diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000007.fa new file mode 100644 index 0000000000000000000000000000000000000000..56f46e522a4d930010e45faf9cc0560c9712ed53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000007.fa @@ -0,0 +1,52 @@ +>GCF_002008305_PROKKA_00158 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_002008305_PROKKA_01033 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKAEDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_002008305_PROKKA_01293 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_002008305_PROKKA_01383 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWR------------------KQNATLKRLLAEAELEKAALKELAEGNF +>GCF_002008305_PROKKA_02076 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_003691675_PROKKA_01016 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_003691675_PROKKA_01103 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_003691675_PROKKA_01111 +MRVVLLPAVADRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_003691675_PROKKA_01115 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_003691675_PROKKA_02022 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_005280335_PROKKA_01213 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_023573625_PROKKA_00589 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_023573625_PROKKA_00591 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_023573625_PROKKA_01251 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_023573625_PROKKA_01338 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_023573625_PROKKA_01886 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF +>GCF_023573625_PROKKA_02204 +MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT +YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000008.fa new file mode 100644 index 0000000000000000000000000000000000000000..247bb0b1c757bb8b26249cc6f28551e1624bc5d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000008.fa @@ -0,0 +1,91 @@ +>GCF_002008305_PROKKA_00711 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_002008305_PROKKA_01398 +MEGS---------------------------------------------------LEGSH +GDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_002008305_PROKKA_01502 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_002008305_PROKKA_02225 +M----------------------------------------------------------- +--------------------------LWK------------------------------- +----------------------------------VRSKAP-------------------- +-----------------TVTASVSKMVVATGEGY--TTIRDSTPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_002008305_PROKKA_02227 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEV-------- +-----------------------V +>GCF_003691675_PROKKA_00092 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_003691675_PROKKA_00343 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_003691675_PROKKA_01013 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_003691675_PROKKA_01394 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_003691675_PROKKA_02284 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_023573625_PROKKA_00606 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_023573625_PROKKA_01016 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_023573625_PROKKA_01158 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_023573625_PROKKA_01349 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN +>GCF_023573625_PROKKA_02164 +MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT +GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP +SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID +DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH +VCQTTGDSVRMTQAMAGKGVMPLN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000012.fa new file mode 100644 index 0000000000000000000000000000000000000000..7623d4c06edc785b18d92a2bb6aba430c103cef3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000012.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_00156 +MK-------------------------------------GA---AQLDFIRRGQAVGLTL +AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC +SPEDVCRYL +>GCF_002008305_PROKKA_00159 +MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVL--------GPAVG--- +------------------------------------------------------------ +--------- +>GCF_002008305_PROKKA_01075 +MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL +AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC +SPEDVCRYL +>GCF_002008305_PROKKA_02063 +MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL +AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC +NAEVICSYL +>GCF_003691675_PROKKA_00297 +MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL +AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC +SADQVCRYL +>GCF_003691675_PROKKA_00338 +MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL +AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC +SPEDVCRYL +>GCF_003691675_PROKKA_00345 +MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL +AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC +SPEDVCRYL +>GCF_003691675_PROKKA_00794 +MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL +AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC +SPEDVCRYL +>GCF_005280335_PROKKA_00720 +------------------------------------------------------------ +-----MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC +SPEDVCRYL +>GCF_005280335_PROKKA_00722 +MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPM--- +---------------------------------------------------------KWC +SG------- +>GCF_020097155_PROKKA_02223 +MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL +AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC +NAEVICSYL +>GCF_023573625_PROKKA_01024 +------------------------------------------------------------ +-----MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC +SPEDVCRYL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000017.fa new file mode 100644 index 0000000000000000000000000000000000000000..313f109af73d45bcc80398cd65c1a127795abbdc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000017.fa @@ -0,0 +1,81 @@ +>GCF_002008305_PROKKA_00542 +MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVTLADEAVALGGETAADS +YLVIGKILDAAERAGADAVHPGYGFLSENADFARAVTDAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT +GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG +DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV +SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGEAVSG +AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS +ALTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGKRGAPVA-AAVSTDALTAPMQGT +VVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATIADAE +>GCF_002008305_PROKKA_01915 +MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT +YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP +DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG +HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV +TEEVFGVDLVREQFRIAAGELLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG +EYDSLLAKLIVWGEDRAQAIARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES +PYLGAE-VPAGGRTSVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPADAAGAG---KPDDDGAVASPVTGT +LASWKVEDGAEVAEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAISRLGA-- +>GCF_003691675_PROKKA_00267 +MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVTLADEAVALGGETAADS +YLVIGKILGAAERAGADAVHPGYGFLSENADFARAVADAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT +GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG +DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV +SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSG +AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS +ALTPAEPAP---ARRAT--------------------------------------------------------------- +-------------------------------------------------------------P +>GCF_003691675_PROKKA_01611 +MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT +YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP +DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG +HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDKQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV +TEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG +EYDSLLAKLIVWGEDRAQAVARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES +PYLSAE-VPAGGRTAVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPAGAAGAG---KPDDDGAVASPVTGT +LASWKVEDGAEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA-- +>GCF_005280335_PROKKA_02407 +MSIADAPQASVIPPRDPKAERRFSRVLIANRGEIAVRVVRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGETAADS +YLLVEKILDAAERSGADAVHPGYGFLSENADFARAVEAAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT +GTEEVVAFADEHGLPVAIKAAYGGGGRGIKVARSREEIPELYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG +GVVVMSTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILKEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV +TEEVTGIDLVREQFRLARGEALGY-EDPVVRGHSFEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDTGVVEGETVSG +AFDSMVAKLIVTGADRRQALQRAARALGEAEIAGMPSVLPFHRAVVTDPAFAPEIAGAAEPFTVHTRWIETEFANHIEPS +EHAPADPTSREPRRTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGRRGAPVA-AAVSTDALTAPMQGT +VVKVAAENGQTVAEGDLIVVVEAMKMEQPLTAHRAGVVSGLEVEPGQTVSAGTVIATIADAD +>GCF_020097155_PROKKA_00880 +MSTPSTT-----------ASRPVTRVLIANRGEIAVRVARACRDHGIASIAVYSDPDAQAMHVAVADEAYALPGSTSAET +YLDIAAVLDVARRSGADAVHPGYGFLSENADFAQAVIDAGLTWIGPSPQAIRDLGDKITARAIAQRAGAPLVPGSDGPVP +DAAAARAFAQEHGLPIAIKAAFGGGGRGIKVVRELSEVEDAFESAVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG +AVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRQRIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV +TEEVFGVDLVREQFRIAAGEPLSIPEDPAPRGHAIEFRLNAEDPAHGFLPVPGPVEAFEAPTGPGVRMDSGVRTGSVVPG +EYDSLLAKLIVVGEDRSQAIARARDALAELRIEGVPTVVPFHRAVLEEEAFT-----SAEALGVYTTWIESEFAAPLAAS +PHLGAS-VPGGGRTTVTVEVDGRAVRLGLPA---DLHAALLGGGGARTGA--SAPAE--------QSVDEGAVTSPVTGT +LASWKVEDGAQVAEGDTIAVVEAMKMETPVRAPRAGRVERAAGDAPAAVTRGQVLASVRA-- +>GCF_020097155_PROKKA_02288 +MTNASAPQASA--DIAEAPGRPFSRVLIANRGEIAVRVIRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGETAADS +YLVIQKVLDAAERSGADAVHPGYGFLSENAEFARAVEAAGLVWIGPPADAIDALGDKVSARRIATKVGAPLAPGTTSPVN +GTDEVVAFADEFGLPVAVKAAYGGGGRGIKVARTREEIPELYESAVREAVAAFGRGECFVERFLDRPRHVETQCLADAHG +NVVVVSTRDCSLQRRNQKLVEEAPAPFLTDEQNTRLVESSKALLKEAGYVGAGTCEFLVGQDGTLSFLEVNTRLQVEHPV +SEEVTGIDLVREQFRIARGEALGY-GDPEARGHSFEFRLNGEDPGRNFLPAPGTLTRFRMPSGPGVRVDAGVTEGETVSG +AFDSMVGKLIVTGADRRQALQRAARALAEAEIAGMPSVLPFHRAVVADPAFAPELAGSEEPFAVHTRWIETEFAHQIEPT +ALTPAAAPDRPERHTVTVEVNGKRVDVTLPTWGEAMHQ--LQGAAARAGAGRRRPRGARRAGAAPAAPGTDSLTAPMQGT +VVKVAAQNGDRVAEGDLIVVMEAMKMEQPLTAHRAGVVSGLEVAAGDALTAGAVIAVIADAE +>GCF_023573625_PROKKA_00545 +MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGESAADS +YLVVGKILDAAERAGADAVHPGYGFLSENADFARAVADAGLVWIGPPAAAIDRLGDKVSARQLATKVGAPLAPGTTSPVT +GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG +DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV +SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSG +AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS +ALTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGKRGAPVA-AAVSTDALTAPMQGT +VVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATIADAE +>GCF_023573625_PROKKA_01835 +MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT +YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP +DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG +HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV +TEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG +EYDSLLAKLIVWGEDRAQAVARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES +PYLSAE-VPAGGRTAVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPAGAAGAG---KPDDDGAVASPVTGT +LASWKVEDGAEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA-- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000019.fa new file mode 100644 index 0000000000000000000000000000000000000000..6985e11dd60dd9fc0f0fc15078aee67a019dd90f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000019.fa @@ -0,0 +1,28 @@ +>GCF_003691675_PROKKA_00342 +MPAPYPQEFRDDVVRVARSREEGVTLAQIAKDFGTHEMTLSKWMRQADVEDGAKPGTTKA +ESAENRELKKRIRLLEQENEVLRRAAAYLSQANLPGKGSTRS +>GCF_003691675_PROKKA_01766 +MPAPYPKEFRDDVVRVAQNREPGTHLKDIAKDFGISESCLTNWIRQADIEAGNIPGTTKA +EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK----- +>GCF_005280335_PROKKA_02275 +MPAPYPQEFRDEVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA +EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK----- +>GCF_005280335_PROKKA_02497 +MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA +EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK----- +>GCF_005280335_PROKKA_02616 +MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA +EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK----- +>GCF_005280335_PROKKA_02634 +MPAPYPQEFRDDVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA +EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK----- +>GCF_020097155_PROKKA_01886 +MSKPYPKEFRDDVVRIARNREPGVELSQIAKDFGIHFTTLYAWMKKADIEDGDRPGTTEA +QYAELREAKRRIRTLEQEVEVLRRAAAYLSQAHLPGK----- +>GCF_023573625_PROKKA_00899 +MSKPYPKEFRDDVVRVARNRGPGVELSQIAKDSGIHVTTLYAWMKKADIEDGDRPGTTEA +QSAELREAKRRIRTLEQEVEVLRRAAAYLSQAHPPGK----- +>GCF_023573625_PROKKA_01543 +MPGPCPREFREDVVAVARSRESGVTIKQIATDFGVSEATLQNWLRQADVEDGNRPGQTAA +DAAEARELKKRIRLLEQENEVLRRAAAYLSQANLRLGGSPK- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000020.fa new file mode 100644 index 0000000000000000000000000000000000000000..139250974806ab95273102adf05917303f317709 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000020.fa @@ -0,0 +1,64 @@ +>GCF_002008305_PROKKA_00524 +MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS +EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP +LSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV +DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAGD +VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA +VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLQ-GTG- +--KGGKKSRRAAR----------AKKG---------------------------------- +>GCF_003691675_PROKKA_00245 +MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS +EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP +LSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV +DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHELFQVAGD +VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA +VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLS-GVGS +SAKKGRRSRRKAR----------TR-G---------------------------------- +>GCF_003691675_PROKKA_00256 +MNIIDFLRVLRANRLVILGCAALGLALGLLYSLLQPTLYTATSTAFVTVEG--EAS----ISGTETAQTRAQSYIPLINS +RTVRERIAAE-GLDTAGATL----SAALVPNSNLITVSAVAPDAQQAAALANGALVATADVANELDPTSN-----VKVTA +MEDALAPAAPSSPDRVRHLLYGLGAGLVLGLIVAFLRRLLDVNVRTTTDAQVAGGAGLLGAI--PLDPSMKAERTAPMAP +-LSPRASEAVRQLRTNLRFAAVDDPPR-TIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQALQFGVDGR +VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHM--VLVDAPPVLPVTDSTLLATA +VDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGGYGADGGSYDAYYQAPRDAAEA-AAGT +A---GDASRR--------------------------------------------------- +>GCF_005280335_PROKKA_01211 +MDLQQYLQTFRKYWRSILTVLSVCVGAALVFTFLQTPKYSSTSSALIAVDT--AATPGELSSGALYAERQVSSFVALADS +ALVLDPVINELGLNVTPQALRSRVSVSAPAGTSIVDVTVTDTNAGRAAEVANAITASLKNVTSDVVPTGPDGDEIVTVTV +VEPAAASSRPVSPRPVVNIALGLIAGVVIGLGQALVRRLLDSRIRTRDDLVEITDAPVLASVVHHKGSDRPKDEAAPARG +-TAWASAESYRKLRTAVGFVALGGERRSSIVVTSSVQGEGKTETSTNLAKVLAETGARVLLVDADLRRPQVGARLGLDDE +LGLSDVLTGRADLNDVLLSV--DDLSVLTAGTVPPNPSELLGSEAMAELL-ALVEAHFEYVILDAPPLLPVTDAAILSHQ +AGGAIVVARSGVARQNQLAEALSILEAADASVYGVVLNDVPVSHIDG--------------YSQYYR------------- +------------------------------------------------------------- +>GCF_005280335_PROKKA_02417 +MNIIDFLRVLRANRLVILGCAALGLVAGLVYSLLQPTLYTATSTGFVTVQG--EAT----ISGTETAQTRAQSYIPLINS +RTVREKIAEG-GLDTAGASL----SAAVVPGSNLITVSAESEDPEQAAALANSALVATAETANGLDPTSN-----VQVTA +MEDALAPTSPTSPDYVRNMLYGLGAGLLLGLVIAVLRRILDVNVRTTTDAQVASGAGLLGAI--PLDATLKAERDAPRGE +-PSPRAAEAVRQLRTNLRFAAVDDPPR-TIAFTSANPGEGKSTVIGSLALAVAASGQPVILIDADLRRPRQALQFGVDGR +VGLSEVLNGDVALQDVLVPVGDHGLLLLPAGRTPPNPSEQLGSARMRDLLTALAETHM--VLVDAPPVLPVTDSTLLSTA +VDGTVLVVRHGKARKEHVEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGSYASKGDDYHAYYQASRDAESR-PSDE +AVPEGPAAQR--------------------------------------------------- +>GCF_020097155_PROKKA_02299 +MNILDFLRVLRANRLVLLGGVVLGLLGGLVYSLLQPTLYTSTSTGFVTVAG--EAS----ISGTETALTRAQSYVPLINS +RTVREKVAES-GVDVSGSTL----SAQVVPNSNLITVTALAPDPQRAADLANTALGATAEVANSLDPTSN-----VKVTA +MEDALPPAGPSSPDHLRNALIGAGIGLLAALAVAFLRRVLDVNVRTTTDATEASGAGLLGAI--PQDGTMKAERTAPLGV +-PSPRAAEALRQLRTNLRFAAVDDPPR-VVMVTSSNPGEGKSTVIAGLAQAVAVSGQPVILVDADLRRPRQASQFGVDGR +VGLSEVLSGDVLLEDAVQDLG-DGLLLLPAGRTPPNPSEQLGSHRMQELLRVLAETHL--VLVDAPP----------GAA +GDG--LHPAGGRRGRDR-------------------AGGAPRQDPEGPCGGGPGHAGQGQRPHAGRGAQRRARLRCGLGL +LRRGLRRGRRQLRRLLPGAPGRRRRRGRDRGRHVATLIAPGGRARSSHRRRRPGDAEGPRL +>GCF_023573625_PROKKA_00524 +MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS +EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP +LSDARVPSAPVSPDTRRNVLLGAVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV +DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAGD +VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA +VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLQ-GTGT +AGKGGKKSRRAAR----------AKKG---------------------------------- +>GCF_023573625_PROKKA_00535 +MNIIDFLRVLRANRLVILGCAALGLAMGLVYSLLQPTLYTATSSAFVTVEG--EAS----ISGTETAQTRAQSYIPLINS +RTVRERIASE-GLDTAGATM----SAALVPNSNLITVSAVAPDAQQAAALANGALVATADVANELDPTSN-----VKVTA +MEDALAPATPSSPDRVRHLLYGLGAGLVLGLIVALLRRLLDVNVRTTTDAQVAGGAGLLGAI--PLDPSMKAERTAPMAP +-LSPRASEAVRQLRTNLRFAAVDDPPR-TIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQAMQFGVDGR +VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHM--VLVDAPPVLPVTDSTLLATA +VDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGGYGADGGSYDAYYQAPRDAPEA-AAGT +A---GDTSRR--------------------------------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000021.fa new file mode 100644 index 0000000000000000000000000000000000000000..90c2662690e7e53b3aad3431863efe4feed6a4d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000021.fa @@ -0,0 +1,73 @@ +>GCF_002008305_PROKKA_00570 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------MHAGWSLG +AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASARGAADQSPA +PS-ETSAPPAPAAQALP--RRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITERGLDP +AAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLAL-APLPGPVAVP +AAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA +VGLAPALTVFLGLAAVGTVLAARLPA---AP--- +>GCF_002008305_PROKKA_00571 +MSEAPPHLPTADDGVAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP +AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG +AGHGAGTAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------- +>GCF_003691675_PROKKA_00294 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------------------MHAGWSLG +AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASARGAADQSPA +PS-ETSTPPAPAAQALP--RRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITERGLDP +AAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLAL-APLPEPVAVP +AAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA +VGLAPALTVFLGLAAVGAVLAARLPA---AP--- +>GCF_003691675_PROKKA_00295 +MSEAPPHLPTADDGVAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP +AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG +AGHGAGTAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------- +>GCF_005280335_PROKKA_02374 +MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA +DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG +R------PWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLG +AGLGAGLGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPD------------DARPA +P-----DADAPEGTAAPAPGPSP------------------------------------- +-----------------------------RRPAR----------------PPPPRP-APP +---------------------------PGWPC---------------------------- +-----------------------------SP--- +>GCF_005280335_PROKKA_02375 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------MAGFGVEEFGNAWTALFLQSERGLDV +AAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTLAGSLAVVVAALVLVLTAP-----AAP +AVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVVSWLMRVAGIGLSPLVGLLATG +LPLPAALAVFPALAVLGLVGTGVVGRRRRRP--- +>GCF_020097155_PROKKA_02254 +MTSAPADTPR--------IDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDP +AGFGLLVTVMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDA +AG-----PWLGA---YAAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLG +AAVGAALGAAAVGAGVPAGLHLGLNGAACVLLLALTLPRFLPDTP----------DHAPA +PALLTADDPGPESEATPASHRHPWLLLAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDP +ATAGLGASTLLGAQFLGRLTGDRVLAALGRTRALTGGLAVVLAGLTVTLLVP-----TPA +AMFTGLALAGLGSAVVVPTAFALADEVPGLPAQTGLAVVSWLMRLAGLGLSPLVGLLAGV +LPLTAALGAFVVLAALGTVLALTLRAPRLAPDFR +>GCF_023573625_PROKKA_00572 +MSEAPPHLPTADDGFAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP +AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG +AGHGAGTAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLG +AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPA +PS-ETSTPPAPAAQALP--RRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDP +AAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLAL-APLPGPVAVP +AAFVGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA +VGLAPALTVFLGLAAVGAVLAARLPA---AP--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000026.fa new file mode 100644 index 0000000000000000000000000000000000000000..e261d99619730853b5f9cf0b2c1385496be1ce9f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000026.fa @@ -0,0 +1,56 @@ +>GCF_002008305_PROKKA_00134 +MS------------------------------TSPSGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY +GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT +TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH +GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF +VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT +VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI-------- +---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED +>GCF_003691675_PROKKA_02148 +MS------------------------------TSPSGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY +GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT +TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH +GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF +VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT +VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI-------- +---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED +>GCF_005280335_PROKKA_00251 +MS------------------------------TSPSGSRVAE---PGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY +GSAGGIQAAGPGVILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT +AYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQAGLANLVDH +GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF +VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT +VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI-------- +---PDSRQA-----LIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVASGEEAAASHR +>GCF_020097155_PROKKA_00186 +MN------------------------------ASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFY +GSAGGIQTAGPGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAVT +KYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIVAMIFGGLILMFTGASFTDGTPAGLHNLVDH +GGFLPHGFGGVLIALTIVTFSFGGIETLGVAAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPF +VQIFEGLGVPFAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLGVMVLGAILIT +VNP-DAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFGIVGTVLGLAFVATVVITMATI-------- +---PESRQA-----LLIGLAWVVALTAAWFVTGVRKTAALHDRTGQLPVVHRHH------ +>GCF_020097155_PROKKA_00187 +MQ------------------------------STPA-----------PEAPAQAQLQRGLNPRHITFIALGTAVGTGLFY +GSAAGIQAAGPGVVLAFMLAGAAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVT +VYMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMFSGASFQDGVTPGPHNLVEH +GGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASALPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPF +VQIFETLGVPFAPHLLNFVVLTAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMS +VKE-DTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFVAVVAGTMAFDQGGAVLGA +LGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHDRHGTPPPLTWDV------ +>GCF_020097155_PROKKA_02180 +MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGLSMRHIQFIALGSAIGTGLFY +GSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPVPGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFG +VYMGFWFPDTPRWIWVTAVILFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH +GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMTMVVIMSLVPWDRITGEASPF +VEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLFGMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNA +VIPEDVFVVVASIATFATVWVWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWF-------- +---SDTRVA-----MIVGLVWLVLLGAAY-----RLFLHGHGR--SRPDLEEGAA--SSP +>GCF_023573625_PROKKA_00142 +MS------------------------------TSPFGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY +GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT +TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH +GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF +VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT +VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI-------- +---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000027.fa new file mode 100644 index 0000000000000000000000000000000000000000..d69cc6e2fd7b73f992aa69b6f9f2fe6c2e4fc898 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000027.fa @@ -0,0 +1,15 @@ +>GCF_002008305_PROKKA_00161 +MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR +>GCF_002008305_PROKKA_01073 +MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR +>GCF_003691675_PROKKA_00336 +MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR +>GCF_003691675_PROKKA_00347 +MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR +>GCF_003691675_PROKKA_00792 +MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR +>GCF_005280335_PROKKA_00724 +MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR +>GCF_023573625_PROKKA_01022 +MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000028.fa new file mode 100644 index 0000000000000000000000000000000000000000..a222845d2231f6bf1b7dd9ac77b452d2022e6f2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000028.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00162 +MSTPATRGRADGGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL +SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV +EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV +GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD +LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ +VEGAGSDGCHDLSW +>GCF_002008305_PROKKA_01072 +M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL +SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV +EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV +GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD +LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ +VEGAGSDGCHDLSW +>GCF_003691675_PROKKA_00335 +M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL +SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV +EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV +GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD +LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ +VEGAGSDGCHDLSW +>GCF_003691675_PROKKA_00348 +M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL +SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV +EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV +GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD +LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ +VEGAGSDGCHDLSW +>GCF_003691675_PROKKA_00791 +M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL +SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV +EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV +GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD +LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLHDRYGIAHATLQ +VEGAGSDGCHDLSW +>GCF_005280335_PROKKA_00725 +M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL +SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV +EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGTKDSLNVKGAYYEVIADAAGSV +GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD +LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ +VEGAGSDGCHDLSW +>GCF_023573625_PROKKA_01021 +M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL +SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV +EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV +GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD +LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ +VEGAGSDGCHDLSW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000029.fa new file mode 100644 index 0000000000000000000000000000000000000000..7450aedc466568fb826fed7b69cd84f8df7846cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000029.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00163 +MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL +CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH +EGQG +>GCF_002008305_PROKKA_01071 +MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL +CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH +EGQG +>GCF_003691675_PROKKA_00334 +MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL +CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH +EGQG +>GCF_003691675_PROKKA_00349 +MSVTLLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL +CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH +EGQG +>GCF_003691675_PROKKA_00790 +MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL +CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH +EGQG +>GCF_005280335_PROKKA_00726 +MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLADPRRARVLYALLEAGEL +CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH +EGQG +>GCF_023573625_PROKKA_01020 +MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL +CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH +EGQG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000031.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1d6bda8bed7b897b77ae7d90d7f765c260ded34 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000031.fa @@ -0,0 +1,64 @@ +>GCF_002008305_PROKKA_00172 +---------------------MPGRLIGW-----PRKPTLLELLFG-------------- +---LAMWEHAVMQIISFFNHKGGVGKTTMLFNAAVEMGRLGKRILMVDFDAQANLTAISI +DDDMLSMIYAPDEDGKTVAHAFAPLVGGSGDVFAPEAIEVREGKVWLAAGDLRLSEFDAI +LPSAWTEALAGNERGFRVTSAPYRLICEIAEE---------IKADY--VFVDLGPNV--G +ALNRAVLLGSDYMIIPMAADLFSIRALPSVGNSVDTWVRQWNTARSVAPRL----NFD-- +IQKGLPKVLGYVSQQFNIYRGEATLAFSHWIDEMPAQIQSGLLEPLAVHSDGKGATLADP +AQSKGPGVGDLKNFHSLVPHAQTLRKAIFELRADDVVRGGQVTRARQSEEQFKELCANII +ARAV +>GCF_002008305_PROKKA_01408 +MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF +PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA--- +-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI +LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G +LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD-- +LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA +TVAATP-ITLFAENHDGAKAYRQLARELIS-------RGG-------------------- +--AP +>GCF_003691675_PROKKA_01138 +MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF +PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA--- +-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI +LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G +LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD-- +LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA +TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG-------------------- +--AP +>GCF_005280335_PROKKA_01488 +---------------------MQTSLEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF +PEPAPLSSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSA--- +-----GLGANPHDLETTVYN-----VLMERSVTA----------------------RDAI +LPTPF-EGMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G +LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD-- +LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDKVFETVIKRS----IKFADA +TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG-------------------- +--AP +>GCF_020097155_PROKKA_01399 +--------------------------------MTPKEPIPVMTVHGEPVLGPTGRPKHEF +PEPTPLAGHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSA--- +-----GLGADPYELDVTVYN-----VLMERKVTA----------------------RDAI +LPTAF-ENMDVLPANIDLSAAEVQLVNEVAREQVLDRALRQVKDDYDVVLIDCQPSL--G +LLTVNALTASDGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD-- +LE-----IDGVLATMFD----QRTLHSKEVVGSLVDGFGDRVFETVIKRS----IKFADA +TVAATP-ITVFAENHDGAKAYRQLARELIC-------RGG-------------------- +--AP +>GCF_020097155_PROKKA_02230 +------------------------------------------------------------ +-----------MHTLMVYSEAGGVAKTTTAVSLAMSWAEQGRQVVLIDLDPRAAATK--- +-----WVDVEPTEPGLHIGA-----VIGNPDPTG-----------WV---------QDLA +VPSGWHENLRVVPSDRSLSHQESDRADHAHLR--LRMALSDLQADL--VVIDC-PNRQGG +PLTQNAFTASDGVIYAARPTSDGCDGVHGARQSVA----------AFKQSMALLGAPDRL +VE-----VGIVVSDYRD----HITPKDQTVAVEELRETGLLLTPLVPARS-----IVPKA +RLACDW-LGRYEKGEPVAAAYADLAGLIFE-------R--------------------I- +--TA +>GCF_023573625_PROKKA_01358 +MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF +PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA--- +-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI +LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G +LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD-- +LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA +TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG-------------------- +--AP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000032.fa new file mode 100644 index 0000000000000000000000000000000000000000..100ef99a279a189b34c69c8b369150429ff8d3a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000032.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_00245 +MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG +AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG +YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR +MIGAEEAERIGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGI +AFERRVFHAAFATADQKEGMDAFTAKREAGWQHR------ +>GCF_003691675_PROKKA_00096 +MST-----------GLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETD +GVVITGSGQKAFAAGADIREL------QHKSVQEMTARGMQHAMTALRESSLISVAAVNG +LALGGGFELALSCDIRLATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQ +PISADRAHQLGLVSELHEAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGL +EIELLAQAAIFGTQEREEGLNAFLERRTPSFIPRPRPRKD +>GCF_003691675_PROKKA_00100 +MTD-----------RIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVR +AILLRGEG-KAFCAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRR +YALGAGLEMALAADLIVAEPQAKLGLPFVLRGI---AAGTSLLPKRAPVQLVQRMLYLGE +MITAEDAHRMGVVGHLAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDAL +AVQVGATAASVLTEDFTEGKVAFTQKRDPEFGGR------ +>GCF_003691675_PROKKA_02257 +MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG +AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG +YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR +MIGAEEAERIGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGI +AFERRVFHSAFATADQKEGMDAFTAKREAGWQHR------ +>GCF_005280335_PROKKA_00124 +MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG +AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG +YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR +MIGAEEAERIGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGI +AFERRVFHSAFATTDQKEGMDAFANKREAGWQHR------ +>GCF_020097155_PROKKA_00093 +MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG +AILLLGSA-KAFAAGADIKEM------KDKDAADMYAADWFRRWEDLARLRTPIVACVQG +YALGGGCELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGR +MVEAEEAERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGL +VFERRVFHGVFSSEDQAEGMAAFAEKRSPVWKHR------ +>GCF_023573625_PROKKA_00245 +MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIG +AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG +YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR +MIGAEEAERIGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGI +AFERRVFHSAFATADQKEGMDAFTAKREAGWRHR------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000035.fa new file mode 100644 index 0000000000000000000000000000000000000000..80de0738986f0d6b41bfda36a26d73db945945e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000035.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_00627 +MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN +EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK +>GCF_003691675_PROKKA_00372 +MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN +EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK +>GCF_005280335_PROKKA_00389 +MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN +EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK +>GCF_005280335_PROKKA_00393 +MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN +EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK +>GCF_005280335_PROKKA_00410 +MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN +EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK +>GCF_020097155_PROKKA_02189 +MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN +EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK +>GCF_023573625_PROKKA_00604 +MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN +EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000036.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c113dbc96fe6fc59ec00b81fe94058f5cf193e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000036.fa @@ -0,0 +1,56 @@ +>GCF_002008305_PROKKA_00631 +MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL--------------------------- +-----------------------AGPPLFHEHLEQA-------------------------------------------- +GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA +GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR +LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL +TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG- +------GSGVGLAISRALIQTHGGTLSATSTT--AGATFTIDLPTKQPPTSPP----------TGAPVYPP-- +>GCF_005280335_PROKKA_00403 +MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL--------------------------- +-----------------------AGPPLFREHLEPA-------------------------------------------- +GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA +GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR +LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL +TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG- +------GSGVGLAISRALIQAHGGTLSATSTT--AGATFTIDLPTKQPPDQPTYRRTRSSTVNTGAP---PLA +>GCF_005280335_PROKKA_01253 +M-------------RTRLSTLLALVLVLSLAVSGITAYAVLRITVNDRIEASLQRAVEQVALLSETGVDPETGEPPDSAA +AFIRLAMLRVLPHDNEGILG---LAPDRAELAASDAVELRLEEDPELVAWALARVGDQEARAETVTTASATYRAVVVPVT +GWGQDDAGALLLAVDVDAEVGRLDRTFLGFAGGALLTTVFALAVGVPLLRRVFAPLESLQEAVGEVTEHDLDRRVEVIGH +-DDVAALGHSFNAMLER-----LEDSFASQRRLLDDAGHELRTPVTIVQGHLEVMDPDDPADV----RETTRLTLDELDR +MSRLVDDLLVLAKAQHPDF-LRPAPVDV--AELTRGVL-----ARASGFDGHVWELDGV-AEATVSLDAQRITQAWLQLA +AN---AVRYSEPGS-----------------VVRLGSAVEGDTLRLWVQDHGVGVRPEDRAQIFERFGRGAHGTRAD--- +------GSGLGLAIVSSIAAAHGGEVSLDSVPG-LGSVFRIELPLSTPSRPAG----------SLTPGKDP-A +>GCF_005280335_PROKKA_01330 +MTRSKPTGRLSASGRARVVAWILGVSALGMVLMLVSIVLTLRWVERDAIETSLTQESDEVAVFAQNGRDPETGEPFATPE +RFVGHYLERQRVEPTELMFGGTAATPVIAQIHGDAA------APVELLAPATRQ-AMEQPRSRGTLVDPTHGRISYANLT +VTTPADTGHVVVAVFHERYEQRVMTQTLLLSALALAALAATAAAAWLVSSRILGHTVEFHRAVDASLKDRGLRRLPENGS +-EEYAGLARRANDLVRR-----ADRRLEEERRFAEDVTFALRTPLTVIEGGL-----RNPGGDEQERRTSYRHIGAEATR +VRGLLEDLVILSRLQQDDVVLERTPVDV--GVLVATAAQAWRERHPDAADEPRLDVEAPAEGLTAVTDRARLVQVLEELL +DNARHAVRFAPGSDLPRDLTAVTPLERTLSVRVREEERDGEPWAVVEVADRGRGIPEEDREEVFERLANASNDPYP---- +------GNGLGLPVAALLSTALDGELTLEPGPGAAGTVARLAVPLTADQDGEDA------------------- +>GCF_020097155_PROKKA_00451 +M------------------------------------------------------------------------------- +------------SPTPALRGRPAPGP-----------------DAALVARAARRIGLRTALACAALVLGGAG--VFFGY- +-------------------------------------------LWWQIAHPGVDPRDA--DATVTVQLDLVDLATAAILA +GAAAVLITGFASLWFSRSAVQPLADALRRQREFVSNASHELRTPLTVLSARTQVLQARVPAGDPL--EPLADELRRDTDV +MAGVVEDMLSTAR-------LDSAPEGMCDAGEVAAAACA--DLSLVGAEERGVRLRADLPSLPVALPEAALRRMLAALL +DN---ALGFAPPGT-----------------EVTVSGERVRGVVELRVADRGAGIQGVEPDHVFDRFARGRPAAVPGSGP +GAVPRSSHGIGLALVRETAHRYRGEVRVESTGP-EGTVMLLTLPAAQEAR----------------------- +>GCF_020097155_PROKKA_02198 +MT-----------SRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL--------------------------- +-----------------------AGPPLFHEHLEQA-------------------------------------------- +GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA +GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGGQLAR +LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLDNLL +TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG- +------GSGVGLAISRALIQTHGGTLSVTSTT--AGATFTIDLPTKQPPDQPTYRRTRLSTVNTGAP---PLE +>GCF_023573625_PROKKA_00600 +MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL--------------------------- +-----------------------AGPPLFHEHLEQA-------------------------------------------- +GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA +GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR +LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL +TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG- +------GSGVGLAISRALIQTHGGTLSATSTT--AGATFTIDLPTKQPPTSPP----------TGAPVYPP-- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000047.fa new file mode 100644 index 0000000000000000000000000000000000000000..60b256cdb332a94f69eeb62741a1722260905089 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000047.fa @@ -0,0 +1,98 @@ +>GCF_002008305_PROKKA_01806 +M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI +VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE +EGGPSPEE-------AVARAQAWLRKRRYRVER----RLE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK +YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFDRESETH---YGQPLDYTAVMDVREGSGGELQ +RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF +FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG +SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVAL +RAAMEKWWPIVAATETADDAAAGAAPQSTPTAPETPAGPA---------------------------------------- +--------------------------------------------------------------------DARS---GD--- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------- +>GCF_003691675_PROKKA_01503 +M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI +VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE +DGGPGPEE-------AVARAQAWLRKRRYRVEH----RPE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK +YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFERQSETT---YGQPLDYTAVMDVREGTGGELQ +RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF +FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG +SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLVISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVAL +RSAMERWWPVAAPESEEEAVASAAAVGHTGTTPETLAGPR---------------------------------------- +--------------------------------------------------------------------TPRS---GD--- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------- +>GCF_005280335_PROKKA_00397 +M------SRTEDQDPG-----RRPEVAL----PALGFWGTLRFAWTQLTSMRTALMLLLLLAVAAVPGSLFPQRPAGPGI +VQDYIDDNPVLGEWLDR--FQMFDVYSSVWFSAIYLLLFISLIGCVAPRAVKHAQALRSAPPRTPRRLSRLPEYGRVVLE +PGGPAPVE-------AVEQAARYLKRRGYRIEV----RQEDAGGASVGAARGYLREVGNIVFHLSLIGVLVFMATGSLLS +YRGQKILVEGEGFANTLVAYDAFTPGSAFSEEMLTPFSMTLKRVEYVYDRQSPTH---YGQPLD---------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------- +>GCF_005280335_PROKKA_01068 +MGDAPVSSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI +VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE +EGGPSPEE-------AVARAQAWLRKRRYRVEH----RPE-ASGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK +YYGQKIIVEGEGFANNLVSYDSFTPGTYFSADDLQPFSLTLDSFDVVFDRESEAL---YGQPLDYTAVMQVQEGGGGEPR +EEILKVNHPLSMDGVRVYLVGNGYAPVLTVRDGEGDIAFQGPVVTRVQDV-NFNSLVTLKVPD------ARPDQLGFVGQ +FMPAAVEDESGVAVSVDPELYNPQLILDSYYGDLGLDGGVPQNVYVLDTETLTELNSRKNENGGIVLSQGQTYELPEGKG +SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVAL +RAAMEKWWPVAAATAPE-------------TTPETPCRPRRRPIRRLTVFNPTAPVNEQLALYSDLFMLIAAFVYAAAFV +LFTIDMATSSATIRRLEEDLAAQRGPARLAPARETVGAGFGGSSLGGSSSVGSTGAGSSAGGPGVLPGEARAAGLGDEPG +LVDEDMDYTGGGRRPIANVAVAVLAVGWALHAFAVIARGLAASRVPWGNLYEFMTTGALVITTVYLLFLFRKDLRFVGTF +VTGLVVAMMCAATMGFPTPVGHLQPPLQSPWLVIHVSIAVLATALFTLTAAMSMLQLIQDRAEKRAAATGERPWAFLRLV +PSAQALENWSYRINAVGFVMWTFTLIAGAIWAEASWGRYWNWDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVG +FLCVVFNYTIVNTYFPGLHSYAGLPG +>GCF_005280335_PROKKA_02641 +M------SRPSDYDDG-----TGAGGTLRAESPELGFAGWLRWFWRQLTSMRVALILLLLLAVAAIPGSLVPQRGADPNG +VVQYQKDHPDLFPILDAFPIQAFDVYGSVWFSAIYLLLFISLIGCVLPRIAHHWKAWRGRPPKTPARLQRMAGFSEIRLS +NPDATPAEREAFAARAVDEAAAILKKLRYRVEVQRASRRG-VDEVSVSAERGYLRETGNLLFHVSLLGVLVSVGLGGVFT +FNGQKVLIEGETMVNQLIDYDTATSGRSFDSSSLEPFSLRLDTLDVTYNTPDDGNVQAIGLVKDYTANMTLISPEGDE-S +EHVIRVNHPLRVHGSPIYLIANGYAPKITIRNAEGTVVYSEAMPFIPQDNLNMTSLGVVKVPDGIVDESGEPVQLGLRGF +FYPTKADLDTGAYTSNYPDLENPVLTLDVFVGDLGINDGIPKSVYALDTSDMEQVTGRAVDLDSIELRPGEQTELPNGFG +TIEFESVPRYASFDVMQNPAQEWILVFAVLALGGLMWSLFVPRRRMWVKALPSEDG-VVLQYAALARGDDPALERAVEEL +RDRHRELL------------------------------------------------------------------------ +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------- +>GCF_020097155_PROKKA_01003 +MGDAPVSSTSAPKDPAPRNRTRDD-VTL----PALGVGGTLRWAWTQLTSMRTALLLLLLLAVAAVPGSLVPQRRAGPEA +VDQWIEDNPFWGPILDA--LQFFDVYTSVWFSAIYLLLFISLVGCVLPRALKHAKALRQPPARTPRNLGRLPESGVVVLE +AGGPAPEE-------AVRQAQRWLKRKRYRVEL----RPE-AGGASVGAERGYLREIGNILFHFSLIGVLAFMAYGGMTK +YTGQKIIVEGEGFANNLVAYDSFTPGMYFDAASLQPFQLTLKSFDATFERQSQTH---WGAPLDYTAVMEVRHGTGGDPE +EQVLKVNHPLEIDGAKVYLVGNGYAPVVTVRDGNGDIAFQGPVVTRVTDQ-NFNSLAVIKAPD------ARPDQLGFVGQ +FMPAAADVGQGVEVSVDPEPLNPKLILNSYSGDLGLDAGVPQNVYVLDTSTLTELNSRRSENGGITLSVGQTHVLPDGKG +SISLDGVRRYVGLDIHYDAGKWGVGVFSVLALIGLAVSLFTRRRRVWVRARTGDDGRTRVEYALLARGEEFGLREEHVAL +REAFEKMWPVSAPEADTGE-----------TTPATPA-PAAAP------------------------------------- +--------------------------------------------------------------------TPRS---GD--- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------- +>GCF_023573625_PROKKA_01727 +M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI +VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE +EGGPSPEE-------AVARAQAWLRKRRYRVEH----RPE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK +YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFDRESETH---YGQPLDYTAVMDVREGSGGELQ +RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF +FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG +SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVAL +RAAMEKWWPIVAATETADDAAAGAAPQSTSTTPETPAGPA---------------------------------------- +--------------------------------------------------------------------DARS---GD--- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000048.fa new file mode 100644 index 0000000000000000000000000000000000000000..638815e34c0b7ae087d50b9cbb5600e235ba4f4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000048.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_01808 +MQ--------------T-PRPSRRTVLTGLSL-LGLAPVLAACS-GDDSLTRQAGNADGK +NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP +HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--EVLLNMTDYVP +PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA----------------- +-- +>GCF_003691675_PROKKA_01505 +MQ--------------T-PRPSRRTVLTGLSL-LGLAPVLAACS-GDDSLTRQAGNADGK +NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP +HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--EVLLNMTDYVP +PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA----------------- +-- +>GCF_005280335_PROKKA_00398 +MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAG-VASLPLLAACS-AEDPLAAQAGKADGK +NYIAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAP +DLQALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGG--QVLLAMTDYVP +PQAVPTTIVLDHQGRVSARILGIAE-RSTLRTLITTVLDEQA------------------ +-- +>GCF_005280335_PROKKA_01066 +MH--------------TPPRPSRRTLLTGLAL-ASLAPALAACSGGDDSLARQAGNADGK +NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP +HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDTRG--DVLLNMADYVP +PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA----------------- +-- +>GCF_005280335_PROKKA_02643 +MN--------------------RRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGK +GYVSGDGSSLSIAPDQRTEPVEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAP +DLVEAYDEFSPQGVKFVGVNTRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVP +LNAVPTTLVLDAEGRVAHRVLGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEAT +EQ +>GCF_020097155_PROKKA_01001 +MP--------------FPPRPSRRAALAGLSA-AALAPLLAACSGTDDSLAQQAGNAGGK +NYIAGDGSVVEYAADQRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAP +HLVKLHGEFEPKGVRFLGVNVRDTVTTAQAFERTFGIPYSSVDDTSG--SVLLAMSDYVP +PQAVPSTLVLDRQGRVAARVLGAVE-EGTLRALLDTVVAEA------------------- +-- +>GCF_023573625_PROKKA_01729 +MH--------------TPPRPSRRTLLTGLAL-ASLAPALAACSGGDDSLARQAGNADGK +NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP +HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--DVLLNMTDYVP +PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA----------------- +-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000049.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba1bd7b258f959d6835ae4e0aeedd42f190aa5c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000049.fa @@ -0,0 +1,63 @@ +>GCF_002008305_PROKKA_02005 +MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR +SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP +DYGWAFETLEDTN-DGEHPVLVTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV +MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEIIRRAQQILRPYTLDVKEV +AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERK +EIAKNLIDFDKEWSTLMATPTSELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERS +CDTNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH +PDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN- +>GCF_003691675_PROKKA_01715 +MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR +SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP +DYGWAFETLEDTN-DGEHPVLVTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV +MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEIIRRAQQILRPYTLDVKEV +AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERK +EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERS +CDTNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH +PDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN- +>GCF_005280335_PROKKA_00837 +MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRSHRLEIGQADGIQAR +SVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEP +DYGWSFESLEDSA-EGEYPVLVTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGV +MDALAVSDFPDIRTKCAIHS-STGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEIIRRAQQIIRPYTLEVKDV +AWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERK +EIAKNLIDFDKEWSTLMAKPTSELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERS +CDTNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQDARFDVKVVYQQKQTEFAH +PDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISRDGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS- +>GCF_020097155_PROKKA_00774 +MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTRIIERRGKRLEIGQADGIQAR +SVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRTSLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATP +DYGWEFVSLDDSDQDAERPVQVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV +MDVLADSNFPDIRTKCAIHS-SSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEVIRRAQQIIRPYTLDVKDV +AWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERK +EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERS +CDTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQDERFDLKVVYQQKQTEFAF +PDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVSRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN- +>GCF_023573625_PROKKA_00173 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------FIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQ +QIAENLIEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGVPIGKRFESAAVRRV +ADTSPRQLGHLFEADGRWRLYAFAD-----EDRTAVGELADWLADSPDSPVRRFTPESADLNSVFDAKVVYQQPYQEVEL +ADVPALFLPKMGPYQLTDKEVVFAA---DLADDIFEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV +>GCF_023573625_PROKKA_00174 +MR---------------------------------------------------------------------GAAD----- +----------------------------P---------RRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGP----- +---------------------------------------QGQERTVRAKYVVGCDGSRSRVRDCTGIEVVRDPSAHAWSV +MDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGFLARFYVSLGSI--DDAPRPRS------------------------ +-------------------------------------------------------------------------------- +---------------------------------------------------------------GG---GIRACSSPATPA +TPTPPR-------------------------------------------------PARA--------------------- +-------------------------------------------------------------------------------- +>GCF_023573625_PROKKA_01943 +MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR +SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP +DYGWAFETLEDTN-DGEHPVLVTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV +MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEIIRRAQQILRPYTLDVKEV +AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERK +EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERS +CDTNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH +PDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000052.fa new file mode 100644 index 0000000000000000000000000000000000000000..e442a0497c7f0b37a12eee4c70022b0e98239183 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000052.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_02160 +MS-SE-ETVPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA +DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP +PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE +EQQAAVASLTPREHEVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV +LIAHRAGLVQ-----------F +>GCF_003691675_PROKKA_01873 +MS-SE-ETVPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA +DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP +PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE +EQQAAVASLTPREHEVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV +LIAHRAGLVQ-----------F +>GCF_005280335_PROKKA_00589 +MT--------TRVLLVDDQPLIRLGFAAILQSQ---DDIEVVGEAGDGAECLERAAALDP +DVICMDVQMPRMDGIEATRALAEAG-TRAAVLILTTFDRDDFLFETLEAGASGFLLKSAE +AEHLIDAVRVLGRGDALLDPQVTRRVLRRMASAAPEGVDGPAGVGQPRDDDGAAPGQAEA +SDAVGKAGLTGREAEILTLMARGLSNGEIAGQLFVGESTVKTHVSNVLMKLGARDRVHAV +IWAFEHGVAG------------ +>GCF_005280335_PROKKA_00598 +MS-TDAENAPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA +DVVLMDVRMPEMDGIEATRTLLQRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP +PEELLAAIRTVHRGDAVIAPSTTRRLMAHMA---------------PRLRSDHARTAECE +HEQAAVESLTPREREVLVLMAQGSANLEIAGELVLSEATVKTHVGRVLAKLGARDRVQAV +LIAHRAGLVQ-----------F +>GCF_005280335_PROKKA_02580 +M--------------VLPDAGVRGGVRVRTSRTGVVGDIRLVEGAVSG------------ +DLDSADLLLGGVNSLGETRQVARQGRDVPPFLLVAEATIVEELSGIDASGAAAVLAYPLD +TVELAS----VAHGIAGSGPFLSPRL--------------------PQLSVEPLG----- +------EGLSAREAEVVVALGEGLSDAEIAQALCVSVKTVHTHVLNLRRKLGARNRAHAV +SLARSVGPLGDACSEPGLVAAL +>GCF_020097155_PROKKA_00520 +MSPDDAQPTPIRVALVDDQALIRSGLAMLIDSQ---PDLTVVAQASDGREAAASVAVAGA +DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEHVMDAIEAGASGFLLKDAP +PEELLAAIRTVHGGDAVIAPSTTRRLLAHMA---------------PRLRQDAARSAECA +DEQAAVGSLTPREREVLVLMGQGAANPEIAAQLVLSEATVKTHVGRVLAKLSARDRVQAV +LIAHRTGLVG-----------F +>GCF_023573625_PROKKA_02104 +MS-SE-ETAPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA +DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP +PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE +EQQAAVASLTPREREVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV +LIAHRAGLVQ-----------F + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000053.fa new file mode 100644 index 0000000000000000000000000000000000000000..830ff25534b685791bbcb467983661c32133af44 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000053.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02246 +MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE +LEYFGEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL +--------VFDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR +GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R +>GCF_002008305_PROKKA_02261 +MD------HKQ--ILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVE +LEYFGETFDRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITAL +--------GADAHGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLR +APGNNLPVWGADRWAAHVDRLTAIAEGSGGPGRN +>GCF_003691675_PROKKA_01948 +MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE +LECFGEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL +--------VLDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR +GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R +>GCF_020097155_PROKKA_00418 +MD------HKQ--ILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIE +LEYFGGTFGRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITAL +--------GADAPGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLR +SPGNNLPPWDADRWAAHVDRLTAIAEGSGGVGWN +>GCF_020097155_PROKKA_00422 +MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA +VYWTAAAASAPGEPVLPED---VNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAV +ADLSAPVPVPDA----PWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSY- +-------------------ELNDLADAAAQ---G +>GCF_023573625_PROKKA_02178 +MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE +LEYFDEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL +--------VFDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR +GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R +>GCF_023573625_PROKKA_02192 +MD------HKQ--ILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVE +LEYFGETFGRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAAL +--------DADAPGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLR +APGNNLPPWDADRWAAHVDRLTAIAEGSGGPGRN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000055.fa new file mode 100644 index 0000000000000000000000000000000000000000..80151f46353221e446227bf71fce739ffddff933 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000055.fa @@ -0,0 +1,70 @@ +>GCF_003691675_PROKKA_01696 +-------------------------------------------------------------------------------- +------------------------------MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTL +SGGEKQRVAVARALINEPPLVLADEPTGALDQARTRDVVD-LLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGELAPQ +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------D +>GCF_005280335_PROKKA_00855 +MT-------LLEVHDVDKTFHSG-GEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPDSGRVLLGGEP-- +----LPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGTRTGHRARTL +SGGEKQRVAVARALINEPPLVLADEPTGALDQERTRDVVD-LLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQ +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------D +>GCF_005280335_PROKKA_01010 +MSDGS-APPLLELAGVLKSFK---GADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLLDRPDGGSYRVSGTD-- +----TMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTPPEQRDAR--AGEALALLGLSHRLDTRAKLL +SGGERQRLAIARAIATRPRVILADEPTGNLDSVNSRIVID-HLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITEL +AGHRTAASASADMAGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASVGLTQTAT +DQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVAQVAPADVVITRHDPSDPEPAVAISLVA +ASSSYAGLAGLTLPSETSRTLLDSPDARLAWATPAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDA +SLVVTPAVMTGVAQAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVLSGVLLVL +AVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGAAVGSGVILAVSQARGWAAVLPPGAVPL +ALGLGLVAGVVSALYPGWVASRQRPADALRG +>GCF_020097155_PROKKA_00792 +MS-------LLEVHDVDKSFTTA-ASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPDAGEVLLEGVP-- +----LPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRAEQRRRAALALDRVGLADRAHHRARTL +SGGEKQRVAVARALINDPPLVLADEPTGALDQARTRDVVK-LLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQ +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------G +>GCF_020097155_PROKKA_00870 +MTA---SAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAGLSRPLAGRIAYRSPDGS +LNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVWIHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRL +SGGEAQRVALVRALSKRPHLIVADEPTGHLDGVTAREAIA-LLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED----- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------- +>GCF_020097155_PROKKA_00943 +MNTAPLTPPVLAARGLTKAY-----GSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGIIAPDGGRVTLAGADGT +VH-EVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLMLN--GVDRRAAEQTAARWLGSLGLAGMEDRRPGEL +SGGQRQRVAIARAQAVEPDVVFADEPTGALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESD +QAQAAAGTTREQV------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------R +>GCF_023573625_PROKKA_00735 +MS-------LLTVHDVHRSYRGP-AGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPDAGSIRVAGRS-- +----LPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKRERRTMAAELLTRLGLGDRLHHPVGRL +SGGERQRVAIARAVIMGPSLLLADEPTGALDEERTDEVMG-LFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE-- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000056.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d292059ed25c90b14d63654c470fa59261f7554 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000056.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_00025 +MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA +PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD +LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPRE---PSPAPR +VGPRPAPRRA------AAPAAPAAPSHADQPTVVMGRPVT-EPAGPALELDGRMLPLDGD +DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD +GDVVTVGQTELLFFGG-TGGR--A +>GCF_003691675_PROKKA_02043 +MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA +PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD +LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRE---PSPAPR +VGPRPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVT-GPAGPALELDGRMLPLDGD +DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD +GDVVTVGQTELLFFGG-TGGR--A +>GCF_005280335_PROKKA_00370 +MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA +PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD +LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDL---------------- +------------------------------------------------------------ +------------------------------------------------------------ +-----------------LGGRT-P +>GCF_005280335_PROKKA_00371 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------MGRPVT-EPSGPALELDGRMLPLDGD +DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD +GDVVTVGQTELLFFSG-TGGR--A +>GCF_020097155_PROKKA_00353 +------MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVA +PNDFTVHFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQ +VEVDARIDDGSSPVPSPPAATSAPA----PAAARTADDR--GPRPSRAPRHGATAAPAPR +RDPSPAPRPAPTPA--RSESARRAPAD-EQATVVMPRRTSPAPAVPWLEADGVRHPLTHE +DMVLGRSSERADVVVPDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLRE +GDRITVGQTDLVFHIDPADGRPRA +>GCF_023573625_PROKKA_00025 +MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA +PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD +LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRK---PSPAPR +VGPRPAPRRA------AAPTAPAAPAHADQPTVVMGRPVA-EPAGPALELDGRMLPLDGD +DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD +GDVVTVGQTELLFFGG-TGGR--A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000058.fa new file mode 100644 index 0000000000000000000000000000000000000000..323770089a197ec23001f3c84237b2383bb6b54f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000058.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_00049 +MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GE +DATVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG +KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDG +ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD---------- +--------------GLVYLRKNQMQLASKMRFVSAQLLALFDGDLYLRSARHANAMAARL +RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRARFRFYDWDAARREVRWVCG +FDTTEEDVDAFTAALRAELVPA--A +>GCF_003691675_PROKKA_02062 +MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GE +DATVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG +KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDG +ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD---------- +--------------GLVYLRKNQMQLASKMRFVSAQLLALFDGDLYLRSARHANAMAARL +RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRTRFRFYDWDAARREVRWVCG +FDTTEEDVDAFTAALRAELVPA--A +>GCF_005280335_PROKKA_00354 +MQQIHD-PASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHF-GE +DAQVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDG +KLTPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDG +ARLANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATT---------- +--------------GMTYLRKSQMQLASKMRFVSAQLLALFDGDLYLRTARHANAMAQRL +QDAVAAGIADGSLPGVALTQRAQVNAVFATLPAGVADRLRRSFRFYDWDEANGEVRWVCS +FDTAEEDVDAFVAALRAELAPA--D +>GCF_005280335_PROKKA_01608 +MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP +DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG +RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG +ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL +PAD--AGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMAREL +AGRV-AGI-----DGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTS +WDTTAADVDSFAAALGEALSPGRRR +>GCF_020097155_PROKKA_01503 +MSAARP-AGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVF-GE +RAFAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDG +RLTGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDG +ARLSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADV +PGGDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVL +ADAV-AGL-----DDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTS +WDTTDADVESFVDALAAALRARRPR +>GCF_023573625_PROKKA_00044 +MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GK +DATAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG +KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDG +ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD---------- +--------------GLVYLRKNQMQLASKMRFISAQLLALFDGDLYLRSARHANAMAARL +RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRARFRFYDWDAARREVRWVCG +FDTTEEDVDAFTAALRAELVPA--V + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000061.fa new file mode 100644 index 0000000000000000000000000000000000000000..864fbd0bcf670452f7032e6ba277df3cfd9e9e7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000061.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00068 +MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV +YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI +EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEA +QPATEEGEATDEPQGR +>GCF_003691675_PROKKA_02081 +MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV +YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI +EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEA +QPATEEGEATDEPQGR +>GCF_005280335_PROKKA_00326 +MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV +LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPA-DKRFDHITELEHIEESLKQEI +EHFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDP +SPATEEGEEKDVPQGR +>GCF_020097155_PROKKA_00266 +MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV +FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPA-DKRFDHIQELEDVEESLKQEI +EHFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEA +APAAEQEA-------- +>GCF_020097155_PROKKA_00684 +MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV +LLPR-PTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEI +EHFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTA--------QNAHTRHP---------- +---------------- +>GCF_023573625_PROKKA_00062 +MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV +YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI +EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEA +QPATEEGE----PQGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000066.fa new file mode 100644 index 0000000000000000000000000000000000000000..567cc428e283c47e5e50d1ae98103ad87b7c5344 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000066.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_00198 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA +AW---AALALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSR---RA +GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV +LRRMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTS- +---------------------RSPGVA---GGGRG------------------------- +---------------------------------------------- +>GCF_003691675_PROKKA_02026 +M----------------------------------------------------------- +------------AVAVYPLAFYTSIHWAGVAIGSVVSLAS-APLASGLLERIVEYRRLSR +WWMLAAALGGTGAALLCLSQLDQ--EAASSTATLAGVLLGLVAGATYATYSWAAHRLIHD +GISRAASMGAVFG--AGGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYG +LTRVPASTATTITLTEPAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTAD +RHGRTPTSEAIQPALAPSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVR +GRFRKPYRLRPVSPDHGRATCGERTEIMRPARGLDARSVLAATMET +>GCF_003691675_PROKKA_02194 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA +AW---AALALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQ---RA +GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV +LRRMPTALFSLLTCLSPIAAALTAWAVRGQQLTPLDLAGMLLV-----IAACAAAVWTS- +---------------------RSPGVS---GGARG------------------------- +---------------------------------------------- +>GCF_005280335_PROKKA_00197 +MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS +RRGWVAVVMLGVTMAGMNLLIYAA--FDRIPQGVAVTFEVLGPLALSVLAN---RRWLSV +VW---AALAFAGIALLGRDGFSA--GMDGAGLDPLGVAFALAAAACWAGFILANR---HA +GTHLPGVQGLALAMVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQV +LRTMPTGLFSLITCLSPVVAALTAWAVRGQRLAVLDLGGMGLV-----VLACGAAVWAAE +RAAR--------------PSRRAPRTS--------------------------------- +---------------------------------------------- +>GCF_020097155_PROKKA_00149 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA +AW---AALALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSR---RA +GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV +LRRMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTS- +---------------------RSPGVA---GGGRG------------------------- +---------------------------------------------- +>GCF_023573625_PROKKA_00198 +MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG +PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA +AW---AALALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSR---RA +GTHLPGVQGLALATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQV +LRHMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTG- +---------------------RSPGVA---GGGRS------------------------- +---------------------------------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000068.fa new file mode 100644 index 0000000000000000000000000000000000000000..93b5eccb961a749a743f91a20fe8bc5ba761a74a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000068.fa @@ -0,0 +1,19 @@ +>GCF_002008305_PROKKA_00216 +M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE +DLFTP--DGNAG----- +>GCF_003691675_PROKKA_02209 +M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE +DLFTP--DGNAG----- +>GCF_005280335_PROKKA_00167 +M---ENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIE +DLFSP--DPPA------ +>GCF_005280335_PROKKA_02206 +----------------MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLR +DLLAP--LDEALERGTR +>GCF_020097155_PROKKA_00321 +MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD +DLTAAAWRGHAGG---- +>GCF_023573625_PROKKA_00216 +M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE +DLFTP--DGNAG----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000072.fa new file mode 100644 index 0000000000000000000000000000000000000000..98003047def632a682d1fe1a9d8c78cb93d87c9f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000072.fa @@ -0,0 +1,54 @@ +>GCF_002008305_PROKKA_00250 +MTVQDPTAVAAPSPTEVFRVARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE +RTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA +EDLAKFAGVGEGLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDAADAATELAPAEPTPADETLLFYFTSGTTSKPKLVEH +THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMARYGVTSFCAPPT +VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVTL +IDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS +PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK +IRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLHR---- +>GCF_003691675_PROKKA_02262 +MTVQDPTAVAAPSPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE +RTFAELSAASSRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA +EDLAKFAGVGEDLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH +THTSYPVGHLTTLYWIGLEPGGVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMERYGVTSFCAPPT +VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTL +LDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS +PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK +IRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLQR---- +>GCF_005280335_PROKKA_00120 +MTVQDRTPADAASPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQDPARQDVPALIIAEDDGRSTE +RTFAELSAASNRAANWLAEQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSADLEDRVSRADAAWAVAGA +EDLAKFAGVGEGLRLVHVPGVFAEGEARRAPEVPGHTVLSYDDAAGASAELSPAEPTPADETLLFYFTSGTTSKPKLVEH +THTSYPVGHLTTLYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMDRYGVTSFCAPPT +VWRMLIKADLAQLKTPPTKTISAGEPLNAEVIDQVQKAWGATIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVVL +IDPLTGQEA---AEGEICLRLDPRPVGLLKSYFGNQEKTDEVFRDGVFHTGDIASRDENGVLTYVGRADDVFKSSDYKVS +PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETAQSILQFTLTQLPPYKRIRRIEFLELPKTISGK +IRRVELRKAEVERSETGTAPSGYGTEFREEDLDLTR---- +>GCF_020097155_PROKKA_00088 +--------MTTTSVTERLRAARDLLVECQEDYDRARAEFEWPRFEHFNFGFDWFDQLAARPDRADVPALIISDAGGGHLS +RTYAELSAASNRAANWLRERGITPGDRVILMLDNQVELWELMLACIKLRVVMVPTTTQMTSADLADRVERAEARWVVASA +ENLAKFDGVDSGLHLVHIPGVAAQGDARTAPVVAGHEVLSYDDAASASPELTPDSPTPADETLLLYFTSGTTSKPKLVEH +THTSYPVGHLTTVYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDAAALMADMDEFGVTSLCAPPT +VWRMLIKADLSLLKTPPVKTISAGEPLNAEVIDQVHRAWGTTIRDGFGMTETTLQIANTPGQKLVIGSMGRPLPGMDVVL +IDPLTGEEA---AEGEICLRLDPRPVGLLKSYYGNEEKTAEVFRDGVFHSGDIASLDESGVLTYVGRADDVFKSSDYKIS +PFELESVLVEHPAVMEAAIVPSPDEVRLAVPKAFVTLAPSYEPTAETARQILQHTLTQLPPYKRIRRIEFRELPKTISGK +IRRVELRKAEAERAETGQAPEGYGIEHREEDLDLKR---- +>GCF_020097155_PROKKA_02472 +-----------MSVTARLRAARDLLVEHQQDYAGARAAFEWPRFETVNFGSDWFDAVAATPERADQDALVIVEEDGTVLR +RSYARMSADTDRVAGWLQHLGVGRGDTVIVMLDNQVELWEAMLACMKIGAVVIPTTTQLVAADLQDRVDRAGARWAIANA +GNLVKFADVVGDCTLIHVPGVYASEAEHALPEVPGHPVHSYGDAASFAGTWSLETPTSADDPLLLYFTSGTTSLPKLVEH +TQASYTVGHLSTMYWVGLRPGDVHLNVASPGWGKHAWSSFFAPWLAEATIFVLNFRRFDAATLMRAMDEGGVTSFCAPPT +VWRMLIKADLTQLQAPPRNAISAGEPLNAAVIDQVQRGWGVTVRDGFGQTESTLQIANTPGQRVVIGAMGRPLPGFDIEL +RDPQTGDRVDGEGEGEICVGLDPRPVGLFQRYHGDPEKTAEAFRDGVYHTGDIARRDEHGIYTYVGRADDLFKSSDYKLS +PFELESVLMTHPAVLEAAVVPAPDELRLSVPKAFVTLAAGHEPGEEAARAILQHVTDRVPAYKRIRRIEFRPLPKTVSGK +VRRVELR-AEEEQRRAGVA--GLGVEHREEDLGIRRQRRA +>GCF_023573625_PROKKA_00250 +MTVQDPTAVAAPSPTEVFRAARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE +RTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA +EDLAKFAGVGEDLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH +THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMERYGVTSFCAPPT +VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTL +LDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS +PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK +IRRVELRKAEVERAQTGAAPDGCGTEFREEDLDLQR---- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000073.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb9a628c77b18b412629d572b45dd2b3da6b8233 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000073.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00258 +M-------------------------------------------------------SEEL +RILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQMPLMDG +MEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE +SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA +ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD +>GCF_003691675_PROKKA_02272 +M-------------------------------------------------------SEEL +RILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQMPLMDG +VEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE +SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA +ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD +>GCF_005280335_PROKKA_00111 +MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL +RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG +VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE +SVLSPAVASKLLASIERDHPVVGPAQARPGDPDG--SDLTDRERDVLRLLARGQSNPEIA +ANLHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD +>GCF_020097155_PROKKA_00079 +M---------------------------------------------------PDSPEDEI +RVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLMDMQMPRMDG +VEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLGAVEAVRRGE +SVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDG--SDLTEREHQVLTLLARGRSNPEIA +AELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD +>GCF_020097155_PROKKA_00526 +M--------------------------------------------------------DAI +TVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMPVLDG +VEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAVEAGT +MALGPSIAREVVDLLLRSG--VAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQEMA +ARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIP-G +>GCF_023573625_PROKKA_00257 +M-------------------------------------------------------SEEL +RILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQMPLMDG +VEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE +SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA +ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000075.fa new file mode 100644 index 0000000000000000000000000000000000000000..8e0facce9c891c439b96874dc8d8cc41b9c821c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000075.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00282 +MT----------GG-----------------DPAALMDALGAWFHPLTALLVALDAPI-- +PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA +WWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS +LAWSSSMVGLGWITGRATGLPWWASAMVGMVFGTLAGLMIAGIMAHRRRGRKG------- +--- +>GCF_003691675_PROKKA_02297 +MT----------GG-----------------DPAALMDALGAWFHPLTALLVALDAPI-- +PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA +WWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS +LAWSGSMVGLGWLTGRATGLPWWASAVVGMVFGTLAGLMIAGIMAHRRRGRKG------- +--- +>GCF_005280335_PROKKA_00071 +MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPI-- +PPVPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGD-VGLYALFRHGLADRLD--RWA +WWRRVHRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS +LAWSGWMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVA-RRRARKG------- +--- +>GCF_020097155_PROKKA_00057 +MT-----------------------------DVTALLEGLGPWFHPLTFLLVALDAPV-- +PPTPSEVLVIGSGSLAAAGRLGLATSVLTAWLGCWAGD-VGLYALFRHRLTSVLD--RWG +WGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGGRTASMAAAGVAGVRWRPFLWLSGTGS +LAWSVYMVGLGWITGSATGLPWWASAVVGVVLGTLLGAAVAAVIAWRRRGKEGA------ +--- +>GCF_020097155_PROKKA_00450 +MPVLTNIL-----------------------DAASILHSLGPWTLGGIGSMVFIESGVLF +PFLPGDSLLVTAAALHVELGIALWAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVL +KTERLAQA-EAFFERRGPLALVLG----RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGA +VAWVCSMVAVGALLGQIPGITKSIDGIMILIIVISVAPIAIQALRARRKARRDAVMTEGQ +PVA +>GCF_023573625_PROKKA_00281 +MT----------GG-----------------DPAALMDALGVWFHPLTALLVALDAPI-- +PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA +WWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS +LAWSGSMVGLGWITGRATGLPWWASAVVGMVFGTLAGLMIAGIMAHRRRGRKG------- +--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000078.fa new file mode 100644 index 0000000000000000000000000000000000000000..49037847b108223a9a2edbfa8e564336787f9ebd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000078.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_00310 +MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ +-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE +YVAVPAGQLMAVPDGVGLVEA------AALPEVACTVHSTLVGRAGVQAGDRVLVHGATG +GIGSFAVQFLTAVGARVLGTAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGH +GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL +RSRSVTDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV +TDPADARRPSGDRA +>GCF_003691675_PROKKA_00025 +MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ +-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE +YVAVPTGQLMAVPDGVGLVEA------AALPEVACTVHSALVGRAGVQAGDRVLVHGATG +GIGSFAVQFLAALGARVLGTAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGH +GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL +RSRSVVDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV +TDPADARRPSGDRA +>GCF_005280335_PROKKA_00027 +MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ +-REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCAL----LAGGGYAE +HVVVPAGQLMAVPPGVDLVTA------AALPEVACTVWSTMSERGGVRAGDVVLVHGGSG +GIGTFAVQYLAAIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGR +GADVVLDVVGGPYLDANVRCLAEEGRIVVIA--VQGGPKADGFNLMRLVSKRGWLTGATL +RARSVVDKARIVAGTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLV +TDPADALWPQEDRT +>GCF_020097155_PROKKA_00023 +MD----TA----PDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQ +-REGHYPVPPGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCAL----LAGGGYAE +HVAVPAGQLMSVPDGLDLVSA------AGLPEVACTVHSNLEGRAGVRPGEWALVHGATG +GIGAFAVQYLSAVGVRVLATAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGH +GADVVLDVVGGPYLAPNVKALAMDGRIVVIA--AQDGPVPEDFHLMRLAARRGWVTGSLL +RPRPPDEKAGIVAAAERAVWPLVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLV +TDDADALLPGG-AA +>GCF_020097155_PROKKA_00654 +MHPS--LP----RTMLAAIIPAPGGRPELR--QCPVPEPGPGEVLVRVMASSVNPTDVMT +WRRGMFVTGQTVPFVGGYDMSGIVVKLG-----RGVTALDVGDAVTGMPRFPAPAAAFAQ +YSAVPARHLARIPTGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASG +GVGSLACQLAVNLGAQVTAVTSDRGR-TLVEVLGTRHVVDR------ATVDW--QRFAG- +CFDVVLDTVGGDTTPRSLAMASPDGVVVALHPYAHDDLAQRDPRLRRMLVE--------- +-----PDHHALELLIEQA-----ARGRLTVQVGAGYPLSDLGDALLHVETNKTPGKTIIH +I--------QGDNA +>GCF_023573625_PROKKA_00317 +MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ +-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE +YVAVPAGQLMAVPDGVGLVEA------AALPEVACTVHSALVGRAGVQAGDRVLVHGATG +GIGSFAVQFLAALGARVLGTAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGH +GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL +RSRSVVDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV +TDPADARRPSGDRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000084.fa new file mode 100644 index 0000000000000000000000000000000000000000..f57b2f7f9e465ef348846381db22b4e9f28bb6fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000084.fa @@ -0,0 +1,54 @@ +>GCF_002008305_PROKKA_00418 +MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERR---------GTTADTADTAGEQAAAPAAPTRLSR +LDEVAAEQDARPAAAVKPAGGPAA------------SETAAAGRETDESVA--GVAGGAGVTVDQQDAPRTDATAET-SR +PTA--APTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDEQTPAADVAAAPASPSPVTETPA--PAAPAAEAPQ +HRSHLTP----APEHVHGTVPAEEVAAEHTPTKEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAE +RSAAGSLRIDGTPGVPGRVAEAGREPARTED-------------HRADAAQPAAVEPAAERPSLEAAAERPSLEATPATR +RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAAAGTAA-TAGTAGTAAPTS +STPTTVAPDT--------STSSAPTNEEPAEDDTEGAALPDLRADRDE-------------TRGSDAEGESKL------- +AQAGAVAASAFETVRDKVAIPLRDNVAVPAK--DKAVKVVKDKLAQAQERRWGK--------------R +>GCF_003691675_PROKKA_00139 +MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERR---------GV---SADTAGEQAAAPAAPTRLSR +LDEVAAEKDARPAPAVRPAGGLAA------------FDTAAADRETDESGA--GVAGGAGVTVDQQDAPSTEATAQTHRR +DAA--APATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQTPAADVPATPASPSPVTETPA--PAAPVAEAPQ +QRSHLTP----APEHVHGTVPADEVAAEHTPTKEFATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTE +RSAAGSLRIDGTPGVPGRVAEADREPARTDD-------------HGADVAQPAAVEPAAERPPLEAA---------PATR +RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAA-------AGTAGTAAPTS +STPTTVAPDT--------STSSAPTDEEPAEDDTEGAALPDLRADRDE-------------TRASDAEGESKL------- +AQAGAVAASAFETVRDKVAVPLRDNVAVPAK--DKVVKVVKDKLSQAQERRWGK--------------R +>GCF_005280335_PROKKA_02541 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------PTDAEPAADDTEGAALPVQDATRADAVRP-------GTARTDASAGDSKL------- +AQAGAAAGTVLETVRDKVAIPLRDNVAIPAK--DKAVKVLKAKLAEAQERRRNK--------------R +>GCF_005280335_PROKKA_02542 +MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERR--RVTPTAAGVGASHEDALEETHDADARPHTVA- +----STGGDVAPAAAAGAAAGTTRLSQLDDVA----PVAAAAADADAESLPADGVAAGSGVTVDQQ-----DASDQS-VR +PAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVAGGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQD +DRADRTAQDAADAEPVKGTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATA---- +--------------------------------------------------------------------------ASRETE +--TETDDSRG-----DDAGQDRDAERAVAEGVAGGTGVTVDQKAV--------AEAAATQGAPASAAGAASAAGAAARRR +DRGRRLDPACGGARLLQDRRH--AGHARPRRLRGAGRGRG---GDR--PARPPRRRP-----------GDARLHHPRDAP +GRRAG------------AGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPRPPRRTAPAR +>GCF_020097155_PROKKA_02410 +MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTVGASTVPATGDAPADRTDGR- +----AAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAAGHAAVP--GVTGGSGVSVDEAEGVAKDATGQD-VT +PVA-------DAQRRNGSSAAPAATGAGLGLAAAGVAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAE--TQAEAAQA-- +--------DAAPAEHT--VVP-------------------GVAGGDAVTVDTADVQSSSAPQGAQAAAGRSDLTDAE--- +---ARTYPVTGLPGVPSAVDPEQVAAARVQDAAELKAAEGQGAEHERGASQPADPESVPGTVPLTGE--EAVIEAPVHTH +--EMPEPVLGTPAYIQDSTTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVPVE +ETETAVVPVA--------ETR--SADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHD-EHRSRLEIVKDAV +AETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQERRWGK--------------R +>GCF_023573625_PROKKA_00421 +MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERR---------GTTADTADTAGEQAAAPAAPTRLSR +LDEVAAEQDARPAAAVKPAGGPAA------------SETAAAGRETDESVA--GVAGGAGVTVDQQDAPRTDATAET-SR +PTA--APTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDEQTPAADVAAAPASPSPVTETPA--PAAPAAEAPQ +HRSHLTP----APEHVHGTVPAEEVAAEHTPTKEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAE +RSAAGSLRIDGTPGVPGRVAEAGREPARTED-------------HRADAAQPAAVEPAAERPSLEAAAERPSLEATPATR +RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAAAGTAA-TAGTAGTAAPTS +STPTTVAPDT--------STSSAPTNEEPAEDDTEGAALPDLRADRDE-------------TRGSDAEGESKL------- +AQAGAVAASAFETVRDKVAIPLRDNVAVPAK--DKAVKVVKDKLAQAQERRWGK--------------R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000086.fa new file mode 100644 index 0000000000000000000000000000000000000000..c424f6c22674e87c297d7d0921171736898ba6e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000086.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00448 +M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA +VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD +LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA +HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES +NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE +LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL +LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR +SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFRG +>GCF_003691675_PROKKA_00169 +M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA +VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD +LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA +HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES +NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE +LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL +LVKVNQIGSLTETFDAISLAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR +SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFRG +>GCF_005280335_PROKKA_02509 +M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA +VPSGASTGEFEAVERRDGDTKRYLGKGVLDAVAAVE-EIADELEDEFAVDQRAVDRLMLD +LDGTPNKGKLGANAILGVSMAVAAAAAQSSDLMLYKYLGGPNAHV--LPVPMMNILNGGA +HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHSLKKVLQEKGLSTGLGDEGGFAPSLES +NRAALDLIAEAVEKAGYTLGED-IALALDVASSEFCE-KGAYTFEGQKRSAEDMVAYYTE +LADNYPIVSIEDPLDENDWDGWRLLTEKLGDRVQLVGDDLFVTNVERLQRGIDDKAGNAL +LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR +SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRYRG +>GCF_020097155_PROKKA_00683 +MNDYISGIHHHGAHQGEYVTHHDHPVTIDAVHGARILDSRGYPTVRVSLELDDGRTVTGD +APAGASTGAHEAVELRDGGSA-FGGRDVTQALHLIDTDISGLLTGRSWSAIGQIDAALAE +LDGTTGYRRLGANSVVATSIAASRALAHAADLPLWQWIAEITGSTPRMPVPHFNVLNGGA +HAANELDFQEFMIAPVNAGSMADAVRIGADVYHALAALVRDRFGSLGLGDEGGFAPSIAA +PEEALDLLVDAIRTAGYEPGVDQVAIALDPAANEFSQGDGSYRVLNDSLDRDGLVDYYRH +LIDTYPIRSIEDAFAEDDHEGFRRMQAALGDRIQIVGDDLYVTDPQRIRDGGEQQLTNAA +LIKPNQIGTVSQTLGAIATAKSIGMASMVSHRSGETTDTFIADLVVGTGTGQIKSGAPGR +GERVAKYNRLTEIAEQ---------HPELPYGLI +>GCF_020097155_PROKKA_02380 +M------------------------AQIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA +VPSGASTGEFEAVERRDGDTERYLGKGVQDAVNAVF-EIAEELEDELATDQRAVDQMMLD +MDGTENKGKLGANAILGVSMAVAVAAADSADLPLYKYLGGPNAHV--LPVPMMNILNGGA +HADSNVDIQEFMIAPIGAPSFREALRMGAEVYHSLKKVLQEKGLSTGLGDEGGFAPNLES +NRAALDLIAEAVQKAGYTLGED-VALALDVASSEFCE-NGSYTFEGRQRSAEEMSAYYAE +LVDAYPIVSIEDPLDENDWEGWEHLTEQLGDRVQLVGDDLFVTNVARLQRGIDEKAGNAL +LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR +SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFQG +>GCF_023573625_PROKKA_00451 +M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA +VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD +LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA +HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES +NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE +LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL +LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR +SDRVAKYNQLLRIEEDLDDAAVYAGRSAFPRFRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000090.fa new file mode 100644 index 0000000000000000000000000000000000000000..d98fb2869eecb2fb8daf90d85173344ddd8c34e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000090.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_00521 +MTPRGSCWSSLPVGARFRLWNTLDPMHLLVTGGAGFIGSNFVHHVVRETGHDVVV----- +-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH +NDNSLNDPSPFIQTNIVGTFVLLEAARKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN +PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP +RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGADGEKNNREVVEILLELFDR +PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP +AKAAVEATYRAQG---------------Q +>GCF_003691675_PROKKA_00243 +-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVA----- +-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH +NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN +PSSPYSASKAGSDHLVRAWV-RSFGVRATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP +RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR +PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP +AKAAVEATYRAQG---------------Q +>GCF_005280335_PROKKA_01219 +-------------------------MRFVVTGAGGFLGSNVVRELLAETDHDVVAVSSQT +DRELAAQLERAPYPALRRFPQVHPRTRL-LEAG----------FLRDGDIVINCAFPWNR +GGRAMADGLEYLTR----LFQSAHAVALH--TFVNVSSQSVYSQARTEAA---DESSPVE +CDTPYSTGKYAMELAAELVLPPKVLVNARMSSLIGPGYDVRIVNRFIARFLAD-----EP +VSIQGGDQVFDFMDVRDAARALIAVALAGPPEGSAALNIGSGAPRTLRDIAQTVADVVRT +HTGHDPRIAWEPSAGDDRTLGLDSGLLRREYGFAPRHTLEDSALS--------------- +---ILQAMTSAQSASVGETPTGSVEGGRR +>GCF_005280335_PROKKA_02428 +-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVV----- +-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAQSDAVVHYAAE-SH +NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN +PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP +RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR +PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPQFTDIRAGLADTVRWYRENEAWWRP +AKAAVEAKYRAAG---------------Q +>GCF_020097155_PROKKA_02311 +-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVV----- +-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH +NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN +PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP +RLYGQGINVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNKEIVEILLELFDR +PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPQFTDIRAGLADTVRWYRENEAWWRP +AKDAVEATYRAQG---------------Q +>GCF_023573625_PROKKA_00521 +-------------------------MRILVTGGAGFIGSNFVHHLVRETDHDVVV----- +-------LDKLTYAGNRDNLVGLPESRVRLEIGDICDAALVDRLVAESDAVVHYAAE-SH +NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN +PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP +RLYGHGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR +PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP +AKAAVEATYRAQG---------------Q + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000092.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ac8bccd34a26dd7aa318b493e2a2e916ad4fc09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000092.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00554 +MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD +RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA +EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP +FLVYRLALD +>GCF_003691675_PROKKA_00279 +MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD +RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA +EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP +FLVYRLALD +>GCF_005280335_PROKKA_00640 +MERPAPTA-------EICPVRPEDTDAVVALWERTLPEY--GDPTRPQRAPRPSIRRKLD +-WGDGLFWLAVSDEEVVGTV--------MAGYDGHRGWIYS-LAVHPDHRRGGLGTALVA +H-AEQELARLGCPKVNLQVLATNADGAEFWAATGYQPDPVLG------------------ +-LGKRLG-G +>GCF_005280335_PROKKA_02391 +MTETAPTVPTPPARPQVRPLRPEDHEAVAAL---TVASYVDGGHIAPGSRYVKTLRDVAG +RAARAEVLVAEVDGQVAGSVVLTPLGSPMAETAAPGEYEFRMLAVHPDHHRRGVARTLMA +VIEERARALPGIEAIALTTMPTMTDAHRLYEALGYVRVPERDWYLRDVIPDLDPADETGP +FLVYRLPLA +>GCF_020097155_PROKKA_02275 +MSDVT-----------VRALRPEDHEAVAAL---TLASYTTGGHFEAESDYLETLADVAG +RAAVAEVLVAELDGQVAGSLVLTPHGSPMAETSVPGEYEFRMLAVDPAVHRRGVATALLA +EVVRRARATPGVEAIALSTMTSMTDAHRMYERLGFVRVPDRDWRLSDLEPGLDPAEDAGP +FLVYRLPLT +>GCF_023573625_PROKKA_00557 +MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD +RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA +EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP +FLVYRLALD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000098.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2de5b4bd66769856ce7670c66813a2f312c7e8d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000098.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00626 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSAREWSDAHAANAVLDAHAGDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVRVRCCHWFRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLALDALQMALARR +GGKAEVQGCRVHSDRGSQGGFNR--SSQHPLGITGGMGD-GKQG---------------- +--------------------------------LGE---------------EDQ +>GCF_003691675_PROKKA_00371 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR +GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLRKLTPVEFEMVQSVQAAAAA +>GCF_005280335_PROKKA_00392 +MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR +GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWQSFDQLRLAIVSWIERTYHRRRRQAPLGRLTPVEFEMVQSVQAAAAA +>GCF_005280335_PROKKA_00411 +MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFLKR-------------------------- +--------------PGSD------------------------------------------ +--------------------------------------------------EDS +>GCF_020097155_PROKKA_02188 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYPWLAEPVSAREWSDAHAANAVFDAHADDP +EFGYRFLADELRGRGLDVSDHQVLKACRLVRVRCCHSIRRGSGKRPGPAVHDDLVRRQFR +ADKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSIDRRMSSQLAVDALQMALARR +GGKAGVQGCRVHSDRGSQFRARRFVETLRVNSLIGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWDSFAQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA +>GCF_023573625_PROKKA_00605 +MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP +EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFA +AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALGRR +GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV +LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000100.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3d93d6ac086d04623e9a1f74e74a44812e9cada --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000100.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_00644 +M-------------TSVPTV-----PFHDGQQIPQLGFGVWKVEDDVAADVVEQAIRAGY +RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDVSLDK +LGTDYVDLYLIHWAKPAQGKYLETWKALIEAQKQGKVRSIGVSNFPAAQLEEIIEATGVV +PVIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEARGATPA +QVVIAWHLAHGFVVIPKSVTPERIVSNLEAAGVELTDDDVARIDALDREDG-RLGPDPAV +IDF-- +>GCF_003691675_PROKKA_00381 +M-------------TDVPTV-----PFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGY +RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDVSLDK +LGTDYVDLYLIHWAKPAQGKYLDTWKALIEAQKRGKVRSIGVSNFPAAQLEEIIEATGVV +PVIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEVRGATPA +QVVIAWHLAQGFVVIPKSVTPERIVSNLEAAGVELTDDDVARIDALDREDG-RLGPDPAV +IDF-- +>GCF_005280335_PROKKA_02319 +M-------------TSVPTV-----PFHDGQSIPQLGYGVWRVEDEVAADVVAQAIRAGY +RHIDTAAIYGNEEGVGRAVAAS----GVPREELFITTKVWNSAHGYDEAL-AALEESLGK +LGTDYVDLWLIHWAKPTQGRYVDTWKALIEAQRQGKVRSIGVSNFPAEQLEEIIEATGVV +PVIHQVETHPYWQQRELRELEERHGILHESWSPLGQGGELLE--DPEITAIAEAHGATPA +QVVIAWHLAKGFVVIPKSVTSERIVSNLAAADVELTEDEVARIDALDREDG-RIGPDPAT +IEF-- +>GCF_020097155_PROKKA_00584 +MSTDSRHTAIPVDETPVPETLTLTGTGVDGVEMPRIGLGTWPLRGAEARDAVEQALRIGY +RHVDTAQNYGNEDAVGEGIAAAIHAGVLDRDQLFVTTKVNREHHGDARTVRAAVECRLRV +LGLEHVDLVLVHWPNPDQDRYLETAWSLSELAEDGRIRAWGVSNFTPAHLDRLAGAGLRA +PV-DQIEVGPLRQSPAWQEGVRAHGAAITAYSPLGRADQDLGALEP-VAAAAARTGRTPA +QVVLRWHLQSGRAAVPKSVDPARQAQNLDVFSFALTAEEMAAIDALDTGEGPRRHPD--- +-EFGH +>GCF_020097155_PROKKA_02178 +M-------------TTVPQT-----PFRDGQSIPQLGYGVWQVEDAVAADVVEQAVRAGY +RHIDTAAVYGNEEGVGRAVAAA----GVPREELFITTKVWNSDQGYDEAL-AALEASLAK +LGTDYVDLWLIHWAKPAQGKYVDTWKALIEAQRQGRARSIGVSNFPAEQLEEIISATGVV +PVIHQVETHPYWQQRELREVESRHGIVHESWSPLGQGGELLS--DPVITAIAEAHGATPA +QVVIAWHLAEGFVVIPKSVTPERIVSNLTAAELELTAEEVDQIRGLDRADG-RIGPDPAS +ITF-- +>GCF_023573625_PROKKA_00614 +M-------------TDVPTV-----PFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGY +RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDASLDK +LGTDYVDLYLIHWAKPAQGKYLDTWKALIEAQKQGKVRSIGVSNFPAAQLEKIIEATGVV +PAIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEARGATPA +QVVIAWHLAQGFVVIPKSVTPERIVSNLEAAGVELTADDVARIDALDREDG-RLGPDPAV +IDF-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000104.fa new file mode 100644 index 0000000000000000000000000000000000000000..0f5c27101e87ff7e56905b5e2ffeb10b3ef9e3ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000104.fa @@ -0,0 +1,126 @@ +>GCF_002008305_PROKKA_00731 +MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSAP-----ARGPELAVVTEHGP +DAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALP +RPVTPEPPAVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA-- +-RADALVRRR------------AQAALSPGAVARAVRSGATDRF-----------------------GLTSG-ADEAVA- +------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW +AVFQLLRHAVAADGAFVVEAGGVRRTWWSGGSGPRLLVSAPEDAA--LDPAWRAWRAAIGGDA--GTTPT-ARADLPWTR +Y------------------------------------------------------DFTGPSPAPGDA-VVDLRGRTVVVP +AEQQRF---------EDVTADGLADGTLVAWLTELADDVVDLGLLP--ADDGDGTLTPPGQVGARDAVDGLTVTLARSGD +-ETGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV +GTASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL +AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ +------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVENYAAG +DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG +GRAETLAAVVEVALRSGRP----VAVLDGTGEAAA-AARS---------GTPVLTPDAEGA--GEAAL------------ +---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRE-LATGRL +LLHLPHRFFVPAGTNAEHRLIW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------- +>GCF_003691675_PROKKA_00462 +MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGRRSVTYAEGVGSAP-----ARGPELAVVTEHGP +DAGRIVPLGEGGLSVGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRATGRLWDGRSPLPVGRTALGLVRGPGSALP +RPITPEPPVVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPMFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA-- +-RADAVVRRR------------ARVALSPGAVARAVRSGATDRF-----------------------GLTAG-ADEAVA- +------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW +AVFQLLRHAVAADGAFVVEAGGVRRIWWSGGSGPQLLVMAPEDAA--LDPAWRAWRAAIGDDA--GTTPT-ARTDLPWTR +Y------------------------------------------------------DFTGPPPAPGDA-VVDLRGRTVVVP +AEQQRF---------EDMAADGLADGTLVAWLTELADDVVDLGLLP--TDDGDGTLTPPGQVGARDAVDGLTVALARSRD +-EAGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV +GAASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL +AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ +------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVENYAAG +DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG +GRAETLAAVVEVAMRSGRP----VAVLDGTGEAAT-AARS---------GTPVLTPDSEGA--GEAVL------------ +---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPAAAGLRLAVFGGRE-LATGRL +LLHLPHRFFVPAGTNAEHRLVW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------- +>GCF_005280335_PROKKA_02222 +MGWTVRILGGRTPETWRVSPLPRDPTLRDRAVRERAPGRSLRAVASGPGSVTYAPWGGAEP-----APGPELSVVTERGP +DGGRLAPLTGGGVSVGRGRARLLLDDPAAPSRPTRLRLAAAGLHVEGAVEGAPRLWDGRRPHRIGRTTLGLVRGPQPPLP +PPSLPAPPCVDLGSPPAGQSLAIPLLTAAAPLVIGVALVLVMRNPIFLLFGLLSVAVALTMLGLQRRARMRHAALLAE-- +-RAAAVTAHR------------ASAALSPGDVARAVRARTPDRF-----------------------GLTGA-AEGPAT- +------LSWGLGMGALGLSRDD-----PDQAWVAAVTARREALTVPSPAARTVVLG-----PPR--------EAAGVCRW +VVFQLLRHAVAAGACLVVESGGSRRCWWAGGTGGALLVTAPADAA--LEAAWTAWTAGIGG------APG-ERTGAQPAR +I------------------------------------------------------DFTGADCAPGET-VVDLRGGMLTDP +GQEQRI---------TGLEADGIAPATLPGWAAELADDVVDLGLLP--ADAGAGALFPPADVGTRDAVDALRVSLEAGSD +GGPGALALDLAAD---GPHLLLAGTTGSGKSDLLLSLLLGVAAHHPPAEAAFLLLDFKGGASFGPLAALPHTMSLETNHV +GAASL--RALNAIRAELHRREALFAEAG----VSDYPAFRRRH-----PEAALPRLVVAVDELRVLVDDHPDAAAVLQRL +AATGRSLGFHLVLATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAATRLDPRRPGSAILSTAGREPVPFRASR +------------------WAVDGGAPVWRR---LG-----------EAAETPAAAPW---------KAVVAQLVERYAAG +RWPTP-PPVVTPALPERWVPDRTRRAGATA---------------LALLDDAAHGRHRPWRWAPGGGGRAAWIVE--PAG +GRAEALAAVLEVGVRGGAP----VVVLDGTGEAAAIAAPE---------GVRLLRPDEEGA--GERAA------------ +---------------ACLRELAAAGGTAVLTGWTTWAGLRLGESYRTLEEDAQGWLGGREAAGLRVAAFGGRE-LATSRL +LLHLPHRFFVPAGTSAEHRLVW-PRLVEV-EPLPGRAVHVSPDVPEPGLPC--QLASPGAHRSGAADAASTL-------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------- +>GCF_020097155_PROKKA_00342 +MTRRL-----------------------------------VHR-----------------P------------------- +--GRTVP-----------PARLLPED--------------------------------------------VITGPQ---- +----PVDPAMDQGSGP-NLLMIVPMVAAAASMLTMMAFRQSPFAAVGALAMVVTLTAMLILYGSQAGKARRRRTTLRETY +TRYLDRQRRRLIAEDEQARAIAASAAPPPGALLDVVR--RPDRLWERRRTDEDFLQTRVGLGARPVRALRVA-VQDNATQ +VQDEFMLKQAESLATRFRTTDDMPVSLPLDSLGNLAVVGPREFGLTA--ARSLVLGACVQQAPEDLVVALLVPPERRADW +PWFDRLPHARVADAA--------------SPTGNRLLVAADADDLMRMLRADLARRAGIAAETLRASTRD-GRAATELSR +LVIVVDSHGEPAAGLPLEGSHLPLVSRGITLITLVSDRLDEPSDVRLRLSATGGTDVTGAAEFQVDD-ARQDEGRPTVSH +GRLDTFDAATALGVATDLQPLRLSADSLEHAEDDLSSTQTFLQMLGLSPELTLEELRRRWRPRGQDEF--LRVPIGEDDR +GDAVHLDLKEAAQLGMGPHGLCVGATGSGKSELLRALVFALLASHAPERMSLLLVDFKGGATFAPFHGAPHVAGIITNLS +DDLSLVERVYASLSGEILRRQEVLKAAGNLANITDYQVHRERELAQGRSVEALPHLIVIIDEFGELLTARPDFIDLFLSI +GRIGRSIGVHLLLSSQRIESGRLRGLETYLSYRLGLRTLSESESRTVLDTADAFHLPP-LPGFGYLKVDTSVYTRFRSGY +VSSPLEEEAAARAEQERVLTADDDVPPALPVPDYGLQLVLPTEGAEPQLSSGAGAAQVMEEPEDHRPTIMETLMD--RLR +EVPSPVEPLWLPPLPEALTLDQAAGDVAVTDHGLRLPAGGDLEVPIGLIDDPEHQWQGLWMLDF-ASGSGHLIVQGGPRS +GKSTLLQTIVTSLALTHSPQQVGVYCVDLLGSSLL-PLQG----LPHVGGVAIRTNREMVTRTLREVSAMLTLREKLFEA +EGIDSMTTLRRRHADGSLPDLGSADVFLVLDGYG-----QVNEEFADLTPVLNGLISRGAAYGIHIITTVARQGEIRSTQ +QTFFTHRVELRLSTPSDSAIDR-KAAEEVREDTPGRGLASTRLHGQVALPRVDGAADPGTAAEGLAETVQRIAESARGEA +MAVRVLPPTTERPPLEQLEDPGRLPVGLLEDDLSVRSLDIDGRERHVVALGDAQTGRSSMLRQFARHFMDTHADTEMMFV +VFDPRGELKGVIPDAYMAGYAGNATVAVPLARALVSELEKRQSTDPKDAGPMRQARIVVLVDDYDVLTVAGDSPLAPLLP +YLPMARELKLHVFLTRRMKGASRGLYEKFLASLVSQDAVTLMFSGDRSEGVLFDGLRPKRLPPGRAVLIGASRRHETVQT +FTGPPAPGRG +>GCF_020097155_PROKKA_02098 +MTWRVRVLGLPVEQDWAVSELPLDVDGQDRVVAEHFAPLRVERARGGGTTLTYVAHPSGTPPVPAAGSGPELAVGTSAGP +DAGRLVPLTAAGLTVGRGRSRMLLDDPQCPSRPVRLALGPSGVSVDDG--RTRRTWDGLDGLPIGDSILRLVRGRQRPLP +PALTPPPAQIDLGAAPAEQSLLVSLAMAVGPVLIGLVLAVTTRSPLFLLFGIVSLLGVGVLLGVQRRTRRRHADLLRE-- +-RALDVVRRR------------VAAVSGPADVSAACRAKAEDRF-----------------------GLVSARPGDGPA- +------LLWGRARGSVAFTRGD-----VADHWRSAACVDQPVLGVAAADRGTVLCG-----TGR--------PAQAAARW +TLFQLLRHAVATGSSLVVRSPDGARVWWPAVPGAPTIALELEDTA-PLAGAWEVWTASLGAEM--SETRRHGCADEVLVR +--------------------------------------------------------CTGTPPADLDADVVDLDARQATLP +GQGLEL---------TDLTPLGISADTLQWWLAELADDVAHLGLGG--PPASAPPLRRPHDVGAHRAVRNLAVPLTSSSA +GDAAPMVLDLAAD---GPHALIAGTTGSGKSDLLLSVLVGLAARHAPAEVSFVLLDFKGGASFGPLRRLPHTMSVETNHV +GAASL--RALQAIGAELRRREALFAEAR----VADYPAFRAAH-----PDTALPRLVVAVDELRVLVDEHPDANAVLQRL +AATGRSLGFHLLLATQRPGGAVSADVRSNLGTTIALRTATEQESWDLVGSAAASRIDPAAPGTALLARGTGAPVPFRASP +------------------WSAGPVRPRWTP---WGV----------PVASAASGTDW---------PSVVEDLVQACRDR +DLPIP-EPVVSPPLPGSFAPDRSRRRSADV---------------LALVDDAARARHVPWRWPLGAQGNGAWIVE--PAG +GRALVLAAVLEAAGRTSPA----VLILDGSGECAA-ALPTVADALPDLADVTLLTPEAQPADVGEQVC------------ +---------------GAVADLAAVGGTLVITGWQSWAGVRVGETYRTLDEELHRLLGTQAARGLRVAAVGGRE-LVTARI +APHLPHRFYVPAGTTPDHRLVWPPKLVEV-EQLPGRAVHVHPGGPTVGVPA--QLAFPAHSAAGAGTDSDDQ-------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------Q +>GCF_023573625_PROKKA_00695 +MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSAP-----ARGPELAVVTEHGP +DAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALP +RPVTPEPPAVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA-- +-RADAVVRRR------------AQAALSPGAVARAVRSGATDRF-----------------------GLTSG-ADEAVA- +------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW +AVFQLLRHAVAADGAFVVEAGGVRRTWWSGGSGPRLLVSAPEDAA--LDPAWRAWRAAIGGDA--GTTPT-ARADLPWTR +H------------------------------------------------------DFTGPSPAPGDA-VVDLRGRTVVVP +AEQQRF---------EDVTADGLADGTLVAWLTELADDVVDLGLLP--TDDGDGTLTPPGQVGARDAVDGLTVTLARSGD +-ETGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV +GTASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL +AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ +------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVEKYAAG +DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG +GRAETLAAVVEVALRSGRP----VAVLDGTGEAAA-AARS---------GTPVLTPDVEGA--GEAAL------------ +---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRE-LATGRL +LLHLPHRFFVPAGTNAEHRLIW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000105.fa new file mode 100644 index 0000000000000000000000000000000000000000..e2407e491d63a2ba21c67a3af7fd9d27aa63cde1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000105.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00747 +------------------------------------------------------------ +----------------------------MLSGFCLALGTWSTVAAEAADAALARRWGAAA +RLWTAHLGLGLVAVVVGWGAGLGLHAVLAG +>GCF_002008305_PROKKA_00748 +MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL +AVPELVYASGG------------------------------------------------- +------------------------------ +>GCF_003691675_PROKKA_00478 +MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL +AVPELVYASESWGDGQGL--MLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAA +RLWTAHLGLGLVAVVVGWGAGLGLHAVLAG +>GCF_005280335_PROKKA_02182 +MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL +ALPSLVYASGLAGDPLGVAGLLVASLTA---GFCLALGTWSTVAGQAADAVLAGRWGAAG +RIWAAHLGLGLLAAAAGWGLGLGARLLVA- +>GCF_020097155_PROKKA_02077 +MS-----AGTVLLTVLLAGLAA--AVGAGLRHLADHRWGGRGVLLANVTASALAG----- +ALFAIGFGPGSA-DPEGPAGAALALGAA--GAFVLALGTWSTVAFQAAQEVLAGRTRRAV +RVWLVHLASGTAAAVVGV---LAVGFLVR- +>GCF_023573625_PROKKA_00712 +MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL +AVPELVYASGGGGDGQGL--VLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAA +RLWAAHLGLGLVAVVVGWGAGLGLHAVLAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000106.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000106.fa new file mode 100644 index 0000000000000000000000000000000000000000..fdfbdfca1cf5b348bfdad239444339ce0dfa4217 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000106.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00762 +MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT +ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG +WFRRFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM +TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMG-GRVVASGSPRDVLT +VENLDIAYGRGALHGPSTAVEDAADFLDDPAG--GRRH +>GCF_003691675_PROKKA_00492 +MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT +ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG +WFRRFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM +TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMG-GRVVASGPPRDVLT +VENLDIAYGRGALHGPSTAVEDAADFLDDPAG--GRRH +>GCF_005280335_PROKKA_02168 +MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ +ALAGVLDPAAGRLEVRG---ESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAG +WFRRLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPV +TGLDIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMD-GRVVASGPPAQVLT +AANLDAVYGRGALHAPLLV------HLDDPADCSPDRG +>GCF_020097155_PROKKA_00528 +MN---PAAPAPAIRLADVSAAYDRRRPVFTG---ADLVIDGPGLVRVHGRNGGGKSTLIE +LVSGYLRPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPL-----------MDVHDHVV +FASRWAGADPAEGLARAERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPF +NGLDDESSAVLAAELAAW-ARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAP----- +-----------------------------PAD-PGVRP +>GCF_020097155_PROKKA_02063 +MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH +ALAGTLEPAAGSLTVRG---ESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVG +WFGRFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPL +TGLDLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMS-GRVVAAGTPRQVLT +EANLEAAYGHGVLHGPRLP------FLDDPVD--GVR- +>GCF_023573625_PROKKA_00726 +MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT +ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG +WFRRFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM +TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMS-GRVVASGPPRDVLT +VENLDIAYGRGALHGPSTAVEDAAEFLDDPAG--GIRH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000109.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec2ddd59a016f13a329cee62d56a2ddd3095500a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000109.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_00886 +MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLGRNGVVPALGHEMRGERAAAL +AALGVDEAGR------PVRASRPGAGNVRGLVHRADAALGMGRPDIAETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGA +AALAARHPRNRHLARRMAGERD----AFRGVAPTVPTEP-----GYRPVPG----RVLHVLTNSLPHTGSGYAQRSHAIL +TSLRDEGFDAAAVTRPGYPVQIGVPWAAQRDVVDGIRYARLLPARLAQG--QAARIQQHAELLAAHVRRHRPALLHTTT- +--HFVNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQER---EAEAARRADGVVTLGAGMRDRLVA +AGVAEDAVVLCPNAVGPAFVAERVDRDEA-RARLGWDLPTDAFVVGTVSSL-VDYEGLDILLRAAARLAPHRPGLRVHIA +GDGVARPGLQALAAELGIAELCAFPGRVDREDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALA +ELVEDERTGLLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLY-------DRLGVHPR--- +------- +>GCF_003691675_PROKKA_00608 +MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLGRNGVVPALGHEMRGERAAAL +AALGVDEAGR------PVRASRPGAGNVRGLVHRADAALGMGRPDIAETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGA +AALAARHPRNRHLARRMAGERD----AFRGVAPTVPTEP-----GYRPVPG----RVLHVLTNSLPHTGSGYAQRSHAIL +TSLRDEGFDAAAVTRPGYPVQIGVPWAAQRDVVDGIRYARLLPARLAQG--QAARIQQHAELLAAHVRRHRPALLHTTT- +--HFVNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQER---EAEAARRADGVVTLGAGMRDRLVA +AGVAEDAVVLCPNAVGPAFVAERVDRDEA-RARLGWDLPTDAFVVGTVSSL-VDYEGLDILLRAAARLAPHRPGLRVHIA +GDGVARPGLQALAAELGIAELCAFPGRVDREDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALA +ELVEDERTGLLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLY-------DRLGVHPR--- +------- +>GCF_005280335_PROKKA_02050 +MDRPGGLEGAFDRHWRKIRRELGSVYRDYRAGRASTGSALKR----ATRIG----------------LKHGVLAPRDA-- +----LAEFLRLRD--EAVGPTLAGAGPMTMLPGELDSERARIWLSVLERHYPSGPART---AYFEQLRRLALRDGQISTA +LDATAELASSNTSMARAAVDVNGRMTELSGWLPRLPG-------PVEPVSGCGTNVVLHLLKESRPYLSNGFTSRTQWNL +LAEKDAGWTPVVLTEPGFPEGMTEGRPSTVEEVDGIEHRRILTGVSYRGVPFDRWLEDFAFLALDHVRNVRPDVLHVSSG +RRGYETALVGLALREKTGLPLVYEVRSFFEGNWT----PDLDIEEHSEVFRRRREVETRCMIAADRVLTLGEAMRDEIVA +RGVPAEKVDIVPNGVQLDRF-TPAPRDPAIAARHGITLPT----FGYVSNMDHPREGHELLIRAALLLQERGVEAQCVLV +GGGRRFDELRALARELGIANRVVFTGPVDHEEVAALYGLIDVFVVPRINERAARYVTPLKPFEAMALRRPVIVSDLPALR +EIVAAPRRGLTFPVGDVMVLAETIARLLEEPAERQRLGAAGREWVEAERQWVHNGPRYDRAYHAAINARRRAG------- +-----KG +>GCF_005280335_PROKKA_02052 +MTSI---LLDFVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVG-------LGR------LAESLPARPGVVL +GAVGLAAAGRHVDLLEHVEAVLPSAG-APDRVRLADVLTAAQEPDRAQAVLDAVPVNTPGLA--AARARVAWHRGDVEAA +ISLLGGTGRDGVVRARFASEVR----ALRGGALPLPRADRDRAVGYRPRPG----SALFVLTNSLPHTGSGYAQRSHSLA +CALRDEGWDVEAVTRLGWPVQTGVLTAARRDMVDGIVYHRLLPSSLARG--FDGRLAQHARMLLDLVLERRPAVLHTTT- +--HWVNAVVTRAVAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAR---EDDAVRSADGVVTLGEQMARRIAV +AGMDRDAVVLSPNGVGGAFLEEPAPREDA-RRRLG--LSMDDEIVGTVSSV-VPYEGLDDLVRAVAALVDERPRLRLAVV +GDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQALDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALS +EIVEDGVTGRVLPAEEPEAWAAALAALLDDPAEARGLGARAREWVLGHRTWAANARRYDALY-------RRLGVMAPSA- +------- +>GCF_020097155_PROKKA_01946 +MSPR---APRVRRLAANAALTGRTVADHLLDDPVVLALQVSRRLPTGLRAR-------VGG------VLADVPARVAVPR +G-IGLAMLGREEQLQAALVDADDAPG-PRERARRAEVLLAAGRDEDAERLLADVPADAPGAA--EARARLRWHRGDMTGA +VLVLSPHGRQGRLRARLAAERD----SLLGRPVCLSAEDRALAADYEPRPG----HVLFVLTNSLPHTGSGYVQRSHSLL +TAVRDAGWSVAAVTRLGWPVQTGVLAAEDVDRVDGVAYHRLLPAALAPG--FGARLDQHAAALLRLVLRERPAVLHTTT- +--HWVNAAVTAAVAEAVGIPWVYEVRGQLADTWASTRGPQALMSERYRAFRTR---EAEAAARADGVVTLAETMRARLAE +DGVDPEDVVLSPNAVGGAFLDAPGERAAA-RRALG--LAPDAEYIGTVSSV-VPYEGLDDLVRVVALLADRRPRLRLLVA +GDGTALPGLAALAEQLGVRDRVDLLGRVERARAPLCHQALDVFCVPRRDTSVTRDVTPMKPLEAMASARPVLLSRLPALQ +ELVAEGETGATVPASDPEAWAEAVEALLADPNAAAAMGDRARAWVLAERTWAANARRYTELY-------ARLGAVVDVAD +RGAVRGG +>GCF_023573625_PROKKA_00842 +MTSI---LLDSVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVG-------LGR------LAESLPARPGVVL +GAMGLAAAGRHVDLLEHVEAVLPSAG-APDRVRLADVLTAAQEPDRAQAVLDAVPVDTPGLA--AARARVAWHRGDVEAA +ISLLGGTGRDGVVRARFASEVR----ALRGGALPLPRADRDRAVGYRPRPG----SALFVLTNSLPHTGSGYAQRSHSLA +CALRDEGWHVEAVTRLGWPVQTGVLTAARRDMVDGIVYHRLLPSSLARG--FDGRLAQHARMLLDLVLERRPAVLHTTT- +--HWVNAVVTRAVAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAR---EDDAVRSADGVVTLGEQMARRIAA +AGMDRDAVVLSPNGVGGAFLEEPAPREDA-RRRLG--LSMDDEIVGTVSSV-VPYEGLDDLVRAVAALVDERPRLRLAVV +GDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQALDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALS +EIVEDGVTGRVLPAEEPEAWAAALAALLDDPAAARGLGARAREWVLGHRTWAANARRYDALY-------RRLGVTAPSA- +------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000112.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d151c6751c9a86dd75530edb8dda7f90d15933c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000112.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_01012 +MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV +TAAFFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA +AGEGLVRYDVEV-DGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAM +QLAPGVAGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGT +DTFTVDFHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAF +RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR +LGLTD +>GCF_003691675_PROKKA_00726 +MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV +TAAFFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA +AGEGLVRYDVEV-DGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAM +QLAPGVAGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGT +DTFTVDFHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAF +RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR +LGLTD +>GCF_005280335_PROKKA_01876 +M----------------------------------------------------------- +------------------------------------------------------------ +----------------------------------------------THLGDRPLVWDSAM +QLAPGVEGAEIVHLVAAPTMENTYAEVVTEPAHGEVFAFRDSEHSELRAWYIPEEGFVGT +---------------------------------------------------DTAAALAAF +RGDEAAPAPEDEEE---------------------------------------------- +----- +>GCF_005280335_PROKKA_01877 +MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGSFQAVDHENV +TTAFFQTYDGYDPEDLTLTITPVAEDGTRLEGGQEVGFTALDVIDGGAVDVLETRRALGA +AGEGLVRYDVVA-DGQMLNMGITLQADADLADDQGTAVHSVEA----------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------RR- +----- +>GCF_020097155_PROKKA_01764 +MFV--TRPSCAPRLAAAVLASGL-AAAALAAPASAEQAYDWTDDHGYPHGLFFGMDPESV +DEATFQTFYGFDPADLTVTVSPSDAEGTPTGPAAAVPFTAVDVLDGGTIDVLETRRVLGE +AGTGTVAYHVFSGDQKELDMALVVGPDADLADATGGALVAAPGPVRAVLGDMPLSWSADV +VMAPGVRAMEVRYPVDPALFDDVHPMVMTEAAHGTVVTFRDREDLSVRTWYVPDAGFTGT +DTFSLDLTSDHVAHLPTVTVHVGQELPAAAAGAPDAQDGVLGGMPLDVEDPAIAAMLQQM +GALPPAP------EATVPETTVSAEQHTRPGKVQTGGEPIWWLASAAVLGAGALVAARRR +PGMAG +>GCF_023573625_PROKKA_00955 +MSVIRTRRPSLRHLPVAVAAAGLVTTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV +TTALFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA +AGAGLVRYDVVA-DGQMLNMGITLQADTDLADDQGAAVHSVDGPQMAHLGDRPLIWDSAM +QLAPGVAGAEIVHLVAAPTMESTYAEVVAEPAHGEVFAFRDSGHSELRAWYIPEEGFVGT +DTFTVDFHSEHVAHVQTVTVHVGEEIPAAYDGFLDAEEGVLNGKPLDLTDPDTAAALAAF +RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR +LGLTD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000115.fa new file mode 100644 index 0000000000000000000000000000000000000000..27f9ba5fd32efedc55b5a9c4c628effee968ae3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000115.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_01030 +MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR +AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE +QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG +GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------ +----- +>GCF_003691675_PROKKA_00745 +MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR +AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE +QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG +GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------ +----- +>GCF_005280335_PROKKA_00186 +MS--EALSRIL--QVWPEIVVALGQTLTMLAVTIPLAVLLGTPLGIWLFTHAPGGLSPSP +RLHRVVD-AAVSMLRSFPFLILLIAIIPVTRLIVGTTIGTAAVIVPLTVNAIPYFARFVE +QNLAQLGPGPVEAARAMGATRGQIVRDVLLVDARPALVGSLTIMSVSFISYSAMAGLVGG +GGIGDFAIRYGYYRYETPLMVVAILLMIGLVALLQFAGTRLSQRLDHRRPRTARRPRRRA +LAPAG +>GCF_005280335_PROKKA_01853 +MTWLETLTTNP--AITDALPEALVETLLMVAISGVATVLIGGLLGIVLHVTRPGGLNPMP +ALYTVLSTVIVNITRSVPYAILMVALIPLTKWLVGTAIGPIAATVSLTIGTAPFFARLVE +SALREIPSGTVDAAQVMGSTRGQVIRKVLLPEAMPGLIAATTTTLVTLVGYSAMAGLIGG +GGLGRLAYNYGYQRFQTEVMVVTIVVIVILVQLIQWIGDLLIRRVDHR------------ +----- +>GCF_020097155_PROKKA_01742 +MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWAFILGGILGLLVGLVLYTTRPGGIFANR +AVYLVTN-FVVNLIRPIPFVILIAALQPLTIAVLGSGIGNTAVVFCMIWASTFGIARIVE +QNLVSLDPGVIEAARAMGASRMRIVRTVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG +GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------ +----- +>GCF_023573625_PROKKA_00974 +MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR +AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE +QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG +GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------ +----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000116.fa new file mode 100644 index 0000000000000000000000000000000000000000..0015cb9daaaa40d9e67d7e03a6dab36bd481a747 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000116.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_01042 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------MLEPEIRSD +NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTKTTSVAGQSQ +PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTANIWRTI +TRNVADDCSVDSSAWGCTGPIESAPAG +>GCF_003691675_PROKKA_00755 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------MLKPEIRSD +NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFRWDYGDGSPTKTTSVAGQSQ +PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTADIWRTI +TRNVADDCSVDSSAWGCTGPIESTPAG +>GCF_005280335_PROKKA_00331 +MP---------------------------------------------------------- +------------------------------------HQLDNADYGSCLNQDESFCPDGE- +-WVQARTVDITRPDADPLYGRPTCTSDVAAGAGGAR----SFTLEEVRTLLLLDPTIESD +NAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSFHWNYGDGTAPRVTHVGGHAQ +AEFNTPTPTSHVYEETGEYTVTLTTVYIGEYREADGDWVLIPGTITLDAAPVTADIWRTV +TRNVAEDCAADPSAWGCTGPIEAPDAP +>GCF_005280335_PROKKA_00544 +MP---------------------------------------------------------- +------------------------------------HQLDNADYGSCLNQDESFCPDGE- +-WVQARTVDITRPDADPLYGRPTCTSDAAAGADGAR----SFTLEEVRTLLLLDPTIESD +NAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSFHWNYGDGTAPRVTHVGGHAQ +AEFNTPTPTSHVYKETGEYTVTLTTVYIGEYREADGDWVLIPGTITLDAAPVTADIWRTV +TRNVAEDCAADPSAWGCTGPIEAPDAP +>GCF_020097155_PROKKA_01735 +MTSRRGDFPACMAVLFALIFLVSAVTLVTPSQAHASSCDTAGRKAQLTDDSLIVGQRCHK +SSIAEIVGDGLADDQEKSAKATSPTTKVTTLQNACYENLPEPGFENCATQQELICGDQNV +AWLQPSTKDTARPEDAPVKGDAFCADGSAAPSAPPQPSRPAVSIDDMGEVIAPEPRILAD +TDGRGVRNAETNFYSPEAVRHETAVIDGVSVEMRLTPVSFIWDYGDGTAPVTTDVGGNPQ +DGFDVRTPTSHVYDETGTYEVTLTTVYTGEIRYPGQGWEAVPGTIRRTATPVTADIWTTS +TRNVADDCSADASAWGCAGPVEAPNGG +>GCF_023573625_PROKKA_00983 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------MSIDEVRTLLVLEPEIRSD +NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTKTTSVAGQSQ +PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTANIWRTI +TRNVADDCSVDSSAWGCTGPIESAPAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000117.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b9e93694209bbca8774b777a1b39f6f0d89cc86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000117.fa @@ -0,0 +1,61 @@ +>GCF_002008305_PROKKA_01102 +MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGP--------------------- +EDPAASHFAAAVERGFYETVPTGAALR-QQLEAHAADGRRRLGVYAPGDDPAARRPAATF +EDFVQPLTTSPGRTVDAWLITDVTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATE +AAIYGRFGFGAATRWHAVRIDVSGAPAF------TGAPAGGRVTVEEPREIPGLVDELYG +RVLPATPGSVQRTSFSVPRWEDREASRNEGRGSGLYAAVHRDDDGRVQGVALYRFEGWEK +E-----PPTITVTAFLAATADARRGLVHHLARLDLVERIEWGRAPEPGWLEALFVDERRV +SRHRGSDDLYLRVLNLPAAMAARGWAGD--GEVVVAVEDALGAIDGTWRLTVRQGRGAAE +RLGPAADAVGLD-AGLRLDAARFSALWLGGHSRGAGAAVLAEAGVVAELRAGAAEAFDGL +VRPSRPLHTLVGF +>GCF_003691675_PROKKA_00821 +MTPHTDTPEGPSLRRLADAAEARLGEHGLALRDLGVLGP--------------------- +EDPAASHFAAAVERGFYETVPTGAALR-QQLEAHAADGRRRLGVYAPGEDPAARRPAATF +EDFVQPLTTWPGRAVDAWLITDVTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATE +AAIYGRFGFGAATRWHAVRIDVSGAPAL------TGAPAGGRVTVEEPREMPGLVDELYG +RVLPATPGSVQRTSFSVPRWEDREASRNEGRGSGLYAAVHRDDDGRVQGVALYRFEGWEK +E-----PPTITVTAFLAATADARRGLVHHLARLDLVERIEWGRAPEPGWLEALFVDERRV +SRHRGSDDLYLRVLNLPAAMAARGWAGD--GEVVVAVEDALGAIDGTWRLTVRQGRGAAE +RLGPAADAVRMG-AGLRLDAARFSALWLGGHSRGAGAAVLAEAGVVAELRAGAAEAFDGL +VRPSRPLHTLVGF +>GCF_005280335_PROKKA_01792 +MSIN---PAAAAHAADATAAQDALARHGLVLR---TLAPLSRGFDGADP------AR--A +EHPAHVRHTAAVEKGFYEEVPQGAAAD-QDLGVSADDAKVLRGVYLSADDPARREPVGTF +VDWTSRLTTSPGAELPVWMISNVTVSPGHRRRGILRAMMTASLEEAVAAGVPVAALTASE +STIYGRFGFGAASTARTVRVDVRGDVVLAADAAGRTDEDAGTVLREDPRELAGVVEALHD +RVRRGTPGSVHRPTGHVIRWEDRSAAKNDGRGSGLFAAVHRDADGAVQGVALYRFDGWGK +E-----PTTVSVEVFLAATDAAARQLWRYLTRLDLIERLRMTRCPDDGGLEQVLADRRRV +RTKSVWDDLYLRVLDVPVCLGGRGYAPEVVGEVVLAVADAAGHAAGTWRLRVADG----- +-VGRAERLADDARADLALDVAHLSAVWLGGVRAG----ALVRAGVVDEREPGAAARLDAL +LAPAAAVHLLTGF +>GCF_005280335_PROKKA_01793 +MTPRTDAPDAWLDPAPATA--EALAAHGLEL--LRVPSPWETG--DADPDAPFDHARRWA +DAPAVRRHTAVLQRNFHEVGDPDFALADRFIGVEQGDRRRLSGVYPQGADPAATDPVGTL +VDFTKDLNVGDGRMLPAWCLTEVTVSPTHRRRGILRAMMTESLRRAHAARVPIALLTATE +ATLYRRFGFGVSTYHRSVWLDVTRGVQL------RGRRPDGSFRFVEPTASGALIDGLWR +RAFEAQAGSVERIRFHAARETDRDPRVGEGRPQGLRAVVYSAPDGEDLGVAVYRVTGSTA +ELVADDPVTATVVALWAATPEAHRALLEFLGNLDLVVRLRLPAVAADRLLEFLVLDESRI +YTRGVHHHLWHRVLDVAACFEARPYLHE--GAVTVTVEDDLGYAAGTWEIAAADG----- +-VGRVRPAPQDA-AELTLDVAELGSVLLGGVKAE----MMREAGILLAHRPGAAADLDTL +LRQARPPYSLTGF +>GCF_020097155_PROKKA_01683 +MRPHTDLQ--PTATPRADA--EVLAEQGLAL----VVAP----------------GR--A +ADPAFERHTTAVERGFYEQVPSGEAMA-QLLEAGEADGRRMVDVLPLGADPATTRPVATF +EDFRSELTVSPGVAVSAWLISGVTVDPGFRRRGLLRTMMTRSLADAVAAGVPVAALTASE +AAIYGRFGFGAATRWRRARLDTRGDVRL------RGAPSAGRVTREEPREVGALADELYQ +HVRRLTPGATQRPTMTAIGWEDRSRFKNDGKGSGLYAAVHRDAAGTAQGIALYRPQGWDV +E-----PPTVTMELFLALTPDARRGLLTHLTSLDLIERIVWERAPEAGWPEALLEDERRL +RTERDGDDLYLRILDVPAALGARADLGD--GEVVVDVTDPLGHAAGAWRIRARDG----- +-VAEVTEAAEGE-AELGLDVADLSAVWLGGHGSAGGVAARVATGLVREVVPGAGARLDAL +LRPSVPVRSLVGF +>GCF_023573625_PROKKA_01051 +MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGP--------------------- +EDPAASHFAAAVERGFYETVPTGAALR-QQLEAHAADGRRRLGVYAPGDDPAARRPAATF +EDFVQPLTTWPGRTVDAWLITDVTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATE +AAIYGRFGFGAATRWHAVRIDVSGAPAF------TGAPAGGRVTVEEPREIPGLVDELYG +RVLPATPGSVQRTSFSVPRWEDREASRNEGRGSGLYAAVHRDDDGRVQGVALYRFEGWEK +E-----PPTITVTAFLAATADARRGLVHHLARLDLVERIEWGRAPEPGWLEALFVDERRV +SRHRGSDDLYLRVLNLPAAMAARGWAGD--GEVVVAVEDALGAIDGTWRLTVRQGRGAAE +RLGPAADAVRMG-AGLRLDAARFSALWLGGHSRGAGAAVLAEAGVVAELRAGAAEAFDGL +VRPSRPLHTLVGF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000119.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d9ddc38ec45bb964fd7fc34f4f17d358f78998c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000119.fa @@ -0,0 +1,90 @@ +>GCF_002008305_PROKKA_01117 +MPKNSSTTVSSAV--EAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA +EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPV +SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFKDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL +AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR +SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAE +RDAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARL +NPTVLNVLVGGLSIADATRLPMREAMEFFSGL------------------RLTDRERQIADQVLKEILARLAFLLDVGLE +YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW +IVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRVPEKGRV-LTVRGAQENNLKDVSVEVPLGVL +TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRSVEGL-----EHLD-----------KVVHVDQSPIGRTPRSN +PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY +KGKNIAEVLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRTIYVLDEPT +TGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPEGGSGGGTIVAAGTPEEVAHVAESHTGRFLAELL +--------A +>GCF_003691675_PROKKA_00373 +MVESSSFV-----------------PPKL-SVQPD-VRVLGARENNLQDVDLTVPRDATVVFTGVSGSGKSSLAFGTLYA +ESQRRYLESVAPYARRLIDQAGVPDVDSITGMPPAVALQQQRGSGNARSTVGSITTLSSLVRMLYSRAG----------- +------------------------------------------------------------DYP----------------- +---------------------------------------------------EGQPM--------------------LYAE +DFSANTVQGACSECHGIGRVYEVNEQQMVPDPSLTIRERAIASWP-----TAWHGHQLRDVLVALGYDVDVPWRDLPKKD +RDWILYTDETPFVPVHSRLTLSESKAAIEAGVEPSYSGTFVGARRYILDTFANTKSASMKRRVAQFLTAAICPTCNGKRL +KPEALSVTFEGFDIAEFSQLPLRELATILSGVVAREEDHEAASSDVRPTASRTPEKRAAAVQLASGVLQRLRPLVDLGLG +YLSLSRTTPTLSGGELQRLRLATQLSSDLFGVVYVLDEPSAGLHPQDVAALLEILDGLKGRGNSLFIVEHSVAVMRHADW +LVDIGPGAGEHGGRVLYSGPPDGLAGVTESVTRGYLFGGRGLPL----RTPREARSWLRLENVTRNNLHDLTVDIPLGVF +TAVTGVSGSGKSSLVSQALPSLLGDRLGLAARADDEPVSDESLLADAPEHLEGRVAGPVTGVQRLVVIDQRPIGRTPRSN +VATYTGLFDHVRRRFADTPEARSRGYKPGRFSFNVAGGRCPTCEGEGSVMVELLFLPSVYTECPDCHGTRYKASTLEVTW +RGRTIADVLSMSVEEANLFFVGDEEITRSLAALSDVGLEYLRLGQPATELSGGEAQRVKLATELQRAQRGDTLYVLDEPT +SGLHCADTDRLVAHLQTLVDAGNTVVAAELDMRVVAVADHVIDLGPGAGDAGGTVVAAGTPAHVADQGVGASAGYLAAAL +QAATNVTPS +>GCF_003691675_PROKKA_00836 +MPKNSSTTVSSAV--EAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA +EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPV +SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL +AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGKKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR +SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAE +RDAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARL +NPTVLNVLVGGLSIADATRLPMREAMEFFSGL------------------RLTDRERQIADQVLKEILARLAFLLDVGLE +YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW +IVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRVPEKGRV-LTVRGAQENNLKDVSVEVPLGVL +TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRSVEGL-----EHLD-----------KVVHVDQSPIGRTPRSN +PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY +KGKNIAEVLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRTIYVLDEPT +TGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPEGGSGGGTIVATGTPEEVARAAESHTGRFLAELL +--------A +>GCF_005280335_PROKKA_01776 +MPKNSSTTVSSAV--ETHAGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA +EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEVYDYLRLLWARVGVPHCPQCGEPV +SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFADLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL +AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEVVAEKGKKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR +SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLAKEMGFSLDTPWRELEPAQ +REAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVVPYVLRKHGETESDGARERYESFMREIPCPVCHGARL +NPTVLNVLVGGLSIAEATRLPLREARDFLAGL------------------ELSARERQIADQVLKEILARLAFLLDVGLE +YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW +IVDIGPRAGEHGGEVVHSGSLEDLKANTASITGDYLAGRRAITAPQTRRAPQEGRT-LTVRGARENNLKDVSVDIPLGVL +TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRAVDGL-----EHLD-----------KVVHVDQSPIGRTPRSN +PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACSGDGTLKIEMNFLPDVYVPCEVCDGARYNRETLEVTY +KGKNIAEVLDMPIEEAAQFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRSVYVLDEPT +TGLHFDDIRKLLQVLQSLVDKGNTVITIEHNLDVVKCADHVIDLGPEGGSGGGTIVATGTPEEVARVEASHTGRFLAELL +--------A +>GCF_020097155_PROKKA_01669 +MPKNSSSAAAPARPDAAARGGLASGPARG-SAQHERIVVKGAREHNLKNVDVSIPRDSMVVFTGLSGSGKSSLAFDTIFA +EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVAHCPVCGEVV +SKQTPQQIVDQLEQLPERTRFQVLAPVVRGRKGEFVDLFSSLSTQGYARALVDGELIQLSDPPALKKQNKHTIAVVVDRL +AVKEGIRQRLTDSVETALKLADGLVAVEFVDVDVVAQAGKKNQGDLAGEDAEGNPRFRTFSEKLSCPHGHPQTVDEIEPR +SFSFNNPFGACPECTGIGSRLQVDPDLVVPNDELSLNEGAILPWSLGKSTSDYWLRVLGGLAKEMKFSLDTPFKDLTAQQ +RDAVL----------NGKDFKVEVSFRNRFGRERRYTTGFEGVLPYVMRKHGETESDNARERYESFMRQIPCPACHGARL +NPTVLNVRVGGLSIADATRLPLRESLAFLDGL------------------QLTERELAIADQVVREIRARLEFLLDVGLD +YLNLERNAGTLSGGEAQRIRLATQIGAGLVGVLYVLDEPSIGLHQRDNRRLIDTLIRLRDLGNTLIVVEHDEDTIAEADW +IVDIGPRAGEHGGEVVHSGSLDELKANTRSVTGDYLAGRRRIEVPAARRPVDPKRR-LTVKGATENNLKDVTVDIPLGVF +TAVTGVSGSGKSTLINEILYKVLADKLNGAKMVPGRHRSVAGL-----EHLD-----------KVVHVDQSPIGRTPRSN +PATYTGVFDQIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY +KGKNIAEVLDMPIEEAAEFFGAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSTGRTVYVLDEPT +TGLHFEDIRKLLQVLQTLVDKGNTVLTIEHNLDVVKCADHVIDLGPEGGSGGGTVVATGTPEEVAAVPESHTGRFLAELL +--------G +>GCF_023573625_PROKKA_01067 +MPKNSSTTVSSAV--EAHPGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA +EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPV +SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL +AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR +SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAE +RDAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARL +NPTVLNVLVGGLSIADATRLPMREAMEFFSGL------------------RLTDRERQIADQVLKEILARLAFLLDVGLE +YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW +IVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRVPEKGRV-LTVRGAQENNLKDVSVEVPLGVL +TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRSVEGL-----EHLD-----------KVVHVDQSPIGRTPRSN +PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY +KGKNIAEVLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRTIYVLDEPT +TGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPEGGSGGGTIVAAGTPEEVAHVAESHTGRFLAELL +--------A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000120.fa new file mode 100644 index 0000000000000000000000000000000000000000..0eac8913ce25100739afaf35eea1c96b055e0127 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000120.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_01118 +MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV +PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV- +--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG +AAWLALA-TGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR +DATAAIMDAIGALSGQERVDAYNAAPGAR------------G +>GCF_003691675_PROKKA_00837 +MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV +PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV- +--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG +AAWLALA-TGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR +DATAAIMDAIGALSGQERVDAYNAAPGAR------------G +>GCF_005280335_PROKKA_00163 +MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALL-------------- +PRQAVFY--ANHTSHLDFVTLWAVLPPALQRRVRPVAAADYW-GSGLRRRVAEGLFHAYL +VERGKTRRRGPGAASGSGVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRG +LHALAAAFPQVPVVPVSLVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPA +SGTAA-TDAPEPGRGEDEAARTAWLERARAVLVQDLSASLRG +>GCF_005280335_PROKKA_01775 +MAT-------------------------------SEPVRRSAAALLRLTCRPEVTGMDQV +PAEGPFIMASNHLSFFDSVILQALAP----RPVHFFAKEEYFTGAGVRGRAQRWFFESV- +--GSVPVRRGEQAASVAA--------LESLVGLLDSGQGVGIYPEGTRSRDGRLYRGRTG +AAWLALT-TGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDFGHPGRRHTLPQRR +DATAAIMDAIGALSGQERLDAYNAAPGAR------------G +>GCF_020097155_PROKKA_01668 +MAT-------------------------------SEQLRRAVAGAIRLSCRPHVRGLEHV +PPEGPFIVASNHLSFVDSVILQALCP----RPVGFFAKAEYFEAPGLRGRAQRRFFEAV- +--GSIPVRRGEQAASVAA--------LEDLVALLDGGHGVGIYPEGTRSRDGRLYRGRTG +AAWLALT-TGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDFGHPGRRHSLPQRR +EATATIMAAIAALSGQERVDEYNAAPAAR------------G +>GCF_023573625_PROKKA_01068 +MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV +PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV- +--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG +AAWLALA-TGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR +DATAAIMDAIGALSGQERVDAYNAAPGAR------------G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000121.fa new file mode 100644 index 0000000000000000000000000000000000000000..e7cabaaf99c0dc330abc5232afb516f009f3f227 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000121.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_01147 +MADQTTTPTADAQAAGRSVLVTGGNRGIGLAIARAFAANGDRVAITSRSGE-GPEGVL-A +VRADVTDAASV----------DAAFREVEEVHGPVEVLVANAGI-THDQLLLRMSEDDFT +SVIDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR +SITRELGARGVTANVVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLA +SDEAAYISGAVIPVDGGLGMGH +>GCF_003691675_PROKKA_00866 +MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGE-GPEGVL-A +VRADVTDAASV----------DAAFREVEEVHGPVEVLVANAGI-THDQLLLRMSEDDFT +SVIDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR +SITRELGARGVTANVVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLA +SDEAAYISGAVIPVDGGLGMGH +>GCF_005280335_PROKKA_00771 +MA----------EFDGKVALVTGGGSGIGEACAKDLARGGAKVLVTDINLE-AAERVAEE +IKADGGEAAAYRLDSASPDDNEKAVAFAEETFGALHLAVNNAGIGAGTEPAGELKIEDWD +RVIDIDLNGVLYGMRHQLPAMERAGGGAVVNMASIHGTVATGLGASAYTAAKHGVVGLTK +QAGVDYGPRGVRVNAVGPGYIETPLLAELPDEVHEALVAKHPIGRLGRAEEVAHLVSFLL +SDKASFLTGAYYLVDGGY-TAP +>GCF_005280335_PROKKA_01745 +MADQTTPTAADAKASGRSVLVTGGNRGIGLAIARAFAANGDRVAVTSRSGE-GPEGVL-A +VRADVTDAASV----------DAAFREVEEAHGPVEVLVANAGI-TNDQLLLRMSEEDFT +SVVDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR +SITRELGARGVTANVVAPGYIDTEMTQSLGEDLKAQYKKSIPAGRFAQPEEVADVVRWLA +SDEAAYISGAVIPVDGGLGMGH +>GCF_020097155_PROKKA_01639 +MAEQT-------EPGGRSVLVTGGNRGIGRAIAEAFLANGDRVAVTSRSGEGGPEGAL-T +VAADVTDAASV----------DAAFRAVEEAHGPVEVLVANAGV-TNDQLLLRMSEDDFT +SVVDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLIGMAR +SITRELGARGITANVVAPGYIDTEMTRSLDEELKAQYRKSIPAGRFAEPEEVADVVRWLA +SPGAGYVSGAVIPVDGGLGMGH +>GCF_023573625_PROKKA_01097 +MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGE-GPEGVL-A +VRADVTDAASV----------DAAFREVEEVHGPVEVLVANAGI-THDQLLLRMSEDDFT +SVIDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR +SITRELGARGVTANVVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLA +SDEAAYISGAVIPVDGGLGMGH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000124.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc9e7acd76d44fb57df7cf15d0b71ffe8a8b9f9f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000124.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_01285 +---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTATLEQAGTDDVVHAALDAGITFFDV +ADVYGAEPGLSEERLGRA---LGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAV +EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEY +VARELGVERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDA +PEGSRLSHVRQHMVAD--ADLEQLAGFGRF---ARERGITEVQAAIGWLAAQGPVSSVIA +GATRAAQVVENAAAAD--WLATAEDLAELDALFPGPEKVALF +>GCF_003691675_PROKKA_01004 +---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTATLEQAGTDAVVHAALDAGITFFDV +ADVYGAEPGLSEERLGRA---LGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAV +EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEY +VARELGVERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDA +PEGSRLSHVRQHMVAD--ADLEQLAAFGRF---ARERGITEVQAAIGWLAAQGPVSSVIA +GATRAAQVVENAAAAD--WLATAEDLAELDALFPGPEKVALF +>GCF_005280335_PROKKA_01600 +---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTVTLEQDGTDAVVHAALDAGITFFDV +ADIYGAQPGLSEERLGRA---LGARRDDVVIGTKFGMDMAGANGVDHDARGSRRYIVRAV +EASLRRLGTDWIDLYQFHTPDPATPIDETLRALDDLVRDGKVRYVGHSNRTGWQIAQAEY +VARELGTERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGAA +PEGSRLSHVRQHMVAD--ADLEQLAAFGEF---ARARGITEVQAAIGWLAAQGPVSSVIA +GATRTGQVAENARAAD--WEATEADLAELDALFPGPEKVALF +>GCF_020097155_PROKKA_01496 +---MRTVRLGRSGLTVSVVGLGC----NNLGRPGTATMEQEGTDAVVHAALDAGITLFDV +ADVYGARPGLSEERLGRA---LGSRRDEVVLATKFGMDMGGAAGADGGARGSRRYIVRAV +EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRSGKVRYIGHSNRTGWQIAQAEH +AAREIGVERFVSAQNHYNLLDR-RAELEVLPASAEYGLGVLPYFPLANGLLTGKYSDGTA +PAGSRLSHVRQHMVEE--ADRGQLAAFGAF---ARERGITEVQAAIGWLAAQRPVASVIA +GATRPGQIAENARAAD--WEATPADLAELDALFPAPPPVALF +>GCF_020097155_PROKKA_02080 +MSDMIYNRLGSSGLQVSQFSFGSWVTFGNQVDMGLAKDQ-------LAAAKEGGVNFFDN +AEVYAG--GESESIMGRAIAELGWKRHEYVVSTKLFWGIHGDV-VNMKNTLNRKYLMQGI +DGSLERLGLDFVDLVFCHRPDPHTPIEETVWAMSDMINRGKALYWGTSEWSADEIRAAWN +IAERHHLHKPVMEQPQYNLLHRTKVEEEYARLYEDIGLGLTTWSPLASGILSGKYVDG-V +PEGSRGALKGYDFVKDSIADQETTAKVRQLVDIAAELDVTPAQLALAWTASNPRVSTVIL +GASSVAQVQENLKALDVIELVTPEVRERLEAVFA-------- +>GCF_023573625_PROKKA_01243 +---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTATLEQAGTDAVVHAALDAGITFFDV +ADVYGAEPGLSEERLGRA---LGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAV +EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEY +VARELGVERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDA +PEGSRLSHVRQHMVAD--ADLEQLAAFGRF---ARERGITEVQAAIGWLAAQGPVSSVIA +GATRAAQVVENAAAAD--WLATAEDLAELDALFPGPEKVALF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000125.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000125.fa new file mode 100644 index 0000000000000000000000000000000000000000..51c3a8d76027c670b5abfa2835cfa575b5b7d613 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000125.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_01334 +--------MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAE +HHNMPSIASSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL +GLGRA-------PGTDQRT-------LQALRRDPS------------------------- +------------AAER------------FPQDVLELQGYLTGQSLIPG-----IDAYPGK +GTNVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF +IAAANVIAADTEEVAEREWQ--AAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGML +ECTAVGTGPTTAAWLHDFAARVQADELIITTAAQDAGVRRRTLELLGEHVVRA +>GCF_003691675_PROKKA_01055 +--------MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAE +HHNMPSIASSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL +GLGRA-------PGTDQRT-------LQALRRDPS------------------------- +------------AAER------------FPQDVLELQGYLTGQSLIPG-----IDAYPGK +GTNVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF +TAAANVIAADTEEVAEREWQ--AAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGML +ECTAVGTGPTTAAWLHDFAARVQADELIITTAAQDAGVRRRTLELLGEHVVRA +>GCF_005280335_PROKKA_01557 +--------MTEHTAPTPLPLSLLDLATVRDGASVAEAVAESVEQAQAAERAGFRRVWYAE +HHNMPAIASSATSVLIAHVAAHTESIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL +GLGRA-------PGTDQRT-------LQALRRDPS------------------------- +------------AAER------------FPQDVLELQGYLTGRTRIPG-----IEAYPGK +GTDVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF +IAAANVIAADTREEADREWE--AARRARIRMMLGRGRTLSDDEVEMLLHSPAGQQVLTML +ECTAVGTGEETATWLRDFAAKVQADELIITTAAQDAGVRRRTLELLGEHVVRA +>GCF_020097155_PROKKA_00131 +---------------MSIPLSVFDPVLLPAETDPREAIDDARTLAAAADALGYRRLWHGE +HHLNPGVLGSNPALTLALVGPVTQHIRLGSAASLVGPRTPLVLAEDFGLLAAAFPGRIDL +GLGRAAAPGGPPPGTRAETPTGDGGPAQDPQREPAGAGASSGQDPAAGPSEVDGVVIPAA +PDLSAALGSPLRAASRALLPTPSTPALDYGAQVDLLLGLLDGTAQHDGAALGQVVARP-- +AVDVEPWVLGSGPGVSAEVAARRGLRFGANYHVSPAGTVAAVRRYRELFRPSPEVPCPVV +SVSAEVLIADTAAEARRRASGYAAWVLSIRSGAGAVPYPSPAHPEPSRTPQEEALVADRL +QTRFVGTAEQVAERLDALARLTGADELLISASAHRVEHRVETLTRLAEIWRTA +>GCF_020097155_PROKKA_01453 +MTADVRPVVPPETAPAGVPLSLLDLATVRGDQRIGEALGQSVELAQTAEAQGFTRVWYAE +HHNMPGIASSATAVLLAHVAAHTERIRVGSGGVMLPNHSPLVVAEQFGTLAELHPGRVDL +GLGRA-------PGTDQRT-------LQALRRSPE------------------------- +------------AADR------------FPQDVLELQGYLRGESRMPG-----IDAYPGR +GTDVPLWILGSS-AFGANLAAQLGLGYAFASHFAPQMLEHAARLYREHFTPTDALDAPHF +IAAANVVVADTDEEAQRLWE--ATRRSRVRMFLGRGRHLTEDELDMLMDSPAGEQVLGML +RHTAVGTPDVVRAWLDDFAARVEADELIVTAAAVDHPARVRTLELLGEHVIRR +>GCF_023573625_PROKKA_01290 +--------MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAE +HHNMPSIASSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL +GLGRA-------PGTDQRT-------LQALRRDPS------------------------- +------------AAER------------FPQDVLELQGYLTGQSLIPG-----IDAYPGK +GTNVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF +IAAANVIAADTEEVAEREWQ--AAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGML +ECTAVGTGPTTAAWLHDFAARVQADELIITTAAQDAGVRRRTLELLGEHVVRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000126.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6e199b699aa2364accf2d290cfa7e5f53dded35 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000126.fa @@ -0,0 +1,49 @@ +>GCF_002008305_PROKKA_01341 +MT-THTSTAQRS----SKYP-TTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQ +TAMPEPVAATLAAITAELDGREKAPKPSAPLGVCFPSIV----------KDGVCLSANNI +DHSWIGTDLRGTFEEHLRRPV-------------TVVNDADAAGLAEARYGAGRGVRGLV +-----HVITLGTGIGGAMIHDGMLVP-----NFEVGSLELD------------------- +-------------GVMAESRASAKARERDQ-LSWAEYAERLQRFFSHVERIFSPDLFIVG +GGISKRPDDYLPLLRL------------RTP-IVPAQLQNNAGIVGAALAAHGSLADG-- +N +>GCF_003691675_PROKKA_01061 +MT-THTSTAQRS----SKYP-TTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQ +PAMPEPVAATLAAITAELDGREKAPKPSAPLGVCFPSIV----------KDGVCLSANNI +DHSWIGTDLRGRFEEHLRRPV-------------TVVNDADAAGLAEARYGAGRGVRGLV +-----HVITLGTGIGGAMIHDGVLVP-----NFEVGSLELD------------------- +-------------GVMAESRASAKARERDQ-LSWAEYAERLQRFFSHVERIFSPDLFIVG +GGISKRPDDYLPLLRL------------RTP-IVPAQLQNNAGIVGAALAAHGSLADG-- +N +>GCF_005280335_PROKKA_01551 +MT-THTTTAQRS----SKHP-TTIGIDVGGTGMKGGLVRLGSGPKSGTLRGDRFRIPTPQ +PAMAEPVAATLAAITAELDARDKAPAPTAPLGVCFPSIV----------KDGVCLSANNI +DPSWIGTDLKAAFEEHLRRPV-------------RVVNDADAAGLAEARYGAGRGVSGLV +-----LVITLGTGIGGAMVHDGVLVP-----NFEVGSLELD------------------- +-------------GVMAETRASAKARERED-LSWAEYAQRLQRFFSHVEHVFSPDLFIVG +GGISKRPDDYLPLLSL------------RTP-IVPAQLRNNAGIVGAALAAHDSLADA-- +R +>GCF_020097155_PROKKA_01415 +MH--RSRPAPPSPPAPSAYPRRLLGVDLGGTAAKAGVLELARDGRARILARSRAAHAGAD +PASAVTRA---------------AADALSRAGVRVPDGAGFACAAWLDPATGRARASPHL +-PSLVGIR-----PAALLTPVLEAAGAAGHGLVPVALNDADAAALAESRLGAARPAPGDL +PGAPTLFVALGTGVGGAVIVDGAVLPGARGMHGEAGHICVDPDGPACPCGARGCWELYAS +ASALARTLPGRPIADVLEAAVAGPGPERDAVLDAGEW---LGRGLAPAVCLLDPVRVVVG +GGLMAAGELLLPTARAALRRALPTAAADRPPELVAAALGNDAGWIGAALADGARV----- +- +>GCF_020097155_PROKKA_01447 +MSFPNTGVIPRLPPAPSKHP-SVLGVDIGGTGMKGGIVRLGHGPKSGTLRGDRFRLDTPQ +PASPATMARTLAQIVSELDHREKAPDADSRVGVCFPSIV----------QHGVCRSANNI +DPSWIGVSLQDTFEEALQRPV-------------TVVNDADAAGLAEARYGAGAGVPGLV +-----MVITLGTGIGGAMINDGVLVP-----NFEVGSLELD------------------- +-------------GVMAESRASAKAREREG-LDWPEYALRLQRFFSHLERIFSPDLFIVG +GGISKRPHDYLPLLQL------------ETP-IVPAMLQNNAGIVGAALAAHADPADGLL +R +>GCF_023573625_PROKKA_01296 +MT-THTSTAQRS----SKYP-TTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQ +PAMPEPVAATLAAITAELDGREKAPKPSAPLGVCFPSIV----------KDGVCLSANNI +DHSWIGTDLRGRFEEHLRRPV-------------TVVNDADAAGLAEARYGAGRGVRGLV +-----HVITLGTGIGGAMIHDGVLVP-----NFEVGSLELD------------------- +-------------GVMAESRASAKARERDQ-LSWAEYAERLQRFFSHVERIFSPDLFIVG +GGISKRPDDYLPLLRL------------RTP-IVPAQLQNNAGIVGAALAAHGSLADG-- +N + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000127.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b0521656b3c25aa376207b09b93b900fd653491 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000127.fa @@ -0,0 +1,120 @@ +>GCF_002008305_PROKKA_01369 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------SSARRDPL---VGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHP +HLAEDPVLVGRFEQEAKTTARLS-HPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSPREALRFLRPL +VDGLAAAHGAGLVHRDVKPENV-LVRDDG---RVTVADFGLSRAATAHTMAGQAVVGTPAYLAP--EHIAGAPADARSDV +YAVGIILFELLTGRQPYTAATALQVAYRHVHERVPVPSTL-HPGLPEDLDDLVLWCTEPDPADR------PAGAGELLHR +IEAVAAGL--------DP-DAPDRRPA--AQP-----AEGPGADPAPAGPAADGLEDAAP----DGNLETRALDAGDHHA +TRVLPALA-ESDLDEDMTDVIDTRVATHGGDPRPAA-------RPAEPIGPLGLDPAPAD------RHPGRGSRRRLRRA +ARRPALDLGQGTGRAAAIGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREA----AEERLTAAGFTAAVTA +RHDELRTEGTVVASSPAAGEPAGRGAPVELTVS-------AGPAPVP-------VPDLTGVVIRQAHGVARDARFTVEVA +ERRTDPAVPAGA-------VIEQHPAPGEQATPGTA------VRVVLSEGRAVRPVPDMTGQDPETAHTTLADEGWDARV +HRLP-LPLSARGESRVLHQSPAAGTAL----------------------------------------------------P +EGT----------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------AVHVWV---------------------------------------------------G +>GCF_002008305_PROKKA_01953 +MSLPDARWHVVSPSPFEHEQQGLDILREVLPDESPFQVWTNFEFPDEDGQWHEVDALVLARTKFILVELKYYSGVLRGTG +LRWERPGHSPQRSPLALAKKKAERFRSLLERTIESKMPGAGRQRIVPYVDYAVFLHHDRFRNEMAPQDSGRLFGLPHNET +ASNLPSIEHLVLAPATDRFPLIGEPREQVLVALMEHLNLADARQPEVGSWLLEERLGEPTPDGQDWLASHRFQERHFARI +RFQQPREGAPSSDLARVREAARREFDLTRALHHEGLLTASDRVDNELGVGLVFPYDESLAPLPLWLESRAATLSQQNRLD +LLRQLAETLEYVHSNGIVHRALSPEALWVKTPKQGEPRILVADWQLAGVADRDKVDHAASLTQLSTQFGTTVRSTEELAP +TSGALFRAPEDARRVSSLGRYKLDVFSVGALAAYLLTGAPAANTVAELHEHLATHQGLDVSVALPSVPEPVRQAILHATD +PRPTARTATLNDFLAGLTEAQATAPQPASPALDPLEAAPGQALDSRFTLVRRLGKGSTAVGLLVDDAQTGSRQVLKV--- +--ALDDEAATRLDDEAQVLRLLPLHKRLVRLLDGPF--DVGGR--RALLLTSAGTRTLSEVLRERQRLSLDHLERFGSEL +LEAAQALDAAGLRHRDVKPANIGVVRTPKHGEHLVLFDFSLARARSTDVRA-----GTPPYLDPFLEQGGRTGYDSAAEL +YAVAVVLYEMASGQKPFYGDPEANPA--AVRDDLTVPDGIFDPSLQAPLSALFERALARDAQARFHTVAELAAAWEALFR +NDA-------------DPVTAQDAETLAARAT-----LETPLSEAGLSARGLSALEAIKV----TAGPGGVAVEPHDVRT +VRDLVLVD-PIKLNSLAGSTTETRAEVRARAKQWRAAFKKELMRQATQV-PQGTLPTPLDAAELLLRHAGAAHAEGVRAQ +LR---LVLGLDGEVPALSTHAVLADARGVT----------------PGLVPQLFGRAQQAWTDVAETRSLLDSLDGALRA +----------------AVAERGGVSTPDELTSALEQTLSPATPAEVRDAEPRRIVQGLLWLLLDRERAAARGEADVPALV +QRRREGRVVAVAEMPVLLDVAETLGAAAEAAVDGAGDPESALVPADLVQTR-VAAVLDAVDGLPEALRSWRRAAALAAHV +SATTCLSAAGEWHHRLLAPATAAHHALQGASGTVQLSRERAAERVGARFPALSPLPRDAALDRVLAEAELGLVFDEDLGP +QGAYRSRQTLAPTTGFATRAETRLVEHQRPLSELGVEGQRLLDSQRNRSYLALGVPAQRLARLESALVRRFHAEPLDLTD +LFIRLLKDQAAAHPKMTWDHVTAADAEPDGSRPAQGLNVLVRNLLPELEQHLSRTIGDPGRAASPVLLTGAAVLARYGHL +GVLARWADLAEYRARPVWLVVPQVAGNVGPRLDGVSVPKNTPGQYVPLTPEWIDGLAALMAAQPLTEESRT +>GCF_003691675_PROKKA_01089 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------SSARRDPL---VGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHP +HLAEDPVLVGRFEQEAKTTARLS-HPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSPREALRFLRPL +VDGLAAAHRAGLVHRDVKPENV-LVRDDG---RVTVADFGLSRAATAHTMAGQAVVGTPAYLAP--EHIAGAPADARSDV +YAVGIILFELLTGRQPYTAATALQVAYRHVHERVPVPSTL-HPGLPEDLDDLVLWCTEPDPADR------PAGAGELLHR +IDAVAAGL--------DP-DEPDRH------P-----AEGPGAEPAVAAPAADGPEDAAP----DGNLQTRALDAGDHHA +TRVLPALA-ESDLDADMTDVIDTRAATRGADRRPAA-------HPAEPIGPLGLDPAPAD------RHPGRESPRRLRRA +ARRPALDLGQGTGRAAAIGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREA----AEERLTAAGFTAAVTA +RHNELRTEGTVVASSPAAGEPAGRGTPVELTVS-------AGPAPVP-------VPDLTGVVIRRAHGVARDARFTVEVA +ERRTDPAVPAGA-------VIEQHPAPGEQATPGTA------VRVVLSEGRAVRPVPDVTGQDPETARTTLADDGWDARV +HRLP-LPLAGRGESRVLHQSPAAGTAL----------------------------------------------------P +EGT----------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------AVHVWV---------------------------------------------------G +>GCF_005280335_PROKKA_01524 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------SSTRRDPL---VGGIVDGRYEVLARLARGGMSTVYLALDTRLDREVALKVMHP +HLAEDPVLVGRFEQEAKTAARLS-HPHVVAVLDQGHTEDASGEVLAYLVMEHVPGHTLRTVIREQAPLTPREALRHLRPL +VDGLAAAHRAGLVHRDAKPENV-LVRTDG---RITVADFGLSRAATAHTSAGQAVVGTPAYLAP--EHIAGAPADARSDV +YAAGIILFELLTGRQPFTAGTALQVAYRHVHERVPVPSSL-QPGLPEALDDLVLWCTEPDPADR------PADAGEVLDR +LDAVAAEL--------GP-AELDRPPV--LVPDAVEGRPGPEHDETTTLDALDRLDPKDPLDDADGD-ETTSLDAGDHHA +TRVLPSLP-ADALPTE---------------------------------------ALAAD------DVVRRSPARRRRR- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------P +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------------------------------- +>GCF_020097155_PROKKA_01419 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------SSTRRDPL---IGDLVDGRYEVLDRVARGGMSTVYRALDHRLDREVALKVMHP +HLAEDPALVGRFEREAKTAARIS-HPHVVAVLDQGHTADEAGDVLAYLVMEHVPGRTLRAVIREEAPVAPRRAVALLEPV +VEGLAAAHRAGLVHRDVKPENV-LVRTDG---RITVADFGLSRAATGHTSAGQTVFGTPAYLAP--ELISGTGGDARADV +YGVGIMLFELLTGTQPFTAATPLQVAYRHVHERVPVPSSV-RPGLPEALDDIVLWCTEPRPADR------PEDAAALLPE +LRRVAALLPQTAPADEAP-AADDAPTVALAVSPTVPTVPVPD-----AADATARLEPRRP--DPRRA-EPVPTPAT---A +TAASPSSDLSSAVPEA---------------------------------------PRPAP------VAPRPASARQRRRT +ARTPEVVLGAGMGRTVAVGAAVTLLLAGMALLLGWILGSGGISGPAGVVVPPLWGLEQQE----AAARLAEAGLTSAVVS +RHDERFSDGVVLDVSPAAGSTVDAGGPVRLTVS-------DGPAPVP-------APDLAGLTVTDAHAVAEDGRVGVVVA +DRVADRAVPAGA-------VVSQSPEAGAEMTPGDE------VAVVLSTGPATHPLPDLGGLTVGEARTRLADLGFVPDV +RTLP-LPGPSGDAARVLRQGTPAGTVL----------------------------------------------------P +EGA----------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------SVQLWT---------------------------------------------------L +>GCF_023573625_PROKKA_01324 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------SSARRDPL---VGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHP +HLAEDPVLVGRFEQEAKTTARLS-HPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSPREALRFLRPL +VDGLAAAHRAGLVHRDVKPENV-LVRDDG---RVTVADFGLSRAATAHTMAGQAVVGTPAYLAP--EHIAGAPADARSDV +YAVGIILFELLTGRQPYTAATALQVAYRHVHERVPVPSTL-HPGLPEDLDDLVLWCTEPDPADR------PAGAGELLHR +IDAVAAGL--------DP-DEPDRR------P-----AEGPGTDPAAAAPAADGLEGAAP----DGDLPTRALDAGDHHA +TRVLPALA-ESALDDDVTDVIDTRAATHGGDPRPAA-------RPAEPVGPLAVDPAPAD------RHPGRGSRRRLRRA +ARRPALDLGQGTGRAAAIGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREA----AEERLTAAGFTAAVTA +RHDELRTEGTVVDSSPAAGEPAGRGAPVELTVS-------AGPAPVP-------VPDLTGVVIRQAHGVARDARFTVEVA +ERRTDPAVPAGA-------VIEQHPAPGEQATPGTA------VRVVLSEGRAVRPVPDMTGQDPETAHTTLADEGWDARV +HRLP-LPLSARGESRVLHQSPAAGTAL----------------------------------------------------P +EGT----------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------AVHVWV---------------------------------------------------G diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000129.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000129.fa new file mode 100644 index 0000000000000000000000000000000000000000..b1ef2bb615da2f3a30fe76b75e8e4d1fa68e3b1b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000129.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01450 +-----------------------------------MPPGPGALLGGRRVRLLPAILALAL +GSFAIGTTEFAMMGLLPQAVADLGVGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVT +SIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVA +WVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVG +-----RELRGLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYG +VGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVAL-TAPWA-PVMIVFLFCVA---- +-VSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL +VGAGIALAGLVLAFLLVRRDVAASPGVRADDGGSPR------------- +>GCF_003691675_PROKKA_01182 +MPTPTPAADGAHDRSPRAPRPTRPDPS----IPPTAPTGPGALLGGRRVRLLPAILALAL +GSFAIGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVT +SIVLMLLFVVGHVAAFLAPDAATMMAARFICGLPHGAYFSAAALAAADLAGPARRGQAVA +WVMAGLSVANVLGVPAATALGQSAGWRWMFVIVATCAALCVAATAWLVPPVPAPEGASVR +-----RELRGLASGRLWATVAVGVLGFAGMFALYTYIAPLLTTVSGLDERWVPAVLALYG +VGMVVGTLVGGALTDRDPVRTLRLSFALSAVFLLGVGL-TAQWA-PVMVVFLFLVA---- +-VSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL +IGAAIALGGLVLALLLVRRT-PAVGAVPHDGPSAATV------------ +>GCF_005280335_PROKKA_01449 +MTTP---ASGDPAASPSV--SARPDPADAAGSPAAGAVGPQSLLGGRRVRLLPAILALAL +GSFAIGTTEFAIMGLLPQAVADLGIGLEAGGVLISMYALGVVVGAPLLAAAFARVDRRTT +GIVLMLLFTVGHTGAFLAPDTATMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAIA +WVMAGLSVANVVGVPAATAIGQAAGWRWMFVIVAACALACVAATAWLVPPVPAPEGASVR +-----RELRGLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLDERWVPAVLALYG +IGMVVGTLVSGALTDRDPVGTLRLSFGLSAVSLLAVGL-TAQWA-PVMVLLLFCVA---- +-VSGSGIAPSLQVLLVDSAPGAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL +VGAAIALAGLVLAFVLVRRASPTSAATAADAR----------------- +>GCF_020097155_PROKKA_01353 +------------------------------------------------MRLLPAILALAL +GSFAIGTTEFTMMGLLPEAVTDLGVGLETGGVLISMYALGVVVGAPVLAAALARMDRKLS +SILLMGLFVVGHLASLLAPSLGALMAARFVSGLPHGAFFSAAALAAADLAGPARRGQAIG +WVMAGLSVANVVGVPAATALGQAAGWRWMFAVVAACALGCIAATALLVPRVPAPAGASVA +-----AEIRGLASGRLWATVAIGVVGFAGMFCLYTYIAPLLTEVSGLHPRWVPAVLALYG +VGMVIGTLVSGALTDRDPIRTLRWSFGVSALGLLAVSL-TAPWW-PALLVSLLVVA---- +-LSGSGIAPALQVLLVDAAPTAPQLSGSLNHSALNMANAMGAWVGAAAVGAGASLRMPSL +IGAGIALVGLLMSVALLRRPASAPPGA---------------------- +>GCF_020097155_PROKKA_01775 +MSAVS-----------NAPRPRLP---------------------------WGALLALSA +SGFLAIFTETIPAGLLPELSRGLGVTESAAGQLVTLYAMGSVVAAIPLVAATQTVNRKKV +LLAAVATLGAFNLVTAAAPWLPVILAARFVAGAAAALVWGVLAGFARSLVAPQLQGRALA +VTGLGQPIALAGGVPLGSFAASVMDWRWVFVAISVAAG---GLAVWIAAAVQNVEGSPRR +QREPLRRVVMLPGVRLIFAVTGCWILAHNM--LYTYAAPLLNRT----DLRLDVGLGLFG +VASMIGISLVGMVIDR----ALRL---VSAICVTAMCLATTVWLLPQVGIALAVASVVAW +GLSFGGAPVLLQTALADRAGEHTDAAQSVFVTVFNLAVAGGGFMGGMLLASSGT------ +--AGIATTSAVLCLVAVGMIVLARAAFPAGHRHKDETDESVVAPSECSA +>GCF_023573625_PROKKA_01400 +MPTPTPAADGAHDRSPRAPRPTRPDPS----IPPTAPTGPGALLGGRRVRLLPAILALAL +GSFAIGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVT +SIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVA +WVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVG +-----RELRGLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYG +VGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVAL-TASWA-PVMIVFLFCVA---- +-VSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL +VGAGIALAGLVLAFLLVRRDVAARPGVRADDDGSPR------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000130.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000130.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c0a06a657c743694b7d07321123bb5249be4a2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000130.fa @@ -0,0 +1,96 @@ +>GCF_002008305_PROKKA_01539 +M------------------------------------------------------------------------------- +----------------TQNSE-------------------HTPASADLDPTVA--------------------------- +--------------------AIAEDI-VTEDAAPVAPEQ--------------------TFADF---------------- +--------------GVHPAIVEALEAKG-------------------------------------------------IVH +PF----------------PIQAMTLPVAL-----GGHDII---------------------------------------- +-------------------------------------------GQA-----------KTGTGKTLGF------------- +-------------------------------------GIP----------ALQRAI-----------------GPGEPGW +DGLEA-KGTAGAPQALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVE------IVVGTPGRLI +DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAMARRYMTQPTHIRAADPEDEG +LTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAR---------- +---------------EQALRAFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV +D-WEDMPRWSLI-------DKALGLGQPEPVETYSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLE-GETLEDLGGPEAKQ +-------------R-------------DGG------------RG--------R---------GREGGRSRDGERGGR-EG +GR----------GGRGGRGRGGRSGEGRDAARGGSRGER-SERSGRGRGEAPAEQ---RAEGRGRGR------GEGRKRT +ASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGRSRTRRRNGEVV-----------DG +>GCF_003691675_PROKKA_01249 +M------------------------------------------------------------------------------- +----------------TQNSE-------------------HTPAPADVDPTVA--------------------------- +--------------------EIAEDI-VTEDAAPVAPEQ--------------------TFADF---------------- +--------------GVHPKIVEALEAKG-------------------------------------------------IVH +PF----------------PIQAMTLPVAL-----GGHDII---------------------------------------- +-------------------------------------------GQA-----------KTGTGKTLGF------------- +-------------------------------------GIP----------ALQRAI-----------------GPGEPGW +DGLEA-KGTAGAPQALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVE------IVVGTPGRLI +DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGTVVAMARRYMTQPTHIRAADPEDEG +LTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAR---------- +---------------EQALRAFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV +D-WEDMPRWSLI-------DKALGLGQPEPVETYSSSPHLFSDLDIPKGTKGRLPQAKRVLEGLE-GETLEDLGGPEAKQ +-------------R-------------DGG------------RG--------R---------GREGGRSRDGERGGRGRG +GRSGEGRDRARGGGRGERTE--RSPRGRDEARA----------EGRGRGEAPAEQ---RAEGRGRGR------GEGRERT +ASRPETPAARTPEPVAGVELTEARRAERAEARAEARRRRGGRTRTRRSNGEVV-----------DG +>GCF_005280335_PROKKA_01386 +MNR------------------------------------------------------AHGASG----PSR-------PP- +------------CRRPNRNASR-----------HDPELRAHPRPGRRRPPQVA--------------------------- +--------------------DIAEEI-VTEEAVETAPEQ--------------------TFADF---------------- +--------------GVHPAIVQALEAKG-------------------------------------------------IVH +PF----------------PIQAMTLPVAL-----GGHDII---------------------------------------- +-------------------------------------------GQA-----------KTGTGKTLGF------------- +-------------------------------------GIP----------ALQRAI-----------------GPGEPGW +DKLEA-QGSAGAPQALIVAPTRELAVQVAGDLTAAAAQRPLRIATIYGGRAYEPQIEELQRGVE------VVVGTPGRLI +DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLGAVPAVRQTMLFSATMPGPVVAMARRYMTQPTHIRAADPEDEG +LTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAR---------- +---------------EQALRAFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV +D-WEDMPRWSLI-------DKALGLGQPEPQETYSSSPHLFADLGIPKGTKGRLPKEKRVLEGLE-GEVLEDLGGPESAP +-------------R-GRGGR-SRDGERDGG------------RGGR-GGRGER---------GGRGGRSRDDERGGR-EG +GR----------GGRGERA-GREGGRGRDAEQSSARGEEAGESKGRGRGGERAGREGGRGESTGRGRG--GRSGESRTRG +ESRTEASEARAAQPVAGVERTEARMAERAEARAEARRRRGGRTRTRRRNGEVV-----------DG +>GCF_020097155_PROKKA_00286 +MKSIDNVNVKLGDDLKAEITAGSKVRIAASAFSIYAFEALREELEGLEELQFIFTDPAFSASSIDGTPRREHRRYFIPPL +DIESSLTGTEFEVRLRNRLTQRAIARECADWVRRKVRFR-SNTSGKGMQPIIGVGDDAAYLPVQDFSTSALGYEAGGALS +NVVGKFEGPLEAAGLLTVFDQVWNDPSALEDVTSTVLERIEQVYAENSPRHIYFLILNSIFSDFLADLSEDALPNDRTGY +RETKVWRALYDFQRDAAESIIQKLETYNGCILADSVGLGKTFTALAVIQYYEKRNKSVLVLCPKKLAENWTTYNNNYVTN +PFVEDRFNYDVLAHTDLSRTRGESLGVRLDRINWGNYDLVVIDESHNFRNATYGEDRDTRYQRLMEKVIREGVRTKVLML +SATPVNNRFNDLKNQLQLAYEGEEENLSQHLNLSTTIDGVFRGAQAAFNEWSKLPAEERTPGRILGMLDFDFFELLDAVT +IARSRKQIQRFYDTAAIGAFPTRLPPLSLQEPLSEDKSVPSYNDIFEQLQALNLAVYTPLAFVHASRRYKYETGPGEENT +DNFRSGRGQAGRETGL----KRLMTVNLLKRLESSVHAFRKTLVSI------ESQVDALHRRLESEALGPLRVDAPAVEE +DILREDD---DVAEALFALPGDLELDLNDV-DVLSWTSALWHDRETL--------------RELIGEMDKI---TPERD- +LKLQRLRRLI-----RDK----ATSPLNEGNRKVLVFSAFADTADYLYEQLSPALSAAGLETGIITGGSHSARSTLDGAV +DFQTLMTLFSPVSKNRSALMPEETREVDVLIGTDVISEGQNLQDCDFLVNYDIHWNPVRIVQRFGRIDRIGSTNERIQLV +NFWPDMDLDAYIQLKDRVENRMVMVDVTGTADDNVLTPQQEQDAAYRTAQLKRMREEVVELEDTQAGVSITDLGLNEFRS +ALMAYVREHGDLTRAPRGLHAVVPADPDAGLPAGVIFALHNLQADPAMHRGNRLHPYYLVYVGEDGATVLEHTKAKP--- +--------------------------LLDLLRSA------------------AEKQ--SVPLADAVRAFNTATAEGTDMA +AYSALLTRAIESMVEADEEQDVASLFTAGPTTALTSAIRG------LEDFELIAFLAVVDTAGTDA +>GCF_020097155_PROKKA_01277 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------TENTAAAEAVAPTAPEQ--------------------TFADF---------------- +--------------GVQEPIVRALSEKG-------------------------------------------------IVH +PF----------------PIQAMTLPVAL-----GGHDII---------------------------------------- +-------------------------------------------GQA-----------KTGTGKTLGF------------- +-------------------------------------GIP----------ALQRAV-----------------GPDEAGW +DTRVA-AGAAGAPQALVVAPTRELAVQVAGDLVAAAKHRPLRIATIYGGRAYEPQIEELQRGVE------VVVGTPGRLI +DLLRQKHLRLDAVNTVVLDEADEMLDLGFLPDVETLLAAVPEVRQTMLFSATMPGPVIAMARRYMTRPTHIRASDPEDEG +LTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVAEELTNRGFAAGPLHGDLGQGAR---------- +---------------EQALRAFRNGKVDILVATDVAARGIDVDDVTHVINFQAPEDAKTYVHRVGRTGRAGHKGTAVTLV +D-WEDMPRWSLI-------DKALGLNQPEPVETYSSSPHLFSDLGIPKGTKGRLPKEKRVLAGLD-AERLEDLGGPEAKE +-------------KAARGGRDERSGSRSGG------------RGERSGGRGGR---------AGGGSRASREDRPPR--- +----------------------------------------EDRTPRGERAPRPEK---TVKAERAPR------AE-RAPR +AEKADRPAA----------------AERSEGASGERRR---RTRTRRRGGDVI-----------DG +>GCF_023573625_PROKKA_01466 +M------------------------------------------------------------------------------- +----------------TQNSE-------------------HTPASADLDPTVA--------------------------- +--------------------AIAEDI-VTEDAAPVAPEQ--------------------TFADF---------------- +--------------GVHPAIVEALEAKG-------------------------------------------------IVH +PF----------------PIQAMTLPVAL-----GGHDII---------------------------------------- +-------------------------------------------GQA-----------KTGTGKTLGF------------- +-------------------------------------GIP----------ALQRAI-----------------GPGEPGW +DGLEA-KGTAGAPQALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVE------IVVGTPGRLI +DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAMARRYMTQPTHIRAADPEDEG +LTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAR---------- +---------------EQALRAFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV +D-WEDMPRWSLI-------DKALGLGQPEPVETYSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLE-GETLEDLGGPEAKQ +-------------R-------------DGG------------RG--------R---------GRDGGRSRDGERGGRGRG +GRSGEGRDRARGGGRGERNRGGRSGEGRDDARGGGRG----ERSGRGRGEAPAEQ---RAEGRGRGR------GEGRERT +ASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGRSRTRRRNGEVV-----------DG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000134.fa new file mode 100644 index 0000000000000000000000000000000000000000..b50e414494d1dd3eda81ff0e00d8b61761301c2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000134.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01581 +MS---------------------TTLDLDHAATAPVRRSALEAMWPALT-GVYGNPSSAH +EAGRAAAALLEDARARVACAIGAR-AGQVVFTSGGTEADALAVLG-----TVRARILAGR +PAGHVLTTGIEHSAVRQSCDQLARLHGVEVEHLALDRDGLTSADDLAARLRPDTALVSVH +LAHNEVGTVQPVAELAAVAREAGVPLHVDAVQAAGQIPVDVRALGADLVALSGHKVGGPK +GVGALWVRPG--HALEPLVPGGGQ------ERGR--------RSGTQNVAGAAGFAAAFE +EAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARRLPRHA-SFALPGVNGE +SVLEEAARRGVLASAGSACS--AHDAEPSPALLALGLSEDEARTALRCTFGPDADAPLLD +AAADAIVDAVRTVSAL-R +>GCF_003691675_PROKKA_01291 +MS---------------------TTLDLDHAATAPVRRSALEAMWPALT-GVYGNPSSAH +EAGRAAVALLEDARARVARAIGAR-AGQVVFTSGGTEADALAVLG-----TVRARILAGR +PAGHVLTTGIEHSAVRQSCDQLARLHGVEVEHLALDRDGLTSADDLAARLRPDTALVSVH +LAHNEVGTVQPVAELAAVAREAGVPLHVDAVQAAGQIPVDVRALGADLVALSGHKVGGPK +GVGALWVRPG--HALEPLVPGGGQ------ERGR--------RSGTQNVAGAAGFAAAFE +EAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARRLPRHA-SFVLPGVNGE +SVLEEAARRGVLASAGSACS--AHDAEPSPALLALGLSEDEARTALRCTFGPDADAPLLD +AAADAIVDAVRTVAAL-R +>GCF_005280335_PROKKA_01342 +MS---------------------AALYLDHAATAPVRRVALEAMWPALT-GVYGNPSSAH +EAGRAAAALLEDARARVARAIGAR-AGQVVFTSGGTEADALAVLG-----TVRARILAGR +PAGHVLTTGIEHSAVRQSCDQLARLHGVEVEHLALDRDGLTSADDLAARLRPDTALVSVH +LAHNEVGTVQPVAELAAVAREAGVPLHVDAVQAAGQIPVDVRALGSDLVALSGHKVGGPK +GVGALWVRPG--HALEPLVPGGGQ------ERGR--------RSGTQNVAGAAGFAAAFA +EAEAERAAAADAWSGLRDRFAARALDGVQELVPDARLTGHPARRLPRHA-SFVLPGVNGE +SVLEEAARRGVLASAGSACS--AHSTEPSPALLALGLSEDEARTALRCTFGPDADEAMLA +AAADAIVDAVRTVSAL-R +>GCF_020097155_PROKKA_01235 +MS---------------------TILDLDHAATAPVRRSALEAMWPALT-GVYGNPSSAH +EAGRAAAALLEDARARVARAIGAR-AGQIVFTSGGTEADALAVLG-----TVRARILAGR +PAGHVLTTGIEHSAVRQSCDQLARLHGVEVEHLALDRDGLTSADDLAARLRPDTALVSVH +LAHNEVGTVQPVAELAAVAREAGVPLHVDAVQAAGQIPVDVRALGADLVALSGHKVGGPK +GVGALWVRPG--HALEPLVPGGGQ------ERGR--------RSGTQNVAGAAGFAAAFE +EAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARRLPRHA-SFVLPGVNGE +SVLEEAARRGVLASAGSACS--AHDAEPSPALLALGLSEDEARTALRCTFGPDADAPLLD +AAADAIVDAVRTVTAL-R +>GCF_020097155_PROKKA_01767 +MALDVAAVRQDFPILRSTLADGRPLVYLDSGATSQRPRQVIEAEVEFLTISNAAVKRGAH +QLAEAATDRYESARETVAAFVGATDPRELVFTRNATEALNLVAYALGNGDDATPEHLRVR +AGDEILVTEMEHHANLVPWQELARRTGATLRHIPLGEDFALDLVDLGSLVTERTKVVAFT +HQSNVTGTVNPVATLGEAARAVGALTVLDACQSVPHMPVDVAALGVDFLAFSGHKMLGPT +GIGALWGRYELLAELPPFLLGGSMIEVVHLDRSTYAEPPARFEAGTPPISQAVGLAAA-- +-CDYLSALGMDAVAEHEHALTARALEHLAGM-DRVRVIGAPAGPERSGAVSFAVEGIHPH +DVGQVLDSLGVQVRVGHHCAWPLHRRYGVPG-------------TTRASFSVYSTLDEVD +AFADGLAQTLAFFQGFGR +>GCF_023573625_PROKKA_01508 +MS---------------------TTLDLDHAATAPVRRSALEAMWPALT-GVYGNPSSAH +EAGRAAAALLEDARARVARAIGAR-AGQVVFTSGGTEADALAVLG-----TVRARILAGR +PAGHVLTTGIEHSAVRQSCDQLARLHGVEVEHLALDRDGLTSADDLAARLRPDTALVSVH +LAHNEVGTVQPVAELAAVAREAGVPLHVDAVQAAGQIPVDVRALGADLVALSGHKVGGPK +GVGALWVRPG--HALEPLVPGGGQ------ERGR--------RSGTQNVAGAAGFAAAFE +EAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARRLPRHA-SFVLPGVNGE +SVLEEAARRGVLASAGSACS--AHDAEPSPALLALGLSEDEARTALRCTFGPDADAPLLD +AAADAIVDAVRTVAAL-R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000135.fa new file mode 100644 index 0000000000000000000000000000000000000000..a19e3d5228db8cdc5403395496b825bb7949227a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000135.fa @@ -0,0 +1,48 @@ +>GCF_002008305_PROKKA_01582 +MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVASRLTLPSGVATGDVTSNSAV +LWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWVDGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVA +RFTTAPGARFGRKTSAAQSFVWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR +NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLEDPRYTQVRDVDTLAARARRAW +QEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKV +IANDLPLGLVVPDGTGQESLSNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE +FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAAGRTVYSRTLTAA +>GCF_003691675_PROKKA_01292 +MRLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVASRLTLPSGVATGDVTSNSAV +LWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWVDGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVA +RFTTAPGARFGRKTSAAQSFVWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR +NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNW---------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------------------------------------------------------- +>GCF_003691675_PROKKA_01293 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +--------------------------------------------------------------------MDTLAARARRAW +QEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKV +IANDLPLGLVVPDGTGQESLSNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFESFWE +FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA +>GCF_005280335_PROKKA_01340 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------MKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE +FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA +>GCF_020097155_PROKKA_01234 +MSLACVPHPGSVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVASRLTLPSGVATGDVTSNSAV +LWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWVDGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVA +RFTTAPGARFGRKTSAAQSFVWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR +NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLEDPRYTQVRDVDTLAARARRAW +QEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENTPGLETHETPILGEEQLQWLIHGLRASTATWKV +IANDLPLGLVVPDGTGQESLSNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE +FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINANGRTVYARTLTAA +>GCF_023573625_PROKKA_01509 +MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVASRLTLPSGVATGDVTSNSAV +LWARSSGRSRLHATLRAVDEDGKALRGRFSRGLTLRSGWVDGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVA +RFTTAPGARFGRKTSAAQSFVWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR +NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYTDVPVIAQWDDHETTNNWWPGEVLEDPRYTQVRDVDTLAARARRAW +QEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKV +IANDLPLGLIVPDGTGQESLSNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE +FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEGGREFRVRLINAAGRTVYSRTLTAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000143.fa new file mode 100644 index 0000000000000000000000000000000000000000..afe41b733da3c4c07af15c7d20cc8192be76125d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000143.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_01687 +M----PDVT---P-PPPSRSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQAT-- +--RLPAPDIITTAQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQ +NAHMGSANDWGDTGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIEC +EGLYMLNPPPQSLYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILRE +DVRLSLASGEYHVSEGFG------AD---------------------------------- +------------------------------NLFDDAHVTP---EYVEE--ERG +>GCF_003691675_PROKKA_01391 +M----PDVT---P-PPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQAT-- +--RLPAPDIITTAQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQ +NAHMSPANDWGDTGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIEC +EGLYMLNPPPQSLYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILRE +DVRLSLASGEYHVSEGFG------AD---------------------------------- +------------------------------NLFDDAHVTP---EYVEE--ERG +>GCF_005280335_PROKKA_01191 +M----PEQS---P-TPSSRPWARRTVLGGTGLAIAAGVAGCSRPEAGEEAEETEAAPK-- +--RLPAPDILTTAQWGALQPNYHLQTLDERPSYLVIHHTTTPNVTDGSREAAESIAKSIQ +NAHMSTLNDWGDTGQHFTVSRGGFALEGRHGSRYTLEQGQTFMLGVHALGFNAYALGIEC +EGLYTLNPPPQSLYAGLVPLAAYICQQYELPPSRIIGHRDVTATSCCGDAFYGKLPVLRE +DVRLSLATGEYHVSEGFG------AD---------------------------------- +------------------------------NLFDDAHVTP---DYLQE--QGY +>GCF_020097155_PROKKA_00038 +MKHALPRHVQHAPVPPAAASPGRRAVLVG-GLA-AAGAAGA--------AAAGAVPAA-- +--AFAGPVVHSTAQWGARSPRSAAEVVRARPTRLVIHHMASPNTAETSLAHAYGLARACQ +QDHMG--RGFDDSGQHFTVSRGGHCLEGRAGSLAALRAGDRHVKGAHVSGQNTGKIGIEC +EGSYVTGLPTPAQYRALVQLAAHICRQYGIRPADIVGHGDLMATQCPGGAFHARLGVLRA +DVARTLATGRLSVSDPSGRAASIPADPRRAATTTPSAAAPASRRVLGPGSRGADVKRVQA +LLTTAGHRVPRTGLYAARTTAAVRAFQRRSGLAQDGFTGPLTWAALEAAGRR- +>GCF_020097155_PROKKA_01121 +M----PDHQ------ILSSSWPRRAVLGGAGLAIAGTVAGCGTGGDAAQSTSADGSAAST +GPRLPEPEILSTIDWGARIPENWQQTLYEKPSYLVIHHTTTPNVTDGSRDAAIALAQRVQ +NQHIN--QQWGDSGQQFTMSRGGFAMEGRHGSLYALQGGETFILGVHALGFNAYAVGIEC +EGFYMVSPPPQSLYAGLVKLSAFICQQYELPPSRIIGHRDVVKTSCCGDAFYAKLPILRE +DVKRSLETGEYQITEGFG------AD---------------------------------- +------------------------------NLLDDAKINV---ENYEDFQKRS +>GCF_023573625_PROKKA_01616 +M----PDVT---P-PPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQAT-- +--RLPAPDIITTAQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQ +NAHMSPANDWGDTGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIEC +EGLYMLNPPPQSLYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILRE +DVRLSLASGEYHVSEGFG------AD---------------------------------- +------------------------------NLFDDAHVTP---EYVEE--ERG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000144.fa new file mode 100644 index 0000000000000000000000000000000000000000..8287c1915a651a1ab7577dc19db693b0a31ffab8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000144.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01779 +MS-----------TAPALPPLPGA-------------PGGPALPSVEELLADAVAVAVPM +RVRFRGTDLRHALLLRGPAGWGEFSPFPEYGPHESAAWLAAAIEAGWQGWPAPVR----- +---------ETIPVNATVP--------------------AVDADDVEAVLARYGDGITA- +---VKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTE +LADVGL--EYAEQPVPG--ITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAA +DLIVVKVQPLGGVRRAAAI---VAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACG +LGTAALFEHDVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRVRAAHA +VLAAQG- +>GCF_003691675_PROKKA_01486 +MS-----------TAPALPPLPGA-------------PGGPALPSVEELLADAVAVALPM +RVRFRGTDLRHALLLRGPAGWAEFSPFPEYGPHECAAWLAAAIEAGWQGWPGPVR----- +---------QTVPVNATVP--------------------AVAADDVEAVLARYGDGITA- +---VKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTA +LADVGL--EYAEQPVPG--ITALAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAA +DLIVVKVQPLGGVRRAAAI---VAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACG +LGTAALFEHDVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRLRAAHA +VLAAQG- +>GCF_005280335_PROKKA_01098 +-----------------------------------------------------------M +RVRFRGTDARQALLLRGPAGWAEFSPFPEYGPAESSAWLAAAIEAGWQGWPAPVR----- +---------DVVPVNATVP--------------------AVEAEAVESVLARYGEGITA- +---VKVKVAEHRPGGGLVPGSHSADLARVRRVRELLPDAHVRIDANAGWTPAEAIAMLTD +LADVGL--EYAEQPVPG--IKKLARVRRELRARGVSTPIAADEAVRKAEDPLAVAAAGAA +DLIVVKVQPLGGVRRAAAV---VAAAGLPAVVSSALDTSVGIAGGAALATHLPALPHACG +LGTAALFDDDVVTPAWTPRQGVLEAPGERAPEPDPALLARVRADERTHAWWRDRVAAAHA +VLAAGGR +>GCF_020097155_PROKKA_01022 +MTVPAAHDDADPRPGSALPPLPGA-------------PGGPALPDVDELLEHAVAVTLPM +TVRFRGTTERRALLLRGPAGWAEFSPFPEYGPAEASRWLAAAVEAGWQGWPAPVR----- +---------SEVPVNATVP--------------------AVDAADVESVLARYGDGITA- +---VKVKVAEHRPGGGLVDPTHAADVARVRRVRELLPEAAVRIDANAGWDEDRAFAVLGA +LQDVGL--EYAEQPVPG--IAGLAALRSRLRAAGIATPIAADEAVRKETDPLAVAQAGAA +DLIVVKVQPLGGVRRAAAI---VAAAGLDAVVSSALDTSVGIAGGAALAAHLPSLPFACG +LGTASLFAHDVVSPAWRPADGSLPAPGERAPEPDPALLAAARADAAEHAWWAERLRAAHA +VLAARGR +>GCF_020097155_PROKKA_01806 +MS-----------PAPGQAPVSVAAVRRHRHRAPLLHPFVTAARRTEAVEYVVVEVELSD +GTVGQGSAAETVAVTGEDAASIETAVDGVFGPALTGA--TGGLDGLLARLPAPARGATSA +RSAVDVAVHDAVARAAGVPLTALLAPAGTAVKQTLENDMTVSLEDPATMAARAAEAVAAG +TRILKIKLGRDV----------AEDRRRLHAVLEAAPQARLRLDANQGWSVEDAIAIISG +MEDEGLPVDLVEQPVAAADVAGLARVRA-----AVTTPIMADEALWSSEDARRLIEAGAA +DLFNVKLAKTGGLADAVAIADLAAEHGIGCMVGSMMEPRISIAAAVQLSLAHPAVTMV-- +---------DLDAPLWFASDA--PAGGYTQEGADLRLLPG-------EGLALERLDPGTD +PV----- +>GCF_023573625_PROKKA_01708 +MS-----------TAPALPPLPGA-------------PGGPALPSIEELLADAVAVALPM +RVRFRGTDLRHALLLRGPAGWAEFSPFPEYGPHESAAWLAAAIEAGWQGWPAPVR----- +---------QAVPVNATVP--------------------AVDAADVEAVLARYGDGITA- +---VKVKVAEHGPEGELVPGSREADLARVRRVRALLPHAQVRVDANAGWTPTEAVDVLTA +LADVGL--EYAEQPVPG--ITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAA +DLIVVKVQPLGGVRRAAAI---VAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACG +LGTAALFEHDVVAPAWRPRAGALPAPGERASAPDPELLDRVRADGARQAWWADRVRAAHA +VLAAQG- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000151.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3c29197bcf4274c8ae58a6c2507bb5c0efedba8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000151.fa @@ -0,0 +1,48 @@ +>GCF_002008305_PROKKA_01921 +M----VLPVLPALATPPLLTALDRLL-AGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAFAIGAAVVYLALQVAR +VVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRPASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQET +GVEHRRERRIRTQTILIRRILNAVIVVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA +IRVGDVVDMEGVFGTVEEITLSNVVVKLWDGRRVVYPSSHFTTQPFENWTRVGTEVSGVVELDVDWRVPMDALRARLAQL +LESTDLWDG-REHALQVTDATGGVVRI----RAVVSARNSGDLWDLRCLVREDLVAFLRHEHPEGIVVQRMVVRHP---- +--AHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAAR-EPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTA +VQRNRELAGPGEEAFAERRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED +>GCF_003691675_PROKKA_01617 +M----VLPVLPALATPPLLTALDRLL-AGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAFAIGAAVVYLALQVAR +VVLVRRPAFQQGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRPASFLMLIAVAAAGAWAAWRLVGVIEKGILGRYQET +SVEHRRERRIRTQTILIRRILNAVIVVVAVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA +IRVGDVVDMEGVFGTVEEITLSNVVVKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVDWRVPMDALRARLAQL +LESTDLWDG-REHALQVTDATGGVVRI----RAVVSARNSGDLWDLRCLVREDLVAFLRHEHPEGIVVQRMVVRHP---- +--AHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAAR-EPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTA +VQRNRELAGPGEEAFAERRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED +>GCF_005280335_PROKKA_00786 +MDLPQITP------------------------------------------------------------------------ +-------------------------------------------------LAVAVGLAVAVVGWLLGRLLGAGVAWLFA-- +----RRGRSPSSARVFGKLVAAGITVLSLGAAVTVVFPSVKPV--DLLGGIGVISIAAGIAFQTVLGNMFAGMVILARDR +FRVGDQIQVGEHAGNVVEMGLSSTAVKTFDGRLVLIPNQMLHSQAVTVQTGFSAVRS---SLRVDVETGNDLARTREIAV +RAMSELPQVLRDPAPQALLASVGVTTVGMDLRFWSGARQMETKEAMDAVIHAVLTAFEKNGVATGDDV-RVVDAGP-ELR +RILEGPGAPRGQG--------------GPDYPG------------------G---------------------------- +------LAGPGE---------------PDRAARP-------------------------GSD +>GCF_005280335_PROKKA_00939 +M----LLAALSGPASPPVLGSLARLF-AGENVPAGVEGNVQDGAAATTAALGVEWGTLLTVLVAFAVGATLVYAALQVTR +VVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRPASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQET +GVEHRRERRIRTQTILIRRILNAVIVVVAIAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA +IRVGDVVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVDWRVPMPALRERLTQL +LDSTDLWDG-RESSMQVTDAIGGTVRI----RAVVSARNSGDLWDLRCLVREDLVTFLRSEHPEAIVVQRVVERHP---- +--AHDDAVPASEGSDAGARGGDPTGEPGPDGSGVAAR-EPRPRTAALPRVEGGEPRPDTVTTPLTRVDDHAGLYTGSITA +VQRNRELHGPGEDAFAERRAQQAKQAAEAATADEAGRRSGAGSHADGLLDDAVTRRRQDDED +>GCF_020097155_PROKKA_00874 +MPVPALLPVLAQTASSDAALSDAVLSAADQVVPGSVEQDVQQGASAASAALGVEWATVAAVLGAFLAGGLVVLGVFLVAR +LALFRRDRLKADAARLTVPVSLFAGFLTARVGLEVMAHGQPWFEAAAFVLLLAVAASAAWAAWRVVDVVESGILARYHQP +GVNDRRERKIRTQTMLLRRVLNAVIVVVALAVVLLAIPQVRSLGAGLLASAGLISVIAGLAVQSTLTNVIAGFQLAFTDS +IRVGDVVDMQGVFGTVEEITLSNVVVKLWDGRRMVYPSKHFTSEPFENWTRTGAAVAGVVEMDVDWRVPMDPLRARLTEL +LESTDLWDG-RENAMQVIDAVGGMVRI----RAVVSAKNSGELWDLRCLVREDLVGFLRAEYPEGIYTQRLVERRPSDPA +PEAHDDPAPDAHDDAAPAAA---PAAPAPSDRGSSTRAEPTPQTRPMPTVTG--------SVPLARAGENASLYTGSIRA +VERNQEMDGPGEEAYAERRARAAER--EDRAARDAGR---GGAHA--------------ARS +>GCF_023573625_PROKKA_01841 +M----VLPVLPALATPPLLTALDRLL-AGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAFAIGAAVVYLALQVAR +VVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRPASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQET +GVEHRRERRIRTQTILIRRILNAVIVVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA +IRVGDVVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTRPFENWTRVGAEVSGVVELDVDWRVPMDALRARLTQL +LESTDLWDG-REHALQVTDATGGIVRI----RAVVSARNSGDLWDLRCLVREDLVSFLRHEHPEGIVVQRMVVRHP---- +--AHGDASPASEGSDAEARGGDRTGEPGPDGSGVAAR-EPRPRTAPLPRVDGADPRPDTLTTPLTRVGDHSGLYTGSMTA +VQRNRELAGPGEEAFAERRAQQAKQAAEAAAADEAGRRSGAGSHTDGLLDDAVTRRRQDDED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000154.fa new file mode 100644 index 0000000000000000000000000000000000000000..2acef14c458bc1956bd1c02db402db69a8b986a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000154.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_01983 +MTPA-LISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLA +VAGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWART +RDARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA +>GCF_003691675_PROKKA_01677 +MTPA-LISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLA +VAGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWART +RDARAALSSSIGALTAMGMGMLVEFCCALGSLTAVGVGALVHGLTA +>GCF_005280335_PROKKA_00875 +MTLAIVVSVLAVLLLIVGVVGTVYPILPGSMLILVTAVAWAWILGSGASWTFGLLAAGLA +VAGMSASAVLTGRRLLRERVTRGPIAAGVVGAIVGFFVIPVVGLFIGFAVGLFGSQWART +KDARAALASSWGALKAMGLGMLVELGCAMLALVSVGVGILVHFV-F +>GCF_020097155_PROKKA_00810 +MTPA-LISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGLIAAGLA +VAGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVAGLFLGFAVGLFASQWART +RDARTALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGVTA +>GCF_020097155_PROKKA_00823 +MTFAILVSLLAVLLLIVGLVGTVYPVLPGSVLNAVVSLAWAWVLGSVASWTFGLIACAFS +IAGMSASAALTGRRLVKERIPRGPILTGVAAAVVGFFVIPVVGVFVGFAAGLFGAEWARR +RDARAALTSSWGALKAMGLGMLVEFGCAMVALASVGAGALVHVLSL +>GCF_023573625_PROKKA_01909 +MTPA-LISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLA +VAGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWART +RDARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000155.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000155.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c9870df781985ee54272287725d66dc7ce8a9f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000155.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01985 +MSP-QKTVGVLALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLA +RIMGMRDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVD +SFEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGD---- +ARLPVAVRQGHLLATAFHPEVTGDWSFHRAFLAGL-------- +>GCF_003691675_PROKKA_01679 +MSP-QKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLA +RIMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVD +SFEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPTSRLSVPAADPGLDGD---- +ARLPVAVRQGHLLATAFHPEVTGDWSFHRAFLAGLRPPRAPRR +>GCF_005280335_PROKKA_00872 +MSA--LLVGVFALQGDVREHVRVLEGLGARTRPVRRAADLTGLDGIVLPGGESSVMDRLA +GLMGLKEPLADAIGAGLPAYGTCAGIILLAREIQNPAPGQGSLGVLDVTVRRNAFGAQVD +SFEADLEVPAVSAEPVHAVFIRAPAVLRAGGEVEVLASVPASRLSAAPPELGLDDA---- +AQVPVAVRQGRVLATSFHPEVTGDHSFHREFLRGL-------- +>GCF_020097155_PROKKA_00808 +MSP-QKTVGVFALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLA +RIMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVD +SFEEDLDVPAVAAEPVHAVFIRAPAVVQAGEGVEVLASVPASRLSLPAADPGLDGD---- +ARLPVAVRQGHLLATAFHPEVTGDWSFHRAFLAGL-------- +>GCF_020097155_PROKKA_00818 +MRAVQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLAGLDGIVLPGEESSVMDRLA +RIMGLRDPLAEAVRAGLPVYGTCAGMILLAAGIENPAPGQGSLGVLDVTVRRNAFGSQAD +SLEADLQVPAVSADPMHAVLIRAPAVVRVGEGVEVLASVPAARAVAASSSTAETDDGAPA +ADLPVAVRAGNVSATSFHPEVTGDWSFHRAFLAGL-------- +>GCF_023573625_PROKKA_01911 +MSP-QKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLA +RIMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVD +SFEEDLDVPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGD---- +ARLPVAVRQGHLLATAFHPEVTGDWSFHRAFLAGL-------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000156.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000156.fa new file mode 100644 index 0000000000000000000000000000000000000000..42444d2e06c3c5ccab100fb6aa9f1f8d2277ec6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000156.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_02014 +MSHTVASPAA--PVPAR---DRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQ +PMGENGSQIAAWVTLGISFLVRPLGAIVAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLP +TYAQIGVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMI +LATGVLFIVRSTMSEEQFLTWGWRIPFLISVILIVVGYLIRKAVEESPVFKEMQQLKVDE +SAPLGELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGG +VGWFIFTLLGGWVSDKIGRKLTFVFGYGFLIVWAFPLFGLLNTAS---LPLFSLGLFVLT +LGLGPSYGPQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKT-GWENVA- +WYIIVISAISLIAVLFV-PKGIQDRELHDEQVVATRS---------NPVVPT------ +>GCF_003691675_PROKKA_01724 +MSHTVASPAA--PAPAR---DRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQ +PMGESGSQIAAWATLGISFLIRPLGAIVAGHLGDRFGRKFVLSLTLIGMGLATTLIGLLP +TYAQIGVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMI +LATGVLFIVRSTMSEEQFLTWGWRIPFLISVVLIVVGYLIRKAVEESPVFKEMQQLKVDE +SAPLGELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGG +VGWFIFTLLGGWVSDKIGRKLTFILGYGFLIIWAFPLFGLLNTAS---LPLFSLGLFVLT +LGLGPSYGPQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKT-GWENVA- +WYIIVISAVSLIAVLFV-PKGIQDRELHDEQVVATRS---------NPVVPA------ +>GCF_005280335_PROKKA_00129 +MAEFSAAPTA-HPAESDTHVSPAQRRKAFVGAIAGHLIEWYDYGVYG-FLAVYVAANFFK +SENPMVGILAAFAVFALSFFVRPLGGLFFGPLADKIGRRKTLMIVLGLMCGATAVIGMLP +TYATIGVFAPILLVLMRLVQGFSAGGEVSTISAFVAEYAVKGRRGFATSFLMVTAASGLL +LGGVVANGLGAIIGTEAMAEWGWRLPFLLAGVLGVVAVFIRMKLEDSPEFRRLHSEGKTS +KTPLRETLRYQRQLFLMGALITLLGSTF-YLVLTYLTTY-MRTILELTPGAIFWLVLLTG +AAAAAFMPVGGAISDRMGDRRPMLAIGAVLVAGAVVWFFLTAPGTDGGLPL-VPSLLALG +ITTGLYCGVPYATMTELMPAHVRSTGIALGYNVPVAVFGGSAPFIASWLINETGDVASPM +YFFLLTAAIALVGVAMLRPTDL----LGHEDVPVTGSIDAVGGKVTRTVAPRPKADAL +>GCF_005280335_PROKKA_00826 +MSHTTVAHGAEHPARTR---DRAEERKVLAGTLVGTTIEWYDFFIYAQAAALVFAPLFFA +PMGEQGAQIASWASLGISFLVRPLGAIVAGHMGDRFGRKLVLSLTLIGMGAATVLIGLLP +TYASIGIWAPILLVVFRLLQGFSAGGEWGGAALLSVEHAPRGKRGLFGSAPQIGVPLGML +LATGVLFAVRASMTNEQFLAWGWRIPFLISVILIFIGYIIRKAVEESPVFKEMQQLKKDE +SAPLGELFRNHTKEVVLAALIFAANNAVGYLVIAWFSKY-GQKNLGMAPNDTLIAALVGG +FGWFIFTLFGGWISDKIGRKTAFVAGYALIIAWAFPMFQMMNTAS---LPMFAAALFILS +IGLGPSYGPQSAMYAEMFPARVRFSGVSIGYAIGAIIGGAFAPLIADLLLNDGGWVPVA- +WYMIIISAVSLIAVLFV-PKGIQDRNLHDEGVVVAET---------GTREPVA----- +>GCF_020097155_PROKKA_00765 +MSHTVASPAV---AAAR---DPREERKVLAGTLVGTTIEWYDFFIFAQATALVFATLFFQ +PMGESGAQIAAWVTLGISFLVRPLGAIIAGHLGDKFGRKLVLSLTLIGMGAATTLIGLLP +TYAQIGVWAPILLVLLRLLQGFSAGGEWGGAALLAVEHAPHGKRGLFGSAPQIGVPLGMI +LATGVLFLVRSTMSEEQFLTWGWRIPFLVSVLLIVVGYFIRKAVEESPVFKEMQQLKVDE +SAPLGELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGG +VGWFIFTLLGGWISDKIGRKTTFVIGYAILIAWAFPMFQLLNTAS---LLLFSLALFVLT +MGLGPSYGPQSAMYAEMFPARVRFSGVSIGYAIGTIIGGAFAPLIADELVKS-GWPSVA- +WYIIGISAISLIAVLFV-PKGIQDRELHDEEVVATRS---------NPVVPA------ +>GCF_023573625_PROKKA_01952 +MSHTVASPAA--PVPAR---DRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQ +PMGESGSQIAAWVTLGISFLVRPLGAIIAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLP +TYAQIGVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMI +LATGVLFIVRSTMSEEQFLTWGWRIPFLISVALIVVGYLIRKAVEESPVFKEMQQLKVDE +SAPLGELFRNHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLIGG +VGWFIFTLLGGWISDKIGRKLTFVLGYGFLIVWAFPLFGLLNTAS---LPLFSLGLFVLT +LGLGPSYGPQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKT-GWENVA- +WYIIVISAISLIAVLFV-PKGIQDRELHDEQVVATRS---------NPVVPA------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000157.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000157.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f4cce4c3e41b2f816c3f05fd9856ead8248af6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000157.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_02018 +MTDQQHTPDTVPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAEAAKERI +EADLAASLERGKIDGD-LDEWAQRLTVSVD-RADFARCDLVVEAVFEDMQVKIDALTDVE +AHLREDAWLASNTSSLSIGEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQA +LSTEWVRGLGKTPVVVK-DAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKF +PVGPLALTDIVGLDVRLGIAEYLESQLGE-RFAPPQLMRDMVARGELGRKSGKGFFDY-- +R +>GCF_003691675_PROKKA_00095 +MGQTQK------------VAVIGAGAMGSQIAMLAAMAG-CQTTMVDVDQERLDAARDQV +LQTAQRQAERGRLEADAVEQAAARLTTEPDLAAAVAEADVVVEAIIEDLEAKRDLFAQLG +EHTRPDTILATNSSSIVSSRLA-QIPHPERVCNMHFFNPALVMRLVEVVGGDHTSQKTIE +TVKALAERMGKTPVVVRQEIFGFIANRIVAAIFDEAISLYEQGIASAEDIDTAVTHGLGH +PIGPFALLDLTGIDVNVGIKRLEAQETGDPSRGPSQTLLDLMAQGRLGRKTGHGFYEYGD +R +>GCF_003691675_PROKKA_01727 +MTDQQHTPDTAPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPRSAEAAQERV +ESDLAASLDRGKIDGD-LDEWAQRLTVTVD-RADFARCDLVVEAVFEDMQVKIEALTDVE +AHLREDAWLASNTSSLSIDEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQA +LSTEWVRGLGKTPVVVK-NAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKF +PVGPLALTDIVGLDVRLGIAEYLESQLGE-RFAPPQLMRDMVARGELGRKSGKGFFDY-- +R +>GCF_005280335_PROKKA_00803 +M---TETPDTSRASVPAVVGVLGGGRMGGGIAHAFLTSGSSEVVVVERDPQSAEAAKERI +ESDLAASLERGKLDGD-LDVWAERLTVSVD-RADFARCDLVVEAVFEDMQVKIDALTDVE +SHLREDAWLATNTSSLSVDEIATHLRRPERFCGLHYFNPVPASKLVEVVIGAQTGDELKA +LTTEWVRGLGKTPVVVK-DAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKF +PVGPLALTDIVGLDVRLGIAEYLESQLGE-RFAPPQLMRDMVARGELGRKSGKGFFDYSK +G +>GCF_020097155_PROKKA_00762 +MTENQQT----TGSVPSIVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAEAAQERI +VADLAASLERGKIDGD-LNVWAQRLTVSVD-RTDFARCDLVVEAVFEDMQVKIEALTDVE +AHLREDAWLASNTSSLSIDEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQA +LSTEWVRGLGKTPVVVK-DAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKF +PVGPLALTDIVGLDVRLGIAEYLESQLGE-RFAPPQLMRDMVARGELGRKSGKGFFDY-- +R +>GCF_023573625_PROKKA_01955 +MTDQQRTPDTAPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAQAAKERI +EADLAASLERGKIDGD-LDEWAQRLTVSVD-RADFARCDLVVEAVFEDMQVKIEALTDVE +AHLREDAWLASNTSSLSIDEIASHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQA +LSTEWVRGLGKTPVVVK-DAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKF +PVGPLALTDIVGLDVRLGIAEYLESQLGE-RFAPPQLMRDMVARGELGRKSGKGFFDY-- +R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000159.fa new file mode 100644 index 0000000000000000000000000000000000000000..4301b6457e5501221a0cf90baf9ff3aca1cc6a79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000159.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_02070 +M-----------------STTTSITAAGLETMNGPEG--------CCTLSAGP--VDSVE +AERIASLLKALSDPTRLRLLSHVAAQGCNSVCA-CDLTEPLGISQPTVSHHMKKLVDAGL +LTREQKGRWAHYSVVPSAFAELRSFLD-------IA +>GCF_003691675_PROKKA_01107 +MDVKVYVPEFAVEFDTCQYVPMSMSGL--SARDAALG-------YCTPLAREP--ITPAQ +AEGVSRMLKALADPVRLRLMSMILSHEGAEACAMCDLTEGFDLSQSTLSHHLKVLHDAGL +VDRDKRGVWVYYKARTEAMDALRTLFSGDLAAPQLA +>GCF_005280335_PROKKA_00560 +M-------------TACSVPVSTAAAP--VLADD-----------CCSLADGP--LGAED +AAELAVLLKALADPMRLRLLSHVAARGCADVCA-CDLTEELGIAQPTVSHHMKRLVDAGL +LTREQRGRWAHYTVVPEAFARLRRVLV-------LG +>GCF_005280335_PROKKA_00743 +M-----------------VATTTIPAP--EDTDRPEGDDALGSVACCSLSAGP--IDAAQ +AQRAAGMFKALADPMRLRLLSHVAAQGCAAVCS-CDLTEELGISQPTVSHHMKKLVEAGL +LTREQRGRWAHYTVVPAAFAELGRMLE-------LG +>GCF_020097155_PROKKA_00486 +---------------------MTTTAP--SPSD------------TCCAPAGPALLPAEH +AARLAAVFKALADPTRVRVLAHVAASPEGTVCA-CHLPEPLGISQPTLSHHLKTLTAAGL +VTREQRGRWAHYTAVPAALDAARAFLADPAGA---- +>GCF_023573625_PROKKA_01998 +M-----------------STTTAITAAGLETMNGPEE--------CCTLSAGP--VDSVE +AERIASLLKALSDPTRLRLLSHVAAQGCNSVCA-CDLTEPLGISQPTVSHHMKKLVDAGL +LTREQKGRWAHYSVVPSAFAELRSFLD-------IA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000161.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000161.fa new file mode 100644 index 0000000000000000000000000000000000000000..25015e0de3f5fe18a9a2c8f8a8ff471415454067 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000161.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_02079 +MPDIIEFPLPASSDDPHWRAYCRLGDEYNHELIGTTEWDETPTDALIQAAAETDHTQRRY +LAYVDGEAVGYARVLINHVDDPDAAALNVYVLPRHRGRGHGRALAERLVQDTAGLTRFET +WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV +ALAEAERVSSDYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM +DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV +KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRR--R +>GCF_003691675_PROKKA_01783 +MPDIIEFPLPASSDDPHWRAYCHLGDEYNHELIGTTEWDETPRDALIQAAAETDHTQRRY +LAYVDGEAVGYARVLINHVDDPDAAALNVYIHPRHRGRGHGRALAERLVLDTAGLTRFET +WPLTPRPVAGQRTLTPPNGAGAVPAEHPGVRLAQSYGFALVQTERVSRYDFADPGIDPAV +ALAEAEGVSSDYELHAWEGAADASLQDDVAVLKARMATDVPSGERTVVEQVWDAARVRRM +DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGRRLGMRV +KAANLIAVRDALPGARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRR--R +>GCF_005280335_PROKKA_00705 +MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY +LAYVDGEAVGYARVLINHVDDPDAASLTVYVHPRHRGRGHGRALAERLVLDTAGLTRFET +WPLTPRPAVGQRALTPPNGAGMVPAGHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV +AVAEAERVSSGYELHAWEGAADASLQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM +DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV +KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRR--R +>GCF_020097155_PROKKA_00615 +MPDIIEFPLPASSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDYTQRRY +LAYVDGEAVGYARVLINHVDDPDAASLNVYVHPRHRGRGHGRALAERLVQDTAGLTRFET +WPLTPRPVAGQRALTPPNGAGVVPAEHPGVRLAQSYGFALVQIERVSRYDFADPGIDPAV +ALAEAERVSSDYELHAWEGAADAALQDDLAVLKARMATDVPSGERTVVEQVWDAARVRRM +DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV +KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLVEASMEAPAPLRR--R +>GCF_020097155_PROKKA_00619 +MPDILEFPLPATADEAHWQAYCRLNRDHNHELLGTTEWDESPDDALLDAAAESDYTLRRF +LALDDGTPVGNGRILVNHVDEPDAASLSVFIHPDHRRRGHGRALAERIAREADGFTRFET +WPMTPLPAEGERALRPSSGAGAVPADHPGVRLALSYGFALGQVERVSRYDVLTPAVDPAD +ALAEAERPGADYEVLTWEGPADEAVRADLAVLKERMATDVPSGDLTVAEQTWDAGRVRRQ +EEQILLTGRLFRAAVRHRDTGRIVGVNELVAPRSRTSGLVDQWDTIVSPEHRGHRLGMRV +KAANLVALRRALTEARAIITWNAEENRPMLDVNEALGFQPILVEAEMQAHGPLRRVVP +>GCF_023573625_PROKKA_02017 +MPDIIEFPLPVSSDDPHWRAYCQLGDEYNHELIGTTEWDETPTDALIQAAAETDHTLRRY +LAYVDGEAVGYARVLINHVDDPDAAALNVYVHPRHRGRGHGRALAERLVLDTAGLTRFET +WPLTPPPVAGQRALTPPNGAGAVPAEHPGVRLAQSYGFALAQIERVSRYDFADPGIDPAV +ALAEAERVSSDYELHAWEGAADASLQDDLAVLKACMATDVPSGERTVVEQVWDAARVRRM +DEQILTTGRLFRAVARHRATGRIVALSELVAPRSRPDGLIDQWDTIVLPEHRGHRLGMRV +KAANLIAVRDALPEARAIITWNAEENRHMLDVNEALGFRPVLAEASMEAPAPLRR--R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000162.fa new file mode 100644 index 0000000000000000000000000000000000000000..1f64cb84efeb7c1e5f459d4cd54ebac5b20401e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000162.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02093 +---------MTDTTTARPKRPAHRDDGPPVRGIGHLRHPAVSGGLIGVIGGGAFLFGGIA +GLPAEHRATLRGIAISLISFTLVVVLLRRRMLPTVPTPARGALRVYGIAVVAMLAFLPVT +RLVALALDAPTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAALGLAGAALAALGDP +VAGPAGAAAAGVAMLVIVAAQGLLASPRQD +>GCF_003691675_PROKKA_01800 +MSHVMRGGTMTDTTTARPMRPAHFDDDPPVRGIGHLRHPVVWGGLIGVVGGGAFLFGGIA +GLPAEHQGTLRGSAIALIGFTLVVVLLRRRVLPAVQAPARGA------------------ +-----STGSPSSR------------------------CW--------------------- +-----------------------RSSP--- +>GCF_003691675_PROKKA_01801 +------------------------------------------------------------ +----------------------------------------------------MLALLPVT +RLVALALDAPTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAVLGLAGAVVAVLGDP +VAGPAGAAEAGAAMLVIVAAQGLLASPRQD +>GCF_005280335_PROKKA_00685 +MSHVTRGGTMTDTTTARPMRPTHHDDDPPVRGIGHLRHPVVSGGLI----DGAMAAQGLL +ASPRPD------------------------------------------------------ +------------------------------------------------------------ +------------------------------ +>GCF_020097155_PROKKA_00555 +MER----------------------DSTHARGIAHPMHPAVLGAVVGMVGGSLFMLLSRP +ELPFPWPTVTLVAWIALLAAAAWAVFLAPRRLRDVGAPSRHAGPIYGLSVLGMVALIIAS +PHLVRALGIEAAQPAVVVMAVGLHFIPFASAFGARVFAWLGGSLTAIGLAGVIAAAVVGA +PAGAVAAVLAGAAMLAFLAVDARRGA---- +>GCF_020097155_PROKKA_00601 +MSHVMRGGTMTATTTARPMRPTHHDDDPPVRGVGHLRHPVVSGGLI----DGAMAAQGLL +ASPRQD------------------------------------------------------ +------------------------------------------------------------ +------------------------------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000163.fa new file mode 100644 index 0000000000000000000000000000000000000000..d061974523212e126a7213a52111c7489c196f28 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000163.fa @@ -0,0 +1,132 @@ +>GCF_002008305_PROKKA_02098 +MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEDG +AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALDDARRKLAEMVTTADALPAPAGRGHD-----GGGPAGLDA- +PAADGAAPPPP-AGLDWRRVMEPLAGLH-GPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRP +LKRGAKGTWIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLAEAREVGVELVPL +GLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPA---------------PPGPGLSGVHAVGGIGFYRV-ELTDEEAVL +HLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRW +SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPD +YRELKAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHPAFDRLRALLSEAATLQ +EWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVERLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDL-G +GILADDMGLGKTVQTLALFAHARQARPEPPPFLVVAPSSVVSVWAAEA-EKFTPDLDVRVLDTTTRKRGTAVADEVAG-- +ADVVVTSYTL-LRIDAGQYGGLDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLSDLWALLDV +VVPGLFPSHRRFRETYVTPIETGGDP---ERMAALRRRVRPFMLRRSKEL---VAKDLPSKQEQILQVELEPA--HRKLY +DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFTSLT--- +-----------------------------------LLRMLALAPQIVDDQYASVPSSKLERFLDDLTEVIGEGHRVIVFS +QFTSFLRVIAEEL-------------------DHLEIEHAYLDGSTRG-----------RADVIRGFR-EGEAPVFLISL +KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS +GAGAFTDSL--------------TAEDI----REMLG------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---AEE--------------------------------------------- +>GCF_003691675_PROKKA_01805 +MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEDG +AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALDDARRKLAEMVTTADALPAPAGRGHD-----GGGPAGLDA- +PAADGAAPPPP-AGLDWRRVMEPLAGLH-GPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRP +LKRGAKGTWIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLAEAREVGVELVPL +GLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPA---------------PPGPGLSGVHAVGGIGFYRV-ELTDEEAVL +HLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRW +SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPD +YRELKAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHPAFDRLRALLSEAATLQ +EWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVERLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDL-G +GILADDMGLGKTVQTLALFAHARQARPEPPPFLVVAPSSVVSVWAAEA-EKFTPDLDVRVLDTTTRKRGTAVADEVAG-- +ADVVVTSYTL-LRIDAGQYGGLDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLSDLWALLDV +VVPGLFPSHRRFRETYVTPIETGGDP---ERMAALRRRVRPFMLRRSKEL---VAKDLPSKQEQILQVELEPA--HRKLY +DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFTSLT--- +-----------------------------------LLRMLALAPQIVDDQYASVPSSKLERFLDDLTEVIGEGHRVIVFS +QFTSFLRVIAEEL-------------------DHLEIEHAYLDGSTRG-----------RADVIRGFR-EGEAPVFLISL +KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS +GAGAFTDSL--------------TAEDI----REMLG------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---AEE--------------------------------------------- +>GCF_005280335_PROKKA_00681 +MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEAG +AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDAHQALDDARRKLAEMVTTADALPAPAGRGHDDAARPDAGPRGAAAG +PDGESAAPEAPHSGLDWRRVMEPLAGLD-APRRLGAPPALAIGVELVAESSRNAFQQWGPAPAGEDQVREGRPLYVTLRP +LKRGAKGTWIKGGLTWKNFQFGRAEFAPAQERAMRLIWRQLQAEDSYPTDAWFGLHSFDSPRIWQLLAEAREVGVELVPL +GLLTDVVLEAPAAVGLDVARAPDGGLDVAPSLDPA---------------PPGRGLAGVHAVGGIGFYRV-ELTDEEAVL +HLIPAERPVPEAVQQLVLAGGPVRVPAVDREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPDHELVLRW +SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVAAARFSEQVLPLLQQAEHVRVDVTGHRPD +YRELKSAPRIEVGTKATKNDWFDLGVQVSVDGHVLPFVELFTALVQGKTTLILADGSYLGLDHPAFDRLRALLSEAATLQ +EWTPENTAVSRHQVGFWEDLKELADEVEEDPEWTAAVGRLAAVERLPEAPEVPGLQADLRPYQEDGLRWLAFLWEQDL-G +GILADDMGLGKTVQTLALSAHARQARPERPPFLVVAPSSVVSVWAAEA-QTFTPDLDVRVLDTTVRKRGTDVAAEAAG-- +ADVVVTSYTL-LRIDAGQFGGIDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLTDLWALLGV +VVPGLFPSHRRFREAYVTPIETGEDP---ERMVALRRRVRPFMLRRSKEL---VAKDLPPKQEQVLNVELEPA--HRKLY +DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFKSLT--- +-----------------------------------LLRMLALAPQIVDEQYASVPSSKLERFLDDLTEVIAEGHRVIVFS +QFTSFLRVIAEEL-------------------DHMEVAHAYLDGSTRG-----------RADVIRGFR-EGQAPVFLISL +KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS +GAGAFTDSL--------------TAEDI----RELLG------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---AED--------------------------------------------- +>GCF_005280335_PROKKA_01500 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----NLPLTDYQAKYYA--HELQRSYAND-----HVGKLAGL--------LFDAQVEPKPHQIDAA--LFALQTPFLPG +VILADEVGLGKTIEAGIVISQYWAER--RRSILIVAPSSLRQQWQQELYEKFL--IPSAILDPKSKD---SLLAAAGGRS +AQVLICSYEFALRHETSLLKA--WDLVVADEAHRLRNYWTGKTKAAEAVAHVVSGAHKTVLLTATPLQNKLEELYGLVSI +FDPNYFYSLDAFRERYVKNRDLGGDDDLVERVATVSKRT----LRRDADKYIHFTKRLP------LTVEFTPSPDEARLY +DLVNDYLQRDELFAFAGSQRHLSALIIRKRLGSSTYAVASTLENIANRLAEEVAAGQRRDGRGGLVTADFTVDDEITSEE +LEEAEEIEGAGPASRPSSSPLDESLLEAMRAEVAELRDYAALARSITENQKAVKLGEALDLGFERLRE-LGAPQKAIIFT +DSTKTQEYIARSLREAGRGDGLVLFNGSNNGPEQTAIYQAWLKANQDGDLITGIAAVDRRKALVDYFRTEG---TIMIAT +EAAAEGINLQFCSMLVNYDLPWNPQRVEQRIGRVHRFGQKHNVVVVNFSNKGNIAEQRILELLTNKFQLFSSVFGASDEV +-LGAIEDGLDFEKTISDILTRCRTADELDAAFRELEGQYASEISREMASAKAKVFDNLDPHVQDRLKAYDTQSGEVLNKF +ERLLLAVTRHELDRFATFEGDGRAFVLNESPVQDVPTGRYFFKSQPLENAHQYRYASSLAQYVVDTSKGHETPARELTFS +LGQSERVSSAIRALEGTSGELTVNLATFRMKARDEDVSESYMLAGALTDDGQWLDEEYVADILDLACISVGEQPVAIDES +RFTPHLDARRAELEKEVQGRNSRYYDQQEELLYRNQQDRKAEHEGKIREYRAKEKEARKLARQADDPMEQLRLKKEARKW +EQRAEEADEDFRDTRKKLRAEADKYLELIEQSLQGTQETEHLFTIRWRITT +>GCF_020097155_PROKKA_00595 +MAPGVSGDPLPHLRTEAIRALVGPTSADRGFDIAAEGGVLRVTYDASRLRLTSAVRGTAPQPYRQAVRLQPS-GETGPDG +E-PLLEPTAGRCQCPVGEDCKHVAAALYEITRRHADAARHAAREELASRVTTADRLPSPE-RA-------GAAPARPDA- +--------PAPEAGLPWRGVLESLAGLDGGPRRLAPPPDLAIGVELVAESSRNAFAQWGPAPAGEEHLREARLLYVIVRP +LKRGAKGTWIKGGLTWKAFQFPRAEYDPAQERALRLIWRQLQAEDSYPTEGWFGLHAFDSPRIWQLLAEAQEAGVELVPQ +GILADVVLDAPVEVGLDVASAPDGGLEVAPSLAPAGGAGEGAPADDAAARPDAERLRDTHAIGSIGFYRADEEEDGTWTL +HLLPAVRRVPEPVQEMVLAGRPVHVPTADREEFLGRIYPRLRAALDVGSADASVELPEFEPPVLRLQADFRPGHRLVLRW +SWLYFDPPRELGL--GHDGLRDPRHEEAVLRAAAQVWPRVGRAEEQELEGVGAARFSESVLPQLQRLDHVRVDVTGERPD +YRELKAAPRIEVSTKAAQNDWFDLGVQVSVDGHVLPFVELFTALVHGKTTLMLQDGTWLGLDHPAFDRLRALLSEAAALQ +EWTPEHTTLSRHQVGFWEDLKELADEAEEDPEWTAAVGRLAAVERLPEAPAVPGLKAELRPYQEDGLRWLRFLHDQDL-G +GILADDMGLGKTVQTLALMAYARAEHPDRPPFLVVAPSSVLSVWASEA-AKFTPGLDVRVLDTTTRKRGTSVTEAAEG-- +ADVVVTSYTL-LRIDAAQHADASWAGIVLDEAQFLKN----RASKVHQVARDLRAPFR-LAITGTPMENSLSDLWALLEV +VVPGLFPSHRRFRETYVTPIETGEHP---ERMASLRRRVRPFMLRRSKEL---VAKDLPPKQEQVLRVELDAA--HRKVY +DRV---LARER----------------RKVLGL----------------------------LGDMDGNRFTIFKSLT--- +-----------------------------------LLRMLALAPQIVDREYAAVPSSKLERFLDDLEEVLAEGHRVIVFS +QFTSFLRVVAEEL-------------------DAMEVEHAYLDGSTRN-----------RAEVIQDFR-EGDAPVFLISL +KAGGFGLTLTEADYVFLMDPWWNPAAENQAVDRAHRIGQERTVMVYRMVSEGTI-EEKVLELQQRKAELFGALMDESDDS +GAGAFTDSL--------------TADDI----RELLG------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---AEE--------------------------------------------- +>GCF_023573625_PROKKA_02038 +MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEDG +AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALDDARRKLAEMVTTADALPAPAGRGHD-----GGGPAGLDA- +PAADGAAPPPP-AGLDWRRVMEPLAGLH-GPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRP +LKRGAKGTWIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLAEAREVGVELVPL +GLLTDVVLEAPVAVGLDVTRAPDGGLDVAPSLDPA---------------PPGLGLSGVHAVGGIGFYRV-ELTDEEAVL +HLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRW +SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPD +YRELKAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHPAFDRLRALLSEAATLQ +EWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVERLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDL-G +GILADDMGLGKTVQTLALFAHARQARPERPPFLVVAPSSVVSVWAAEA-EKFTPDLDVRVLDTTTRKRGTAVADEVAG-- +ADVVVTSYTL-LRIDAGQYGGLDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLSDLWALLGV +VVPGLFPSHRRFRETYVTPIETGGDP---ERMAALRRRVRPFMLRRSKEL---VAKDLPSKQEQILQVELEPA--HRKLY +DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFTSLT--- +-----------------------------------LLRMLALAPQIVDDQYASVPSSKLERFLDDLTEVIGEGHRVIVFS +QFTSFLRVIAEEL-------------------DHLEIEHAYLDGSTRG-----------RADVIRGFR-EGEAPVFLISL +KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS +GAGAFTDSL--------------TAEDI----REMLG------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---AEE--------------------------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000171.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee81487e431b6d81ab8a93e2b83d5b77603c7b0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000171.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_02305 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREVFDEDHMAELV +TSIREVGILQPIVVREVDG-PTPHELIMGERRWRATQKAGLDTIPAIVRQTPDQDLLRDA--LLENLHRSQLNPLEEAAA +YQQLMEDFACTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVR +STEEAVAQLQGGLRPGRTPRRSTDDA-RHERLDHYATALTSRLDTAVK-------------------------------- +-----------ITLGARKGRIAIDFTTVEDLNRIMDLIQ---------------GGQDG--------------------- +---------------------------KGKGKKS---------------------------------------------- +-------------- +>GCF_003691675_PROKKA_01998 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREVFDEDHMAELV +TSIREVGILQPIVVREVDG-PTPHELIMGERRWRATQKAGLDTIPAIVRQTPDQDLLRDA--LLENLHRSQLNPLEEAAA +YQQLMEDFACTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVR +STEEAVAQLQGGLRPGRTPRRSTDDA-RHERLDHYATALTSRLDTAVK-------------------------------- +-----------ITLGARKGRIAIDFTTVEDLNRIMDLIQ---------------GGQDG--------------------- +---------------------------KGKGKKS---------------------------------------------- +-------------- +>GCF_005280335_PROKKA_00432 +MKTSRRGGLGRGLGALIQSTAEPVDEAPQEADATAEDATAPTAAPAEKKAATSTARRLSKETSEAKTPAPRAASASKSSG +GAAKEAPADKKAGSAGRAPAAAKKATPTKKASSSAGEAKANSAAAPAAARKTPDRAAQRPVDVFF------SPDPEDAPA +ARRGTKARPAMPTVKAPTKREAASSSGEEAAAGA---STAAEGTVSTDIAVLREIPVGDIHPNPRQPREVFDEEHMAELV +TSIREVGILQPIVVREVDG-PTPYELIMGERRWRATQKAGLDAIPAIVRQTPDQDLLRDA--LLENLHRSQLNALEEAAA +YQQLMEDFACTQEELAERIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQAEGLSVR +ATEEAVAQLQGGLRPGRTPRRTADDA-RHERLDHYATALTSRLDTSVK-------------------------------- +-----------ITLGARKGRIAIDFTTVEDLNRIMDVIQ---------------GEKGG--------------------- +---------------------------RGAAS------------------------------------------------ +-------------- +>GCF_005280335_PROKKA_01948 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------------------------MV +ASVKTQGLLQPLVVAPNPTLEGDYTIIAGHRRLDALKRAGRDDAPVIVRTDLDTEEKQVAAMLQENLHRQDLTAVEEADA +FAQLSLFEGWDVKRIARETGVAQTRVRSRIKLTYLSEATLASLHDGQVTLERAQALAEFAGSPEEELL-----EEHLTAT +ATNWDFYLARAKQTRDRRKALSAEQK-AHEEAGFEVVPMPESLYTPEREWDRQDFESPTAALEAGAVVAFDPDYDAPVYL +VKHAEQELEKDAAAAERKAEAAERAARNEALERELATAQETVRLWLVDTVFPKAAAGDERILRVAARHLAATACEETHFR +RAGLAAIFCPDLGAYAPELRTAVAEVLAGKSAQELAVIIAVATRWTSTARVHAWRDATREDSSPAVWLAMRQELGRELAA +PEQVAFDAAKAGEL +>GCF_020097155_PROKKA_00384 +M-STRRGGLGRGLGALIQNTAE-IEQPPTREDSSPSAASSNKTTAAPAKRSTRTAR--TAESSQNGLPASDGAT------ +---------QQDHSSDRAEKTASSGTGSQKTSRSTG-SKGAKTPEPTATRSAQEEVP-RPADIFFGGGEGTSDEPPESGR +HRPTRSARPSMPTVKAPSKPAPKSETEQAAP----VRKDEPEGTVSADIAVLRELPVGDIHPNPRQPREVFDEDHMAELV +ASITEVGVLQPIVVREVEGAATPYELIMGERRWRATQRAGLATIPAIVRQTPDQDLLRDA--LLENLHRSQLNPLEEAAA +YQQLMEDFSCTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGALTAGHARALLGLTDPAEMERLAQRIVSEGLSVR +ATEDAVAQLQGAVRPAPKSTRSREESTRHERLDYFATALTSRLDTQVK-------------------------------- +-----------ITLGARKGKIAIDFASVEDLNRIMDLIQ---------------GGGDS--------------------- +--------------------TPV----KG--------------------------------------------------- +-------------- +>GCF_023573625_PROKKA_02246 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREVFDEDHMAELV +TSIREVGILQPIVVREVDG-PTPYELIMGERRWRATQKAGLDTIPAIVRQTPDQDLLRDA--LLENLHRSQLNPLEEAAA +YQQLMEDFACTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVR +STEEAVAQLQGGLRPGRTPRRSTDDA-RHERLDHYATALTSRLDTAVK-------------------------------- +-----------ITLGARKGRIAIDFTTVEDLNRIMDLIQ---------------GGQDG--------------------- +---------------------------KGKGKKS---------------------------------------------- +-------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000172.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd0273e3a6bc3ef667f5f35369bc3b7630657858 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000172.fa @@ -0,0 +1,78 @@ +>GCF_003691675_PROKKA_02019 +MK--------------------------------------------------------------------------RSPK +GRLEL----TWM---------GKDSALIPVEDGKYDYSFVDPNDPRALEVKSIEV--------------------LEQVG +EVEGPTGANENLLIIGDSGDALRSLGTIPEYAEKYGGKVKLVYIDPPFNTE-QAFDHYADQLE----------------- +------------HSIWLTMMRDRIRDFKPLLHPDASIW-VHLDDSEVHRMRALMDEEFGAE--NFIATVVWQKKYSRDNR +PA-IGTVHDYILVYAPAGAQRW--------KTLRNR--------------------------IPRISAAQYRNPNNDPNG +----------PWRPVPMDVQGGHATASQFYDVITPSGKIV----RPANGRA-WSVTAPVMQAMRDRGEVYFGL----DGS +GKPNTIRY-----LKD---------------------DEGLVPWTWWPHEEVGNNDDAKKEIIALFGEDQVFDTPKPERL +LERVIRIAT--NADDLVLDCFAGSGTSAAVAHKLG------RRWLTVELSQ------------------------EVADT +FTVPRLRKVQRGTDSIGISV----------REAEGFA----DADMDGRVKPDDAKALLRAIKEVQKVGLKSLSP----EA +GAA----LVQELRERLKPVSARQSVCQDGGF-------TVAKMG-----PSMYEVDDEHGMVFLSPEATNGAWSKAIAGQ +LKF--TLTPDDPVFCGVRKRQRLAVIDGVADETVVRTVVEHLGEKERAVIVAKGVLP------EAGDLLQRLSPGSRIKK +APEDMFPKGTVN +>GCF_005280335_PROKKA_01501 +MT---DEIYETPSTTPNFQTELAAQLAD------LIPEAIADGK---------VDV--------EKLK-ELLDGDAADSN +ERFGL----FWP---------GKKRALRAA------------------QEPTTAT--------------------LKPDF +EDSKDWDTTQNVFIEGDNLEVLKIL------QKHYHAKIKLIYIDPPYNTG-KDFVYPDNYKEGLDTYLEWTRQVNEEGK +KVTTNAETEGRYHSNWLNMMYPRLKLARNLLTDDGVIF-ISIDDNEIDNLLRLAKEVFGEP--NVSTTFIRQKKKKPSFL +HANVGSMTEYLVCITRNKAFTF--PFSVDTTTAGKK--------------------------YPINNAGNSLGKLTFPAG +-AVRFSQKFAEYEP--QDMSEGNIVTRLLDHVVVSEGVNR----NAFTLEGEWRYSQVTLDEFITAGDLITIS----KAP +FRPNHVKA--------------GGEIKKM--------HNLLTPSTY----GVGTNEDGTAELEDLM-EGSYFDNPKPTSL +VRVLAQAVTYDDPSAIVLDFFAGSGTTADAVFRLNAQDGGNRRVISVQLPE-PLDERSEAWAAGYRT----------ISQ +LAKERIRRA-------GVRV------LD--REALLLEGRGVPLDTGFRAYKLSDTNFSK-----WRLSSD-VEE----DA +LQQHLLSLRDSATDDANADELLTEILLKQGYSLTEAVSPAEVAG-----LDVRFVRDRDGDV-----AVLAYLNEHVKPT +LEQLRALVDEEPT---------------------------------RIIVLEDAFQGDDELKTNLAQLAK--SKGIELW- +----------TA +>GCF_020097155_PROKKA_00288 +ME---MSMDKLRGTSPDLTQDNVARLAE------LFPTVVTEARDEDGQVTRAVDF--------DLLRQELSDHVVEGPQ +ERYHL----DWP---------GKRAAAFAA------------------NAPTTAT--------------------LRPDR +EESVDFDTTKNVFIEGDNLEVLKVL------QESYLGKVKMIYIDPPYNTG-NDFVYADDFAESTADYLQRSGEIDDDGA +RLRANPETNGRFHSDWLSMMYPRLKLARNLLTEDGAIL-ASIGEREVSNLRAILNELFGET--NFVGELVWEKKKKGAFL +SSHVTNVKEYILVFCRDRSSFG--GLIGEVTHAAET--------------------------YPVIKSTNSRGIRTIPAG +IASNYSERDHEVGA-GTRLTSGNMEMILLSDLIIRDGRLA----HDVEVESNWIYSQTLIDQFSLSGDLYIT-----RDL +YIRRHVREPRTKMLKD-LLMMRGESTSGS--------TFTLEPSLH--SDGWGTNEDAFGELHSILGEQNLMDFPKPSKL +IAKLIRSVTWADSDAIILDFFAGSGTTGQAVTQLNAADGGRRQYLLVQLNE-AAEESSALRRAGFSS----------ISA +LSRERLRRS-------AAAV----------RETSGTE----RLDLGFRAFRLDASPFVE-----RNHSADSITP----DM +LAE----LENPVLADRSPEDLLTHVLLAWGLDLSATIETVSLAG-----EEVYDVEDG---------ALLAALGSTVSDE +LAH--AMAERHPD---------------------------------RALFLDSGFVS-DAARINVEQIFREVSPGTDVK- +----------VL +>GCF_020097155_PROKKA_00347 +MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEEHRPE------AVELPSREVRKGDKVR-------ILPPR +GETKKGDQTLWRVQRINRADD--IAHLVEVD-----------GEQG-------AEAALADLVVVAEFRDHMYPGLVETGR +VERGG-DKPFHTVINAENFHALEML------TYTHRHQVHCIYIDPPYNTGAKDWKYNNDYVASDDDYR----------- +------------HSKWLSFMERRLQVARELLNPEDSVLIVTIDEKEYLRLGMLLEQTFPQARMQMVSTVINPK---GSHR +AGGFARSDEYVFFLFVGASQPAPMPLSSEWKVVQDSRALGLRWADLLRTADGSTRAARPNMFYPVFIRLAGDGPVFVSVG +EPF-YDADLTAVEA--------------------PEDAVAIWPIKADGSQGRWQIGADTLRDLITKGYVRIGRWR--GSK +TTLTYLKAGEQAKVEDGRFPVRGRRADGSVLVDASEYSASFVPTSQWRISSHNAEQGGTNLLKSIM-GDKRFPFPKSLYA +VEDALRFLIKKNPDAVVLDFFSGSGTTAHAVMRLNKQDGGRRQCISVTNNEVSAEEQKGLRKQGLRPGDPEWEQWGICDY +VTKPRVTAAITGRTPTGDPIKGDYKFTDEFPMSDGFE-----ENAAFFTLTYESPLMVR-----QDLAFKRIAPLLWMRA +GSRG--RVITEVHAR--------------GWDVAEAYGVLTKVDRATPFAEAV-AEAGVGTVYVVTDDERRYQAVC---- +-----ALLPEDVT----------------------------------PVRLYESYLT------NF-EINTGGRAG----- +-----------A +>GCF_020097155_PROKKA_00694 +MSRLTDLLAQARKTDPQLAADLEAEFRQLTQRS-QFGLVFERHQPE------AVELPGRPVRRGDTVR-------VLPPR +GTLTIGDTRHWVVTDLERTPDGKQAHLTEAD-----------VDPE-VREPATSTAALEDLVVVARFEDPIYPGLVETGR +VENGGPDKPFHTVINAENFHALEML------TYTHRHKVDCIYIDPPYNTGAKDWKYNNDYVEADDDYR----------- +------------HSKWLSFMERRLQVARELLNPDDSVLIATIDEKEYLRLGMLLEQTFPEARIQMISAIINPK---GSSR +RDQFSRFDEYIFFVMNGSARPA--AVAGDMTMRQARSKEKVRWAGLMRQGANGRRSARPNLFYPIFV--ANETGRVHSVG +DSLPLDVPRSEVSP--------------------PPGTTAIWPLSKAGGESTWGRDPESLRKALSAGYVKIGRFTPGSER +CGFTHLQSGQIKAIEEGALVVTGRDSDGSLQVEFAEGGQTAMPGTAWHRPAHSASEHGSTLLNAIL-PDRKFPFPKSLYA +VEDAVRFFVHGKPDAVVLDFFSGSGTTAHAVMRLNRQDGGRRQCISVTNNEVSAEEQKGLRKKGLRPGDPEWERWGICDY +ITKPRITAAITGKTPAGDPIKGNYKFTDEFPMADGFE-----ENAAFFTLTYEAPRQVR-----RNRAFARVAPMLWFKA +GSRG--RIISSLPER--------------GWDVAQAYGVLEDMDHAPEFLAALEADPQVGMAFIVTDSEVAFQSVA---- +-----RQLPEHAT----------------------------------AVRLYESYLH------NF-QINRRA-------- +------------ +>GCF_023573625_PROKKA_00111 +MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEGHRPE------AVELPSRPVRKGDKVR-------ILPPR +GETKKGDQTLWHVDHIDRTTG--TARLTAVD-----------GEQE-------AQAAISDLVVVAEFRDHMYPGLVETGR +VENGG-GKPFHTVINAENFHALEML------TYTHHRKV----------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------DS-------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------------------------------------------------------------C-- +------------------------------------------------------------------------------RA +SDLG--HV------------------------------------------------------------------------ +-------------------------------------------------------------------------------- +------------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000173.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5f356770e5e0555fd44fb55c0ddc039d0addf2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000173.fa @@ -0,0 +1,48 @@ +>GCF_005280335_PROKKA_00092 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------MDLTYKLWEGSWDEGAVLQDKGGSRHADPEKVHKIHHVSERYRVEGPHLPAPSP-QRTPVLF +QAGSSGPGRAFAARNAEAVFLIAPSVEAARQQIEDPRRQAVEFGRRPEDIKFFQGLSFVIGDTEEEAQAKLEEYERYVSV +DGYLA-HAALV---DPDGRVYPPDTPLRELETNTQ-KGFAESLQKAITDREPVVADVA--------------WRSHRDSR +VVGTPEQIADELQRWQ-DAGVDGVNVINWVIPGSFEEFIEKVLPVLRERSLAQSDYG--EGTLRHRLFGEGDRLPDRHPA +AKYRGAFTGTPRSQRAPRTEPQGADPAPAA +>GCF_005280335_PROKKA_00093 +MT---------KTARRRPLHLNAFAMNTTSHIHHGQWRRPDARQHEFADLRTWTELARTLEDAAFDAMFFADVVGHYGDA +DADYAVYVEEGLQIPSNDPTVLLGALAAVTERIGLATTSNVFQAHPFQFARQLSTLDHLSRGRIAWNIVTGT-------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_005280335_PROKKA_00195 +-------------------------MMTPVHQSPGLWRHPESRIAEFDRLAYWTGLARTVEDGGFSALFLADVLGLYDVY +GGGIEATVRGGVQWPVLDPAVAVPAMAAATERIGFGVTASVTYERPYLLARTLATLDHFTGGRVAWNIVTSYQDSAARNL +GLDRQIPHDARYDLADEALDALYRLWEGSVEPGAVAFDRAAGVVADPDRVHPAAVAGAHVRVPDAALTHPGP-QGTPYLF +QAGASARGRRFALDHAEAVFAIGPTPAHVRRFVDQTRAGLTEAGRSADAIRVLAMVTVVVAETDEAAAQRLAGYAEHVDV +AGALALWGGWT---GVDVAGLDPDAPLEHVVTDAN-RSALAAFTEDPSGRTWTLRDVAEF-----------VAIGGRGPV +IVGSPETVADELQRWQAETGVDGFNVSAAVRPADLERFAALVSPELRRRGVLREPEP--GRTLRENLSGAGPALPADHRG +HAFRTA-----------------------G +>GCF_020097155_PROKKA_00133 +MTGTHPSTPRPRTADRQLILGAHF----PGVNNTTVWSDPESGSQIAPE--SFIRFAEIAERGRLDFIFLAEGLRLREQR +GLLHDLDVVGR---PATLP--ILAALAAATEHIGLIGTLSTTYNEPYELARQLAGLDALSGGRAGWNVVTSPDAFTGENF +RRGGYLPRERRYQHAGEFLATAQQIWDAA---------SGRPPHVDVD--------VEDFSVHGT-VDAPAPVHGRPVIL +QAGDSDEGRDLAAREADAVFTRHGDWEAGQEFTADMRRRAAAAGRPDGAVRVLPGVTVVVGDTDEEAAAEAEQIRR-AQV +SGATA-VLTLERIWNRDLSGWDPDGPLPDVEPVLEDTGLSQGRVRHVADPHAEVARLREISQRQGLTLRETVIATGQRQD +FVGSPETVAQELIRHVEHDVCDGFILIPHLTPGGLEPFVDRVVPLLQERGALRTDYPEDGGGLRGLLGAA--VHPTAGRA +S----------------------------- +>GCF_020097155_PROKKA_00146 +MT---------ATPAPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLADILGLYDVH +GGGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLARTLTSLDHFTGGRIAWNVVTGYQDSAARNL +GLDRQPGHDERYDRADAYLDAMYRQFEGSVERDAVVADRESGVFADPAKVHPIDVEGPHVRLPGVALAHPGP-QGTPFLF +QAGASSRGRRFALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLASYHEHVDV +ESALALFGGWT---GVDLSGLDPDAELEHVESEAS-RTALAAFTTQSPDRRWTVREVAEF-----------VSVGGRGPV +IVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELRRRGVLREPEA--GRTLRENVAGAGPLLPEDHRG +AGFRR------------------------- +>GCF_023573625_PROKKA_00201 +MT---------AT--PAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLADILGLYDVH +GSGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLARTLTSLDHFTEGRIAWNVVTGYQDSAARNL +GLDRQPGHDERYDRADAYLDAMYRQFEGSVERDAVVADRESGVFADPAKVHPIGVEGPHVRLPGVALAHPGP-QGTPFLF +QAGASSRGRRFALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLAEYHEHVDV +ESALALFGGWT---GVDLSGLDPDAELEHVESEAS-RTALAAFTTQSPDRRWTVREVAEF-----------VSVGGRGPV +IVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELRRRGLLREPEA--GRTLRENVAGGGPLLPEDHRG +ARFR-------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000175.fa new file mode 100644 index 0000000000000000000000000000000000000000..c87ffa39fee863069a4dd6cb801479215e465430 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000175.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00002 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA +>GCF_003691675_PROKKA_02007 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA +>GCF_005280335_PROKKA_00422 +-----------------------------MPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETDGQVLVSGRLLNDIVRALPHAQVTVELDGGKVVVTCRSSRFALATMPVGDYPAL +PELPTPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSISTSLLVKARTLTEVAKSLGAGGDLEILLGEGTDLVGFSSGGRRTTSVLV +DGEYPKIRSLFPETSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA +>GCF_020097155_PROKKA_00375 +---MKFTVARDILSDAVSWAARSLSPRPPVPVLSGLLVTAEAGLVSIASFDYETSARLQI +EADVEDEGQVLVSGRLLNDIVRALPNAPVTLELDGGKVLVTCRSSRFQLATMPVADYPAL +PELPEPAGTVDGAAFAHAVNQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMT +EIRWNPADPAISTSLLIKARTLTEVAKSLGGGGRLEIMFGSSHDLVGFSSGGRRTTSVLV +DGEYPKIRSLFPETSPIQAAVDTEELIAASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DATANESVPCTLEGEEITVAFNPAYLSEGLAVVDQPQVRFSFTAAPKPALLTGVHEEDGT +VSDHRYLVMPVRLT +>GCF_023573625_PROKKA_00002 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000179.fa new file mode 100644 index 0000000000000000000000000000000000000000..49f2a324a88efe4cdec03b5b94a5db06a7bc7e63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000179.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_00006 +MSDETTPQT-PDEPVEGAPTPQPPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMAVIVGRALPDVRDGLKP +VHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYT +ETKMAPLAMEMVRDIDEDTVDMQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA +TREELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELPYMTNPDNLAAKIAEMV +RDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQID +VIVRRTAFRKRKAEERAHILRGLLKALDMLDEVIATIRRSASAEVAREALKELLDIDDVQAQAILQMQLRQLAALESQKI +QDEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEEEMVVSITRGGYVKRTR +IDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQ +IQPLVDY-GRAPYLVLATRGGLVKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEA +LRPMGRATSGVTGMKFRDDDSLLTMDVV---EEDGYVFTVTDGGFAKRTHVDEYRPQNRGGLGIKVAKLVDDRGELAGGL +VVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVAVTLNNEQEMEAKADAEAEAGP----------- +----------------------DVPLDADIDPTDPVAAPEDALTQDA-GEGADGGEQ +>GCF_003691675_PROKKA_02011 +MSDETTPQT-PDEPVEGAPT---PQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMAVIVGRALPDVRDGLKP +VHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYT +ETKMAPLAMEMVRDIDEDTVDMQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA +TREELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELPYMTNPDNLAAKIAEMV +RDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQID +VIVRRTAFRKRKAEERAHILRGLLKALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKI +QDEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEEEMVVSITRGGYVKRTR +IDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQ +IQPLVDY-GRAPYLVLATRGGLVKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISRKGQSLRFTATDEA +LRPMGRATSGVTGMKFRDDDSLLTMDVV---EEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAKLVDDRGELAGGL +VVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVAVTLNNEQEMEAKADAEAEAGP----------- +----------------------DVPLDADIDPTDPVAAPEDALTQDA-GEGADGGEQ +>GCF_005280335_PROKKA_00418 +MSDETTPQT-PDESAE---VPETPETGQDVAVEQYVLPEGAADKVEPVDLESEMKRSYLDYAMAVIVGRALPDVRDGLKP +VHRRVLYAMYDGGYRPDRSFNKSARVVGDVMGNYHPHGDTAIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYT +ETKMAPLAMEMVRDIDEDTVDMQDNYDGKQQEPAVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA +TREELLEALLTRVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELPYMTNPDNLAAKIAEMV +RDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQID +VIVRRTVFRKRKAEERAHILRGLLKALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKI +QDEYDELMARIAEYDRILESPQRQREVISEELGEIVAKHGDDRRTEIMAGYDGDMSMEDLIPEEEMVVSITRGGYVKRTR +IDQYRSQGRGGKGVRGATLRGDDIVEHFLTVSTHHWLLFFTNFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQ +IQPLTGY-DRAPYLVLATRNGLVKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEA +LRPMGRATSGVTGMKFRDDDALLTMDVV---EEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAKLVDDRGELAGGL +VVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVAVTLNNEHEMEAQADAEAAEDPVSEGSAAAAGV +LPEGEPEALVGAEATAGAAADADVRLDADIDPTDPAAAPEGLFEEDADGEGADGGEQ +>GCF_020097155_PROKKA_00370 +MSDETTPGTAPGTPQDGHDADQTPQIGQDVAVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMAVIVGRALPDVRDGLKP +VHRRVLYAMYDGGYRPDRSFNKSARVVGEVMGNYHPHGDTAIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYT +ETKMAPLAMEMVRDIDEDTVDMQENYDGKQLEPTVLPARFPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA +TREELLAALMQRIKGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELPYMTNPDNLAAKIAEMV +RDGKIAGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIE +VIVRRTAFRKKKAEARAHILQGLLKALDMLDEVIATIRRSASAEVAREALKTLLDIDDEQAQAILQMQLRQLAALESQKI +QDEYDELMARIAEYTAILESPQRQREVVSDELGELVAKHGDERRTEIVAGFDGDMSIEDLIPEEEMVVTITRGGYVKRTR +IDQYRSQARGGKGVRGAALRGDDVVEHFLTVSTHHWLLFFTNLGRVYRIKTYELQEAGRDAKGQHVANLLAFQPDERIAQ +IQPLAGYDGDAPYLVLATRNGLVKKTPLEDYDTNRQAGLIAIKLREGDELVSARVVSAQDDLLLISRQGQSVRFTATDEA +LRPMGRATSGVTGMKFRGDDALLAMDVIRAGDEDSYVFTVTDGGFAKRTHVDEYRTQGRGGLGIKVARLVDDRGELAGGL +VVGEDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVVFAKPDKRDRIVAVTLNNEDEIEATADERAAA----EGAA----- +-----PEA-------AGAADGAGVPLDAVNDQTDPAAAAE---AEAA-GEDADGGEQ +>GCF_023573625_PROKKA_00006 +MSDETTPQT-PDEPVEGAPT---PQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMAVIVGRALPDVRDGLKP +VHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYT +ETKMAPLAMEMVRDIDEDTVDMQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA +TREELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELPYMTNPDNLAAKIAEMV +RDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQID +VIVRRTAFRKRKAEERAHILRGLLKALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKI +QDEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEEEMVVSITRGGYVKRTR +IDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQ +IQPLVDY-GRAPYLVLATRGGLVKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEA +LRPMGRATSGVTGMKFRDDDSLLTMDVV---EEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAKLVDDRGELAGGL +VVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVAVTLNNEQEMEAKADAEAEAGP----------- +----------------------DVPLDADIDPTDPVAAPEDALTQDA-GEGADGGEQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000181.fa new file mode 100644 index 0000000000000000000000000000000000000000..000ea5d60212464750606fc9bd2cb925cc812fec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000181.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_00009 +MGRLARVALVVSAAAAAYGARLWRENSARKDVWATATDDL-PEDADGVEPAPED------ +>GCF_003691675_PROKKA_02014 +MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDL-PEDADGVEPAPED------ +>GCF_005280335_PROKKA_00415 +MGRLARVALVAGAAAAAYGARLWQQNREGKDIWATATDDL-PEDAEGVEPAPED------ +>GCF_020097155_PROKKA_00367 +M-RLARIATLVAGAAAAYGVRSWRQQREDKAVWASATDSLEPRKAPAEDGRGEDEETPQG +>GCF_023573625_PROKKA_00009 +MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDL-PEDADGVEPAPED------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000182.fa new file mode 100644 index 0000000000000000000000000000000000000000..550ad84ac56f3a711332113f6aaa4e3139e51f60 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000182.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00011 +------MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYG +PTVPVISDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAAL +TYTVVSWTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAF +RLILSTVVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRAL +KRREPTYRAPGFEIHRDDDPALAPAASR---- +>GCF_003691675_PROKKA_02029 +------MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYG +PTVPVISDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAAL +TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAF +RLILSTVVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRAL +KRREPTYRAPGFEIHRDDDPALAPAASR---- +>GCF_005280335_PROKKA_00386 +MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG +PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL +TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF +RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV +KASEPTYR-----------PASSPARAAADAA +>GCF_020097155_PROKKA_02181 +------MNTT--PASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYG +PTVPGVSDVFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAAL +TYRLVALTTPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAW +RLIASTLVGEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWL +KRHEPTYRA-----QPTPAPVSAPTA------ +>GCF_023573625_PROKKA_00011 +------MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYG +PTVPVISDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAAL +TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAF +RLILSTVVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRAL +KRREPTYRAPGFEIHRDDDPALAPAASR---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000184.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b546a873ab92fa56c6b5050e90ac1a43811fac7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000184.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00015 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA +>GCF_003691675_PROKKA_02033 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA +>GCF_005280335_PROKKA_00382 +MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA +>GCF_020097155_PROKKA_00363 +MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA +>GCF_023573625_PROKKA_00015 +MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL +YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS +QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000185.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000185.fa new file mode 100644 index 0000000000000000000000000000000000000000..45bfa897cba5e1519e4f8c86b8e9a1b50b614cca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000185.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00016 +MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAG-PAP----TVAP-AGAAA-SVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQ +ASGVTEALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGW +WRFLALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLI +GLNLVFSFLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGR-------ARVPSVGAQVA +GLVVVAAALAALTVLGAARVTVAGLLG +>GCF_003691675_PROKKA_02034 +MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAG-PAP----TSPPAAGAAA-TVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQ +ASGVTEALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGW +WRFLALYVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLI +GLNLVFSFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGR-------ARLPSVGAQVA +GLVVVAAALAALTVLGAARVTVAGLLG +>GCF_005280335_PROKKA_00381 +-----------------------------------------MDCAAQGGA--PAGTTTSP +AAVGS-PGP----GGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTVAAYVAQWATRDT +VPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALWVIGRVLEPALGW +WRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRVRGGQVRSIAVLI +GLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGR-------ASAPSAGAQAA +GLVLVAAVLAVLTVLGADRIGLDAVLR +>GCF_020097155_PROKKA_00362 +MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA +RLAAGVPGPASGTTTSPAPASAG-AGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGS +RTGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGW +WRFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLI +GLNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGG-PPGRSAAADGTARRSSAGVHVA +GLVLLAAVLAVLTLVGAARLSPAALLG +>GCF_023573625_PROKKA_00016 +MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS +GVVAG-PAP----TVAP-AGAAA-SVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQ +ASGVTEALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGW +WRFLALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLI +GLNLVFSFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGR-------ARVPSVGAQAA +GLVVVAAALAALTVLGAARVTVAGLLG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000186.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c053e63d375e2a26c63d5770c3385ff0707069a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000186.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00017 +MAAPAGKRKDSARRKREELE----AARRSRSA-VRTDLGDVDPGPKPLSPVYKAVMFGLL +ILGLLWIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE +>GCF_003691675_PROKKA_02035 +MAAPAGKRKDSARRKREELE----AARRSRSA-VRTDLGDVDPGPKPLSPVYKAVMFGLL +ILGLLWIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE +>GCF_005280335_PROKKA_00380 +MAAPSGKRKDSARRKHEELEDARRGARRGSSA-VTTDLGDVDPGPKPLSPVYKAVMFGLM +IVGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE +>GCF_020097155_PROKKA_00361 +MATTSGKRKDSARRKRRELEQAR--SRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLL +ILGLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE +>GCF_023573625_PROKKA_00017 +MAAPAGKRKDSARRKREELE----AARRSRSA-VRTDLGDVDPGPKPLSPVYKAVMFGLL +ILGLLWIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000189.fa new file mode 100644 index 0000000000000000000000000000000000000000..efacbd890fd437c6d151c467b179a0f437db07b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000189.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00020 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRAEAQHTALLNHPGVANVYDYG +EEKGSAYLVMELVPGQPLSSILEKEKVLSPERTLRIIAQTAAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARL +ADQVPLTATGQVMGTAQYLAPEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV +RALIMCMLSKDPKERPSDATALSEAADALRRKDTRGAVEAVPGLAVFLEEQGV---ADPSGAETAPLDYDGLRTTHPRTE +-GIRTD-GSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA----ASASTRDHEIAAVRDQQ-TRPGDVVDPGPPA +GGGSAPARRRRANPWPLWALLGLVVFALLGALLWPLLTGGRGDGGSAPATSQEESSVNVDPEAYKGRPVSEVRAELEGLG +LAVREEDRDAQSPQGTVEEINPVGALQRGETVTLAVSTGEGVIPEGLVGQPVDSAIQTLRDRGFTVDRVDDPSADGADGE +VVRVVPGEGERHRYDTHVQLIVA--TGGSDAAPTREASQPASEPVPSASEEPSSEPSPSASDEPSPSPTAESPTATADPE +PTQEPTEEPTT-PTGDPTTESSGESTA-----PTGEPTTDPSADARGAEASSADATPSA +>GCF_003691675_PROKKA_02038 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRNTAVKILKEEYTGDPNFLRRFRAEAQHTALLNHPGVANVYDYG +EEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQTAAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARL +ADQVPLTATGQVMGTAQYLAPEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV +RALIMCMLSKDPKERPSDATALSEAADALRRKDTCGAVEAVPGLAVFLEEQGV---ADPSGAETAPLDYDGMRTTHPRAE +-GTRAD-GSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAAGAAGAVASTRDHEIAAVRDQQ-TRPGDVVDPAPPA +GGGSAPARRRRANRWPLWALLGLVVFALLGALLWPLLTGGRGIGGSAPATSQDESSVRVDPEAYRGRPVSEVRTELEGLG +LAVREEDRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRVDDPSADGADGE +VVRVVPGEGERHRYDTHVQLIVA--TGGSDAAPTREASQPASEPEPSASEEPSTEPSPSASDEPSPSPTAESPTATADPE +PTPEPSEEPTT-PTGDPTTESSGESTA-----PTGESTTDPSADARGAEASSADATPSA +>GCF_005280335_PROKKA_00376 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRAEAQHTALLNHPGVANVYDYG +EEKGSAYLVMELVPGQPLSAILEKEKVLSPERTLRIIAQTAAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARL +ADQVPLTATGQVMGTAQYLAPEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDAPPPLPSTVPAPV +RALIMCMLSKDPKERPTDATAASEAADALRRKDTRAAVEAVPGLAAFLAAEGV---ADPSGAETAPLDYDGMRTAHPRPE +-GTRAD-GTPATAALPVTAAQPRTDDGARGSAATAAGAAGAAGLAGAAAAGARPANEEIAAVRDPQ-TRPSDVVQEAPPA +GQGSAPVKRRRANRWPVFALLGLVLFALLGALLWPWITGDRTPGGSTPSGTSQASSVSVDPEAYKGRPAAEVRAELERLG +LVVREEDRDARNPRGTVEEVNPVGSLQRGETVTLAVSTGEGVVPDGLVGQPVDSAIQLLRDRGFTVDRVDDPSADGAEGE +VVRVVPGEGQRHRYDTHVQLIVAGGAGGDEPAPTPEPSEPA-EPTAEPSDEPTTEPTSEPTEEPTTEPTAPS------EE +PTEEPTEEPTTEPTSDPTGE------------PTGEPTADPTDDAGGSASPTAEESPTA +>GCF_020097155_PROKKA_00358 +MRPTSGITLGGRYALTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRAEAQHTALLNHPGVANVYDYG +EEKGSAYLVMELVPGQPLSAILEKDRTLSTDRTLSIIRQTAAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARL +ADQVPLTATGQVMGTAQYLAPEQATGQQATGSSDIYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPALPDTISAPV +RALIMCMLSKNPKDRPANATALSEAAEALRRKDVAGAVAAVPTLAAFLADQGVHSTGGPGDAETTALDAAPRTAPQPTVP +LGTTTEPAAPATAALPVAAARP-----------------------------------DVAATRSPRAAEPARSVPAAAPA +DPAPRTAKPRRRNRWPLFALLALVAFAVLGALLYPLLSGESGAGAGASSSTGTDAQVEVDAAAYRGRPADEVRAELEGRG +LAVEEEQRDANDPQGTVVEVTPTGTLRRGDTVTLAVSTGQGTIPQDLVGQPADTVVGILRDRGFSVDRVDDPNADGATGQ +VVRVVPGEGQTHRFDTPVQVIVA---GGTGSSPVTQSVVTAPTAAP-ASESPA-EPAPASSSSGDPAPSSAQPTPS---- +---EASTEPSP-ESPAPTSESAAPSTEPSAGTPSTPDASGPSSQGSDAGSPSTD--PAG +>GCF_023573625_PROKKA_00020 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRAEAQHTALLNHPGVANVYDYG +EEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQTAAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARL +ADQVPLTATGQVMGTAQYLAPEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV +RALIMCMLSKDPKERPSDATALSEAAEALRRKDTCGAVEAVPCLAVFLEEQGV---ADPSGAETAPLDYDGMRTTHPRAE +-GIRTD-GSPATAALPVTAAQPRTADDARGPGAAGAAAVGAAGAAGAA---ASTRDHEIAAVRDQQ-TRPGDVVDPGPPA +GGGSAPARRRRANRWPLWALLGLVVFALLGALLWPLLTGGRGVGGSAPATSQEESSVHVDPEAYRGRPVSEVRTELEGLG +LAVREEDRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRVDDPSADGADGE +VVRVVPGEGERHRYDTHVQLIVA--TGGSDAAPTREASQPASEPEPSASEEPSTGPSPSASDEPSPSPTAESPTATADPE +PTPEPSEEPTT-PTADPTTESSGESTA-----PTGEPTTDPSADARGAGASSADATPSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000190.fa new file mode 100644 index 0000000000000000000000000000000000000000..43901d3bccea5f788dc98ff4ea3252d87a3561e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000190.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_00021 +MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN +ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA +ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT +E +>GCF_003691675_PROKKA_02039 +MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN +ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA +ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT +E +>GCF_005280335_PROKKA_00375 +MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN +ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA +ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT +E +>GCF_020097155_PROKKA_00357 +MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT +PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA +LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN +TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV +LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA +ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM +EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA +AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA +E +>GCF_023573625_PROKKA_00021 +MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN +ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA +ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT +E + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000199.fa new file mode 100644 index 0000000000000000000000000000000000000000..163aa9d817d368c96bb908bc74f2d221c89c5469 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000199.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00040 +M-------------------------------------------AKGVKP-----AGRAG +GEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHDDAAQLAHL +AHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSELPVVCVGRDHLL +AAWDVDADGPVPPAELDPDEELDPARFAPAP--SPEPMDAAELPGAGERMALEIAASGAG +HVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAEAEAGAA +VVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASSR +>GCF_003691675_PROKKA_02053 +M-------------------------------------------AKGVKP-----AGRAG +GEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHDDAAQLAHL +AHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSELPVVCVGRDHLL +AAWDVDADGPVPPAELDPDEELDPARFAPAP--SAEPMDAAELPGAGERMALEIAASGAG +HVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAQAEAGAA +VVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR +>GCF_005280335_PROKKA_00360 +MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG +GEGRRR-APSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHL +AHDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLL +AAWDAEADGPVPLAELDSHEELDPARFAAAP--VEDPLDSAELPGAGERMALEIAASGAG +HVVLPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATR-------AEVEADAGDA +GTAAAGPGEADDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR +>GCF_020097155_PROKKA_00301 +------------------------------------------------------------ +-------MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHL +AHDAAGAPLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLL +AAWDLEADGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVG +HVVLPQSVARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAE-------EGDGV +VPDGAD--APATTAPRHPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR +>GCF_023573625_PROKKA_00035 +-----------------------------------------------MKP-----AGRAG +GEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHDDAAQLAHL +AHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVVCVGRDHLL +AAWDVDADGPVPPAELDPDEELDPARFAPAP--SPEPMDAAELPGAGERMALEIAASGAG +HVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAEAEAGAA +VVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000200.fa new file mode 100644 index 0000000000000000000000000000000000000000..162990b59ec4a3f68de0a2194173a0b5ef261b0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000200.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00042 +M--SPTPTRPSRG--PG-------WRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVM +AMFGATVLVPALTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIG +GTGAALGGILVTGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ +EVPVTTFGTALAVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLP +PFHGPELRWDLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSG +AGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG +IILYGMIGMMGVRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVA +ALVVYHLMTAIARARGTEPVPEDEE---QFEASEAGRLG +>GCF_003691675_PROKKA_02055 +M--SPTPTRPSRG--PG-------WRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVM +AMFGATVLVPALTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIG +GTGAALGGILVTGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ +EVPVTTFGTALAVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLP +PFHGPELRWDLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSG +AGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG +IILYGMIGMMGVRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVA +ALVVYHLMTAIARARGTEPVPEDEE---QFEASEAGRLG +>GCF_005280335_PROKKA_00358 +M--SSSPSRPAPG--FG-------WRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVM +AMFGATVLVPALTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAG +GVGAALGGVLVTGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ +EVPLTTFGTALAIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLP +PFHAPELHWNLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSG +LGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG +IILYGMIGVMGVRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIA +ALVVYHLMTAIARVRGTEPVSEDDE---AYEASEAGRLG +>GCF_020097155_PROKKA_00300 +MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM +AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH +GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ +EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP +PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG +LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG +IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT +ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG +>GCF_023573625_PROKKA_00037 +M--SPTPTRPSRG--PG-------WRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVM +AMFGATVLVPALTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIG +GTGAALGGILVTGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ +EVPVTTFGTALAVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLP +PFHGPELRWDLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSG +AGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG +IILYGMIGMMGVRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVA +ALVVYHLMTAIARARGTEPVPEDEE---EFEASEAGRLG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000204.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7886b2b86ce1c51a5f3a10fb0a5d26d2919f4a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000204.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00046 +--------------------------------------------------MSERTTYLLI +DGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAI--DGEIPIPFV +QALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLTDLAATPGR +RTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYEFL +>GCF_003691675_PROKKA_02059 +--------------------------------------------------MSERTTYLLI +DGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAI--DGEIPIPFV +QALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLTDLAATPGR +RTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYEFL +>GCF_005280335_PROKKA_00349 +MGRRADAPAGPGRAVVVPTTTSSPAPASAPVHTPAPAPATSSAPAGSLGQVSESTTYLLV +DGENIDATLGTSILQRRPQPDERPRWNRLLSFMGEHWDQPVKGLFFLAI--DGDIPVPFV +QALTAIGYKPIMLRGAGKVVDIGIQKTMEALQEREDDVVLVSHDADFAPQLTDLAATPDR +RTAIIGFEEFLSHELRRIPDVEFFDLEYGVGAFDTPLRRLRVIDIDEFDPLEFL +>GCF_020097155_PROKKA_00294 +MSRRADLPTGPATAV--------PAAPAAPV-SPTAEDRSAATPADTLDTMSARTTYLLV +DGENLDATLGMSVLNRRPNPEERPRWNRVLRHVERAWGQEVRPLFFLAVDEDGDIPFGFV +QALTTMGYQPILLRGAGKVVDIGIQRMAEALIGRDADVVLASHDADFAPQMLDLAAH-GH +KIAVMGFDEFMSAELRAVNGMEVWDLEHDVAAFDVPLPRLRVIDIDDFDPRDFL +>GCF_023573625_PROKKA_00041 +--------------------------------------------------MSERTTYLLI +DGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAI--DGEIPIPFV +QALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVILVSHDADFAPQLTDLAATPGR +RTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPNEFL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000205.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2495d41734fea7f5b0fcbdb6a52121b8a1aaa25 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000205.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00047 +MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA +ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGHFGAAVVNVLAHLAVLTVIMAL +LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLVPLAQALGLSRATLTPYV-----SA +FLTDGPYRLPLFLTWALLGAVLVRTVHGTTTAA---------PARSARLTGLAWAAGGIA +LAGVVLALSRTQTGAAPVPYTATPAEALLDTGLVLTVLGACAALAPRRAG----LLAVPG +AMTLSVYVAHLWYLGWVRRLGPGPWRSATGTDDTWFNLAVLVAGALLLPLLWRAVVRIGP +FRAGPLEGVVRLLTAPFDRA----R +>GCF_003691675_PROKKA_02060 +MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA +ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGLFGAAVVNVLAHLAVLTVLMAL +LAALPLAAHLVLAVLAGGGGLLLAATSTADVVDRLVPLAQALGLSRATLTPWV-----SA +FLTDGPYRLPLFLAWALLGAVLVATVHGTTTAA---------PARRARLTGLAWAAGGIA +LAGVVLALSRTQTGAAPVPYTATPAEALLDTGLVLAVLGACAALAPRRAG----LLAVPG +AMTLSVYVAHLWYLGWVRRLGPGPWRSATGADDTWFNLAVLVVGALLLPLLWRAVVRVGP +FRAGPLEGVVRLLTAPFDRA----R +>GCF_005280335_PROKKA_00348 +MPRVSSR----PHTGRDRLVWVDVARGVALVSMFVAHVAPSGGPAGVLNLSEHLTAALFA +ALVGVSARLEVQGLGVGRALVRAMVRAAALLGAAWLTSLFDAAVVDVLTHLAVITVLMAL +LAALPLAVHLVLALLAGGGGILLTASGTLAVADALAPAARALGLDPAELVPAV-----AG +FLTAGPYRLTAFLGWALLGAVLVRTVHGTTTAL---------P-RSGRLVGLGWGVGGVV +LAGLVILLSRVQTGAAPVPYTGTAAEILVDTGLVLGVLGLCAAVVPSRPSPATDLLAVPG +SMTLSVYVAHQAYLGWVLTAGPGPWVDGRGADDTWFNLAVLLAGGILLPLLWRGLVRVRP +FRAGPLEGVVRLVTDPIGRRSRGEH +>GCF_020097155_PROKKA_00295 +M----------TLAAGHRLTWVDVARGLALVSMFVAHTAPTGGPGGVLNLSEHLTAALFA +ALVGVSAHLEQRRHGFWRAFLRAVVRAAALCGAAWLTSHFGAAVVDVLTHLAVLTVLMSV +LALLPGLVQLLLVPAAAWAGVRVGALTADDVAARLEP-ARALVPAQVRPGPAVVAEQAAA +FFTVGPYFLLFFTAWALLGAVVVRSVQGGGLRAALRLGGHPGPGLGGRAAGGVWAGVGLL +VGGAGVALARQRTEDSPVPYEATWDYALLAAGLVLIVLGACAAVVPSHVPWLTAVLAVPG +SMTLSVYVAHQAYLGWVLRAGPGPWLSELGTDDTWFNVGALCAAGLLLPLLWRALVRAEP +WRRGPLEGPVALVTHGLARR----- +>GCF_023573625_PROKKA_00042 +MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA +ALVGVGARLEVEWLGRGRAVPRALVRAAALFGAAWLTGLFGAAVVNVLAHLAVLTVLMAL +LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLLPAAQALGLSRATLTPWV-----SA +FLTDGPYRLPLFLAWALLGAVLVATVHGTTTAA---------PARRARLTGLAWAAGGIA +LAGVVLALSRTQTGAAPVPYTATPAEALLDTGLVLIVLGACAALAPRRAG----LLAVPG +AMTLSVYVAHLWYLGWVRRLGPGPWRSATGADDTWFTLAVLVAGALLLPLLWRAVVRIGP +FRAGPLEGVVRLLTAPFDRA----R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000208.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0e3dd3ab947dfeba2185780a3bfb8708ec5a043 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000208.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00055 +MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFTTSFNDDHIAAITQAVVEYRA +HHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDG +LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID +VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG +HAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVG +FKWFVPGLLTGTGVFGGEESAGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA +TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTEDVYKIYAESFRGPEHLKQVQ +AEAQKLVDAVIG +>GCF_003691675_PROKKA_02068 +MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFTTSFNDDHIAAITQAVVEYRA +HHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDG +LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID +VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG +QAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVG +FKWFVPGLLTGTGVFGGEESAGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA +TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTEDVYKIYAESFRGPEHLTQVQ +AEAQRLVDAVIG +>GCF_005280335_PROKKA_00342 +MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALKTSFNDDHIAAITQAVVEYRA +EHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDG +LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID +VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMDCSSPHAMASLIERMTPDADG +QAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVG +FKWFVPGLLTGTGVFGGEESAGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA +TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTEDVYKIYAESFRGPEHLKQVQ +EEAQRLVDAVIG +>GCF_020097155_PROKKA_00281 +-----MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFNDDHIAAITQAVVEYRA +EHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFTPTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDG +LVITPSHNPPADGGFKYNPPHGGPADTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVID +LDAIREAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG +HAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRSQWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVG +FKWFVPGLLSGTGVFGGEESAGASFVKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPA +TAEQKAALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKIYAESFLGEEHLKQVQ +QEAQAIVDAVIS +>GCF_023573625_PROKKA_00050 +MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFTTSFNDDHIAAITQAVVEYRA +HHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDG +LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID +VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG +QAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVG +FKWFVPGLLTGTGVFGGEESAGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA +TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTEDVYKIYAESFRGPEHLTQVQ +AEAQKLVDAVIG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000211.fa new file mode 100644 index 0000000000000000000000000000000000000000..dad78dc043aac5e8b20380a6ec39034b2c3e0173 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000211.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00058 +MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSALRDGARVHVLVATAGEASHPH +SPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARDRLTWASLALPDSGVAEHEDAVRDAVAAALDAHP------G +PAVLASHDPGDGHADHEAVGRAVGAVAGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVR +PLSAAPGDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARKRALTLAALPRPRYG +TVVEAGASIGVLTADVAARADRVVGLEASSTAVERAAARLAGAPHAEVRRAVLPADWPADV--------AGADLVIASEI +GYFLQPEELDALIDDADAALAPGGELLLCHWRHPIEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHA +VVVVPAKDEQERLPAALAALAAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAGQAGVGR +ARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGHDEV----LVLGTVDV---HQGPLRQAWLRGYRHE +EGHPHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRALAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSG +YLKAVGRPG---------- +>GCF_003691675_PROKKA_02071 +MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSALRGGARVHVLVATAGEASHPH +SPTHTPADLVRLRRDEMEHALDALAAGLPASAGPGSPARDRLTWASLALPDSGVAEHEDAVRDAVAAALDAHP------G +PAVLASHDPGDGHADHEAVGRAVGAVAGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVR +PLSAAPGDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARKRALTLAALPRPRYG +TVVEAGASIGVLTAAVAARAGRVVGLEASPTAVERAAARLAGAPHAEVRRAVLPADWPADV--------AGADLVIASEI +GYFLQPEELDALIDDADAALAPGGELLLCHWRHPIEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHA +VVVVPAKDEQERLPAALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAGQAGVGR +ARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEA----LVLGTVDV---RQGPLRQAWLRGYRHE +EGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRALAGERDGGEGRRVRVIATDTTRVLTSSRLEGRTPGGFSG +YLKAVGRPG---------- +>GCF_005280335_PROKKA_00337 +MVSFSHTDAGTSEEAWAAAGVGALPVLESPAWDADTLLLVAVAHPDDETLGATGLIRSALRGGARVHVLVATAGEASHPD +SPTHAPEDLVRLRRAEMEHALDALAADLP---GPGEDRRSALTWESLGLPDSGVAGREDAVRAAVVAALAAHP------G +PAVLASHDPGDGHADHEAVGRAVGELAGERDLPLCAFPIWFWHWADPAELPARRYRRLALTDDDRAARRAALDAHASQVR +PLSDAPGDEAVLGPQVLAHHDRPFEAHRLSGPDDADAHRAAAVFDRLYREHEDPWRYLSSPYEARKRALTLAVLPRPRYG +TVVEAGASIGVLTGEVAARADRVVGLEASPTAVERAAARLADTPHAEVRRAVLPGHWPDDV--------AGADLVIASEI +GYFLQPEELDALVDDADAALAPGGELLLCHWRHPIEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHA +VVIVPAKDEQERLPAALAALGAALDRWEEHHAQGSAAVVVAADRCDDATVAAAVAARHADPRVHVLELGEPGPGEAGVGR +ARAEAARRARALFPDVPAQRLWLASTDADSRVPADWLLAQTTAAGPDGA----LVLGTVDV---REGALRRAWVRDYRHE +EGHPHVHGANLGLPWSLYEAAGGFPPVAEHEDVRLVEAVRALA---------EARVRATDTTRVLTSSRLTGRTPGGFAG +HLQEVGGEAVPRRGAQARP +>GCF_020097155_PROKKA_00277 +MVSFDHRDDGTAEAVWMAAGVGELPALPARAWTRADTLLVAVAHPDDETLGAAGLIRAALRGGAAVHVAVATAGEASHPD +SPTHTPADLVRLRRAEMDHALAALADGLGPDAG-------ALTWESLALPDGGLTDRPDEVRAALERVLAGRTPAEEGGG +AVVLVSHDPDDGHGDHDAVGAAAAALAADHDLELYAFPLWLWHWGAPEDLAPRRYRRLELAAGDDAARLAALDAHASQTR +PLSAAPGDEAILPERMIAHFTRGFETYRRTAPDDADASRASAVFDRLYREHEDPWRYLTSPYEARKRALTLAVLPRPRYG +TVVEAGASIGVLTAALAERAERVVGLEASQVAVERAAAHLAEIPHAEVRRAVLPADWPADVGPAEEGAGAPADLVVASEI +GYFLQPEELDALVDAADASLGAGGELLLCHWRQPITGWPLDGDAVHDRVAADPRWRLLSEHVEADLRLSVHARAAAATHA +VAVVPAMDEAEHLPAGLDALSAALDLWEAQHTQGSAAVVTVVPADDAPTLEAAHAARARDPRIRVLELA---PGAGGVGR +ARAAAARHARGLFPDVPAEALWLASTDADTRVPADWLVGQPALAARRRADGQVLVLGTVDLPAHADDDLAHRWRADYEHR +EDHPHVHGANLGLPWGLYERAGGFAEVAEHEDVRLAEAVRALG---------EDRVLATDRVRVHTSSRLEGRTPGGFAG +FLRGLLEEGA------AEG +>GCF_023573625_PROKKA_00053 +MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSALRGGARVHVLVATAGEASHPH +SPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARDRLTWASLALPDSGVAEHEDAVRDAVAAALDAHP------G +PAVLASHDPGDGHADHEAVGRAVGAVAGECDLPLYAFPIWFWHWADPADLPARRYRRLRLTDDDRAARRAALDAHASQVR +PLSAAPGDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARKRALTLAALPRPRYG +TVVEAGASIGVLTADVAARADRVVGLEASPTAVERAAARLAGAPHAEVRRAVLPADWPADV--------AGADLVIASEI +GYFLQPEELDALIDDADAALAPGGELLLCHWRHPIEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHA +VVVVPAKDEQERLPAALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAGQAGVGR +ARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEA----LVLGTVDV---RQGPLRQAWLRGYRHE +EGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRALAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSG +YLKAVGRPG---------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000213.fa new file mode 100644 index 0000000000000000000000000000000000000000..5002daaf7b5c2278269e79cf1f13f8f19eb22059 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000213.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00061 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>GCF_003691675_PROKKA_02074 +MSAFETVDVNEIPADATILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>GCF_005280335_PROKKA_00334 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHLPLGQLPDRLEELDPDTDYYVIC +RTGGRSARAAEFMVGRGYTAINVAGGSGAWLEAGKPMEADGGAEPTVK +>GCF_020097155_PROKKA_00275 +MSHFETVTVDQIPADAAILDVREDDEWALGRAAGAQHLPLGQLPERIEELDPDTDYYVIC +RTGGRSARAAEYMVGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>GCF_023573625_PROKKA_00056 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000214.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c86d48010319ac78c6305d70d3739e0258a1165 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000214.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00062 +MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVPAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVAISFVLVGRPGVAIEDVRRVTTHPH +AWAQVRGWAETALPGVEFTPAPSTAAGAGLV---AQGD-----FDAAVCAPLVAEQTGLP +VLAERIEDVPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGV +NLSRIESRPTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPT +RVPAEFTDAAYRSGRAWVESLRSR +>GCF_003691675_PROKKA_02075 +MTGTGSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVSAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAMEDVRRVTTHPH +AWAQVRGWAETALPGVDFTPAPSTAAGAGLV---AQGD-----FDAAVCAPLVAEQTGLP +VLAERIEDVPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGV +NLSRIESRPTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPT +RVPAEFTDAAYRSGRAWVESLRSR +>GCF_005280335_PROKKA_00333 +MTRDDAAPLG----RCTFLGPAGTFTEAALRAVPGAEQAELIPATSVPAALAAVRAGEAD +HAMVPIENSVEGGVSATLDDIASGDDLQILREELVQISFVLVGRPGVELADVRRVSTHTH +AWAQVRGWVEANLPGVEYTPSGSTAAAARAL---ADAEPGSEPFDAAVCAPLVAEQTGLP +VLARAIEDVTGAVTRFVLVGRPGPLPAHTGSDKTTLTVPLPDDHPGALREILDQFATRGI +NLSRIESRPTGEGMGKYFFSIDLEGHLAEERVAAAMGALHRIFPGVRFLGSYPRAEHRPV +AVRRHTSDDAYRAGRAWVDGLLAR +>GCF_020097155_PROKKA_00274 +M-----SPAP----RYAFLGPAGTFTEAALRQVASPEDVDLLPASSVLAALAAVRVGEAE +RAVVPIENSVEGGVTATLDDIGADEPLQILAEVLVPISFVLVGRPGVALEDVRRVTTHTH +AWAQVRGWMEAHLPGVEFTPAGSTAAGARALLPSAGGDGAVASFDAAVCAPLVAEQTGLP +VLAEAIEDVTGAVTRFVLVSRPGPVPEPTGADKTTLTVPLPDDHPGALREILDQFATRGI +NLSRIESRPTGEGMGRYFFSIDLEGHVAEERVGAALAALHRTFPGVRFLGSYPRAEGRPP +TVPEHVTDAAYRRGTAWVRGLRSR +>GCF_023573625_PROKKA_00057 +MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAKAEFVSAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAIEDVRRVTTHPH +AWAQVRGWAETALPGVEFTPAPSTAAGAGLV---AQGD-----FDAAVCAPLVAEQTGLP +VLAERIEDVPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGV +NLSRIESRPTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPT +RVPAEFTDAAYRSGRAWVESLRSR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000218.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5497dae4f236dfb5c9a7b84dcc017edb223228b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000218.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_00069 +MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACG--PVTAPPA-PSSAPASSTT +AAPTSSSPSAGPTA--------------AEVAAAVEPGLETSPGTASAEFRDLATGEVLY +ARDADEPVAPASSLKVLAAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLG +TGASDSTHVSGRAGLRTLAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPE +SGNIAPVQPLATYGGREAPGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTL +PATEVPRATVLAAAPVAAVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGA +TRLLTATVEDLGVDTAGMALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRP +GEDSTLGDRFPDAPARQAVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPA +RAAVDEAVSAVAGL +>GCF_003691675_PROKKA_02082 +MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACG--PVTAPTA-PSSASASTST +AAPTSSSPSAGPTA--------------AEVAAAVEPGLETSPGTVSAEFRDLATGEVLY +ARDADEPVAPASSLKVLAAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLG +TGASDSKAVSGRAGLRTLAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPE +SGNIAPVQPLATYGGREAPGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTF +PATEVPRATVLAAAPVAAVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGA +TQLLTATAEDLGVDTAGMALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRP +GEDSTLGDRFPDAPARQAVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPA +RAAVDEAVSAVAGL +>GCF_005280335_PROKKA_00323 +MTPG------------------SPFASLLAALAAALLSAA--PVLTPLAGPAALAPGNPV +TAEAVAAPS--PDA--------------RALASAVDAALDASPGRVAAQVRDAATGEVLH +ARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRVVAVPAADDGATELVLVGGGDVLLG +DGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVVVSVDLRLF-DGAAVNPAWTPDLLE +DGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVFQRLLDEEIERTGADLDLGLRDSI +PATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSENQVAEALGHLSAYAVGRPATHEGA +ADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQLAAVVSAASRVPWLAPVLDGLPRP +GEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVTTQDGRVLAFSIVASDLDWRLDEA +REAVDAAVTAMAGL +>GCF_020097155_PROKKA_00265 +MTPSN--RAAR-----VAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPV +PA---ASPSGGATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLY +ARSADQAVAPASALKILTAVTAVDVLGADRALTTSVVALPG--GGATELVLVGGGDALLG +AGASDPGRVDGRAGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVE +SGNITAVQPLATYGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVV +PATSAPRGDVLATEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAV +PGLLRDRAAAHGVDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRP +GEDSTLAERFPGSPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPA +RAAIDEAVSALAAL +>GCF_023573625_PROKKA_00063 +MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACG--PVTAPPA-PSSAPAASTT +AAPTSTSPSAGPTA--------------AEVAAAVEPGLATSPGTVSAEFRDLATGEVLY +ARDADEPVAPASSLKVLAAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLG +TGASDSTHVSGRAGLRTLAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPE +SGNIAPVQPLATYGGREAPGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTL +PATEVPRATVLAAAPVAAVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGA +TRLLTATAEDLGVDTAGMALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRP +GEDSTLGDRFPDAPARQAVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPA +RAAVDEAVSAVAGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000221.fa new file mode 100644 index 0000000000000000000000000000000000000000..060759fad8b694d4ee06d3f717a3fbac449460f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000221.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00072 +MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL +HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>GCF_003691675_PROKKA_02085 +MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL +HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>GCF_005280335_PROKKA_00320 +MDAQDVQNDLTHVLMRREEVQETVKDLAAQIDRDYEGKDLLIVAVLKGAIMVVADLTRAL +HSHVQIDFMAVSSYGSGTKSSGVVRILKDLDADLTGRDVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPDAMKVEIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>GCF_020097155_PROKKA_00262 +MDAQDVQNDLTHVLMSKEEVQDTIRDLAAQIDRDYEGKDLLIVAVLKGAVMVVADLTRAL +HSHVEMDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +TRGPASVEICTFLRKPDAMKVDIDVKYVGKDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>GCF_023573625_PROKKA_00066 +MDAQDVQNDLSHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL +HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000222.fa new file mode 100644 index 0000000000000000000000000000000000000000..44cee865a83aaae325417f4bcd44c65c41ab99e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000222.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00074 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQRVDLTLREPYKQDDRDLGKEV +YFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGFMVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDN +PDVLFKDVAGADEAVEELQEIKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFDASTNVIMIAATNRPDVLDPA +LLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDLRSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALD +EAVDRVMAGPQKRTRLMNEHERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVGGAAGGSSREYSEELAYLVDA +EVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQEAIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRS +RHDGGEQTPVGVEGTTVPVRPEGAPPSSLGGDAAGPGLPPHGGPSNTPG---PGEGPTF +>GCF_003691675_PROKKA_02087 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQRVDLTLREPYKQDDRDLGKEV +YFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGFMVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDN +PDVLFKDVAGADEAVEELQEIKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFDASTNVIMIAATNRPDVLDPA +LLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDLRSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALD +EAVDRVMAGPQKRTRLMNEHERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVGGAAGGSSREYSEELAYLVDA +EVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQEAIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRS +RHDGGQQTPVGVEGTTVPVRPEGAPPSSLGGDAAGPGLPPHGGPSNTPG---PGEGPTF +>GCF_005280335_PROKKA_00319 +MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQRVDLTLREPYSQDGRDLGKEV +YFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGFMIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDN +PDVLFKDVAGADEAVEELQEIKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFDASTNVIMIAATNRPDVLDPA +LLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDLRSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALD +EAVDRVMAGPQKRTRLMNEHERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVGGGGGGSSREYSEELAYLVDA +EVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQEAIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRS +RHEGGEQTPVGVEGTTVPVHPEGAPPSSLGGDAPTPGLPPHGGPSSSPG---AGEGPTY +>GCF_020097155_PROKKA_00260 +MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQRVDLTLREPLSQDGRDLGRDV +YFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGLMIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDN +PDVLFKDVAGADEAVEELHEIKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFDASTNVIMIAATNRPDVLDPA +LLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDLRSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALD +EAVDRVMAGPQKRTRLMNEHERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL +AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLGG-GGAASREYSEELAYLVDA +EVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQIAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERAS +RLEGEQPEAVGVEGTTVPDAPEGAPPTALGGAGGSA-----GGPGDLPGQHSPTPGPTY +>GCF_023573625_PROKKA_00068 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQRVDLTLREPYKQDDRDLGKEV +YFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGFMVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDN +PDVLFKDVAGADEAVEELQEIKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFDASTNVIMIAATNRPDVLDPA +LLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDLRSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALD +EAVDRVMAGPQKRTRLMNEHERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVGGAPGGSSREYSEELAYLVDA +EVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQEAIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRS +RHDGGEQTPVGVEGTTVPVRPEGAPPSSLGGDAAGPGLPPHGGPSNTPG---PGEGPTF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000223.fa new file mode 100644 index 0000000000000000000000000000000000000000..6de4f6e942c3a435b762851300d1fceb535480bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000223.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00075 +M----------------------------TAHTPDD------AVPGTFDPDSTAVDRPRI +EAAVREILLAIGEDPDREGLADTPARVAKAYAEFFAGLHQSPDQVLGTTFDIAHEELVLV +KDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV +EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG +>GCF_003691675_PROKKA_02088 +M----------------------------TAHTPDD------AVPGTFDPDSTAVDRPRI +EAAVREILLAIGEDPDREGLADTPARVAKAYAEFFAGLHQSPDQVLGTTFDIAHEELVLV +KDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV +EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG +>GCF_005280335_PROKKA_00318 +MTEQTHHDDAARGPV----PAADGSAAAPTASTPAA-----AGVPGTFDPDSTAIDRPRI +EAAVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLV +KDIPFYSTCEHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVV +EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG +>GCF_020097155_PROKKA_00259 +MTEQ--HRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRI +EAAVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLV +KDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV +EALMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG +>GCF_023573625_PROKKA_00069 +M----------------------------TAHTPDD------AVPGTFDPDSTAVDRPRI +EAAVREILLAIGEDPDREGLADTPARVAKAYAEFFAGLHQSPDQVLGTTFDIAHEELVLV +KDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV +EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000224.fa new file mode 100644 index 0000000000000000000000000000000000000000..151123e426414dc730ec1dbc3d0ab83f722700be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000224.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00077 +MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA +DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVTAVEVTVHKPQAPIPHDFADAAVTVHR +TREDLA +>GCF_003691675_PROKKA_02090 +MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAADDDLARTANYAEVA +DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR +TREDLA +>GCF_005280335_PROKKA_00316 +MSARDRIRLTGLSAVGHHGVFDHERRDGQPFVTDVVLHLNAGPAAAGDDLARTANYAEVA +DTVVRLVTGEPVDLIETLAERIARAVLAEQPVVEAVEVTVHKPQAPIPHDFADAAVTVHR +TRRDAS +>GCF_020097155_PROKKA_00257 +MS--DVIRLTGLTATGRHGVFEHERRDGQPFTTDVALTLDAGPAAARDDLARTANYAEVA +ETVVRLVTGEPFDLIETLAVRIAEAVLAEQPVVTAVEVTVHKPQAPIPHDFTDVSVTVAR +RR--GA +>GCF_023573625_PROKKA_00071 +MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA +DTVVRLVTGEPVDLIETLADRIARTVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR +TREDLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000225.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2ef72b4a87d53e1b924387727448b03272858e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000225.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00078 +MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV +RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL +DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG +VRRQEPERHRLLAG------TDDVVPLRPACPDALG-------REDT----- +>GCF_003691675_PROKKA_02091 +MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV +RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL +DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG +VRRQEPERHRLLAG------TDDVAPLRPARPDALG-------REAT----- +>GCF_005280335_PROKKA_00315 +MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV +QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL +DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG +VRRAEPERHRLLAG------RDDVVPVRPRAVRAPG-------RDAIDGSGP +>GCF_020097155_PROKKA_00256 +MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV +AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL +DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH +VRR-EPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT----- +>GCF_023573625_PROKKA_00072 +MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV +RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL +DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG +VRRQEPERHRLLAG------TDDVAPLRPARPDALG-------REAT----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000227.fa new file mode 100644 index 0000000000000000000000000000000000000000..d8753c4921b248122dcd09fcad4012d3f4ffe296 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000227.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00080 +MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL +>GCF_003691675_PROKKA_02093 +MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL +>GCF_005280335_PROKKA_00313 +MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL +PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL +>GCF_020097155_PROKKA_00254 +MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL +PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL +LRWAGLQKLTLKT-AGGADVELVGLPRETCDRLREVLMARGQARLAGL +>GCF_023573625_PROKKA_00074 +MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000228.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000228.fa new file mode 100644 index 0000000000000000000000000000000000000000..3356e3dabb72d354e4bdd10a3fdab94547ff0cc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000228.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00081 +MSAAAP-------------------PPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGG--- +GDGSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVDLQHPLVARLLGLATVKVE +AAD-GGESALELSFLRRAEAEAVRREILDRASGMLGGA--------GADASA-----------PERAAEPGLP----DAD +A----A--------------------DAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVALLPEAVLDEGE +T-LTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVN +MAVAGYL--QESDGARDVALPVGPWEDVLRVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWW +FNWFAWRRTGFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDEDVAVDLYA +REARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVV---GGAVVGEESGAHVPAVRGEEER- +>GCF_003691675_PROKKA_02094 +MSAAAP-------------------PPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGG--- +GDGSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVDLQHPLVARLLGLATVKVE +AAD-GGESALELSFLRRAEAEAVRREILDRASGVLGGA--------GADASA-----------PERAAEPGLA----DAD +PDAVDA--------------------DAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVALLPEAVLDEGE +T-LTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVN +MAVAGYL--QESDGARDVALPVGPWEDVLRVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWW +FNWFAWRRTGFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDEDVAVDLYA +REARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVV---GGAVVGEESGAHVPAVRGEEER- +>GCF_005280335_PROKKA_00312 +MSAAAPVP---AT------------RPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRF-GAGAGGGSGE +GEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYDRIQAVDLQHPLVARLLGLAVVKVE +AAD-GGESALELSFLPKARAEQVRREILDRASGVLVGPASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADAD +PTTPRADAPEGAAPSSSDPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLEGED +TPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPPGRVQGVTVSQPLFWRPFGWHRVK +VSVAGYG--EDAAGKRSTALPVGPWEDVLRVLTVVAPDPGLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWW +FNWFAWRRRGFTTTRALLVVRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELFA +EEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVA--RPAAPAGGVAGTDPEPRTSHEERP +>GCF_020097155_PROKKA_00253 +MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDVVERWIGGLF-GADAGGGPGV +DGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIELKQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVE +AADGGGDSALELAYLPKAQAAAVRRQILDRASGAAAAR--------PVPSAA-----------PEAAGGPAAAGPVR--- +-------------------GLLVDPEEQGPVLLRVPAGRLIGSVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEA +G-VWAVTLGSTFPLLFSLAGAVWSGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVK +VSVAGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAA-----GELMRTAMTGSGEEGGFRHVPRRAAWW +WHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQRRLRVATLRVHMAGGAARLRGLDEDVLAELFE +VESRHAAVSRRLTDRNRWMLPEELERFERRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA- +>GCF_023573625_PROKKA_00075 +MSAAAP-------------------PPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGG--- +GDGSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVDLQHPLVARLLGLATVKVE +AAD-GGESALELSFLRRAEAEAVRREILDRASGMLGGA--------GADASA-----------PERAAEPGLP----DAD +A----A--------------------DAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVALLPEAVLDEGE +T-LTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVN +MAVAGYL--QESDGARDVALPVGPWEDVLRVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWW +FNWFAWRRTGFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDEDVAVDLYA +REARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVV---GGAVVGEESGAHVPAVRGEEER- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000229.fa new file mode 100644 index 0000000000000000000000000000000000000000..1c8466e394f830a738cbe03f3c8873ed7f23d5c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000229.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00082 +MTGGLDLS--LDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRD +RAEMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYG +VGVMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGE +PVVVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTD +GDGALTGPVARGDVDTLRTHRETLGELEAGGLPPDVRAVWETLARATTDRAETRGTLRAD +TAARLREVLDDSDDPHDD-- +>GCF_003691675_PROKKA_02095 +MTGGLDLS--LDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRD +RAEMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYG +VGVMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGE +PVVVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTD +GDGALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRAD +TAARLREVLDDSDDPHDD-- +>GCF_005280335_PROKKA_00311 +MTGGLDLT--LDPTDPTQRPGRLGVGVVGAGRVGAVLGAALRNAGHTITGVHAVSEASRT +RAEALLPEAPVLEIPEILRRSEMVLFAVPDDVLPELVAGLAAAGHVQTGHLVVHTSGRHG +VGALNPVRAHGAIPIALHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALAVEMGGE +PVVIKEADRGVYHAALSHGSNHLVTLTAQAAQLLRSIGVQDTERLLRPLMHASLENALAD +GDGALTGPVARGDVETVRGHRETLRELVAEGMPADVLAVWETLARATADRAEARGALRPD +VAARLREAL-----APDA-- +>GCF_020097155_PROKKA_00252 +MS-RMDMSPELTGADPADRPGRLGVGVIGAGRVGAVLGAALRGAGHTITGVHAVSEASRT +RAEALLPGVPVLELPEILRRSEMVLFAVPDDALPELIAGLAAAGHIQTGHLLVHTSGRHG +VRVMDPVRAHGAIPLAVHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALVVEMGGD +PVVVKEADRAAYHLALSHGSNHLVTVTAQARQILEEIGVAEPERMLRPLMQASLENALTD +GDGALTGPVARGDVETVRGHRDTLRELVDGGMPADVLAVWESLARATAQRAARRGALRAD +AAERILAVLDGADDGPDATG +>GCF_023573625_PROKKA_00076 +MTGGLDLS--LDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRD +RAEMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYG +VGVMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGE +PVVVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTD +GDGALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRAD +TAARLREVLDDSDDPHDD-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000231.fa new file mode 100644 index 0000000000000000000000000000000000000000..a06fb99f3c123710deabfa65b73874a5a81d6262 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000231.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00086 +MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDTWMQGK-----KEHPGRG---------VGKTA----- +--------------QRGLKVR +>GCF_003691675_PROKKA_02099 +MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDVWMQGK-----KEHPGRG---------VGKTA----- +--------------QRGLQGR +>GCF_005280335_PROKKA_00305 +MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER +LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ +VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDTWMQGK-----KEHPGRG---------VGKSA----- +--------------QRGLQVR +>GCF_020097155_PROKKA_00250 +MTALRT-TARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAE--------RPDVVAHRG +ASAYRPEHTLAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRK +TTKTVDGVEITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREE +LSAKYGREIGIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAE +MNTRLGLQADTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQ +VIALNQDGSLGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYIT +EVLDAGVDGFFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPA +GLAAAAAGVLVALRRRLTAAR +>GCF_023573625_PROKKA_00081 +MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDVWMQGK-----KEHPGRG---------VGKTA----- +--------------QRGLKGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000232.fa new file mode 100644 index 0000000000000000000000000000000000000000..35ba89d9e71deff72b4dc68e8293478862005e37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000232.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00087 +MTTNTPKNAHGSSAEGRD-AKDQAKDKAQQAAGEAQGQAKAVAQDAKDKAQDLAATAKHE +AGQVKDEAADQVQSLVGSAQEQVGAQVQTQQERFAGQVRSYTDDLHRVVSGEQPQTDLVR +QGVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRD +AVQPDSAA-STSPR----RHTTRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAG +PRRAAGVGDTPYGTQA-----PVQQGLTAERPFDQTRPGGDA +>GCF_003691675_PROKKA_02100 +MTTNTPKNAHGSSAEGRD-AKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHE +AGQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVR +QGVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRD +AAQPDSTA-STSPR----RHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAG +PRRAAGVGDVPYGTQA-----PVQQGLTAERPFDQTRPGGDA +>GCF_005280335_PROKKA_00304 +MTTNTPKNAHGSSAEGRD-AKDQAKDKAQQAAGEAQGQAKAVANDAKDKVQDLAATAKHE +AGQVKDEAADQVQSLVGSAQEEVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVR +QGVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRD +AAQPDAAA-PTAPR----RRDTRPEAVHADVTPHHLDSQAPAYSSDSLSQADGRVASGAG +PRRAAGVGDTPYGVEA-----PEQHGLTAERPFDRSQPGGRA +>GCF_020097155_PROKKA_00249 +M-------AKNHSARAADPQQSETRQKAEAAAGAAQDQAAGVAQDAKAHAQDLAQSAQQE +AVAVKDEAVQHAKSLAGSLQDQAAQQASTQQGRLAEQSRGITDDLHRLLSGEQPQGDAVR +QAVAAVADRAETLTQRLETAQPMDLVDDVRRFAARRPGTFLAIALGAGVLAGRMTRGVRD +ASQDGPASLSSAPRTPQHRRELEPQGVQADVTPHHLDSQIPAHTGDDAPRPVSDTAAG-- +---------LPYGTEPLPTIDPLTGEPVAEDPYDQTRDGGRA +>GCF_023573625_PROKKA_00082 +MTTNTPKNAHGSSAEGRD-AKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHE +AGQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVR +QGVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRD +AAQPDSTA-STAPR----RHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAG +PRRAAGVGDVPYGTQA-----PVQQGLTAERPFDQTRPGGDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000235.fa new file mode 100644 index 0000000000000000000000000000000000000000..490da699e8a60aac90c3fc04c414a40b7d4032c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000235.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00090 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPA-LRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALS +SRNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRD +TFAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP +>GCF_003691675_PROKKA_02103 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPA-LRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALS +SRNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRD +TFAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP +>GCF_005280335_PROKKA_00301 +MTPLDRVPDRTPVPPRTGLTLEDQVPE-----AGG--TRPRLTTTKADFRAAVAELVGRA +AAEDPGEEVSVGLVPTMGALHGGHAALARQARSENDVVAASIFVNPLQFGDRADLEHYPR +TLEADLDLLGAVGVDVVFAPSVDEMYPGHPDAPIVSVSAGRMGEVLEGASRPGHFDGVCT +VVAKLWNLSMPPAPAVLRSYFGQKDAQQLAVLRRLAHDLDVAVDVRAVPIVRSPEGLALS +SRNTRLDEAGLHAALVLNRALTRLEEAAVAGRVLDVQAAREEVAAEPGVTLDHLVVVDRE +TLEELGAELLCQPLRRDALALVAAHVPPVRLIDNRVLPAAGPLP +>GCF_020097155_PROKKA_00246 +MTPLDRTPDRRPVPAGTGLTLEDALPV-----ADG-ARRPRLARTVAEARAALRELTAAA +GQERGGAPVVVGMVPTMGALHGGHAALIRQARAENDVVVASIFVNPLQFGDPADLENYPR +TLEADLDLLGAAGADLVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGVSRPGHFDGVVT +VVAKLWNIVRPAVPA-LRSYFGQKDAQQLAILRRLAHDLDVDVEVRAVPIVRSPEGLALS +SRNTRLDADGLEHALVLSRALRALVDAAEAGEPIDVRAARQMVSDEPGVTLDHLVVVDRE +TLEELGPELLCQPLRREALALVAAHVPPVRLIDNMVLPAAGPLP +>GCF_023573625_PROKKA_00085 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPA-LRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALS +SRNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRD +TFAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000239.fa new file mode 100644 index 0000000000000000000000000000000000000000..d1e83ae19fbe60b53ce06d3c24607e1dfc1119f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000239.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00094 +MAD------------GAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSP +ALSVGAMKAFMMLANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSA +LLSASPEGLARLDAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAES +E +>GCF_003691675_PROKKA_02107 +MVD------------GAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSP +TLSVGAMKAFMMLANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSA +LLSASPEGLARLDAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAES +E +>GCF_005280335_PROKKA_00297 +MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP +GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA +LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA +G +>GCF_020097155_PROKKA_00242 +MAD---PADHGSDGRGT--GADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHP +GLPLGAMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSA +LLTATDEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACR +P +>GCF_023573625_PROKKA_00089 +MAD------------GAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSP +ALSVGAMKAFMMLANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSA +LLSASPEGLARLDAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAES +E + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000240.fa new file mode 100644 index 0000000000000000000000000000000000000000..27ac236394e66f17609887e8477aaf9c34a1a3f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000240.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00095 +M---------------------TPTSPAPEAVAPA------GAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVV +STSMPVIIHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTHDPTFLIVCRTVQG +LGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPH +RERQKVSIDYLGIVFLTAATALLLIWVTSAGRDFDWASTTSAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLA +TIASIATGLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVIGAVLLIAGTALLG +TLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASSGVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERR +ADLAAALRSLGPDAAEWSESLQSSTLPRVAEMPDSLRVIFEDVYAQGIALAFLVAVPLAIVALIAILFLPNLPLGRMTTS +ERLHATRADLATHATAEAMQTLPATGPIPVVTAAQG-----------------------QHPAEDPEESRSVSAERPATA +-----VADRPVVPA-------------------ALAVAGTALLAAVVTALVRARRG +>GCF_003691675_PROKKA_02108 +M---------------------TPTSPAPEAVAPA------GAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVV +STSMPVIIHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTHDPTFLIVCRTVQG +LGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPH +RERQKVSIDYLGIVFLTAATALLLIWVTSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLA +TIASIATGLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVIGAVLLIAGTALLG +TLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASSGVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERR +ADLAAALRSLGPDAAEWSESLQSSTLPRVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTS +ERLHATRADLATHATAEAMQTLPATGPIPVVTAAQG-----------------------QHPAEDPEESRSVSAERPATA +-----VADRPVVPA-------------------ALAVAGTALLAAVVTALVRARRG +>GCF_005280335_PROKKA_00296 +MIDHRQSLTAVNHSDDPAEGPHEPHLPAVAGTAPA------GAPSLERAAADAARHRAVLQALTGLLLGMFVSMIANTVV +STSMPVIISDIGGNQNDYTWVITAALLATAVSTPVWGKLADLMDRKMLFQVALVIFVGASAAAGFTNDPTFLIVCRVVQG +LGGGGLAALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFALVALVMVQRTLHLPA +REPRKVSIDYLGIVLLGVATSLLLIWVTTAGQQFPWASWTTAWMVGGAVLAAALFVVVELKVTEPLIPLTLFRNRTFTLA +TIASIATGLAMFGAGVYLAQYMQLARGATPTQAGLMTIPMIAGLLITSTVIGRVITRTGVWKRWLIVGAVLLTAGMALLA +TLHYDTPFVLVSLHMLLLGAGVGMTMQNLVLVVQNTTDPRQMGVASSGVTFFRSLGGSVGVAAMGAVVANVVPSRFEARG +ADLAAALQSLGADGPVWAQRLQSGTLPRVAEMPEPLRVVVEDVYATGISQAFLVGVPLAVVAVVAIVFLPNIPLGRMTTS +ERLDASRADLATVTAPAAMQKVPATGEIPVVAPAAGGAGGTDDACTAEDADGTEGVPAAQGPTTAPAEPTAERAERPAVQ +PAAESVPARVVAPAAAAPSTAAASGRSGGARPGARAAAAVALLTAIAVLMRQARRG +>GCF_020097155_PROKKA_00241 +M---------------------STTTAPPATAGPAAVGNSPAVPSLERAADDAARHRTVLRALTGLLLGMFVSMIANTVV +STSMPVIISDIGGDQTAYTWVITAALLATAIATPIWGKLADLVDRKVLFQVALVLFVAASAAAGFTTDPTFLIVCRVIQG +LGGGGLAALSQVIMADIISPRERGRYAGLFGAVMAVATVGGPLAGGIITDLWGWRWNFFVSLPFALVALVMVQRTLHLPA +RESRKVSIDYLGIVLLSTATALLLIWVTNAGHQFDWASATTAWMLGGAALAAVLFVVVELTVAEPLIPLTLFRDRTFTLG +TIASIATGLAMFGASVYLSQYMQLARGATPTQAGLMTIPMIVGLLVSSTVIGGVITRTGVWKRWLVIGAVLLIAGAAMLG +TLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASSGVTFFRSLGGTIGVAVMGAVVANVVPDQVEQRR +TDIGAALASLGPAGAEWAQRLQSGSLPRVAEMPDALRVIFEDVYATGISQAFLVGVPLAVVALAAILFLPNIPLGHMTTT +ERIDAERADLATVSVPQAMQTLPATGSTPVVAQAQV-----------------------QEAAPASTTTTPAPAARALRV +PA--GLRERRIAPA--------GTGRSTAWRATASALAAGAAAAAFVPLLRRSRRG +>GCF_023573625_PROKKA_00090 +M---------------------TPTSPAPEAVAPA------GAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVV +STSMPVIIHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTHDPTFLIVCRTVQG +LGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPH +RERQKVSIDYLGIVFLTAATALLLIWVTSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLA +TIASIATGLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVIGAVLLIAGTALLG +TLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASSGVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERR +ADLAAALRSLGPDAAEWSESLQSSTLPRVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTS +ERLHATRADLATHATAEAMQTLPATGPIPVVTAAQG-----------------------QHPAEDPEESRAVAAERPATA +-S--PVAGRPVAPA-------------------ALAVAGTALLAAVVTALVRARRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000241.fa new file mode 100644 index 0000000000000000000000000000000000000000..a9e92362aa5ce2cc823d3e6b21cf59356aa13a39 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000241.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00096 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH +REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN +TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEAPALVNPEVRG +>GCF_003691675_PROKKA_02109 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN +TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEVPALVNPEVRG +>GCF_005280335_PROKKA_00295 +MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD +VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE +GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN +TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA +AMAELTARNAIAMATGGEVPALVNPDVRR +>GCF_020097155_PROKKA_00240 +MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD +LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE +GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH +REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN +TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA +AMAELTARNAIGMATDGEAPALVNPEARG +>GCF_023573625_PROKKA_00091 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN +TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEVPALVNPGVRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000245.fa new file mode 100644 index 0000000000000000000000000000000000000000..a2b3940b1773e24954fdafdc6ce06d1ec9914291 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000245.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00101 +-MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGD----E +GEQQA +>GCF_003691675_PROKKA_02114 +-MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGD----E +GEQQA +>GCF_005280335_PROKKA_00289 +-MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGE--KNE +GEQQA +>GCF_020097155_PROKKA_00235 +MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE +GEQQA +>GCF_023573625_PROKKA_00096 +-MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGD----E +GEQQA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000247.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bda9ff1f5f78a9caa94fd5e479ec9ef18a54b1d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000247.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00103 +MPAPAPLVPPTVDVPHLHDAMLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAVVGRHDGRVPADPA +ALRALPGIGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR +DDDGGLTFPA +>GCF_003691675_PROKKA_02116 +MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA +ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPARANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGRLGSHRPDDAQWARCVAGLVSDGLLAR +DDDGGLTFPD +>GCF_005280335_PROKKA_00287 +MPAHETAVPPSVDVPRLHDAVLDWFAVHARDLPWRSPDCPPWGVLVSEIMLQQTPVARVL +PRWHAWLERWPTAADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHSGEVPADPA +ALRALPGIGEYTAAAVSSFAFGLPETVVDTNVRRVIARAVGGQALPGRSLTRAEMRRAHA +LMPEDPDRAQAWNAGVMELGALVCTARSPACERCPLADACAWVAAGSPPPEQAPRGQAWA +GTDRQVRGAVMAAVREHGRVAGDGLRAVVVAGGRLGAHRPGDAQWERCVAGLLADGLLAR +DDDGALAFPS +>GCF_020097155_PROKKA_00233 +MPAHDD-AAPRPDLTALQDEVLDWFAAHGRDLPWRDPDCPPWGVLVSEIMLQQTPVVRVL +PRWRAWMERWPTPADLAAAPTADVLTAWDRLGYPRRALRLQEAARAIVERHGGEVPADPA +ALRALPGIGEYTAAAVSSFAFGIPETVVDTNVRRVLARALRGEGLPGRTLTRAEMAAAHA +ALPADEHRANRWNAAVMELGALVCTARSPACDRCPIRARCAWVAAGSPAPEVARRGQAWV +GTDRQVRGAVMAAVREHGRVPRGGLREAVDGTGRLGAHTPDDAQWERAVAGLLGDGLLVA +HDDGALAFPA +>GCF_023573625_PROKKA_00098 +MPAPAPLVPPTVDVPRLHDAVLGWFAVHARDLPWRSPDCSPWGVLVSEIMLQQTPVVRVL +PRWREWLERWPTPADLASAPTADVLTAWDRLGYPRRALRLQEAARAVVERHDGRVPADPA +ALRALPGVGEYTAAAVASFAFGVPETVVDTNVRRVIARAVAGEALPGRSLTRAEMRRAQA +LMPEDPTRANAWNAAVMELGALVCTARSPACDRCPLAETCAWVAAGSPPPVEVPRGQAWA +GTDRQVRGAVMAAVREHGRVAEAEVPAVVVAGGWLGSHRPEDAQWARCVAGLVSDGLLAR +DADGGLTFPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000251.fa new file mode 100644 index 0000000000000000000000000000000000000000..0ac3de665e50cdf9d946a6cc0dde1236299c59af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000251.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00108 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +---GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGF +VIDLLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVL +AVMVLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGR +ALGETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIIT +LAVNMIARAIVNKHKEFSGAN +>GCF_003691675_PROKKA_02121 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +---GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGF +VIDLLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVL +AVMVLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGR +ALGETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIIT +LAVNMIARAIVNKHKEFSGAN +>GCF_005280335_PROKKA_00282 +MTSPATEAPPRATTLKSSRGGAAGDKVFSGLSLAAGVLILLTLAFVAIFLVVRSLPALFP +DAYGTQLKSADTFFQYVWPLMAGTIMAAVIALLLATPVAVGVALFISHYAPPKIAQPVGY +VIDLLAAIPSVIYGIWGWLTLAPVMVPIYQWLNEYLGFIPFFGGPVTGTGRVIMTSGVVL +AVMILPIITALCREIFRQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSVMLGLGR +ALGETMAVTLVLSAGGFSLSLIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT +LVVNMTARWIVNKHKEFSGAN +>GCF_020097155_PROKKA_00223 +MSHTATEAAPSSSALKSSRAGAAGDKVFSGLALAAGVLILLILAFVAIFLVSEAWPALFP +-AEGANLESGDSFWGYVWPLMAGTVMAAIIALLLATPVAVGVALFISHYAPPKIAQPVGY +VIDLLAAIPSVVYGIWGWLTLAPLMVPIYEWLNEYLGWLPFFGGSVTSTGRVLMTSGIVL +AVMVVPIITALCREIFSQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGR +ALGETMAVTMVLSPGKFSPSVIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT +LVVNMVARWIVNKHKEFSGAN +>GCF_023573625_PROKKA_00103 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +---GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGF +VIDLLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVL +AVMVLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGR +ALGETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIIT +LAVNMIARAIVNKHKEFSGAN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000252.fa new file mode 100644 index 0000000000000000000000000000000000000000..13842f8310cc56f1c599fe725e8d82717cbcec87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000252.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00109 +MSTV--STSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGA----- +-FNVVGFVIIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVL +SAGLPTLIANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLI +SVPIGMLTSIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKS +TALQSVQMGLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLP +TAISGIASGVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSP +TAADPSTARAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR +>GCF_003691675_PROKKA_02122 +MSTV--STSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGA----- +-FNVVGFVIIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVL +SAGLPTLIANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLI +SVPIGMLTSIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKS +TALQSVQMGLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLP +TAISGIASGVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSP +TAADPSTARAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR +>GCF_005280335_PROKKA_00281 +MSTAIDDVSTRQDTPPSKHRQNSLTAGQKPGWVWMAIAAAAVLLGLGIEALLSGAAPFSE +DFSLARFVVLAGVLYIAGMYLVTRVMENRRRASDGLWKNLVWTAFLIALVPLVSVIWTVL +EGGGPTLLSNPQVLWNDMDGVTGATDAAYDQAGSPAGGLPGGFAHALIGTLVITIIATLI +AVPIGLLASIYLVEYGRDGWLSRAITFFVDVMTGIPSIVAGLFAYAAMTVLLELIMGPGP +AALQAVKMGFTAAVALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP +TAISGIASGVTLAIARVTGETAPILVTAGYAMTTNWNAFDNWMTALPVYIYRQIVSPTSP +TAADPSMARAWSAALVLIFIVMALNLLARVIAKAFAPKTGR +>GCF_020097155_PROKKA_00222 +MSTALNDTPTRENTPASKHTQNSLTAGQKPRWTWMAVAAGAVVLGLGLEALLAGGFA--- +DFSIARFIILAAILFVAGMYVATRVLENRRQATDGLWRNLVWAAFLIALVPLISVLWSVV +ADGGATLFGNPQLLVNDMQGVTGVTDAQYVQAGEPMGDLPGGFAHALVGTFLITVIATVI +AVPIGLLTSIYLVEFGRDGWLSRAIIFFVDVMTGIPSIVAGLFAFAAMSVVLEMVMGSGP +KALQSVKMGLTAAIALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP +TAISGIASGITLAIARVTGETAPILVTAGFASAVNWNPFDNWMTALPVYIYRQLVAPTSP +TAMDASTSRAWAAALVLIIIVMVLNLLARIVAKAFAPKTGR +>GCF_023573625_PROKKA_00104 +MSTV--STSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGA----- +-FNVVGFVIIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVL +SAGLPTLIANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLI +SVPIGMLTSIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKS +TALQSVQMGLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLP +TAISGIASGVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSP +TAADPSTARAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000255.fa new file mode 100644 index 0000000000000000000000000000000000000000..539cbfcfb940fba754cafbaacbf6f67a5e311894 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000255.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00112 +MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA +TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE +TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR +EVAWALHAALEALSRVNMDLGMVLVRES +>GCF_003691675_PROKKA_02125 +MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA +TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE +TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR +EVAWALHAALEALSRVNMDLGMVLVRES +>GCF_005280335_PROKKA_00278 +MSPRMPWPVTRDTPALRHIVDLAEALRRSVHLVAQVAGARGPEADRTARELEDLDAASTA +SLMSFLTALRSAYVTPLPRQDLYRLAGGVHAATQRVVSAGVLIQRADLEHLPAHALDVLE +TVGRQAELLGRSTTELRDLDALEATWMQLLRASRRTERIMVQWLADLGMDLLQRDFNRQR +EVAWALQSALEALGRVNTDLGMVLVRES +>GCF_020097155_PROKKA_00219 +MTPRPAWLVTRDSPALGHLTDLCDTLGRAVRAVAQAVAADGSERDRVERDLSALDAAATA +ALMAFLTALRSAYVTPVPRPDLYRLADGVKTAAHRVVGAGVLVHRADLDALPRNAVELLE +TLGRQAELLAHGTRQLRDLDALEDTWMQLERGIRRMERLMVDWLAALGTDLLQRDYNRQR +EIASALRDAVLALDRVNTDLGVVLVRES +>GCF_023573625_PROKKA_00107 +MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA +TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE +TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR +EVAWALHAALEALSRVNMDLGMVLVRES + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000256.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0f41c8d5e64243566b15b3d7ffbdcc159387b7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000256.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00113 +MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW +YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV +EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD +>GCF_003691675_PROKKA_02126 +MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW +YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV +EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD +>GCF_005280335_PROKKA_00277 +MARHRQTTGRGASSSASGLVRPHRPRLSEPDELAHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPEVVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATARDGERWAAW +YRAGHAAHAARAVAGAVEPPGPDELRRLTDTILTGAYRSEIDVAFERAGAYGRVVALGQV +EHAEAAEAADPALAAGLTRRAARLVSTSEALEEAARAFRNGSLD +>GCF_020097155_PROKKA_00218 +MAHHRAPAGRGASSTASGLVRPHRPRLTDPGLIADLADGEDPQEIAAAASRLAHALVAGG +RAEEDPDVVARLVGLVREVGVETLAGLWADAPAVSLAGALWRLYALQEATARDGERWAAW +YRAGHAAHAARAVAGAVEPPGPEELRRLTDTILTGAYRSELDVALERAGAYARVVALGQA +EHAAAAEHADPAHAARLTLRAARMISTAEALEAAARSWRDGSLD +>GCF_023573625_PROKKA_00108 +MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW +YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV +EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000258.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2b2d53ef826d2e215b2a9e1407110506013fa54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000258.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00116 +MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH +PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA +QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPY----DPQSSLNAL-- +AGTASGT----GISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGK +AVMENAAELFGPLPMVIPGEIREGVAQGRAGGES--AGAKDDGGVLGAIRRALPGGKDEK +DDRQKKGKPAA +>GCF_003691675_PROKKA_02129 +MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH +PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA +QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPY----DPQSSLNAL-- +AGTASGT----GISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGK +AVMENAAELFGPLPMVIPGEIREGAAQGRAAGES--EGTKDYGGVFGAIRRALPGGKDEK +D------KPAA +>GCF_005280335_PROKKA_00271 +MAKNSMIGRYTSGKVKDFALKSALDENGEPTEGFEKVVSKVLGIQRPLVLKHIQNVAAKN +PELTAEQIAERLGQQYLNTVTGAGAAVGGTAIVPGVGTVAALGLSAAATVGFMEATALYA +QSLAELHGITMEDPQRAETLVMALMLGDDAKELLREAAAKAGRPF----DPNASLNAL-- +AGSAAGTGGGAGISAFVMDRLKRTFMKKMLVRQGAGFLGRAVPFGVGAVIGGVGNRAMGK +AVMENAQELFGPLPTVIPGEIREGAA--RQAQED--DG---EGGVFAAIRRALPGGDDKK +D------AAKA +>GCF_020097155_PROKKA_00203 +MAKNSIIGRYASGKAKDFAMKSAFDENGNPTEGFEKLVFTTLDIQRPLVLKNIQRLHESH +PGETPEQLAERLADQYVTASTGAGAAVGGTAIVPGIGTVAALGLSAAATVAFLEATALYA +QSLAELHGLTTKDPARSKALVMAVMLGDDTKELLKDISRKSGVKNTGTPDSAAGLAAMMN +GGAAGQAAGGAGLGAVAIEQLKKQFVKKVLVRQGAGFLGRAVPFGVGAVIGGVGNRAMAK +AVVKNSRDLFGPLPAQIPGEIVAASAKGQDVGQSAEDG---KGGLVSGLIKALPLG--KK +D------EKKA +>GCF_023573625_PROKKA_00121 +MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH +PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA +QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPY----DPQSSLNAL-- +AGTASGT----GISAFVVDRLKRTFMRKMRLRQGAGFVGRAVPFGVGAVIGGVGNRAMGK +AVMENAAELFGPLPMVIPGEIREGAAQGRA------DGTKDDGGVFGAIRRALPGGKDEK +DDRQKKGKPAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000260.fa new file mode 100644 index 0000000000000000000000000000000000000000..6812fdfdd4dab7dbd2681b488c8b2e5a6a1f3f46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000260.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00122 +MATR-------ADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLV +ATLTAGSRYGYMLLWAVILGVIFKIVLVEGVGRWYLSTGKTIFQGWRSLGSWTSWYFGPY +ILIWGFVYGATAMSSAALPLAALFPGVDMKVYAIGLGLVGLGLVWLNRYGLIEKLMAVLI +GVMFLTVLLSAALTAPNVGDILAGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYAYWL +REKGWNVPKYMRVMKFDNATSYILTGIFVIATMIMGVELLHSAGLAISSGDRGLLDVGNV +LAERYGQAYSVVFLVGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS +KPGRFFLLWLTFPPMTLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNKKEVPAQFRN +GWIRNTLLGLTAAVFVAIGVNELWKALQPLIGG +>GCF_003691675_PROKKA_02136 +MAHA-------VDPGRPVHNPDIVGFTDAELNETPIRPRWNSLGPGIVAAATGVGAADLV +ATLTAGSRYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPY +ILIWGIVYGATAMSSTALPLAALFPGVDSKVFAIASGLIGLGLVWLDRYRLIEWLMTVLI +GVMFVTVLLSAALTVPNLGAILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWL +REKGWNVPKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDV +LAERYGSAWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSS +KPGRFFLLWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRN +GWVRNTLLGLTAAVFVAIGVNELIKALQPVLGG +>GCF_005280335_PROKKA_00263 +MPHT-------ADRGHPVHNPDIVGFTEAELNETPIKPRWNSLGPGIVAAATGVGAADLV +ATLTAGSRYGYMLLWAVVLGVIFKIVLVEGVGRWYLSTGKTIFQGWRQLGSWTSWYFGPY +ILIWGFVYGATAMSSTAIPLAALFPAVDAKVFAIAAGLIGLALVWLNKYGLIEKLMTALI +GVMFVTVLISAALTAPNVGEILSGLVPRIPSGDPQVMFYVLGLAGGVGGTITLGAYAYWL +REKGWNVPKYMKVMKFDNATSYVLTGIFVIATMIMGVELLHSAGLAISSGDKGLLDVGNV +LAERYGQVWSYVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS +KPARFYLLWLTILPMSLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNRKDVPVQHRN +GWIRNILLGLTAAVFVAIGVNELIKALQSVLGG +>GCF_020097155_PROKKA_00197 +MSHTTPPGHGLVDRHHPVHDPDIVGFTEAELNETPIKPKWNSLGPGIVAAATGVGAADLV +ATLTAGSRYGYMLLWAVVLGVVFKIVLVEGVGRYYLSTGKTIFQGWRGLGSWTSWYFGPY +ILIWGFVYGATAMSSTALPLAALFPGVDSKVFAIASGLVGLGLVWLNRYGLVEKVMTVLI +GVMFVTVLISAALTVPNLGDILGGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYGYWL +REKGWNTPKYMRVMRFDNTVSYVLTGVFVIATMIMGVELLHSAGIAISSGDKGLLDVGDV +LAQRYGDVWATVFLIGFFAASFSSVIGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS +KPGRFYLLWLTFPPMVLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNSRRVPGKFRN +GWVRNVLLALTTAVFLVIGGNELLKALKPLIGG +>GCF_023573625_PROKKA_00130 +MATR-------ADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLV +ATLTAGSRYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPY +ILIWGIVYGATAMSSTALPLAALFPGVDSKVFAIAAGLIGLGLVWLDKYRLIEWLMTVLI +GVMFVTVLLSAALTAPNLGEILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWL +REKGWNVPKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDV +LAERYGSAWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSS +KPGRFFLLWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRN +GWVRNTLLGLTAAVFVAIGVNELIKALQPVLGG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000261.fa new file mode 100644 index 0000000000000000000000000000000000000000..bebe44e8b848062fd6b0ebc4e6ed88ede13555f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000261.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00123 +MIVAFSVAPSGQPADSAHLP-GDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDW +DEVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR +------ +>GCF_003691675_PROKKA_02137 +MIVAFSVAPSGQPADSAHLP-GDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDW +DEVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAP +HDGDAG +>GCF_005280335_PROKKA_00262 +MIVAFSVAPSGTPADAAHQP-GDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDW +DEVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS------ +------ +>GCF_020097155_PROKKA_00196 +MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW +DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALT--DGTPATPDR +FRA--- +>GCF_023573625_PROKKA_00131 +MIVAFSVAPSGQPADAEHLP-GDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEW +DEVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAP +RDGDAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000262.fa new file mode 100644 index 0000000000000000000000000000000000000000..bb5d00e95a0ff3f98e6a45934c20b37fdddfdf88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000262.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00124 +--------------------MAVTVRPATSDDVEPLLRVKAQAWREAYGGLLPAAHLDAV +DAGVPEQVPGWAALVGS-DRELWVA--DDGGRLLGMALAGPRRSQG-------------- +GGLPDLELMALYVLAEAYGTGLGALLLDAVVGKRPAVLRVLAENPRAVAFYAKHGFAPEG +GPEPMTGPWAGLHEQLMVRR-------G +>GCF_003691675_PROKKA_02138 +M---------------P---ESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAI +EARIPEDVPAWTALIGP-DRDLWVA--DDGGRLLGVALAGPRRSAAETGRTGADDAAASP +ADLPDVELMVLYVLAEAYGTGLGARLLDAVVGERPAMLRVLAENPRAVAFYAKHGFAAVG +APEPMTGPWAGLHEQLMVRRRPHDGGAA +>GCF_005280335_PROKKA_00261 +--------------------MAVVVRPARREDAEALLRVKAQSWREAYGAHLPAEVFDRA +DARVPQDAPAWAALVGS-DRDLWVAEDDDGGRLVGVALAGPSRIED-------------- +EGLPPRELMVLYVLAEAHGTGVGARLLDAVVGDGPAVLDVLAENPRARAFYAKHGFEDHG +APAPMDGAWAGLHEQRMVRR-------G +>GCF_020097155_PROKKA_00195 +MRETDGASDAVVRDVNPPSAPAPTVRPAGADDLPAVLAMKNAAWRETYAHLLEPGFLAAQ +EAELPRAVEAWTRLLGEPGMEVWLA--EGAGVVVGMAAAGPADDPA-------------- +LGPEGRELIALYVRARLHGAGLGAALLRAAVGGRPARLDVLVGNERAIAFYERHGFVAVG +EPAVLGGPWGDAREQRMVRR-------- +>GCF_023573625_PROKKA_00132 +M---------------P---ESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAI +EDRIPEDVPVWTALIGS-DRDLWVA--DDGGRLLGVALAGPRRSAAETGRTGADDAAASP +ADLPDVELMVLYVLAEAYGTGLGARLLDAVVGDRPAVLRVLAENPRAVAFYAKHGFASVG +APEPMTGPWAGLHEQLMVRRLPHDGGAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000263.fa new file mode 100644 index 0000000000000000000000000000000000000000..125cf4efde98c1e0dd17f36dbae313a2c6b06738 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000263.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00125 +MSRRSGRSSGRSSAASSSSRGSAARRGR----AAEPEGIVPGVHEISHGTAEIREDPYEP +GAFVLYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHW-PEPTPLRALHLGGAGCALAR +WVDHAHPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIR +DVFAPDPTDLTG----ARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRAD +VAAVVAAFEHVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRM +DAFPARLAEDPRGFPAGVAPGITGLVPGPEA--------------- +>GCF_003691675_PROKKA_02139 +M-----------------SRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEP +DAFILYVNGVESSPLDPERPERMAFEYMRWAAAAVRAHW-PEPTPLRALHLGGAGCALAR +WVDHAYPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIR +DVFAPDPTDLTG----ARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRAD +VAAVVAAFEHVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRM +DAFPARLAEDPRGFPAGVAPGITGLVPGPEA--------------- +>GCF_005280335_PROKKA_00260 +M-------------------------------------ITPGVFAISSGTAEILPDPWTD +GVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAHRFAPDAERLRVLHLGGAGCTFAR +WVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLKIRVGEAGQVLAGLREATREVVFR +DVFA--PADPLSLAPDSPHVTPAHLTGADAAAHAARVLVPGGVYVLNIGGGPDLASVRRE +VAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLA---AEELGG---RAALARALRS +DALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPAQ +>GCF_020097155_PROKKA_00194 +M-------------------------------------ITPGTFPISSGTAEIVPDPWTD +GVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTHRFAPDA-RLRVLHLGGAGCTFAR +WVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKIRVGEAGEVLAGLRDATREVVFR +DVFAPDPADPTG----ALHVTPAHLTGLDAAAHAARVLTPGGVYLLNIGGGPDLTSVRRE +VAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLS---ADGLGG---RSALARALRS +DALPAQLLDDVVAFTAGLTPDATPLVTPAEG--------------- +>GCF_023573625_PROKKA_00133 +M-----------------SRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEP +GAFILYVNGVESSPLDPERPERMAFEYMRWAAAAVRAHW-PEPTPLRALHLGGAGCALAR +WVDHAYPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIR +DVFAPDPTDLTG----ARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRAD +VAAVVAAFEHVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRM +DAFPARLAEDPRGFPAGVAPGITGLVPGPEA--------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000266.fa new file mode 100644 index 0000000000000000000000000000000000000000..497bffb69ff68f0a1708ec3f9392b56155162843 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000266.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00131 +MPDSPSA-------RATGGETALVVIDVQHSYFEHPALAAQQA-ELTAAVVELLRTAREA +GRPVFLVRTEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSA +FHGT-GLAAELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIAS-EEPALA +AAMLDFLRDEMRQPLLGQDEALTLLRTGLVPD----------RG +>GCF_003691675_PROKKA_02145 +MPDSPSA-------RATGGETALVVIDVQHSYFEHPALAAQQA-ELTAAVVELLRTAREA +GRPVFLVRTEHARDRSTWTLNMLADGEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSA +FHGT-GLAAELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIAS-EEPALA +AAMLDFLRAEMRQPLLGQDEALTLLRTGLVPD----------RG +>GCF_005280335_PROKKA_00254 +MPDSAPAPEPIAGERPSGGETALVVVDMQYSYFEHPDLAARQA-ELTEAVVELVRTAVEA +GRPVVLVRTEHERDRSTWTLNMLEDGEGFAFPGTRQAAVLDEVARAARGAVEVVKTRDSA +FHRT-DLDAQLRRRGVGRLLLCGVSTHSCVFQTATDAFARDFHAATAVDAIAS-EDPRLS +AAMLEFLRDEMRQPLLGREDALALLRTGLVPD----------QG +>GCF_020097155_PROKKA_00651 +MNTLQNP--------------ALIVVDVQRGFDDVEYWGSRDNPDCETNISSLLTHWRDR +SWPIVFVRHDSTNPESTLAVGT---------PGNEFKEVITG----DPDLL-VSKTVNSS +FHGTPDLDDWLRAEGIEQVVICGITTNHCCETTARIAGNLGYDTYFAIDATHTFDRPALD +GTVLPAATVSAMTAANLHGEFATVVSTRTLIDGNSYAPRYEQEK +>GCF_023573625_PROKKA_00139 +MPDSPSA-------RATGGETALVVIDVQHSYFEHPALAAHQS-ELTAAVVELLRAAHEA +GRPVFLVRTEHARDRSTWTLNMLADDEGFAFPGTRQAALLDGVAAAAPDAVEVVKTRDSA +FHGT-GLAAELRGRGVDRLLLCGVSTHSCIAETATAAFALDFHAAIATDAIAS-EEPALA +AAMLDFLRDEMRQPLLGQDEALTLLRTGLVPD----------RG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000267.fa new file mode 100644 index 0000000000000000000000000000000000000000..52807b84dd99c86fd1b86f6078fe7d71a4518be6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000267.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00133 +MSDPTPPSTEPMIPEQPGNHPSS-------ATAPDAGV---APATSAAAGRDRV-LLPWVFWPSAVIVLSFVGATLLAPA +QMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEKPEFSTLSWFSLLFAAGMGIGLVFFGMTEP +LMHFTSPRPDLAAANPTQAEAAQSALATTFLHWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGH +LIDNIALIGTVFGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSNTNLILAAGL +LLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRE +FIAGVLLVPTLVCVVWFGILGGTAIFLETTRPAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSA +DSGSLVMGMLATGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRSLGYSVARVE +AVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAAAGVPASE----------GPRRPRLRRHE- +--H +>GCF_003691675_PROKKA_02147 +MSDPTPPSTEPMIPEQPGNHPSS-------ATAPDAGV---APATSAAADRDRV-LLPWVFWPSAVIVLSFVVATLLAPE +QMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEKPEFSTLSWFSLLFAAGMGIGLVFFGMTEP +LMHFTSPRPDLAAANPTQAEAAQSALATTFLHWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGH +LIDNIALIGTVFGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSNTNLILAAGL +LLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRE +FIAGVLLVPTLVCVVWFGILGGTAIFLETTRPAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSA +DSGSLVMGMLATGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRSLGYSVARVE +AVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAAAGVPASE----------GPRRPRLRRHE- +--H +>GCF_005280335_PROKKA_00252 +MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAV---APASSDAATGARV-LLPWVFWPSTIVVLLFVGATLLFPE +PMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAITLGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEP +LMHFVSPRPDLAATDPNPAQAAQAALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGH +LIDNIALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVERGMKWLSNVNLVLAAGL +LLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQ +FLAGVLLVPTLIGVVWFGVLGGTAIYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSA +DSGALVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVMCLATFRSLGYSVARVE +AVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQRTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR--- +--- +>GCF_020097155_PROKKA_00188 +MT-PAPAGRD----------ADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLFVVATLAFPA +QMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEKPEFSTMSWFALLFAAGMGIGLVFFGMTEP +LMHFTSPRPDLAAANPTEAQAAQSALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGH +LIDNIALIGTVFGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSNINLVLAAGL +LLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWTAYYWGWWMSWTPFVGIFIARISRGRTVRE +FLMGVLLVPTLVCVVWFGILGGTAIWLETVRPAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSA +DSGALVMGMLATGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRSLGYSAARVE +AVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLASPGPDDEIRLH-EDATATSARPDTTRGGS +TAR +>GCF_023573625_PROKKA_00141 +MSDPTPPLKNPLDPERADTRPSS-------APTADGAV---APATSAAAARDRV-LLPWVFWPSAVIVLSFVGATLLAPE +QMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEKPEFSTLSWFSLLFAAGMGIGLVFFGMTEP +LMHFTSPRPDVAAANPTQAEAAQSALATTFLHWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGH +LIDNIALIGTVFGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSNTNLILAAGL +LLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRE +FIAGVLLVPTLVCVVWFGILGGTAIFLETTRPAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSA +DSGSLVMGMLATGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRSLGYSVARVE +AVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAAAGVPASE----------GPRRTRLRRHG- +--H diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000268.fa new file mode 100644 index 0000000000000000000000000000000000000000..edc327a86e4839b76a560e34562bef0f0e2f4ade --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000268.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00135 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD +VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNW +ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF +TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV +ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPTRGVLAFTVTSGGGRHLGSGEPIPAR +TVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDAAAWLLMD +>GCF_003691675_PROKKA_02149 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD +VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNW +ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF +TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV +ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPTRGVLAFTVTSGGGRHLGSGEPIPAR +TVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDAAAWLLMD +>GCF_005280335_PROKKA_00250 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD +VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNW +ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF +TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV +ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPARGVLAFTVTSGGGRHLGSGEPIPAR +TVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDAAAWLLMD +>GCF_020097155_PROKKA_00185 +MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLGVDAIWLSPFYLSPQHDAGYD +VADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHTSSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNW +ESTFGGGAWSRVTEADGTPGQWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT +RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVSPLPRTFRYVRPGEMHQAFNF +TYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTVRHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMI +ELALPGSAYIYQGDELGLPEHTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDAD----------AA +PWLPQPDSFRVLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRHLGSGVPIPAR +TVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR +>GCF_023573625_PROKKA_00143 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD +VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNW +ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF +TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV +ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPARGVLAFTVTSGGGRHLGSGEPIPAR +TVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDAAAWLLMD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000269.fa new file mode 100644 index 0000000000000000000000000000000000000000..22de27cf4c01fbbacb13ef29765847a125c2b801 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000269.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00136 +MTHDD--------------GGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAE +VEAEAAERARRRLARPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEE +TMLPRLHSAAIPPAARAMNRGRALVALEDEWGLSPDPDA-AVEDP-------QDEDGAPE +HHRVQTRTATWGVPHGWLTVFDPEEPVQRLVDGERTAYRRAPIVAARERAGHAAAVLARH +APDAELIGELTVMVEWLGAFHPDSWVELDYG-GLTRHVWPDDSVFDLWTLIDALEEGDEA +TAGVAQERLNRRWATVGMLARLT +>GCF_003691675_PROKKA_02150 +MTHDD--------------GGPPPGVARGTAHLRVFQPLATFPDAVQARLIAGGHRTRAE +VEAEAAERARRRLARPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEE +TMLPRLHEAAIPPAARAMNRGRALVALEDEWGLSPDPDA-AGQDP-------QDEGGAPE +HHRVQTRTATWGVPHGWLTVFDPEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARH +ALDAELIGELTVMVEWLGAFHPDSWIELDYG-GLTRHVWPDDSVFDLWTLIDALEEGDEA +TAGVAQERLNRRWAAVGMLARLT +>GCF_005280335_PROKKA_00248 +MVHDDGADGPAPGGGRVPGGAPPPGIAHGTAHLRVFQPLAAYPDAVQARLIAGAHRTRAE +VEAEAAERARRRLARPVTDPFPEPGEDDLVRVLQDEQGSAFYCPDEFGLRAEMAAAQLEE +TMLPLAYEAAVPTAARAMNRGRVLVALEEEWGLSPDPDA-DRAHPDEEDGPGRDEDGPSG +RHRVQTRTATWGVPHGWLAVFDPEEPVRRLVDGERTAYRRAPALAALERAGHAAAVLSRH +APDAELIAELTVMVEWLGAFHPDSHVELDYG-GLTRHVWPDDSVFDLWTLIDALGEGDEA +TAGVAQGRLNRRWAAVGMLARLT +>GCF_020097155_PROKKA_00182 +M-------------------------RTAAANLRVFQPLSAYPDAVAARMVAAAHRTRAE +VEAEAAERARRRLLRLPADPFPAPGEDDLVRVLE-RGGSAFYCPDELALRMEMAAEMLEA +SAPEALYAAAVPAAARAMNRGRALVALEDEWGLSPDPDAPAPDDP--QDAAHQDQDADAG +THRLQTRTSLWGVPHAWLAAFDPEEPARRLVDGEDVAYRRTPVAEAVERVGHAAAVLAGA +APDAELLGELAVMIPWLQAFHPDAVLELDYGRALTSLVWPDDSVFDLWTLLDALEEGDEV +GAGMAQERLNRRWARVGMHAHDG +>GCF_023573625_PROKKA_00144 +MTHDD--------------GGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAE +VEAEAAERARRRLARPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEE +TMLPRLHEAAIPPAARAMNRGRALVALEDEWGLSPDPDA-AGQDP-------QDEGGAPE +HHRVQTRTATWGVPHGWLTVFDPEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARH +APDAELIGELTVMVEWLGAFHPDSWIELDYG-GLTRHVWPDDSVFDLWTLIDALEEGDEA +TAGVAQERLNRRWAAVGMLARLT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000274.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3a00e8341af03eebc08ce65abab865ccd198fa2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000274.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00141 +--MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLA +VEDALAGGERAKLDRYGEDSFMVLHPARYIDRTETVEFGELSVFTGEHYVVTVRHAEEPD +LAAVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHV +SRRIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDE +ELSEQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNSALELDSTLASKRLAEQSIAQN +EQVKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRA +DWL +>GCF_003691675_PROKKA_02155 +--MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLA +VEDALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPD +LAAVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHV +SRRIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDE +ELSDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQN +EQVKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRA +DWL +>GCF_005280335_PROKKA_00243 +--MIDNAVYVDGRRVHAPSTLEDTWEAAEASGGMAWLGLYRPDADELRAVADELHLHPLA +VEDALEGGERAKLDRYGEDLFMVLH----------------------------------- +------------------------------------------------------------ +-------------FQHAIRALPVIVEQLQGGARARLREEEHRREV-GAPRTGDVHEWDQD +ELSEEGVFEVENLRRLRDVHDHAVQINERVAAMRQMLANALELDSTLASKRLAEQSIEQN +EQVKQISSWAAIIFAPQLVGSIYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRA +DWL +>GCF_020097155_PROKKA_00177 +MTLIDNAVYVDGRRVFAPTSLSDTWDAIERTGGMAWLGLYRPHPDELQEVADELPLHPLA +VEDALTPGQRAKLERYGDDWFMVLHPARYIDATETVEFGELDVFTGKDYVVTVRHAEEPD +LADIRAGMEQRHTDRLAQGPSQVAFEILDHVVDAYFPVAEGLEQDIREIEDQIFSGDAAV +SRRIYELSREIIGFERATRPLPRMIEQLQEDMRARLGDAANGSHASHL------EAPEPE +PGEEERAELVETLRALRDIHDHAVQVTDRVAAMRQMLENALELDSTLASKRLAEQSIAQN +EQVKRISSWAAIIFAPQLIGSVYGMNFQHMPELEWPLGYPWALGLMLGVAVALYALFKKA +DWL +>GCF_023573625_PROKKA_00149 +--MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLA +VEDALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPD +LAAVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHV +SRRIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDE +ELSDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQN +EQVKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRA +DWL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000275.fa new file mode 100644 index 0000000000000000000000000000000000000000..39b8c239d8b0fee3b969dee42fa0a80d7f2dc764 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000275.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00142 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR +>GCF_003691675_PROKKA_02156 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR +>GCF_005280335_PROKKA_00242 +MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA +GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA +-R +>GCF_020097155_PROKKA_00176 +M-SKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYA +GRTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDG +RR +>GCF_023573625_PROKKA_00150 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000276.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae6d14bdfef1e5140120f531ab13058991f0b752 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000276.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00143 +------------------------------------------------------------ +-------------------MAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM +VTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL +SAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAA-VP---- +>GCF_003691675_PROKKA_02157 +------------------------------------------------------MLDHYR +YWSLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM +VTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL +SAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAA-VP---- +>GCF_005280335_PROKKA_00241 +MGPGTSENSPETREKREEREGREEREVGVGPWEGPWPEDPRYDPELLRDGDRRNVVDGYR +YWTLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHVIGRRRWNRRGAM +VTDRYLHVRHHATVEEFTAWAAAEGLPVLGVDLFPESVPLESFELPRECVLVFGQEGPGL +SEEVRAASAAVLSIAQYGSTRSINAGVAAGIAMHAWVRQHGG-VPTSSS +>GCF_020097155_PROKKA_00175 +MGSGEGVDAREV-----------GREVGAPPWEGPWPEDPRYDPALLRDGDRRNVADRYR +YWTVEAIVADLDRTRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM +VTDRYLHVHHHETVEAFTAWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL +SEEVRAASEAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHGGPAPV--- +>GCF_023573625_PROKKA_00151 +M----------------------PREVGVGPWLGPWPEDPRYDPELLAHGDRRNVLDRYR +YWRLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM +VTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL +SAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAA-VP---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000279.fa new file mode 100644 index 0000000000000000000000000000000000000000..1cf875b129056ef83ea77f4d9d11210bdf91a65e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000279.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00147 +MDHGNGPPLVKNVTFFPKHVISSPVPSTVPRMMTRPLPEDSA----TVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGS +HLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAG +LEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDL +PHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQ +KRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQ +AFSRNDRFRAHAQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAW +GGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEER----------EG------ +>GCF_003691675_PROKKA_02161 +-------------------------------MMTRPLPEDSA----TVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGS +HLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAG +LEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDL +PHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQ +KRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQ +AFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAW +GGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEER----------EG------ +>GCF_005280335_PROKKA_00236 +-------------------------------MMTRPLPEDSA----TVDAVALGRRVRHLRKQAGLTLDQLADRTGVSGS +HLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAG +LEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAQRLLDAIGHTGGPLGLHAVSSLAEHLGFTLSFVANL +PHSTRSVTDLKHGRIHVSGGRASDHDRRTVVLQALAAAVLGHGEPRDYEDFLSQRVAVNYLAGALLMPQRPASALLRAAQ +KRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGLVFPADHTGAIEGQAACRRWGARQ +AFGRSDRFRAHTQYTDAPNGTYWCTSMVEHGPDGLFALSVGTAFEHARHFRGADTRHRITSTCPDPRCCRLPDPALEAEW +GGHVWPAARMHAHLLAAMPTQAFPGVDEVEVFEFLESQRDRTPGAPGADAPDGAGGVTP +>GCF_020097155_PROKKA_00821 +-------------------------------MAT---PTDPAHEPPRVDPLVLGRRLRHLRRVSGATLSDVAEKVGVTAS +HLSLVENGHREPRLTLLTALADVHGVGVEDLLTPEAPSRRAALEVAVERAQRGPLFQRLGLPALKIGPRTPDEVLEVIAG +LQAELDRQMAERVSTPEEARRANSALREEMRACGNHYADLERRAQELREAVDVADGPLTHHHVSALAEHLGFAVRFVPDL +PHSTRSVTDLKNRRIYLARARRPDHDPRAVLLQAVCSSVLGHGEPADYADFLRQRVYTNYLAAAMMMPERGTVRALREAK +ERRDLSVDDLRDRFGVSWESAAHRFTNLATEHLGLTCHFAKVHESGVFHKAYENDGIPFPTDHIGAIEGQTACRHWTSRQ +VFSVADHLGAFPQYTDTPAGTYWSAAVVEPTSTGFYSLTVGVPFDDAKWFRGRETSARTRSTCPDPKCCRLPSAELEAAW +GGQAWPAARANAHLLAAMPGGAFPGVEEVQVFEFLQTQESRWP-------PEGSGAA-- +>GCF_023573625_PROKKA_00155 +-------------------------------MMTRPLPEDSA----TVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGS +HLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAG +LEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDL +PHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQ +KRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQ +AFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAW +GGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEER----------EG------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000282.fa new file mode 100644 index 0000000000000000000000000000000000000000..11896b5940dd15ef28fd6b41861bc57bd5b51fd3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000282.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00150 +MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP +TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS +VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA +QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA +WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD +FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP +RPFQGAAREAAESQRAAEASASASASPSPTKSASASASPSPSTS-----------GD +>GCF_003691675_PROKKA_02164 +MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP +TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS +VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA +QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA +WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD +FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP +RPFQGAAREAAESQRAAEASASASASPSPTK--SASASPSPSTS-----------GD +>GCF_005280335_PROKKA_00233 +------------------------------------------------------------ +----------MREARESASAEGTPRAQPRQALETLGPGIRDGAATTAWENTAAVRNDTVS +VMDCTRDVLDQRTLDAVATHIPDGSNIEIVQLFAAQDETHEFLTCAYNGYFEYSPGMPLA +QVQYQHNLDSTRLDWCEDEPATVADEYTFDPETGKGLLALLRPGMIGGQDGAPLMPQRTA +WACSEDGTELVSVTMGSMEGYGDANGGLTQVENSPVAGSTTLVTEARDHLADTVLKDASR +FHEVIKLSSPFFLNASMDEESLAKAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP +RPFQGAAREAAESQRAAEASASA-AEASASRAASGSGTPSPSSTPASRTPSPSGTGG +>GCF_020097155_PROKKA_00172 +MTHPTSAPHRAAAALGAAALALTLAGCSDSGQP-SPASSTSTA---TAAAGSSASATGDP +QSPASAAASEIRAARASEKADGSERPQPREALETQGPGITSGAASAGWKSVAARYNDTVS +VMDCTQDVLDQTTLDAVATHIPVANDIGIVQLFASRDQTHEFLTCQYQGSSSRSEGAPLV +MVHYQHNLDGRRLEWCRPEAPVMADEYSYDESTRKGLLALLRPGMVGGADGAPLLPQRTA +WACNEDGTQLVSVTFGAMKGYGSVNEGLTQVTNSPIANSTTLATQARDHLADTVLKDPSD +FQADIETSSPFFLNAQTDQETLDKAKGLPTGIIPQDQLSDQSTIDRPEGAPEPVAPGQPP +RPFVGAARDAAESAAAESAASSS-GSDSASPSDDGDGNPVVSES---GTPSPSNTTD +>GCF_023573625_PROKKA_00158 +MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP +TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS +VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA +QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA +WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD +FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP +RPFQGAAREAAESQRAAEASASASASPSPTK--STSASPSPSTS-----------GD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000283.fa new file mode 100644 index 0000000000000000000000000000000000000000..c514a4f22fd30d5db3be8c756cbd08882c3992d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000283.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00151 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEAGQGRARG +>GCF_003691675_PROKKA_02165 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEAGQGRAQG +>GCF_005280335_PROKKA_00232 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR +TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV +ERIRTFLKDSDPTAAEKIEATQGRSGS +>GCF_020097155_PROKKA_00171 +MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR +AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV +DRIRTFLKDSDPTAAQQIEAAQA---- +>GCF_023573625_PROKKA_00159 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEADQGRAQG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000284.fa new file mode 100644 index 0000000000000000000000000000000000000000..6633ab579a4f23e36dc52161e9cf3b52123c2d4f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000284.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00152 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG +>GCF_003691675_PROKKA_02166 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG +>GCF_005280335_PROKKA_00231 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF +LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF +VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG +>GCF_020097155_PROKKA_00170 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF +LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED +VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF +VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG +>GCF_023573625_PROKKA_00160 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000287.fa new file mode 100644 index 0000000000000000000000000000000000000000..53c66030b657e86512c730e52dc9d359ef5f71cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000287.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00178 +MSTAAPHTQHSDFPSPTPTR---KGPSVGTWRPWAVLPWALALLALPLIALALRSNFGAN +GWMTVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGVSWGSFA +LAAIIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGIVGGLALVAVSALTGLAVIVVCVVR +RIRAV--R +>GCF_003691675_PROKKA_02174 +MSTAAPGTQHSDFASPTPTR---KGPSVGTWRPWAVLPWALALLALPLIALALRSNFGAN +GWMTVIYMVFGALPHELALVLMVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGISWGSFA +LAAIIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGLVGGLALVAVSALTGLAVIVVCVVR +RIRAV--R +>GCF_005280335_PROKKA_00223 +MSTAAPHTQHSDSASPAPTR---KGPSVGTWRPWAVLPWALALLALPLIALALRSNFGAN +GWMTVIYMVFGALPHELFLMLMVGSLFLLPRVNPLDEQRGGIRLGRLLHTLLGVSWGSFA +LAAILFPDAGDHPDSAATTPVLMDLLGKSTAMDVGSVAGLALAAVSALTGLAVIVVCVVR +RIRAV--R +>GCF_020097155_PROKKA_00169 +M--AVPHPVMPPPGTPLPHQLRPAGPSVGTPRWLPAVLWIVAFALLPLCVIVGRFATENG +GWLLFTYIMFGWMVQGGLGVLAAASLFLLPRVNPPVERRAGVRTGVVVHLLLGASWLTGL +LGMLAFGDYGDAPGSETAPAPLVDLYGMDRAVEIGDAVGPPLVGISLLTGLAAVVLVVVR +RLAAAVRS +>GCF_023573625_PROKKA_00175 +MSTAAPGTQHSEFASPAPAR---KGPSVGTWRPWAVLPWALALLALPLIALALRSDFGAN +GWMTVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGLRLGRLLHTLLGVSWGSFA +LAAIIFPDGGDHPESGATTPVLMGLLGTSTAMDVGIVGGLALVAVSALTGLAVIVVCVVR +RIRAV--R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000289.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6312456ac3e519c9c4a1f9ed31fea1039c3b984 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000289.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00180 +MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS +LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS +MDLARDTRGFATKFYTDEGTWDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW +NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDPDFHRRDLADAIEAGAFPEWE +LGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS +YLDTQLTRLGGPNWNQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD +VQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV +VASPAAPAADAAPGLDQKAGAADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGK-GVESAADGASAVSRLT +ELLPAHRVWDRFPTTGRLAD +>GCF_003691675_PROKKA_02176 +MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS +LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS +MDLARDTRGFATKFYTDEGTWDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW +NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDPDFHRRDLADAIEAGAFPEWE +LGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS +YLDTQLTRLGGPNWNQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD +VQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV +VASPAAPAADAAPSLDQKAGAADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGK-GVESAADGASAVSRLT +DLLPAHRVWERFPTTGRLAD +>GCF_005280335_PROKKA_00221 +MTTQQPDIPGTPGPRTPDLEERTAPTSSDD-AAMPAPDQRGPASVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS +LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS +MDLARDTRGFATKFYTDEGTWDLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIW +NMSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPDYHRRDLADAIEAGAFPEWE +LGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS +YLDTQLTRLGGPNWTQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD +VQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV +VASPAAPAADAAPGLDEKAGAAASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGK-GVESAADGASAVSRLT +ELLPAHRVWERFGTTGRFAD +>GCF_020097155_PROKKA_00166 +-MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS +LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS +MDLARDTRGFATKFYTDEGTWDLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIW +NMSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPDYHRRDLADAIEAGAFPEWE +LGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS +YLDTQLTRLGGPNWTQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQQVADGLGMPVPAPADAPAD +VQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGIHGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVV +VLGATPPAGDAQHGLDAKAAADAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLK +ELMPAHRVWERFPTTGRLAD +>GCF_023573625_PROKKA_00177 +MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS +LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS +MDLARDTRGFATKFYTDEGTWDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW +NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDPDFHRRDLADAIEAGAFPEWE +LGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS +YLDTQLTRLGGPNWNQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD +VQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV +VASPAAPAADAAPGLDQKAGAADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGK-GVESAADGASAVAALK +QLLPAHRVWDRFPTTGRLAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000290.fa new file mode 100644 index 0000000000000000000000000000000000000000..9e7486f87e72e88bdb83bf125bc3c5eef4766fea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000290.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00181 +MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADER--EAVATAEV +TRERIDEVREFLPSLANRRTDVL---------- +>GCF_003691675_PROKKA_02177 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADER--EAVVTAEV +TRERIDEVREFLPSLANRRTDVL---------- +>GCF_005280335_PROKKA_00220 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADER--EAVVTAEV +TRERIDEVRKFLPSLANRRTDVL---------- +>GCF_020097155_PROKKA_00165 +MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS +WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH +RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK +VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV +TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG +>GCF_023573625_PROKKA_00178 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADER--EAVVTAEV +TRERIDEVREFLPSLANRRTDVL---------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000291.fa new file mode 100644 index 0000000000000000000000000000000000000000..e586f18b16d93a748219f919e0f044aca1e5e053 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000291.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00182 +MTINADGSHAVQPHTANAHTTPARPVRHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI +IGNVVRVLTGGLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA +RSVVRYVVGGVVGGFLGAVGLFAVFSNTVVYGSGVHLFWMLPVAGLLGGLWAGLVSSRR +>GCF_003691675_PROKKA_02178 +MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI +IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA +RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR +>GCF_005280335_PROKKA_00219 +MTINADGSHAVQPHSANAHTAPASPARHAVVEEEVLEPLRPVDGWGFTNRVILVSVLVVI +IGDVVRVLTGGLGDPNGSVALGETGRGWVVLVQSFMFGLVGGALAGAAGYLIVLLMGGAA +RSVVPYVVGGVVGGFLGAVGVFAVFSNTALYGSGLHLYWMLPVAGLLGGLWAGVVSSRR +>GCF_020097155_PROKKA_00164 +MNTQAHGAHAVQTVGGTA--APQAPARRAVVAPEAVEPARPVDGWGFVNRILVVATVLIV +AFELWRAATGLLSD--GPRVLGEDGVGWVAVLEAFMFALVGGAIAGAAGYGIVLLMGGAA +RSAARYAIGGLIGGFLAAVGVIFVFSNTAALSVGGHLFWMLPLAGLIGGVWAGITSAKS +>GCF_023573625_PROKKA_00179 +MTINADGSHAVQPHAANAHTAPARPVRHAVVEEEVLEPLGPVEGWGFTNRVILVSVLVVI +IGNVVRVLTGDLGDPNGSVALGETGHGWVVLVQSFMFGLVGGALAGAAGYLVVLLMGGAA +RSVVRYVVGGVVGGFLGAVGLFAVFSNTVLYGAGLHLFWMLPVAGLLGGLWAGVVSSRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000292.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e790d5dee22dc6db5a0bd7c16a66ad4afbf5967 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000292.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00183 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS +>GCF_003691675_PROKKA_02179 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS +>GCF_005280335_PROKKA_00218 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS +>GCF_020097155_PROKKA_00163 +MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ +EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV +EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV +VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPED--AD--------- +>GCF_023573625_PROKKA_00180 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000293.fa new file mode 100644 index 0000000000000000000000000000000000000000..56bd61a60487a83a744342b259f9eaaffd33f62b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000293.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00184 +MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED +ETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEFRELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR +KRYDGSLQGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV +GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD +IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD +GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAAEVAKERGVRVPME +ATIRD +>GCF_003691675_PROKKA_02180 +MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED +ETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEFRKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR +KRYDGSLQGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV +GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD +IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD +GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAVEVAAERGVRVPME +ATIRD +>GCF_005280335_PROKKA_00217 +MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED +ETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEFRKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR +KRYDGSLKGTLTLTGGCGGMGGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV +GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETFTKKAQESMARQVEAMVGFQD +IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD +GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAAEIAAERGVRVPME +ATIRD +>GCF_020097155_PROKKA_00162 +MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAFDAIVETLKDLEED +ETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTFRELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR +KKYDGTLKGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV +GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD +IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD +GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVDAGYSRAVEVAAERGVRIPME +PTVRD +>GCF_023573625_PROKKA_00181 +MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED +ETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTFRELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR +KRYDGSLKGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV +GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD +IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLD +GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAAEVAKERGVRVPME +ATIRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000295.fa new file mode 100644 index 0000000000000000000000000000000000000000..72634e2ac496e1408578b2d371de9eedb7812c1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000295.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00186 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>GCF_003691675_PROKKA_02182 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA +GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>GCF_005280335_PROKKA_00215 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPDADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLEAVREHAGWADVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDTDVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>GCF_020097155_PROKKA_00160 +MASTLITDIAELTTVDPEGRVLRDAAVVLDDEDVAWIGPAAQAPAADERVSVAGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGLTMEATRAASDERLRELVLGRVADAVR +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDVEDYLDDVV +GPMLEAVREHVGWVDVFCDTGAFDAAQTRRVLAAGVAAGLRARLHGNQIEQGPGVALAVE +FGAASVDHVNHLSDADVEALAGTWSGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>GCF_023573625_PROKKA_00183 +MRSTLITDIAELTTVDPEGRVLQDAAVVVEDERIAWIGAAADAPDADDRVSVGGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA +GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLEAVREHAGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000296.fa new file mode 100644 index 0000000000000000000000000000000000000000..60fb70e8374cd63eb8d4e1d0c9339c621eadfdfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000296.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00187 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL +QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA +LMGEGDVVGTDGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN +PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS +DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH +>GCF_003691675_PROKKA_02183 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL +QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA +LMGEGDVVGEDGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN +PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS +DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH +>GCF_005280335_PROKKA_00214 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL +QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA +LMGEGDVVGADGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN +PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS +DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH +>GCF_020097155_PROKKA_00159 +MTT---TVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL +QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA +LMGEGDVVGADGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN +PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS +DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH +>GCF_023573625_PROKKA_00184 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL +QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA +LMGEGDVVGTDGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN +PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS +DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000297.fa new file mode 100644 index 0000000000000000000000000000000000000000..454b646756d384b98f90817ad65644b46951ebd6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000297.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00192 +M------------------------TSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPAD +GRGEPTTPQRDPGAGAPTSGARSTALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAY +LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS +ITGLTGSTRVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI +SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAA +VAPGVSAPAGFGVPYEVIHACALEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTI +VSRHRTDASLLA +>GCF_003691675_PROKKA_02188 +M------------------------TSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPAD +GRGEPTTTQRHPGAGAPTSGARSTALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAY +LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS +ITGLTGSTRVGAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI +SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAA +VAPGVSAPAGFGVPYEVIHACALEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTV +VSRHRTDASLLA +>GCF_005280335_PROKKA_00208 +M------------------------TSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPAD +GRGEPTTTQRHPGAGAPTSGARSTALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAY +LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS +ITGLTGSTRVGEGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI +SEANNTRVLFDTAREHGVTWVTDEQAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAA +VAPGVSAPAGFGVPYEVIHACAVEAATSGKLALADVVELNPSLDVDGRTAKAAARLIHTI +VSRHRTDASLLA +>GCF_020097155_PROKKA_00155 +MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD +GGAPAQTVDAAP--------ARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAY +LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYAS +ITGLTGSTRVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGI +SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAA +VAPGVSAPAGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTI +VSRHRTDASLLA +>GCF_023573625_PROKKA_00192 +M------------------------TSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPAD +GRGEPTTTQRHPGAGAPTSGARSTALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAY +LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS +ITGLTGSTRVGAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI +SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAA +VAPGVSAPAGFGVPYEVIHACALEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTI +VSRHRTDASLLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000298.fa new file mode 100644 index 0000000000000000000000000000000000000000..7693f95b31ad6bf2db80cb3d94f2528ba9305fab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000298.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00193 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDGLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>GCF_003691675_PROKKA_02189 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>GCF_005280335_PROKKA_00207 +MSATHPERTWTGPSAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGQEILGHRVYASLDDLPVTPDLVEVFRKASDAPEMVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>GCF_020097155_PROKKA_00154 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>GCF_023573625_PROKKA_00193 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000300.fa new file mode 100644 index 0000000000000000000000000000000000000000..654a0eb140826b6a1209c4316bc8ed2afe9625a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000300.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00195 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS +E-VLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPAS +PVVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQR------- +---AGFGRIVGL-----------------------VRRRLARTR-------- +>GCF_003691675_PROKKA_02191 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS +E-VLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPAS +PVVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQR------- +---AGFGRIVGL-----------------------VRRRLARTR-------- +>GCF_005280335_PROKKA_00204 +MTARAPLPPALARAAFGVDELLDAGLPWDRTRAADLHRIWRGVYTAADPAALTWDRAAAL +CRVTGGVISHTTAAAWHGIPLPRRLEASEELHLTVDRGRRQHRSARPGVVTHRLRLPPQE +IRQVGGGLRVTSPERTWLDLAVLLRPWELDWLVVAGDHLVHHPWHPDGRR-PSATTPALL +DAALGRHVGRHGIRRAREALADVRVGADSAPETRLRLALIRAGLPEPALQIAVDPSDPRS +PEADLGYRDARIALQYDGAAHRTPEQQARDARREAYCLELDWLPLRCTQEDLR------- +---EGFIRVIGL-----------------------VRRRLGPRGAFGATSRR +>GCF_020097155_PROKKA_00152 +MTARTPLPPALAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL +ARLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRSDLGGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMFRPHEVDWLIAAGDHLVRPPWTPTGRADPVATVPGLS +E-VLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPAS +PVVDLGYRAARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQR------- +---AGFGRIVGL-----------------------VRRRLARTR-------- +>GCF_023573625_PROKKA_00195 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLTRPAGLHLTFDRSARTHRTDLGGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIAAGDHLVRPPWTPTGRAHPVATVPGLS +E-VLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPAS +PVVDLGYRGRAW------PSSTTAPATARLSSR------------RGTPVGTRTASSGNG +RPCAAPGRTSALGSGGSWGWSGVGSPARADPPPRPTRVELSRVPSNAG---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000306.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e9bf7abe474c787f0e35db1282780c2a458ced7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000306.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00208 +MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA +ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR +VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAEVRAEEVD +WDDGTAYRYAVPEEVADAAMVEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ +IEPAEAPEEVAE +>GCF_003691675_PROKKA_02201 +----------------MQRRRAVRAAGLGVVGALALAGCGSEPQSVGEAWHQARTQVDEA +ETVRLETAYTTGRQGPQSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR +VEVDGSDVPDDVQLMYADPQWRRVSAGEGQEPPLKSLLDQVGFPAADALDGAEVRAEEVD +WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ +IEPAEAPEEVAE +>GCF_005280335_PROKKA_00183 +----------------MQRRRAVRAVGLGVAGVLALAGCAAEPQSAGEAWQQARTQLDEA +QTVRLETAHTTGRQGPNTVRWDIAGRLDGSNGDAKGVIQAGHESHMTMETRTVGEDSYVR +VSIDGADFADDVQLAYADPQWRRTPAGQEQERPLKELLEQIGLPSADALEGAEVRAEEVG +WAGETAHRYAVPQEVAAAAMGQGDSTLLHSFTVDDDGGLLALTVDDGRSLRQYALSDWNE +IDPAEAPEEVAE +>GCF_020097155_PROKKA_00129 +----------------MQRRRAVHAAGLGVVAALTLAGCGTDQQDVGEAWQHARAQIDGA +ESVRMTMASVNDSQGPSVVAWDVAGPLEGADGTTTGRMQVGRDSWMTVRSVSADGKTWAR +VDTEGQDVPEQIASMYRTDGWTETQ--QSGQNALRATLDAVGLPAADALDGVDVQPEKVD +WSGGTAYRYAMPGDVASAARGDSQFS-VRAFTVDEDGDLVGLRVEDGGVIQEFALSDWNE +IEPAEAPEEAQH +>GCF_023573625_PROKKA_00208 +MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA +ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR +VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAQVRAEEVD +WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ +IEPAEAPEEVAE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000307.fa new file mode 100644 index 0000000000000000000000000000000000000000..b123b9e970cd9dd384b8b38bd5834c1ef6753eb6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000307.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00209 +MRQRQTQT-----RRTRRGLSLAALG-AAALLLTGC-ASGDDAPGAWDRARTQLEEADSV +RMVTELRSEAPSNGRAVPDAVDISGPVDGSSMRYVSVYKDDGLITRDESRIVDGTAYSRF +TVERVGA-SGEDHPAYAERWTAT-PYEGDPSATGMGAMVSSLLGSLPESGGLDDVEADAD +GIRRSGQDAIRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGG +VDPVQAPPADEVLKQD---------------------------------G +>GCF_003691675_PROKKA_02202 +MRQRQTQT-----RRTRRGLSLAAVG-AAALLLTGC-ASGDDAPGAWDRARTQLEEADSV +RMVTELRSEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRF +TVERAGA-SGEDRPAYVERWTAT-PYESDPRATGMGAMVSSLLGSLPESGGLDDVEADAD +GIRRSGQDAIRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGG +VDPVQAPPADEVLKQD---------------------------------G +>GCF_005280335_PROKKA_00182 +M-PRQNPT-----GRARRGLPLAALGAAAALVLTGCGASGEDASAAWDRARTQLEETDSV +RMVTELRSDAPQAGNRTPESVDLSGPVDGSSMRYVSTYEDGDLITRDESRVVDGTAYSRF +TVERRGA-SGEDRPAYVERWTAA-PHTGDPRATGMGAMVSSLLGSLPESGGLEDVAVDAD +GIRRSGQDAVRYVLDEPLSVADDGVAMTAFTVSEEDGRLLTVETESAGTKAVVTVSEMGD +VEPLQAPPSDEVLPQQQGQGAPGAVPPGGAPQDGTAPGGTPAEPVPPTDG +>GCF_020097155_PROKKA_00128 +MRPTTPRTPAPHGGARRRALSLAALGAAAALSLSACGASGEDASAAWDAARTQLQDASSV +RLTTEARNDSGAA-PGTPDGVEIAGDVHSSDLSYTGVFRTDGYITRDESRTVGGQRYERF +TLEQPGGVSGEGRPAFAEKWKKAEPLPGD---ASMRSILDGVLTAVPQAGALQGADVRAT +DIRRQGRDATRYVLDTPVKGGTTDSSLTAFTVADDDGTLLTVETTGPGTRGTVTFSDWNA +VEPVTA-PATEDMAQD------------------TA-----------TAK +>GCF_023573625_PROKKA_00209 +MRQRQTQT-----RRTRRGLSLAAVG-AAALLLTGC-ASGDDAPGAWDRARTQLEEADSV +RMVTELRSEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRF +TVERAGA-SGEDRPAYVERWTAT-PYESDPRATGMGAMVSSLLGSLPESGGLDDVEADAD +GIRRSGQDAIRYVLDEPVSGPQEGVALTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGE +VDPVQAPPADEVLKQD---------------------------------G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000309.fa new file mode 100644 index 0000000000000000000000000000000000000000..09dc13a549434c3189f998b3c32bd26a9e6de762 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000309.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00211 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHCSYKSSKVHLRQFGEKLTDEM +KQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQGAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARV +FHGVVAGIGGYGNSLGLPNIGGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELASNGEGGMRVELTDVLLRDSTL +TPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWLGEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARP +AWQDELQADTFRSSEAGQDLPATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEAVRGLADGCQTLGIPVTGGNV +SLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADGQAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLL +GELLVNMSRDGMIDAAHDVSGGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG +>GCF_003691675_PROKKA_02204 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHCSYKSSKVHLRQFGEKLTDEM +KQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQGAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARV +FHGVVAGIGGYGNSLGLPNIGGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELASNGEGGMRVELTDVLLRDSTL +TPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWLGEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARP +AWQDELQADTFRSSEAGQDLPATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEAVRGLADGCQTLGIPVTGGNV +SLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADGQAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLL +GELLVNMSRDGMIDAAHDVSGGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG +>GCF_005280335_PROKKA_00175 +MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHCSYKSSKVHLRQFGEKLTDEM +KQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQGAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARV +FHGVVAGIGGYGNSLGLPNIGGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELASNGEGGMRVELTDVLLRDSTL +TPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWLGEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARP +GWQDRVQADTFRASEAGADLPATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEAVRGLADGCQVLGIPVTGGNV +SLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADGQAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLL +GELLVNMSRDGMIDAAHDVSGGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG +>GCF_020097155_PROKKA_00124 +MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHCSYKSSKVHLRQFGDTLTEEM +KEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQGAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARV +VHGVVAGIGGYGNSLGLPNIGGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELASNGEGGMRVELTDVLLRDSTL +TPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWLGEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRP +SFQDALQADTFRSSAAGQDLPATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA +VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEAVRGLADACQVLGVPVTGGNV +SLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADGQAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLL +GELLVNMSRDGMVDAAHDVSKGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD +MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG +>GCF_023573625_PROKKA_00211 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHCSYKSSKVHLRQFGEKLTDEM +KQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQGAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARV +FHGVVAGIGGYGNSLGLPNIGGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELASNGEGGMRVELTDVLLRDSTL +TPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWLGEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARP +AWQDELQADTFRSSEAGQHLPATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEAVRGLADGCQTLGIPVTGGNV +SLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADGQAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLL +GELLVNMSRDGMIDAAHDVSGGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000310.fa new file mode 100644 index 0000000000000000000000000000000000000000..4295e1f5bac2a053654ebfe94a99f23fff6a5507 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000310.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00212 +-MTELPLIGDYSTPATPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQR +TLAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQI +LTESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADE +TTLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAG +PRSGVDGLGFFTSVLTTLASRGGHA +>GCF_003691675_PROKKA_02205 +-MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQR +TLAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQI +LTESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADE +TTLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAG +PRSGVDGLGFFTSVLTTLASRGGHA +>GCF_005280335_PROKKA_00174 +MTTDLPLIGDYSTPTTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHADEDPQR +TLAGVDAVVIPGGFSYGDYLRAGAISRFAPMMDAVATAAGGPEGAADGLPVLGICNGFQI +LTESHLLPGSMIKNDHLHFICRDQELTVENTDTAWTRDYERGQTITVPLKNQDGQYVADD +ATLDALEAEGRVVFRYRGWNPNGSRRDIAGIANAAGNVVGLMPHPEHAVEPGFGPDTADG +PRTGTDGLGFFTSVLTTLASRGGHA +>GCF_020097155_PROKKA_00123 +-MTEIPLIGDYSTPSTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHAEADAAA +TLATVDAVVIPGGFSYGDYLRAGAISRFAPMMGAVAQAAGGPEGSEDGLPVLGICNGFQI +LTESHLLPGSMIKNDHLHFICRDQQLAVESTDTAWTRDFEQGEVITVPLKNQDGQYVADE +KTLDALEAEGRVVFRYVGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEAGFGPDTEAG +PRSGTDGLGFFTSVLTTLATRGGAA +>GCF_023573625_PROKKA_00212 +-MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQR +TLAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQI +LTESHLLPGSMIKNDHLHFICRDQELVVESADTVWTRDFEQGQTITVPLKNQDGQYVADE +TTLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEPGFGPDTAAG +PRSGVDGLGFFTSVLTTLASRGGHA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000311.fa new file mode 100644 index 0000000000000000000000000000000000000000..6456ce1ca4c543067837150f2677fe4cdc410df6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000311.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>GCF_003691675_PROKKA_02206 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGKVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>GCF_005280335_PROKKA_00173 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDAVLDQAR +RAAEELLSNPVIEDVVNVAVLDEAEGAR +>GCF_020097155_PROKKA_00122 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTEEVLAAAR +TAAEEMLSNPVIEDVVNVAVLDE--DAA +>GCF_023573625_PROKKA_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000316.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5f5478a5ed185432b835c85f39b4c845d6ee6ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000316.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00222 +MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR +>GCF_003691675_PROKKA_02235 +MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR +>GCF_005280335_PROKKA_00158 +MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGHRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMMTDTSYGRARIVKVNPHR +VQEALDAGGVAIVAGFQGVSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPSARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPIHVRSSFSDHEGTW +IMPDPNDTITLKEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAESNVNI +DMIVQNVSREGSGTTDISFTLPIVEGKDAMAALRAAQERIGFQDIVSDKEIGKLSLIGAG +MRSNPGVSATFFKALSDAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHTAFGLDAEEEA +TVYGGTGR +>GCF_020097155_PROKKA_00116 +MRLIVQKFGGSSVADAEGIQRVARRIVATQQAGNQVCVVVSAMGDTTDELLDLAAELTAD +APAREMDILLSAGERISMSLLAMAIDAQGVPARSFTGSQAGMMTDAAYGRARIIEVNPHR +VRAALDEGAVAIVAGFQGMSRESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVSSARKLPQLSSEETLELAASGAKVLHLRSVEYARRFGVPIHVRSSFSDHEGSW +IMPDPNDTIHLKEGAPMEQPIVAGVAHDRSEAKVTIVGVPDVPGKAAEIFRVIAESNVNI +DMIVQNVSRQDSGRTDISFTLPIVEGKAAIEALRAAQESIGFEEIVPNKEIGKLSLIGAG +MRSNPGISATFFKALSDAGVNVDLISTSEIRISVVTSEDKLDDAVRAVHTAFGLDTDVEA +TVYGGTGR +>GCF_023573625_PROKKA_00223 +MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000317.fa new file mode 100644 index 0000000000000000000000000000000000000000..39802d2f24ecc25722e097fe8491e9ff4a89a53c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000317.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00224 +MSTAVATSIHDRRP---P-QPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVV +VGAVTLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALA +ANAISGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFPAAALPWLAVAAVVGRVSP +WAVLVGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFL +QTEVRANEADYGSTT-AEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVT +TRTIPDPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVR +DVECLDGELRGLDQSGVP----DRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRL +PAGTRVA +>GCF_003691675_PROKKA_02237 +MSTAVATSIHDRRP---P-QPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVV +VGAVTLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALA +ANAISGDRAGGTLAITQVTLLRTGHLMTGKWLAAWIASAAFLAAALPWLAVAAVVGRVSP +WAVLVGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFL +QTEVRANDAEYGSMT-AEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVT +TRTIPDPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVR +DVECLDGELRGLDSTGVP----DRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRL +PAGTRVA +>GCF_005280335_PROKKA_00156 +MSTVVADPTRQGPP---PLRPPGGGRLSTASAVRTVVGMELRQRLRSRGWYVLLGVFFLV +VGAVTLGALGLRATTLGDLQSQGMDPAAAEVQMRSAGQWLFDGVLLFVLTLSLLVSPVLA +ANAISGDRAGGTLAITQVTLLRTGQLMAGKWIAAWIASAAFLVAALPWLAVAAVVGRVSP +LFVLVGLLMILVEFGVITGIGVAVSAIAGRTLFAVVVTYLIVAALSIGTLVAFVLSLQFL +QTDVRANMPEHDGMTMADPLEGQDVENMTQAEIDAAWAEWERQNPDAYDGIADACVGPVG +VQSVPDPRRVGWLLAANPYAVLADASPWDPTGASMQFTPETGPLNMMSAALRLTQQDPAE +TTECLDGQLRRIDTTSVP----DREGTWPVWPLGLAMQAALTGGLLWWGHRRLDTPAGRL +PAGTRVA +>GCF_020097155_PROKKA_00114 +MSAVLHTPPPAAAPAGGP-TPLGSGRLGVVDALRTLVGMELRQRLRSRGWYILLGVFFLL +VGGVTLGALGLHAW------TGGNSPD----STMVFGRWLYDGVLLFVLTLCLLVSPALS +ANAISGDRSAGTLAITQVTLVSTWQLMLGKWLAAWIAAVAFLVAAAPWLIVAAVVGQVPP +LAVLAGLAMILVEFAVVTGIGVAVSAITGRTLFAVVVTYLLVAMMTIGSLIAFTISLQFI +ETRLQTNQVTYG------------------------YAE------DA--GSTKSCAGPLR +DTTVPDPRRVAWLLAGNPYVVVADAVPL-PELREDSAGEEFGALNLISLGMRVAQIDPRE +YTDCVDGQVNEGSVTDSPVTLVDR--TWPTWPLGMLLQGGFLAALLWWGRRRLDTPAGRL +PTGTRVA +>GCF_023573625_PROKKA_00225 +MSTAVATSIHDRRP---P-QPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVV +VGAVTLGALGLRSLGVTEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALA +ANAISGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFLAAALPWLAVAAVVGRVSP +WAVLVGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFL +QTEVRANDAEFGSMT-AEPFTEAELEKMTPEEADQAWAEWEAANPELFDGIADRCVGPVT +TRTIPDPRRSGWLLAANPYAVLADASPWEGGLVEDGTWAEPGPLNLLSVGLRWTQRDPVR +DVECLDGELRGLDQSGVP----DRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRL +PAGTRVA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000320.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6a5a6351d1922c9a69fc8fd920297e80831af79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000320.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00228 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATNRAFLLRVEDLDRVRSGAEADQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAVHGPDAVYECFCSRKDIAEATSAPHPRP--DD +GAPASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGETPRATA +VDVLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAE +ALCAARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLSAQDPAWTPERVRDRLLES +LGLPAGPLAAAVPAF----DPAALPRVPWVF-----TGL +>GCF_003691675_PROKKA_02241 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRIEDLDRVRSGAEAGQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRP--DD +GAPASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATA +VDVLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAE +ALCDGRGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLES +LGLPAGPLAAAVPAF----DPAALPRDPWVF-----TGL +>GCF_005280335_PROKKA_00153 +MPAGRYAPSPTGALHLGNLRTAIVAWLAARATDRTFLLRVEDLDRVRSGAEAAQLSELAA +VGLDWDAEPVRQSERTGLYDDAVAALRAAHGADAVYECFCSRKDIAEATSAPHPAPADDD +GAPGPAGAAPLRPPGFYPGTCRGLTAAQRAERRRVRPAALRIDAVQVAGLPEGEIPRAEA +VDLLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSTPRQRWLAA +ALCAARGEALPQTSYLHVPLVLNAEGRRLAKRDGAVTLEDLAAADPSWTPERVRDRLLSS +LGLPPGPPADAVPAFARMLEDGSLPREPWMFDPAAFAGA +>GCF_020097155_PROKKA_00110 +MPAGRYAPSPTGTLHLGNLRTALVAWLAARATGRTFLLRIEDLDRVCSGAEAGQLADLAA +VGLDWDGEPVHQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRP--DD +GAPASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATA +VDVLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAE +ALCVARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLGDLAAQDPAWTPARLRDRLLES +LGLPAGPLAVAVRAF----DPAALPRDPWVF-----TGL +>GCF_023573625_PROKKA_00229 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRVEDLDRVRSGAEAGQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRP--DD +GAPASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGEIPRATA +VDVLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAE +ALCSARGEPTPAVEYLHVPLVLNAAGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLES +LDLPPGPLAAAVPAF----DPAALPRDPWVF-----TGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000325.fa new file mode 100644 index 0000000000000000000000000000000000000000..95b807d323799facee3b0572d3a58829008112cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000325.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00234 +M-------PLARLRAALPAAALSLLLLTGCT---ATDDGVTPASDADTSASVSTMP----ITSTPSVDAAATSRAAASSL +AA--SSSAAQSSRAAASSSSGAAESRA---------AEGSR----------------------SAEPAAPAAPADVEGDV +VTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDRRLYDRYDRLLAGV +YADGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRFSG--ECG-------------------------- +------------------------------------TAAEPIPEAAPAPAPEAAPA------------------------ +-------------------------------------------------------------------------------- +-------------------------------------------------AGDAGPVSGADSVCPDSHPVKANDNSGIYHM +PGQQHYGKTNARHCYASASAAQAGGYRAARR +>GCF_003691675_PROKKA_02247 +M-------PLARLRAALPAAALSLLLLTGCT---ATDDGVTPESAADTSASVSTMP----TTPTPSVDAAATSRAAASSL +AA--SSSAAQSSRAAASSSSGAAESRAARAAEESRTAEGSR----------------------SAEPAAPAAPADVEGDV +VTVESISDGDTLRVTLGEVSTRVRLLNIDTPETRHPSKPVECMGPEATAALKSMISPGDTVVLRYDRRLYDRYDRLLAGV +YADGVLVNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRFSG--ECG-------------------------- +------------------------------------AAAEPIPEAAPAPAPEAAPA------------------------ +-------------------------------------------------------------------------------- +-------------------------------------------------SGDAGPVRGADSVCPDSHPVKANDNSGIYHM +PGQQHYGKTNARNCYASAAAAQADGYRAARR +>GCF_005280335_PROKKA_00137 +M------TPRLFPRAGLVAAAALSLVLTGCTPAASGDDVAAPASAGAPSSGAAATTAAPAVSSTASAEAADRSRAAESSR +AAAQASEAEQSRRAEESRAAEARRAEESRAAEASREAERSRRAEESRAAAAAAAEEEDLDAAGSAEDAAWGGTAGVEGDV +AVVQSVADGDTLRVSLDGVSTPVRLLNIDTPETVHPSKPVQCQGPEATAALKSMIGPGDTVVLRYDRRVYDRYDRLLAGV +FADGRLVNAEMARLGLGEPVVFDGNVRFLPEVEAAWEQARADGVGLFSG--ECAVE------------------------ +------------------------------------EAPEPVEDEAPTAVAEPAPA-P---------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------AAGSGPVPGADFVCPDDFPVKGNDNSFIYHV +PGQQHYGRTNARNCYASAAAAEVDGYRAAKR +>GCF_020097155_PROKKA_00102 +MPSSRPPAPRVRTRL-LVSAALVLLAATGCT--------ASPATSSSTSSTSSAAPAALAASASPPASGASSA------- +-------------------------------------------------------------------------AAVEGDA +ATVVRVVDGDTVDVRRGAEDVRVRLLNIDTPETKHPSRPVECLGPEATRKLEELLRPGDEVVLQYDEERFDRYGRTLAGV +VEGETLVNAEIVRAGLGVPVVFEPNRRFLPPVEAAWAEAQREGAGLNQPGLECSLQTLQESVAQDPAPAAVSELAQALEA +VEAEGQEWMKVHYAAVIPLAVSLVQQHGGRADVPSAGAASVAPRASTAPAVPAAPQAPAVGAGSDAAERDRQRAAEAQAA +ADRAERKRQAEARAEAQRQAQAQEQVQARERAAQASREAEAAASAREKQKGASSGSSTAKGFADTSARDTSSGSPSSSGG +TSQKAPNRCYAPGGETFVYCGEGSTGSSSGGSSSSASAGASSSGAGTSSGGAGGPVSGADGVCPAGYPVKVS-SSGKYHV +PGGQYYDDTSAKRCYASTAAAAADGAVASKR +>GCF_023573625_PROKKA_00235 +M-------PLARLRAALPAAALSLLLLTGCT---ATDDGVTPESDADTSASVSTMP----TTPTPSVDAAATSRAAASSL +AA---SSAAQSSRAAASSSIEAAQSRAARAAEESRTAEGSR----------------------SAEPAAPAAPADVEGDV +VTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDRRLYDRYDRLLAGV +YAEGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRFSG--ECG-------------------------- +------------------------------------TAAEPIPEAAPAPAPEAAPA------------------------ +-------------------------------------------------------------------------------- +-------------------------------------------------AGDAGPVSGADSVCPDSHPVKANDNSGIYHM +PGQQHYGKTNARHCYASASAAQAGGYRAARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000328.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca53be64fdbacf329c5b6b62f0be19202e584e4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000328.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00238 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +VSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELIGTVATSDADVRAAVALPAVASLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKI +TDDGTAAERLVEFLAGRGLV +>GCF_003691675_PROKKA_02251 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV +TDDGTAAERLVEFLAGRGLV +>GCF_005280335_PROKKA_00133 +MKILVLAKQVPDTWQERELSLDTGWVVRDGAAEPVPDEISERVMEVALGWRDAGTDAEIV +ALTVGPEDSSKTLRKMLAMGADAAVQVTDDALVGSDAVETARVIAAAVEREGADLVLAGT +VSTDGGTGVVPAMVAELLDRPYLPHAEAPQLADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGAKV +SDDGTAAQQLVDFLAGRGLV +>GCF_020097155_PROKKA_00098 +MKIAVLAKQVPDTWQERTLDMETGMAVRDGAAEPVPDEIGERVMEVALAAREAGLEAEIV +AVTMGPADATKTLRKMLAMGADSAVHVVDDALDWSDAVQTARVLAAAVEHLGVDLVLAGS +ESTDGATGVVPAMVAELLDRPLLPSVEAVEITPEEVRGVLVTEDARLRASVPVPAVVALT +EKTAEPRFPNFKSIMAAKKKPLETLTLADLGLTAGPLDADRRSVMVSAAARRERAAGEKI +VDDGTAGEQVAAFLAARGLV +>GCF_023573625_PROKKA_00239 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV +TDDGTAAERLVEFLAGRGLV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000329.fa new file mode 100644 index 0000000000000000000000000000000000000000..6470b517d393e8ccabc8316faa7a3466308418d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000329.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00239 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPVVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAAAARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCTDAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITMRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +F-AIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAG +MKTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG +>GCF_003691675_PROKKA_02252 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +F-AIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAG +MKTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG +>GCF_005280335_PROKKA_00132 +MSANVEESEMTMQNDAANSGQTVLVHAELGADGALRPVVAELLGAAATVGVPEAVLVTGA +ASQDAAVARLGELGAARVHVLVAEDAAGTLGDAAVQALAAVTARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVALRWADDEVIARHSVFGGDFLSESTGEGGPRIITMRPGAVSD +RAPAVASPEVVEVAAAELGAVTAGARVLETTRRVQQADRPALRGAKTVVSGGRGVGSEEG +F-AIVEELADALGAAVGASRAAVDAGYTAADRQVGQTGVIVSPNLYIALGISGAIQHLAG +MKTAKTIVAIDKNEDAEIFEYADFGVVGDIFKVVPQVIEQLRARRG +>GCF_020097155_PROKKA_00097 +MT----DLPVT----------PVLVLAELTAAGDLRPAVAEALGAAARVGVPHAVLVTDA +DADDALVARLGELGAAVVHTAVAQDPA-ELGTAQVAALAAAVDAVLPEAVVLPNTPESRA +VAGRLAVRARGAVTADAVGLHRADGEIVARHSVFGGDVLAESTVEGGPNIVTLRPGAVAD +RARPVAAPEVRPLDVAGR-TVTAGARILSSEPAAPSADRPDLRTARAVVAGGRGVGSAEG +FTTLVEPLADALGAAVGASRVAVDSGFTAPEGQIGQTGVTVAPDLYVALGISGAIQHLVG +MKTSGTIVAVDSDEDAAIFEHADLGVVGDVNEVVPQLIAALAARRG +>GCF_023573625_PROKKA_00240 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +F-AIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAG +MKTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000330.fa new file mode 100644 index 0000000000000000000000000000000000000000..f686a81948708a819fa7d2da3573e5efa588a7c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000330.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00240 +MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRRMAGYVPFAREAEWLGGAPAP +AAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPDVAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPF +AREGEWFTELAAVGGPTAPEMVAQEVDAPEQA---------TAEP-TAEPAAAAPARPVVAELADVEPADAEPAVAAPVA +AA--SAPEPAPTAPDTRSAPPASAVQPPR----AATGTPARTA-ETDAAESA-VPSRLRKALPAVAGVVVLALLAVLAAR +WLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLFSARGNTPK +KFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVPTDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVV +FVAAPLAALTGWRMSSWFPTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWG +LVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR +>GCF_003691675_PROKKA_02253 +MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRRMAGYVPFAREAEWLGGAPAP +AAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPDVAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPF +AREGEWFTELAAVGGPTAPETAAQEV---------------VAEPATAEPAAA-------------EPADAEPAVAAPVA +AA--PAAEPAPTAPDTRSAPPASTAQPPRAAPGAATGTPARAA-ETDAAESA-APSRLRKALPAVAGVVVLALLAVLAGR +GLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLFSARGNTPK +KFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGIQYLSLDWPTENGWVHYNALQMLSYSLVV +FVAAPLAALTGWRMSSWFPTKATGLNKAFPMEVARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWG +LVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR +>GCF_005280335_PROKKA_00131 +MARRR-----------------------------------------------------RRPGGRSGLGH----------- +-----PAGAPA--AAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVARPAAAAPVAVESDLVPLGQRRRMGGYVPL +AREGEWFAELAAADAAPAGETAEPTVLEAAHDDAAPAAEAAVTEPAAPTTTAA-------------AAAATTAAAQAPAA +PAQPAAAAAAPTAPDTRSAPPASAAQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAAR +WLRTLDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANFTPKKDGAFSARGNTPK +KFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVFHHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVV +FVAAPLAALTGWRMSSWFPTEAKGLNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWG +LVVFLVSVAVTAAAWFLLRPSFTAPAASKFGTVGR +>GCF_020097155_PROKKA_00096 +MP-QRMQGYTEFRG-------EPWPPRDRVPQAPAPT--------TTPAVAADERRPGRRMVGYTAFR-------GEPWP +-----------------PVREAAQPAPAPAAAASPAEVTE-AAAAAVPLEATAPAGIAVP----------GRRMAGYTAF +R-----------------------------------------GEPWPPARVGA-------------APQAPEPAPMATVE +PA--VATGPTPTVEPVAAGAPETTPKP--------------------------APSTGRRVAAAVGGVVVLGLLAVLGAR +WLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQVRHETRPPATFTPHQPGPFAPRSATGG +TYSLTVWIHQALDALWLLNGLVFVVLLFATGHWMRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVV +FVLAPLAALTGFRMSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARNAA-DAWG +LAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR +>GCF_023573625_PROKKA_00241 +MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRRMAGYVPFAREAEWLGGAPAP +AAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPDVAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPF +AREGEWFTELAAVGGPTAPEMVAQEV---------------VAEPATAEPAAA-------------EPADAEPAVAAPVA +AA--PAAEPAPTAPDTRSAPPASTAQPPRAVPGAATGTPARAA-ETDAAESA-APSRLRKALPAVAGVVVLALLAVLAGR +WLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLFSARGNTPK +KFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVV +FVAAPLAALTGWRMSSWFPTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWG +LVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000333.fa new file mode 100644 index 0000000000000000000000000000000000000000..8fefed663156b9a197de08010a1a679395b0f1c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000333.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_00246 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKA +RAAGVETVTDTAAAAAEADVVLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA +DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL +QHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPVNRDFQPGFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAA +GEGAARDFSGIIEDIRASHTDRSEA +>GCF_003691675_PROKKA_02258 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKA +RAAGVETVTDTAAAAAEADVVLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA +DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL +QHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAA +GEGAARDFSGIIEDIRASHTDRSEA +>GCF_005280335_PROKKA_00123 +MSEKTATTTTAPVIPHFVHGERVDGSSGRHSDVYHPATGQVEGRVPLASVEEIDAALASSEKGFAAWSALNPQRRGRILL +KWVDLINENVDELATLLSQEHGKTVPDAKGDIQRGVEVVEFAAGAPHLLKGEFSSNAGSGIDVHSIRQPLGIAVGITPFN +FPAMIPLWKAGIALAAGNAFVLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA +QSIYAHAGRMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPVGEETADRLVALLSERIRRLK +VGPSLDESSDFGPVVSKDAKERIEGYIAAGAAAARRPGRGRPRRRRRGPRGRLLRGRHPLRPRHRGHEHLPRGDLRPGAL +RGPRRGLRGGAHPRQRARVRQRRGHLHPRRRRRPRLRHPRGDRHGGRQRADPRPDRLLHLRRLEGLRLRRPEPARHRRPE +VLHQDQDHHHALALGRARGRQLRDARRLLTAVHPLPQEDPMTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKA +RMAGIETVTDTAAAAAEADVVLTMLPNGRLVLDVYRGREGAPGLLDAARPGTVFLDCSTIDVAEAREAAQAAEAAGMRAA +DAPVSGGQVGAEAGTLAFMVGAADEVYAEVLPLLEVMGGRIVHCGGSGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL +EHQALYDVMSKASGQCWALTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAA +GEGAARDFSGIIEDIRASHTDRSEA +>GCF_020097155_PROKKA_00092 +MSQSQT-------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------------------PSASLPGTVAFIGLGNMGGPMAANLVAAGVTVRGFDLVPAAVEAA +RATGVEIADDAASAVPGADVVITMLPNGALVRGVYEGTADAPGLLGAADPDTLFLDCSTISTSEAQEVAALAEAAGHRAA +DAPVSGGVVGAQAGTLAFMVGGSVEVFEEIRPLLEVMGSRIVHCGGNGLGQAAKVCNNMLLAISQIGVAEAFVLGERLGL +EHQVLFDVMSEATGRCWSLTANCPVPGPVPTSPANRDFEGGFAGALMAKDLGLALKALDEQHVGAEMGRLAQRTYAAYAD +GEGARKDFSGIIETVREAGKDTA-A +>GCF_023573625_PROKKA_00246 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKA +RAAGVETVTDTAAAAAEADVVLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA +DAPVSGGQVGAEAGTLAFMVGASDEVYTEVLPLLEVMGARIVHCGGAGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL +QHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAA +GEGAARDFSGIIEDIRASHTDRSEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000340.fa new file mode 100644 index 0000000000000000000000000000000000000000..cd3c234f14c20026f7aeb17cd443d67c357b0db4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000340.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00261 +MTTPAPVASAARARRRAAR--SGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQ +AFGSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA +AGILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPE-----------PSPAEP------- +--A +>GCF_003691675_PROKKA_02274 +MTTPAPVASAARARRRAAR--SGPRPQLRMGLNGFLVAWLLPNLVMAAVVAILAVVPGLQ +AFGSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA +AGILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPE-----------PSPAEP------- +--A +>GCF_005280335_PROKKA_00106 +-----------------------------MGLNGFLVAWLLPNLVMAALVAVLAVLPGLQ +AFGSLTPLLTVVGIAGLVVGLPLCLLVNFAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA +AGILPMLIPVIGFPAAVLMALGRMAARPLVQVVTPGQEAEARSAAQTASPADPEPSERAA +RGA +>GCF_020097155_PROKKA_00076 +MTTPAPVKSTARARRKAARAVSGPRPRLRMGLNGFLVAWLLPNLLMAAVVLALTLIPSLQ +RFGTLTPLLTVVGIAGLVIGLPLCLLVNRAFRHVLNQWVHVLAYALVGMLYGLVVLAQGV +GGVLPMLIPVIGFPAAVLMGLGRLAARPLV-DVVPG-----------AEPR--------- +--S +>GCF_023573625_PROKKA_00259 +MTTPAPVASAARARRRAAR--SGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQ +AFGSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA +AGILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPE-----------PSPAEP------- +--A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000341.fa new file mode 100644 index 0000000000000000000000000000000000000000..bddf31c80e734424e29aa39d521768fbe8a5d9ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000341.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00262 +MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALR-------- +------------------GLGGLAVGGAVAAVALRTAGLNDRIDGAVVRGLQRV-----G +VPAPRVALAAAASLAMLLANEDARRTRRDAVEL-----------AVTGPAGLDEDPVDEV +EPE------------ATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPHARTVAS +VAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELRLQVIDG +EIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA +>GCF_003691675_PROKKA_02275 +MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALR-------- +------------------GLGGLAVGGAVAAVTLRATGLNDRIDGALVRGLQRV-----G +VPAPRVALAAAASLAMLLANEDARRTRRDAVEL-----------AVTGPAGLDEDPVDEV +EPE------------ATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPHARTVAS +VAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELRLQVIDG +EIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA +>GCF_005280335_PROKKA_00105 +MRQNSPVPG-------SLPARYVDDPAAAFPALRQRALAPGGRPYGLLAAAVVGALTLVD +PHRMGAAERRGLARTEAAASGAFVAAEAASSLRLAGLP-GRVGPAA-------------- +--------------------GGLAAGAATAALALSTVPLNDRIDGALVRFLERA-----G +ASAPRAVLAGTAALSVLAGNESVRRERRNALEE-----------A-AWPAW--DDLSEEE +QSE------------PTAPLPVEVRVLLETLLDPALAEGRELPGAAALRAQLPHVRTVAS +MAEAIRDEDEVPDWTPLVVETDGPVDRAVPHDHVWPVRGRFAVGE-DGHEVELRLQVIDG +ELGALVITLPADEDADPDAWDAFQELEAFPGVEDLTFQVDGERRD +>GCF_020097155_PROKKA_00075 +METP------------RTPE------------------------------------TRTD +PPADRLAEPQHPAHADAPVVHDTAVPESERIERTVSTRTGETRP-PVVRTVVTESERIER +PVVEVRDARVPGRLLWWIGGGTLAAGSLAALVRV----LRERLATPEPTPLERLADAGRG +AGLP-LALSLAGTAAGVGVSLRARRRRRTEEVLAAPAVPFLLGEAVSAEAG--EDDVDGL +PPVNEASDAYPAGALETEALPLEVVVLLDTLLDPSLDEGRELPGAAALRAQLPHVRTAAS +VAEEIREDGKVPDWTPLVVEEETGVARAIPNDMVWPVRGRFT--TEDGHELELRLQVIDG +ELGALVITLPEDVEDGVAAWDAFQELEAFPGVEELTFTVDGDRRP +>GCF_023573625_PROKKA_00260 +MKLPSPAPSVPGEVHHSASSVPVDDAEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTFLAAETAGALHTAAIAEGEVAPSPAARALR-------- +------------------GLGGLAVGGAVAAVALRATGLNDRIDGAVVRGLQRV-----G +VPAPRVALAAAASLAMLLANEDARRTRRDAVEL-----------AVTGPAGLDEDAVDEV +EPE------------ATAELPVEVCVLLETLLDPALAEGRDLPGAEALRSQLPHARTVTS +VAEAIREAGEVPDWVPLVVETDDDIRRAVPNDCVWPVRGRFASGSAGGHELELRLQVIDG +EIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLTFHVDGDRRV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000344.fa new file mode 100644 index 0000000000000000000000000000000000000000..6cb3f9f1ab08c3756e4f006b1c0e2d5927d1a3b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000344.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00265 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID +>GCF_003691675_PROKKA_02278 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID +>GCF_005280335_PROKKA_00098 +MDRMILINLKYTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYLLIEGF +TDEGAKAHVESPHFQEGIDAMRPLLASTPQIISEHVDAEGFGPMGELQID +>GCF_020097155_PROKKA_00069 +---MILINLKFTVKPELADQWMDAVAKYIADVRSEPGNMFFEWYKPVEGGDNEFFLLEGF +TDEGAQAHVASPHFQEGIDAMRPLLQSTPQIISEQIGAEGFGPMGEIQID +>GCF_023573625_PROKKA_00263 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000347.fa new file mode 100644 index 0000000000000000000000000000000000000000..8960620fe41c09746293274f3435b587a763db66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000347.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00268 +MTETLPTVEPEYDVAT-PLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDR +HEYPLDLVARLGQADLLRDGVPVDGLPEISRVAAGLAMMELSRLDGSIATMTGVQGGLAM +RSIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKK +WIGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVF +VPDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQ +SVQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLG +GNGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>GCF_003691675_PROKKA_02281 +MTETLPTVEPEYDVAT-PLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDR +HEYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAM +RSIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKK +WIGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVF +VPDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQ +SVQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLG +GNGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>GCF_005280335_PROKKA_00095 +MTENLPTAEPEYDVAA-PLDTDFYLALGDVSDDEKEVWRRARAFALEPDVLPRIREAWDR +HEYPLDLVARLGAADLLRDGVPVDGLPEVSRVAAGLAMMELSRLDGSIATVAGVQGGLAM +RSIQLCGSDEQRAELLPAMSRGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLRGHKK +WIGNGAAGGVSVVWARSAEDEQVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVF +VPDADVLPEARSFKDTSRVLFATRVGVAWSALGQAVGCYEAAVQYAGQRIQFGRPLAAAQ +TVQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASLAKYSATRAARSIAANARDLLG +GNGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>GCF_020097155_PROKKA_00066 +MTETLPTAEPDYSTITGPLDTDAYAVFAELPDEDLALARAARAF-LTPEVQKRLQEAWDT +GEYPTELIAGLAEADLLRDGVAVEGKPAQSRLACGLAAMETSRIDGSLATVVGVQGGLAM +RSIEMCGSDEQKAKYLPAMDRGELFGAFALTEPTHGSDSVSLQTTATKVEGGWRISGHKK +WIGNGAAGGITVTWARSAEDGQVKGFIVQQDAEGYSAEVIRGKMSLRAIHQAHITYDDVF +VPDEDVMPGAQSFKNTAAVLFATRLGVAWAAVGHALGCYEAAVQYAKQRVQFGRPLAESQ +IVQERLARMLSELTQVQLLVLRAARLEDAGKLTGPQASLAKYSATRTARSIAANARDLLG +GNGILLENEVGKHFADIEAIHTYEGTETVQALIVGRDITGVGAFA +>GCF_023573625_PROKKA_00266 +MTETLPTVEPEYDVAT-PLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDR +HEYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAM +RSIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKK +WIGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVF +VPDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQ +SVQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLG +GNGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000349.fa new file mode 100644 index 0000000000000000000000000000000000000000..befc2ee80f1300b58db4548e4f7264fe16665624 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000349.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00270 +MPDTPQP----PA-------VPAHPDHFGFEVTHRLETPGHDGAPLGRTGVITTPHGRIQ +TPAFIPVATQATVKAVLPESMKDLGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP +TFTDSGGFQVMSLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT +GDRHRFTPEVSVGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL +TGVRAARPYQALFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGA +LEKENLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFY +TRDGRYNLPGAKYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFT +VSLVDRIRAAMQDGTLAELKAETLGRYYAPKG +>GCF_003691675_PROKKA_02285 +MPDTPQP----PA-------VPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQ +TPAFIPVATQASVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP +TFTDSGGFQVMSLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT +GDRHRFTPEVSVGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL +TGVRAARPYQALFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGA +LEKENLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFY +TRDGRYNLPGAKYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFT +VSLVDRIRAAMQDGTLAELKAETLGRYYAPKG +>GCF_005280335_PROKKA_00087 +MPDTSPG----PAPSSSSSGAPAHPSHFGFEVTHRLEAGGVDGAPLGRTGVISTPHGQIQ +TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP +TFTDSGGFQVMSLGSGFKKVIDMKGPSAPDGQGADDAVAPGKERLANVDDDGVWFKSHLT +GDRHRFTPEVSVGIQHRLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL +TGVRAARPYQALFGVIQGAQYEDLRRKACRDLAAMRADFPSAGELDGVTSGFDGYGVGGA +LEKENLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFY +TRDGRFNLPGAKYRRDFGPLDPACDCYTCAHYSRAYIRHLFKAKEMVAHTLISIHNERFT +VSLVDRIRAALQDGTYAELKEETLGRYYAPKG +>GCF_020097155_PROKKA_00064 +MPETSAPGTAGPTSSSAVTSDPAHPDHLGFEVRERLDAPGADGIALGRTGVLRTPHGEIQ +TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP +TFTDSGGFQVMSLGSGFKKVIDMKGPAAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT +GDRHRFTPERSLQIQHNLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL +TAERAGRPYQGLFGVIQGAQYEDLRRKACRDLSGMTAEFAAAGERPATAHGFDGYGIGGA +IEKENLGTIVGWCAQELPEDRPRHLLGISEPDDLFRAVENGADTFDCVSPTRVARTGAFY +TRDGRYNLPGATYKRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLISIHNERFT +VSLVDRIRASIQAGTFAELKAETLGRYYAPKG +>GCF_023573625_PROKKA_00268 +MPDTPQP----PA-------VPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQ +TPAFIPVATQASVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP +TFTDSGGFQVMSLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT +GDRHRFTPEVSVGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL +TGVRAARPYQALFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGA +LEKENLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFY +TRDGRYNLPGAKYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFT +VSLVDRIRAAMQDGTLAELKAETLGRYYAPKG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000353.fa new file mode 100644 index 0000000000000000000000000000000000000000..b4f0dcc4eb5f315d59d12e214dbaa2aa976be458 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000353.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00280 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>GCF_003691675_PROKKA_02295 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>GCF_005280335_PROKKA_00073 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR +>GCF_020097155_PROKKA_00059 +MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH +RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSA---R +>GCF_023573625_PROKKA_00279 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000354.fa new file mode 100644 index 0000000000000000000000000000000000000000..d88178808a07418f12ea71a36f0b922471b6ddde --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000354.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_00281 +MQDASSESRAALERLRAA-----------------------------------------SAPRPDDAETRA------PAA +RPRRALAAPGEI---------SRRDLRRHERALRSG--RSETAAERRVREDHRADVHRAMD--------RLRT------- +-PGAPAEQRPRRDLSEILDRLGSPDLARFADPLVGTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAG-------- +--RAAEHERPVAEAA-------------------------------------------AAAQAR---------------- +------DAARARDAAALQARLDEEARR----------------------AQAARVARRRREEEKQRRRREAERRRRVAAE +EKARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERRRLEAERVEA +ERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARLLEDRAREAERRAAEDAARRRREHEERESR +ALARAARELEGPEVFPAAADRPLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSA---GPVTGAL +PLIPGYT-PAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGASVFGLS +PLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLG +ARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGM +AWTLLCLALPRLLPSPLGAQQSVWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPH--PAG----A +>GCF_003691675_PROKKA_02296 +MQDASSESRAALERLRDA-----------------------------------------SAPRPDDDATRA------PAE +RPRRALAAPGEI---------SRRDLRRHERALRSG--RPETAAERRVREDRRADVHRAMD--------RLRT------- +-PGAPAQQRPRRDLSEILDRLGSPDLARFTDPLVGTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRERAAEAA +RRRAAEHERPVAEAA-------------------------------------------AAAQAR---------------- +------DAARARDAAALQARLDEEARR----------------------AQAARVARRRREEEKQRRRREAERRRRVAAE +EKARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERRRLEAERVEA +ERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAYTVLHAERALAQARLLEDRAREAERRAAEDAARRRREHEERESR +ALARAARELEGPEVFPAAADRPLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSA---GPVTGAL +PLIPGYT-PAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGASVFGLS +PLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLG +ARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGM +AWTLLCLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPH--PAG----A +>GCF_005280335_PROKKA_00072 +MQDPSSESHAALERLRGAPKPVPAPEEAAGAPRTPDQDDDGAATAEDPVPAAARTPADDPAPAPSPSPPQDAETAPAPDA +SPASDADAPADVEADVEAPRPARRATPPRPRRPRPD--LPPRPAPPRARPAHRLSPRRPMRGACARAAARTSTRRWSGRA +PPAPPRSSAPRRDLSDILDRLGSPDLARFTAPLVGTVERILPAPGADPQKAAQAARRREEAEARRRARLQSGRERAAESA +RRRAAEHDRLAAEAAEREAALRD-DDARSEARRADEEAAAAKEACRQERLRERRTAGRAAAEERARLAAEAVEADRERER +REAEEAAAAAAREEAALQARLQEEARARRERAEQEERLAQERAAEEARLAQAARIARRRREEERERQRREAERRRRLAQE +AKARAAADQEKRRQQEQERRRREAKVAEERARVQAERRAREEAELAERERRRLEAEAEAERRRQAQEAERRRREAERAEA +ERRARAEEAERRRREAEEAARRAAEARRLHAERTRAHTVLHAERALAQARLLEDRARDAERRAAEEEARRLREHQDRESR +ALYRAARELEGPEVIPAASQRPLLARPEEGLTDEELVARARQALPEWRHRQRLATKARAVGAETAAGRSA---GPPTGPV +PLIPGYT-PAAPEEPAGPATVRDRRGQLVLTLAWAAFVLAGVWGLGLFRFVPGLDALDAGPYPAAGDGRHGSGATVFSLF +PLHPVIWPVLWLLTGLHVARQWGPGQGAAPRHRRTRGPMAGTLLALALWFPLTVLVPWGLESVLWLVALALMLGAVRRLG +ARPAAGRLARLAEDGAPGALLGTLLAGAPTALAATLHAWGVHVGRFPTELVAALVLLTLLPGAVRLVLGGRGRMGVAVGM +AWTLLCLALPRLLPSPLGAQQSAWVGFAAAFGALLLLTAAAVRRSWVRQIERDAARRPP--PAV----A +>GCF_020097155_PROKKA_00058 +M-----------------------------------------------------TSQDDDAPRPAPPAPRH-------AA +RPRRALAEPGRL---------APEQLERHTRRLRGEPLPPETPEEAAARAGRRHDLAAALD--------RLPA------- +-ESAPAAPRPRADLSDLLDRIGTPDLARFADPLLGTVGRILPS-GPSPERAAAAARRRAEHEGRRRAERAAGRARAAEAA +RRRAEETARREAEAAERARAARTVEESRAEAVRAAEDAAREAERHRAERLRERREAARAAAADKARRVAEAAERARVEEE +ALLAVEADAQAREVAAAQAEPDALARERRERADQEE-----------RRRRAALLARRRRDEERRRRRREAERARREAEE +QRERAA---------------------------RAE--------------------------RSAAEAARRRQAEEAAEA +ERRQMAVEAARARAEAERLAQEAARERRRRIAAARALPRTVAARHIAAGTAAEDRRRQAAARASEEAARVLAAHHDRETR +ALMAAARELDGPDVVPPAHLRPLLADPAEGLDDAALLERARAALPQWRRTGRLLTKADAVRAQ-TAHGAADGTGPATGAF +PIVPGYVPPSGPPEPRAPATREDRRHQLELTGAWLLFVLASAWGLGLFRLVPGLRVVDQGSYTAAHGGRYAFTTSVLSLF +PLHPAVWPVLWLALGVYVAHQWGPGQGAAARQRQTRRSVAGALALTALWFPLAVLVPWGLEFMVWLAALALMIRVMRGLT +AVPARTRAAQTCTDGVLGGFLGLLLAAAPTTLASPVAATGVFWGWFPSALVAAALLWAVVLTGARLALQDRGRLGLALGM +AWTLLCLALPRLLPSPLGAWQSAWVGLSAVAGGLGVLLLVVVRRTWVREIEEQAAAAPQGVPAGRVNGR +>GCF_023573625_PROKKA_00280 +MQDASSESRAALERLRGA-----------------------------------------SAPRPDDDATRA------PAA +RPRRALAAPGEI---------SRRDLRRHERALRSG--RPETAAERRVREDRRADVHRAMD--------RLRT------- +-PGAPAEQRPRRDLSEILDRLGSPDLARFADPLVGTVERILPAPGRDPEKAAEAARRRAAAEERRRARLRAGRERAAEVA +RRRAAEHERLAAEAA-------------------------------------------AAAQAR---------------- +------DAARARDAAALQARLDEEARR----------------------AQAARVARRRREEEKQRRRREAERRRRVAAE +EKARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERRRLEAERVEA +ERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARLLEDRAREAERRAAEDAARRRREHEERESR +ALARAARELEGPEVFPAAADRPLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVQAEATAHSSA---GPVTGAL +PLIPGYT-PAPPEEPAGSPTRADRRGQTLLTVAWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGASVFGLS +PLHPAIWPVLWLLTGMYVLRQWGPGQGASPRHRRIRGAVAGTLLALALWFPLAVLAPGGLDVVPWLLALVLMLRVVRRLG +ARPAARRLARVAEDGALGVLLGTLLAGAPTAVGAALHAWGVHVDWFPTELLALLVLMALLLAALRLVLGGRGRLGVALGM +AWTLLCLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPH--PAG----A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000357.fa new file mode 100644 index 0000000000000000000000000000000000000000..41214c64062037c0e212108241082bb4ca38d550 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000357.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00288 +----MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI +LGAVGADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRV +WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>GCF_003691675_PROKKA_02310 +----MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI +LGAVGADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRV +WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>GCF_005280335_PROKKA_00066 +----MSVRVLAIGKKHEAWVSEGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI +LGAVGADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTVVIGGAYGVDARVHARADRV +WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>GCF_020097155_PROKKA_00045 +MMVLMAVRVVAIGKRHESWVSEGITRYEKRLKKPWDLTWQLLPHSSRQEDAARAEESERI +LAKVGPDEQLILLDERGRGFDSPGLSAHLQGQFDLGRTVTLVIGGAYGVDASVHARADRV +WSLSGLVFPHQLVRLILAEQVYRAQEIAGGRPYHHA +>GCF_023573625_PROKKA_00294 +----MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI +LGAVGADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRV +WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000359.fa new file mode 100644 index 0000000000000000000000000000000000000000..9bdfc344b91356975ab73d17459615a99e8106e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000359.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00291 +MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR +AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHQVQVRAGVRSEESAALLRGFFAAQR--D +>GCF_003691675_PROKKA_02314 +MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR +AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHRVQVRAGVRSEESAALLRGFFAAQR--D +>GCF_005280335_PROKKA_00063 +MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL +AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHAVQVRAGVRAEESAALLRGFFAVQR--G +>GCF_020097155_PROKKA_00042 +MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL +AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHTVQVRAGVRGDECAALLVDFFAARRPGG +>GCF_023573625_PROKKA_00298 +MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR +AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP +RFNHQVQVRAGVRAEESAALLRGFFAAQR--S + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000360.fa new file mode 100644 index 0000000000000000000000000000000000000000..27fd1c39a4c1d9a706d6c1e882057a0137b661b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000360.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00292 +MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE +>GCF_003691675_PROKKA_02315 +MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE +>GCF_005280335_PROKKA_00062 +-------MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVE +IQTPVATTTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESL +GDVEVDLYLAAQDERLDENAYIVPGLGDAGDRLYGLAE +>GCF_020097155_PROKKA_00041 +-------MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVE +VKTPVATTVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEAL +GDVDVELYLAAVDERLNEKSYIVPGLGDAGDRLYGLAE +>GCF_023573625_PROKKA_00299 +MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000361.fa new file mode 100644 index 0000000000000000000000000000000000000000..955d474cfa787b7bcc348907490f80b75ad163e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000361.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00293 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGT--DAPDSQTAPTPVLAPNGIPG +PQAVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPA +GAEGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLT +FKEFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRT +VRGQGYRFYRHPEVVVWAAPEYSI +>GCF_003691675_PROKKA_00001 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGT--DAPDSQTAPTPVLAPNGIPG +PQAVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPA +GAEGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLT +FKEFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRT +VRGQGYRFYRHPEVVVWAAPEYSI +>GCF_005280335_PROKKA_00061 +MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGT--DAPAAQTAPTPVLAPNGIPG +PQAVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPS +GAEGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLT +YKEFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRT +VRGQGYRFYRHPEVVVWAAPEYSI +>GCF_020097155_PROKKA_00040 +MGETAGYVHISVRNAQRRANVSRAR---RGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPG +PQAVARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPA +GAAGRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLT +FKEFELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRT +VRGQGYRFYRHPEVVVWAAPEYSI +>GCF_023573625_PROKKA_00300 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGT--DAPDSQTAPTPVLAPNGIPG +PQAVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPA +GAEGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLT +FKEFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRT +VRGQGYRFYRHPEVVVWAAPEYSI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000362.fa new file mode 100644 index 0000000000000000000000000000000000000000..322bd536f307c0f665eacb968cdc2752799256cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000362.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00294 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR +>GCF_003691675_PROKKA_00002 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR +>GCF_005280335_PROKKA_00060 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR +>GCF_020097155_PROKKA_00039 +MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA +LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN +LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR +>GCF_023573625_PROKKA_00301 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000365.fa new file mode 100644 index 0000000000000000000000000000000000000000..1433c4126e1228048b221f4a92c2e9236b7c0c28 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000365.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00299 +MDATSHPDAGPRLPETSVPGG---------------DAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRRRALVV +QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATEWDEVRARLAADEVDVLLISP +ERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQ +LGVASEQDVFVLRGPLARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT +DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY +FATASMPDEEQARAVLGALADHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVA +EARRAEERLMLDYQTTDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRMWPSGM +DRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAVDVLAGWGWRTRPIAVVAMPSRTRPQ +LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRW +SLAEAARVLREAGAQGVLPLVLAQAG +>GCF_003691675_PROKKA_00007 +MDATSHPDAGPRLPETSAPGG---------------DAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRRRALVV +QRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATEWDEVRARLAADEVDVLLISP +ERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQ +LGVASEQDVFVLRGPLARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT +DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY +FATASMPDEEQARAVLGALADHGGALSVAALEPAVRIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVA +EARRAEERLMLDYQTTDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRMWPSGM +DRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAVDVLAGWGWRTRPIAVVAMPSRTRPQ +LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRW +SLAEAARVLREAGAQGVLPLVLAQAG +>GCF_005280335_PROKKA_00055 +MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFKDGQFEAIEALVAHRRRALVV +QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISP +ERLTNPRFREEQLPDLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ +LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAEDTARALREAGHEAVAYTGRT +DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY +FATASMPDEEQARAVLQALAQHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA +EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAEAALRRTGVPIEPRRMWPSGM +DRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLDKEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPL +LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW +SLAEASRVLREAGAQGVLPLVLAQAG +>GCF_020097155_PROKKA_00033 +M------STSPQDPARPAAVA---------------DPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVV +QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEWEDVRRSLEADEVDVLLISP +ERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPDYRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQ +LDVESRQDVFVLRGPLARASLRLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT +DPEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGTDHADVLLLPGQEDRAIWEY +FATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTALELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVA +EARRAEERLMLDYQTTQTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGM +DRLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEWGWQERPIAVVAMPSRGRPQ +LVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLASVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRW +SLAEAARVLRGTGAQGVLPFVLAQNG +>GCF_023573625_PROKKA_00306 +MDATSHPDAGPRLPETSAPGG---------------DAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRRRALVV +QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATEWDEVRARLAADEVDVLLISP +ERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQ +LGVASEQDVFVLRGPLARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT +DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY +FATASMPDEEQARAVLGALADHGGALSVAALEPDVRIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVA +EARRAEERLMLDYQTTDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRMWPSGM +DRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAVDVLAGWGWRTRPIAVVAMPSRTRPQ +LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRW +SLAEAARVLREAGAQGVLPLVLAQAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000367.fa new file mode 100644 index 0000000000000000000000000000000000000000..0a79f8d7cec7617bc93bcfa3058494c96707d209 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000367.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_00301 +MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF +EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY +LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTA-PAR-- +------------------------------------------------------------ +---------- +>GCF_003691675_PROKKA_00009 +MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF +EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY +LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTA-PAR-- +------------------------------------------------------------ +---------- +>GCF_005280335_PROKKA_00053 +MPPQ--PPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSA +DLGVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTF +EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVA +EAFTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVY +LQAALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRL +PVLTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTS +LYNLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTA-PARCA +GAVRGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRT +PPAWSAPRPG +>GCF_020097155_PROKKA_00031 +--------------MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSS +DLGVPSHRAALLVSAGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSI +ELLMGMRLLEGMAHGGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVG +EWAGWRAGMLAVTAAGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALY +LQAALLMGGFVALYNYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRL +KVLTGSTALMAVGVVLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTS +LYNLAYYAGSSLFGWLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPS +AVAEGAAA---------------------------------------------------- +---------- +>GCF_023573625_PROKKA_00308 +MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF +EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY +LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTA-PAR-- +------------------------------------------------------------ +---------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000368.fa new file mode 100644 index 0000000000000000000000000000000000000000..a0d501baa8471ef58ab408cca26d0926ba55d347 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000368.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00303 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDI---GPERARLAAGLL +DEDAHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATS +AGA-----AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDR--EPSDAV +AEDDARQDTDHASAAPRPTATP---ADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESV +RLSSRDLPPWLRDQLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHR-GEG +>GCF_003691675_PROKKA_00011 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDI---GPERARLAAGLL +DEDAHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATS +AGV-----AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDR--ETSDAV +AEDDARQDSDHASAAPRPTAPS---ADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESV +RLSSRDLPPWLRDQLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERR-GEG +>GCF_005280335_PROKKA_00051 +MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEI---GPERARQAAALL +DEDAHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPE +EAEVRDPRTRPTPP---EPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLS +AEEGRVDDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSV +RLSSQDLPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERR-GED +>GCF_020097155_PROKKA_00030 +MEYLVPILAVVVIGGITLLVARRLS---GRSQAPTRSATGTGADTVEASPERARTAARRL +DEATHRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADD +ASPAAADMPSGPPR---GPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAP------- +GGDAAADPEADGATSRRPGRQA---PEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESV +RLASQDLPPWLRDQLSAMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG +>GCF_023573625_PROKKA_00310 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDI---GPERARLAAGLL +DEDAHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATS +AGV-----AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDR--EPSDAV +AEDDAQQDTDHASAAPRPTATP---ADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSV +RLSSQDLPPWLRDQLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERR-GEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000369.fa new file mode 100644 index 0000000000000000000000000000000000000000..a05b110bdbe5df7fffd27a4d03512c9da9e7f203 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000369.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00305 +MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAAD-HDGDVR +RDD-VRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVT----------DA +DSVVVKDEHLNVGTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEART +AGRDGDVEVTTYEETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDL +DGRNDRKDRI +>GCF_003691675_PROKKA_00020 +MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYS------AAD-HDGDVR +RDD-VRTDAGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVT----------DA +DSVVVKDEHLNVGTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEART +AGRDGDVEVTTYEETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDL +DGRNDRKDRI +>GCF_005280335_PROKKA_00032 +MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYS------NVD-HDRDVR +HDDGLRADAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDR +DSMVVKDEHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEART +AGRDGDIEVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDL +DGRTDRKDRI +>GCF_020097155_PROKKA_00028 +MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ +TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYS------AVDTHD---- +RRD-VR-DAAAAGTAGGV----VTDRERRDVVDADRRDVVDNDRRDLV--------DGDA +DSVVVKDEKLNVGTERRATGRVRLRKQSYTTTETVEVPVTREEVVVERESVDPNSAEART +AGRDGDIEVTTYEETPVVNKTVEAEKVSLGKRTVQDTETVSEELTHEDVKIDGD----DV +DGR-----RR +>GCF_023573625_PROKKA_00312 +MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ +TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYS------AAD-HDGDVR +RDD-VRTDAGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVT----------DA +DSVVVKDEHLNVGTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEART +AGRDGDVEVTTYEETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDL +DGRNDRKDRI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000373.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5a56cf0fc35b03bacf71a6f50d2f664d9219c34 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000373.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00311 +-MRGPFARFRQERADDRELGTGLWRRAHDRLGRAMDRYWQVLAGQRGTDVLSPEERNGVV +HAGNVLTERLPAVRALCVRLHRDHEGDGE-HIPAEAADVHRELSRAAHELAATAQALALY +RLGQGSAESVGRHAERTLGHLDRAEELGAGL +>GCF_003691675_PROKKA_00026 +-MRGPFARFRQERADDRELGTGLWRRAHDRLSRALDRYWQVLEGQRGTDVLSPEERNGVV +HAGNVLTERLPAVRALCVRLHRDHEGDGE-HIPAEAADVHRELSRAAHELAATAQALALY +RLGQGSAESVGRHAERTLGHLDRAEELGAGL +>GCF_005280335_PROKKA_00026 +-MRGPFARFRQSCSDDRELGTGLWRRAHDRFVRAMDRYWQVLEGDRGPDLLRTEQRNGVV +HAGNVLAERLPAVRALCVRLHRDHAGDGE-HIPPEAADVHRELSRAAHELAATAQALAMH +RLGQGSSDSVGRHAERTLAHLDRAEELAARL +>GCF_020097155_PROKKA_00022 +MIRGPFARFRQGRSDDRELGTGLWRRSHDRYVRALDRYWQVLEDGRSAGGFTPEERNGLV +HAGNVLAERVPAVRALAARLHAAHPGDGEQHIPPVTAPVHRELSRASHELAAAAQAVAMF +RRGVSGSEAVSRHAQRTLDHLDRAEGLAADL +>GCF_023573625_PROKKA_00318 +-MRGPFARFRQERADDRELGTGLWRRAHDRLGRALDRYWQVLEGQRGTDVLSPEERNGVV +HAGNVLTERLPAVRALCVRLHRDHEGDGE-HIPAEAADVHRELSRAAHELAATAQALALY +RLGQGSAESVGRHAERTLGHLDRAEELGARL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000375.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0201db848b7b4cd75ca99f657bac7c2c0551b1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000375.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00314 +MTA-SAPVPPVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ +CEVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWR +IFLMEDADRMTERATNVLLKAIEEPPARTIWMLCTPSPADVLPTVRSRCRLITLSIPAVE +QVAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDA +MALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRR +RRRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGTAGDSAEVLAR +IDAVTTTRERIAANVPEQLALEAMMLALLPRRVRTPRRR- +>GCF_003691675_PROKKA_00029 +M---TAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ +CEVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWR +IFLMEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVE +QVAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDA +MALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRR +RRRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLAR +IDAVTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR- +>GCF_005280335_PROKKA_00023 +MTALPDAVPAVFADLAGQGSAVEQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ +CEAPDPAARGCGRCHACRTVLAGTHPDVTVLATEAVTYRIEDVRSLVEAAQSTPATGRWR +IFLMEDADRMTERATNVLLKAVEEPPARTVWMLCTPSPADVLPTVRSRCRLVTLSIPAVE +DVADLLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLEATSVSDA +MALAATLADVSKAEAESSAEARDAEELETLRRSLGLEPGEPVPPKLRQHVKRLEEDQTRR +RRRSVRDSLDRAMIDVMGLFRDVLRVQLGAEGELINEHRRAEVEAYARGAAGDSAEVLAR +IDAVATARERIAANVPEQLALEAMMLALLPRRVRTPRRR- +>GCF_020097155_PROKKA_00019 +MTG----APDVYSDLAGQDAAVAQLRRAATEDRPTHAWLFTGPPGSGRSTAARAFAAALQ +CEQPDPANRGCGACHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAAQSTPATGRWR +IFLMEDADRMTERATNVLLKAIEEPPPRTIWMLCSPSPADVLPTIRSRCRLVTLRIPAPE +DVAALLHRRDGLDEATALMTARISQSHVGMARRLARDPEALARREDVLSLPLQATAVSDA +MAMAARLAEVSHAEAESSAAARDAEELAALRRQLGVAEGEAVPPKLRQQVKRLEEDQSRR +RTRVTRDALDRAMIDVIGLFRDVLRVQLGAGGDLVNEHRRAEIERYAAGAAGSSAEVVAR +IDAVHLARERLGQNVPEQLALEAMMLALLPARVRTPRGRR +>GCF_023573625_PROKKA_00321 +M---TAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ +CEVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWR +IFLMEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVE +QVAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDA +MALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRR +RRRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLAR +IDAVTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000377.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd766d9314d596af7e8959be0cde22314b7b74e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000377.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00316 +MHVALLFDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG +LLGVLAG--GGMGMFGLVAACVACVYLAGPRQDM---GPALRR +>GCF_003691675_PROKKA_00031 +MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG +LLGVLAG--GGMGMFGLVAACVACVYLAGPRQDM---GPALRR +>GCF_005280335_PROKKA_00021 +MHLALTFDQWLFRILAIVGLVLEVWAFLDALRRSPGDFARIGGRDKSFWMILTGVAAAVG +VLGVLSG--GGMGMFGLLAACVACVYLAGPRQEM---GPATRR +>GCF_020097155_PROKKA_00017 +MHLAIVAGNWLFYALAVVAFLLELWAFADAARTSQETFLRTGGRTKGFWLALTGAAAAVG +LVGVLLGPTGGFGILGLAAVCVASVYLAGPRDDLRFYGGRRGR +>GCF_023573625_PROKKA_00323 +MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG +LLGVLAG--GGMGMFGLVAACVACVYLAGPRQDM---GPALRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000384.fa new file mode 100644 index 0000000000000000000000000000000000000000..6230e839b2b85cc5c9339110c8aeb1c24bdde581 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000384.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00324 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLDLDAVVVLTPP +AGADAGRVAAEVDAGPR--LDVPVHCVPGGAERADSVRAGLAAASHALADLA-PAG-APR +RVLVHDAARALTPPSVFGAVTAALETGAVAAIPGLPLTDTVKQVTPGRGGVDVVAATPAR +AGLRAIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFK +VTAPADLDLARLELARRA----PQEEAPMDQ------------PARPAAAPAP---LPRV +GIGTDVHAWAPEDAPRPLWLGGIHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV +FGVDRPEMADASGADMLREVLRLLTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAAL +GGAPVSVSAATTDRLGFIGRKEGLVGIATALVIPAA +>GCF_003691675_PROKKA_00039 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLGLDAVVVLTPP +AEADAGRVAAEVDAGPR--LDVPVHCVPGGAERADSVRAGLAAASGALADLA-PAG-APR +CVLVHDAARALTPPSVFGAVTAALGTGAVAAVPGLPLTDTVKQVTPGRGGVDVVAATPAR +AGLRAIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFK +VTAPADLDLARLELARRA----PQEEAPMDQ------------PARPAAAPAP---LPRV +GIGTDVHAWAPEDAPRPLWLGGIHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV +FGVDRPEMADASGADMLREVLRLLTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAAL +GGAPVSVSAATTDRLGFIGRKEGLVGIATALVIPAA +>GCF_005280335_PROKKA_00013 +MPTALVIAAAGAGTRLGAGMPKALVPLADGRTLLRHCLDSVAAARAAGAAVDAVVVLAPP +AEEDAARVAAEVDAGPG--LGAPVACVPGGAERADSVRAGLAAAADALNALG-PAA-GPR +RVLVHDAARALTPPAVFAAVEAALDAGAVAVVPGIAVTDTVKQVAPGPGGAEVVTTTPPR +AALRAVQTPQGFDLDALLAAHEAVRADPALDAAALTDDAMVMEAAGHPVAVVAGDAAAFK +VTAPADLELARLELARRADAPTPEEDPAMDQYGTAPGTGPEADAATDPAGPRPGAALPRV +GVGTDVHRWAPEDAPRPLWLGGVHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV +FGVDRPEMADASGTAMLAEVLRLLTEAGLAVGNVAVQVVAPRPKVGTRRAEMEAALSAAL +GGAPVSVSAATTDRLGFIGRGEGLVGIATALVAPTA +>GCF_020097155_PROKKA_00009 +MPTALVIAAAGSGTRLGAGVPKALAPLTDGRPLLDHCLESVAAARATGLGLDALVVLVPP +A-ADHARAVADVVARHETAVGAPVTCVPGGVERADSVRAGLAAADAALADRGHPAGQGVR +HVLVHDAARAFTPPAVFEAVAGALVSGEVAAVPGLPLTDTVKEVT-GADGREVVVATPAR +SALRAVQTPQGFDLDVLLAAHAAAQADPAADAAALTDDAMAMEAAGHAVVVVPGDERAFK +VTSPADLEAAARILAVRD----AQSGPGTPS------------PAAVPAAP-P---LPRT +GIGTDVHRWAPDDAPRPLWLGCVEWPGQNGVAATSDGDVAAHAACNALLSAAGLGDLGAV +FGVDRWEMRGASGAAMLAEVLRLVTEAGCRIGSVAVQVVAPRPKVGTRRAEMEAAMSAAL +GGAPVAVSAATTDGLGFIGAGEGLVGLATALVVPAA +>GCF_023573625_PROKKA_00331 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLHHCLASVATARAAGLALDAVVVLTPP +AEADAGRVAAEVDAGPR--LDVPVHCVSGGAERADSVRAGLAAASYALADLA-PAG-APR +RVLVHDAARALTPPSVFGAVTAALETGVVAAVPGLPLTDTVKQVTPGRGGVDVVAATPAR +AGLRAIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFK +VTAPADLDLARLELARRA----PREEAPMDQ------------PARPAAAPAP---LPRV +GIGTDVHAWAPEDAPRPLWLGGIHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV +FGVDRPEMADASGADMLREVLRLLTEAGVAVGNVAVQVVAPRPKVGTRRAEMEAALSAAL +GGAPVSVSAATTDRLGFIGRREGLVGIATALVVPAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000385.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6ba5215d9b525de01dd4cdf4bffdc25bda4ac7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000385.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_00325 +MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD +>GCF_003691675_PROKKA_00040 +MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD +>GCF_005280335_PROKKA_00012 +MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL +RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM +ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV +PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT +WRLAD +>GCF_020097155_PROKKA_00008 +MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL +RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR +RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD +VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM +ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPEL-TAPLAEH +VPAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDV +PEASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGAT +WHLAG +>GCF_023573625_PROKKA_00332 +MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000386.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000386.fa new file mode 100644 index 0000000000000000000000000000000000000000..481c94062bd9b69806b6641e1e884ade3d8537d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000386.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00326 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRG----PVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALR +LCLEQGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTP +PLLIALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA +GNLNTTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI +VSIPIDSTMESLNASMAVGISLYEISVQRAGGR---- +>GCF_003691675_PROKKA_00042 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRG----PVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALR +LCLEQGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTP +PLLIALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA +GNLNTTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI +VSIPIDSTMESLNASMAVGISLYEISVQRAGGR---- +>GCF_005280335_PROKKA_00009 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGKGPTPKAEDRVYHKAYRAKQLSERSAA +KRGG---PVRPS---RPKLTDETVSGRNPVVEALRAGIPAKALHVAVRIEMDDRVKEALR +LCLEQGVPVMENTKPELDRLSGEAIHQGLVLQIPPYEYADAMTLATDALEKHEKGHLRTP +PLLIALDGITDPRNLGAIIRSGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA +GNLNTTLVELHRAGYFVLGLDGGGDVSLPGLSLATEPLVLVVGAEGKGLSRMVREHCQQI +VSIPINSDMESLNASMAVGISLYEISVQRAGGR---- +>GCF_020097155_PROKKA_00007 +MSTAPRSGGSRAPKGKKGPQKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KHGGGRVPVRDQVRGRVKLTDETVSGRNPVVEALRAGIPAKALHVATRIEVDDRVKEALR +LCAENKVPVMENTRPELDRMSGEAVHQGLVLQIPPYQYADALTLGREAMEAQEKGHLRTP +PLLIALDGITDPRNLGAIIRSASAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA +GNLNTTLVELHRMGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI +VSIPIQSEMESLNASMAVGISLYEIAVGRAGGRPVAS +>GCF_023573625_PROKKA_00333 +MSTAPRSGGSRKPKGKKGPVKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRG----PVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALR +LCLEQGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTP +PLLIALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA +GNLNTTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRLVREHCQQI +VSIPIDSTMESLNASMAVGISLYEISVQRAGGR---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000387.fa new file mode 100644 index 0000000000000000000000000000000000000000..2649b004ddc53112827b2cec172460a9ce52ef3f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000387.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00330 +M---K------PDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSVRATVRLLDPAG +AEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAATVKIAAGIDVELMLAEGAALFRRAAEDAERSA +EDRAVFEEVVRGLEDESLIPAQRLASAESAEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEA +SGTWSSGTFATAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDAAHPDLGTVEDF +EAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAENPPKKYQDIYPLNFDNDPDGLAQAVLDVVRGW +VARGVHIFRVDNPHTKPLWFWEWLIAKVRAEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEIS +HETPAFYRPNLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNEKYEYRPRDWEG +AEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRSARPEGAHRDAEAVTDAGPAEDTLIVVVTTNP +HDVAEATLDLDLEALRLRPEDRDASGAVEVEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRIVRNG +>GCF_003691675_PROKKA_00046 +M---K------PDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSVRATVRLLDPAG +AEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAATVKIAAGIDVELMLAEGAALFRRAAEDAERSA +EDRAVFEEVVRGLEDESLIPAQRLASSESAEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEA +SGTWSSGTFGTAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDAVHPDLGTVEDF +EAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAENPPKKYQDIYPLNFDNDPDGLAQAVLDVVRGW +VARGVHIFRVDNPHTKPLWFWEWLIAKVRAEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEIS +HETPAFYRPNLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNEKYEYRPRDWEG +AEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRSARPEGAHRDAEAVTDAGPAEDTLIVVVTTNP +HDVVEATLDLDLEALRLRPEDRDASGAVEVEDLLTGQRWRWGRTPYVRLDPNVEPAHVLRVVRNG +>GCF_005280335_PROKKA_00005 +MSNSK------QAAQSTPVPDVRLQTVTGRIPVTGVQPVVQDGRFPAKAVVGEDIPVRATVFGEGHDAVRATVRLLDPSG +AEVQRVHMRPGRPGLDEFLATLRPSETGVHHFVVEGWHDPVGTWLHAATVKLAAGVDVELMLAEGAALFRAAAEDAERSA +QDRAAFEETARVLADEGLVPAQRLAGAESAELAAVLGARPLREHVTSSELLPLDVQRELAGRGGWYEFFPRSEGARFDEA +AGTWSSGTFTTAARRLPAVARMGFQVVYLPPIHPIGTAHRKGPNNTLTAGPQDPGSPWAIGAAEGGHDAVHPDLGTIADF +EDFVAAAADEGLEVALDLALQCSPDHPWVAEHPEWFTTRVDGTIAYAENPPKKYQDIYPLNFDNDPEGLAQAVLEVVQGW +VGRGVHIFRVDNPHTKPLWFWEWLIARVRAEEPRVVFLAEAFTRPAMMHALGTVGFQQSYGYFTWRNTAAELAEYLEEIS +HETPAFYRPNFFVNTPDILTEYLQHGGPGAFRIRAVVAALANPLWGVYAGYELFEHVARPGAEESIDNEKYEYRPRDWEG +AEAAGASLAPYLTRLNEIRAAHPALRDLQNLTLHRSTHQDLLVFSKTRTARPEGEHRDAEAVTDAGAHEDTVITVVTVNP +HHVAEATLDLDLSALRLRPEDLDESGSFEVEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRVVRHG +>GCF_020097155_PROKKA_00006 +MSTSKPRPAAHPAPPAPALPDVRRTTLTGRIPVSNVQPTVEEGRFPAKAIVGEDVPVRANVYREGHDAVRATVRLLGPDG +AEVQRVHMRPGRPGLDEAVATLRPSEPGVHHFVVEGWDDPVGTWRHNASVKLAAGVDVELMLDEGAALFRAAAQDPERGA +ADRAVFEEAVRGLEDASLAPVQRFAVTQSAEVSAVLDARPVRRWVTSSELYPLDVQRPLAGRGAWYEFFPRSEGARYDEA +AGLWHSGTFRTAAERLPAVAAMGFQVVYLPPIHPIGVAHRKGPNNTLTAGPQDPGSPWAIGGEAGGHDAIHPGLGTFEDF +DAFQERVRELGMELALDLALQCSPDHPWVTEHPEWFTHRVDGSIAYAENPPKKYQDIYPLNFDDDADGLARAVLDVVLGW +VRRGVHIFRVDNPHTKPLWFWEWLIREVRAVEPEVVFLAEAFTRPAMMHGLGRVGFQQSYGYFTWRNTREELEEYLEEIT +AETAGFYRPNFFVNTPDILTDYLQHGGPGAFKARAVIAATSNPLYGVYAGFELFEHVARPGAEEYIDNEKYEFRPRDWAG +EEAAGRSLAPYLTRLNRIRAEHPALQDLQNLTLHSATDPELLVFSKTRSALPEGDHRDAAAVTDAGSAEDTVVVVVACDP +HRVAEATLRLDAEALRVRPEDRDEEGRFEVEELLTGARWRWDEQPYVRLDPAVEPAHVLRVVRRG +>GCF_023573625_PROKKA_00337 +M---K------PDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSVRATVRLFDPAG +AEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAATVKIAAGVDVELMLAEGAALFRRAAEDAERSA +EDRAVFEEVVRGLEDESLIPAQRLASAESAEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEA +SGTWSSGTFATAAGRLPAVARMGFQVAYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDAVHPDLGTVEDF +EAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAENPPKKYQDIYPLNFDNDPGGLAQAVLDVVRGW +VARGVHIFRVDNPHTKPLWFWEWLIAKVRAEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYYTWRNTAEELAEYLQEIS +HETPAFYRPNLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNEKYEYRPRDWEG +AEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRSARPEGAHRDAEAVTDAGPAEDTLIVVVTTNP +HDVVEATLDLDLEALRLRPEDRDASGAVEVEDLLTGQRWQWGRTPYVRLDPHVEPAHVLRIVRNG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000389.fa new file mode 100644 index 0000000000000000000000000000000000000000..8fe7ce0714541a381b400155ada8bae4eea32e36 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000389.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00335 +MSWWPFPR-PSASPSP-DDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQ +AAEYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQG +TEHGRLRRRLTRALTARLRAGEEL---- +>GCF_003691675_PROKKA_00051 +MSWWPFLR-SSASPSP-DDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEH +AAEYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQS +TEHGRLRRRLTRALTARLRAGEEL---- +>GCF_005280335_PROKKA_02680 +MAWWPFRG-PSGAPRD-DDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITER +AAEYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQ +TEAQRLGRRLTRALSSRLRARGEL---- +>GCF_020097155_PROKKA_02492 +MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR +SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE +GDLSHHAARLTQVLTARGRAVRELDERQ +>GCF_023573625_PROKKA_00342 +MSWWPFLH-SSASPSP-DDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEH +AAEYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQS +TEHGRLRRRLTRALTARLRAGEEL---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000390.fa new file mode 100644 index 0000000000000000000000000000000000000000..865dc1140be2ec64c4916a3c7cae505f90b68388 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000390.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00337 +MTEQTPSLEHPQVRKNAERYEIVVDEAGTVAGYTVAIDYDTGDGPT-----QRIFPHTKV +DHGYEGRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVNEH-DDVAGEVDPAGPEHLQF +LESR-----QD +>GCF_003691675_PROKKA_00053 +MTEQTPSLEHPQVRKNAERYEIVVDDAGTVAGFTVAIDDDTADGPA-----QRIFPHTKV +DHQYEGRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVDEH-DDVAGEVDPARPEHMQF +LESR-----QD +>GCF_005280335_PROKKA_02676 +MTENTPTLDAPQVRKVGEKYEIVVDGDGTVAGYTLAIDYEGTDGVA-----QRIFPHTKM +AEEYGGRGLASVLVREALKDSVAAGFRIVPVCPYVKQWTQKH-DDVAGDVDQARPEHLQF +LEEHARRRSEG +>GCF_020097155_PROKKA_02488 +MTEQTSSLDHPQVRKNAEKYEIVVDADGTVAGYTLAIDYTAEDGTAEDGTEQRIFPHTKL +EDAYEGKGLASTLVREALRDTEAAGRRIVPVCPYVKQWADKHADEVEGQVDQPRPEHLQF +LEKHAQERKQG +>GCF_023573625_PROKKA_00344 +MTEQTPSLEHPQVRKNGERYEIVVDDAGTVAGFTVAIDDDTADGPA-----QRIFPHTKV +DHEYEGRGLASNLVREALKDTVAAGRRIVPVCPYVKDWVDEH-DDVAGEVDPARAEHLQF +LESR-----QD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000391.fa new file mode 100644 index 0000000000000000000000000000000000000000..5930704b4a1a265db40fcaa306d54caed9788b1b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000391.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00338 +MTAA--DTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARGAAEQAGLDRQLVELVNLRVS +QLNGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQE +QLNYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG +>GCF_003691675_PROKKA_00054 +MTAA--DTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARAAAEQAGLDRQLVELVNLRVS +QLNGCGFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQE +QLNYVQASTAAVLTDAQYAAVQWVAMVMNLTNRISILSHHPVRRRDD +>GCF_005280335_PROKKA_02674 +MSAA--ENPATRKDPLAFYLDKAVPDAWKAVGGLAAAVRTAAEEAGLDRQLVELVNLRVS +QINGCGFCLDLHAREGAKAGLNAQRMALLPAWREAEAVYSEQERAALELAEAVTELPEQE +QLHYVQASTAAALTDAQYAAVQWAAMVMNLTNRISILSHHPVRRRED +>GCF_020097155_PROKKA_02486 +MSSPHDDAAPARKDPLAFYLDKAVPEAWVAVGGLAAAARRAAVEAGLDEQLMELVNLRVS +AINGCAYCLDVHTRKGVGAGLSDQRRGLLSAWREAPEVYTELERAALELAEAVTELPEQE +QQQYVQLSTHGVLTDAQYAAVQWLAIVMNVTNRISILSHHPVRRHDS +>GCF_023573625_PROKKA_00345 +MTAA--DTPAPRQDPLAFYLDKAVPEAWHAVGPLASAARDAAEQAGLDRQLVELVNLRVS +QLNGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQE +QLNYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000394.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000394.fa new file mode 100644 index 0000000000000000000000000000000000000000..10cce5fd9853a3bcb9b92d3b206d40477de8b2aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000394.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00341 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE +MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA +KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR +GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE +LVSYASQLITLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV +>GCF_003691675_PROKKA_00057 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEERRE +MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA +KFAQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVEDAPEHIAGYAVANDISMR +GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFSADARVLTHVNGELRQEDRVADVVFSPAE +LVSYASQLVTLNPGDLILTGTPAGVALARRDAEGRRPWLRPDDVVEVEITGLGRQRNELV +>GCF_005280335_PROKKA_02628 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPECRDVGEYLTAEPQEQRE +MVESALRAAQEDRSLLLDTSTLVYDTLIPFPTKVFCVGLNYTNHIEETGQNQPEHPTLFA +KFTQSLTGALDPVEVPEEDHLVDYEGELCIVIGEPGRRIAVEDAKEHIAGYAVANDVSMR +GWQGRTSEWLQGKVWEASTPVGPWLVTPDELTADARIITRVNGVERQDDRIADVVFSPEE +LVAYVSQMITLNPGDLIMTGTPAGVAVARKGADGRRPWLQAGDVVEVEITGLGRQRNELV +>GCF_020097155_PROKKA_02480 +MKLATFRQPDSDASYPGATFAAVLTSFHPQDPQVAVRAVALPECRDVGEFLTAEPQEQKD +MVREALEAAKEDHGLLLDVSTLVYDTLVPFPTKVFCVGLNYADHIRETGQEKPEHPTLFA +KFAQSLTGALDPIEVPEEDHRVDYEGELCVVIGEPGRRIAVEDAKDHIAGYAVANDVSMR +GFQGRTPEWLQGKVWEASTPVGPWLVTADEFPKDARIVTRVNGEVRQDGKVKDVVFSPAE +LVSYVSQLVTLNPGDLIMTGTPAGVAVARRDGDGRRPWLRADDVVEVEITGLGRQRNELV +>GCF_023573625_PROKKA_00348 +MKLATFRQPDSDAAYPGATFAAVITSVHPEDPEVAVRAVALPDCRDVGEYLTATPEEQRE +MVEGALRAAQADRSLLLDTSGLVYDTLVPFPTKVFCVGLNYTNHIDETGLERPEHPTLFA +KFPQSLTGALDPIEVPEEDHRVDYEGELCIVVGEPGRRIAVADAPEHIAGYAVANDISMR +GFQGRTSEWLQGKVWEASTPVGPWLVTPDEFPADARVLTHVNGELRQEDRVADVVFSPAE +LVSYASQLITLNPGDLILTGTPAGVALACRDAEGRRPWLRPDDVVEVEITGLGRQRNELV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000399.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000399.fa new file mode 100644 index 0000000000000000000000000000000000000000..e5675e6db0d989e118b99053563c1fbdb6a6fb68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000399.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00347 +MA-RNTSGSHTSATDARARARQIQEEQRRKDRRRRTGVIWGSVLAAVLVIGLVVAFALTR +N-GDDAAAAGPIPAAANEQGGIELTSATGLAE-GAGEREVDPSEIEVPKQA-ASSQPETL +PNTEARGDGEPTRIVLYADFNCVHCADFESSNAEQIEQWLEQGEVTVEYRMVDFLSAPNN +QNYSARAANAAYCVADQKPEAYNGFVAALFAAYDEHQGKGLDNAALTQLAQEQGVDISSC +VEDGTFRSAVEHTTRQARVAGVAGTPTVFVDGKNWALDGEDKTFTDWAGAKIAD +>GCF_003691675_PROKKA_00063 +MA-RNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNR +N-GDDAAAAGPIPAVANEQGGIELTSATDLAE-GAGEREVDPSKIEVPKQA-ASSQPETL +PNTEARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNN +QNYSARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASC +VEDGTFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG +>GCF_005280335_PROKKA_02622 +MA-RNTSGSHTSATDARARARQIQEQQRKKDGRRRTAVIWGSVLAAILVIGLIVAFALNR +G-GDEPAAAGPIPAAANEQGGIELTSATTLAE-GAGAREVDASTVEVPEQG-AAQQPETI +PAAEAPAEGEPSEIVLYADFNCVYCADFETSNAAQIEQWLEAGEVTVEYRMVDFRSAPNN +QNYSARAANAAYCVADQKPEAYNGFVTALFGTYQEHGGKGIDNAALTQLAQDNGADIASC +VEDGTFRSAVEHTTRQAQAAGVGGTPTVFMDGENWAIGGPDQSFQEWAQSKISG +>GCF_020097155_PROKKA_02474 +MASRNPA---PSEVDARARARQMQVDQQKKARRRRTATIWGAVLAAVLVIGLIVGFVVKG +NQGTEISATGPVPGVVNEEGGVEMTSATALADSGKSERQVDSSSVAVPETATAPEELTTI +PAAGEPADGEPAQIVVYADFNCVHCAEFESQNSEQLQSWLRDGKATVEYRMVNFLSAPNN +KNYSARSANAAYCVAAAKPEAYNEFTTGLFMAWEGHGGKGLSDDELIQRADALGVDIEGC +LKDNTYRPAVEWATNKAKAASVAGTPTVFVNGKNWSTDGGDKSFVDWAKPMVEG +>GCF_023573625_PROKKA_00354 +MA-RNTSGSHTSATDARARARQIQEEQRRKDSRRRTGVIWGSVLAVVLVIGLVVAFVLNR +N-GDDAATAGPIPAVANEQGGIELTSATDLAE-GAGEREVDPSKIEVPKQA-ASSQPETL +PNTEARGDGEPTRIVLYEDFNCVHCADFESTNGDQIEQWLEQGEVTVEYRMVDYLSAPNN +QNYSARAANAAYCVADQKPEAYNGFVSALFAAYDEHQGKGLDNAALTQLAQEHGADIASC +VEDGTFRSAVEYTTRQARAAGVAGTPTVFVDGKNWALDGEDKTFIEWAGAKIAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000404.fa new file mode 100644 index 0000000000000000000000000000000000000000..065aa1c063f85ac123feab77d77e46281e04e565 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000404.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00354 +MAYQPDRFDEVPEYTDQRGAHRESFAV-------AGATATG-----GG-RRLSPLLWVAG +LVLLAGLFVGVVLPWLTGDRSEPVAAESSTTA---PAAAP----STSASSVSSSASSASA +STASATESATPSEDAVEASRS--A-----------AAAESSRAAQEA--AAAEA---AES +SQAAASSRAAAEAQAAEASRSEAAAQSAEASRAAAEAQAAEASRSEAAAQSAEASRSAAA +VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSA--AVRGTHVT +VYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELG +FPVMQTPNLQVNGIAVVVTS +>GCF_003691675_PROKKA_00070 +MAYQPDRFDEVPEYTDQRGAHRESFAA-------AGATAAG-----GG-RRLSPLLWVAG +LVLLAGLFVGVVLPWLTGDRSEPVAAESSTTA---PAVEPSPSTSTSASSESSSASSASA +STASATESATPSEDTAEASRSAAA-----------AAAESSRVAQEA--AAAEA---AES +SRAAESSRAAAEA--------------AESSRAAAEAQAAEASRSEAAAQSAEASRSAAA +VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSA--AVRGTHVT +VYNATRSQGLAASYAQRLTSAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELG +FPVMQTPNLQVNGVAVVVTG +>GCF_005280335_PROKKA_02607 +MAYQPDRFDEVPEYTDQRGAHRASFAA-P-----AGAAAAG-----GGARRFSPLLLVAG +LVLLAGLFVGVVLPWLTGDRSEPVAAESSASS---PAADP----STSSEPASPTEGAATT +EPASPSEDAAAAE----ASRSQAAAQSAAEQSAAEAAAASSRAAEEA--AAAEASRSAEA +AQAAEASRSAAAA--AEASRSAGAAQAAEASRSAEAAQAAEASRSAAAA--AEASRSAEA +AQAAEASRSAAAAAEASRSAEAAQAAEASRS-AAAQAAEASRSAAAQAAA--AARSTNVT +VYNATRTTGLAASYAQRLRSAGFTSVSAQNWGGYGIQSSTVLYNGSGNQAAAEAVAAELG +FPVLQTPNLQVNGVAVVVTG +>GCF_020097155_PROKKA_02466 +MAYPADRFDDVPEYTDQSGAHRESFAAAPAAAGAAGATAAGTEAAAGG-GILKWLLAAAA +AVLLVGLFLGLVLPRLNGGDDKPVAGAASSSSSSEPAADA----SSSSSDAPSSDASSSA +GPDSAAPAAPSSD----AGAESAAAPSSDAAVESRAAAESSQAAAESSQAAADAQRSRDD +AARA-ASESAQAA--ADASSADAAARERAASESAQA--AADASRA------AEASRSAEA +SRSAEASRS----------AEASRSAEASRSAEASRSAAASRSAAAQESADRAVKSTPVN +VYNATRRNGLAASYADRLTGAGYTRVTADNWPGFRVTSNTVMYNGADKRAAAEAVGRELG +MPVQQVPNLQVPGIAVVVVR +>GCF_023573625_PROKKA_00361 +MAYQPDRFDEVPEYTDQRGAHRESFAA-------AGATAAG-----GG-RRLSPLLWVAG +LVLLAGLFVGVVLPWLTGDRSEPVAAESSTTA---PAVEP----STSASSESSSASSASA +STASATESATPSEDTAEASRSAAA-----------AAAESSRVAQEA--AAAEA---AES +SQA------------------------AASSRAAAEAQAAEASRSEAAAQSAEASRSAAA +VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSA--AVRGTHVT +VYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELG +FPVMQTPNLQVNGIAVVVTS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000407.fa new file mode 100644 index 0000000000000000000000000000000000000000..9d10b95b007be56fca321c9a909c1391dd7dab47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000407.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00358 +MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAVRQLDEDMAANRDTVSMYLAN +VAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADEPALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSS +GDGTMAVALPLQSVTSSVERVTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREEEDVAAAMQRIESEATRMTRL +VEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPDRKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYT +PAGTPIEIAVGTVDHLGGQ-AGADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ +HGGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERLPARDTDDDAAG-PPTGPLALAAPSGAGASAADAARSSRLLR +AAERFRRASAERRRRA--SAPAQAPQADPPSPGEDDPAAERDARP +>GCF_003691675_PROKKA_00074 +MRARLDAAAAHVRHPRAWLRGTWQGQSLRTKLVVMIAALMLALVAVTALATAALFRQEAVRQLDEDMAANRDTVSMYLAN +VAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADEPALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSS +GDGTMAVALPLQSVTSSVERVTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREEEDVAAAMQRIESEATRMTRL +VEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPDRKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYT +PAGTPIEIAVGTVDHLGGQ-AGADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ +HGGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAG-PPTGPLAQTAPSGAGASAADAARRSRLLR +AAERFRRASAERRRRV--SAPAQAPQADAPSPGGDDPAAGRDARP +>GCF_005280335_PROKKA_02603 +MSGRLDAAAARARLPRAWLSSAWRGQSLRTKLVMMITVLMLALVAVTAIATAALFRQEAVRQLDEDMAANRDTVSMYLAN +VAQTGEYYMPQLPILRYYGVVWDNDGDRVVQTPVVPGSDEPDLPSITPERALEIGSASFEVAGTQDESSRWRVQLYGLSS +GDGTMAVALPLEGVRSSVERVTSLVVTIGLLGTAGTVIVANLAVQRAFRALNRVERTAAKIAAGDLTQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEVSEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREEEDVAAAMQRIESEATRMTRL +VEDLLTLARLDEQRPLELAPVDLLILAMDSMMDASVNAPDRKVTLVGLDGGRAGSAPIVGDENRMRQVVVNLMANALRYT +PAGTPIEIAVGTVDPLGGPGAAGDGEGRTSVIEIRDHGLGVSEEDAARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ +HGGSVRLLETEGGGATFSVHLPWAPFEDDDDLEDEDDAGPVSESENAAEV-SHTGPLGLVAPSGAGASVVDAARRSRLLR +AGERFRRASAERRPRA--GTPAQAPAEGAASPGEEEPGPAAPDRP +>GCF_020097155_PROKKA_02462 +MGPRLGVAAARLRHPRTWLWGWWGARPLRTKLVVMITALMMVLVAVIALVTAVLFRTELLRQLDDDLSHNRDEVSIYLTT +MSQTGGYYTPQQSILRFYGVVWDTSGRAVVSTPLMPGADGPALEGMTPEQVDAQGSASFEVPGTTAGSDGWRVQLYHLRS +GEGSLAIALPLHGVRTSVERVVTLVVTIGLLGTAVSVVASNLLVERAFRALNRVERTAAKIAAGDLSQRVAYAPPSTEVG +RLSRSLNAMLAHIETAFRDKEASEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGITREEDVAAAMGRIESEAGRMHRL +VEDLLTLARLDEQRPLEHEPVDLLVLGMDSMMDASVNAPDRKVSLVGLDGGPAGSAPLMGDENRMRQVVVNLMTNALRYT +PEGTPIEIAVGTRDAFGGD-SGVDGT-RHSVIEIRDHGAGVSEEDAARIFERFYRADASRHRETGGTGLGLAIVAAIVAQ +HGGSVRLLETEGGGATFSVHLPWAALEDDADDDLDLEDDDARPGAGVPAGRPPTG----GSTAAGSAGALETGQRRRLAW +AGERFRRASAARRQAQAGTSPAQAARDGA---------------- +>GCF_023573625_PROKKA_00365 +MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAVRQLDEDMAANRDTVSMYLAN +VAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADEPALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSS +GDGTMAVALPLQSVTSSVERVTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREEEDVAAAMQRIESEATRMTRL +VEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPDRKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYT +PAGTPIEIAVGTVDHLGGQ-AGADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ +HGGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAG-PPTGPLAQTAPSGAGASAADAARRSRLLR +AAERFRRASAERRRRV--SAPAQAPQADAPSPGGDDPAAGRDARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000408.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ca11d8c74f40b2ea782652ef0246ba74df19e54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000408.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00360 +MTSQDSPTRVAGMPRTSTLPAPA----PADHRGGRGVVLVLGVAVTAVSALALVALLVAY +FL-AWPA-SPALFALALFGLPVGFGLMLLHVVLGAVRRSRP +>GCF_003691675_PROKKA_00076 +MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY +FL-AWPA-SPALFALALFGLPVGFGLMLLHVVLGAVRRSRP +>GCF_005280335_PROKKA_02601 +---------------------------------------MLGVTVTAVSFVALLGLLAAY +FF-SWPA-VPALYALAMFGLPVGFSLMLLHVVLGAVRRSRL +>GCF_020097155_PROKKA_02460 +MPS----------PRTSPQPRPDAAPAPSGARRALRVLLTAGVVLTVVSGLGLLGALAAY +FLHATPAFLPALYAVSLFGLPLGFTLMVLHVVLSAVLRARS +>GCF_023573625_PROKKA_00367 +MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY +FL-AWPA-SPALFALALFGLPVGFGLMLLHVVLGAVRRSRP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000412.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000412.fa new file mode 100644 index 0000000000000000000000000000000000000000..9bdc61218448ec8b281cbbd2364d4b36999ad27e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000412.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00364 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGMDR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPDL +LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAAATAAHVWVERLDG +>GCF_003691675_PROKKA_00080 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGTDR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSREMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPEL +LAQLAGAGVTPGRVVRAQAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG +>GCF_005280335_PROKKA_02597 +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------MGLAGTRLSEEAATPGRFRVRGLAEGVQTDPEL +LAQLAAAGVTPGRTVTAQAAIDPGYVRVEGEAADG-APESGALELAVETAAHVWVERLDA +>GCF_020097155_PROKKA_02456 +MTDLIDTTEMYLRTILELEEEGTVPLRARIVERLEHSGPTVSQTVARMERDGLVHVGSDR +RLLLTDEGRERAVAVLRKHRLAERLLSDVIGLDWAYVHDEACRWEHVMSDRVEQRLLEVL +ENPTATPYGTPIPPRPEAQSAGEWSRDLGLAGEPLATAAATPGRFRVGSLSEGVQADPEL +LAELQDAGVLPGGVLEAQPALEAGYVRVQGEGS------AEALELSAGTAAHVWVQRL-- +>GCF_023573625_PROKKA_00371 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGADR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGARLSEEAATAGRFRVRGLAEGVQTDPEL +LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000413.fa new file mode 100644 index 0000000000000000000000000000000000000000..f69b08def58dd516ae30594959704ffd346f91c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000413.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00365 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>GCF_003691675_PROKKA_00081 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>GCF_005280335_PROKKA_02596 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDAHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNALK +ADRSLESMGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>GCF_020097155_PROKKA_02455 +MRTLVLNAGYEPVSVVSDRRALLLVATGKASVLEDGDAPMHSPTRAWGRPLVILLHQYVR +VPHADAAAVSRKGVLRRDGHRCAYCGAHATTVDHVHPRSRGGQNTWENLVACCLRCNSAK +ADRSLDALGWRLRVVPTRPCGVQWRLRELERPAPAWEGWLQFAA +>GCF_023573625_PROKKA_00372 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000419.fa new file mode 100644 index 0000000000000000000000000000000000000000..363917c33bf7af40d8c8fac6aa53a4a490a647ae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000419.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00374 +MTS------EHTSE------------------------------------TRRLRS---- +-----RTSFVLLAVF-GVAAIVALLTSA----VEPWPPLVLAPGL-----------IAGL +WLLSQWHREVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWS-----RH +ARAVVTLLVLTVGSAA----GALVFVTDP--QALWVYVGMGALLTGVACVTIPVSRISFD +LMRLQDQR----AEQERAASLDAERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTD-TD +AAQRELDEAQQTLRQTMAETKALAQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRG +--EEFEHVAGVVIREGTTNILRHSDARRVEISLAPG-------HVVISNDGAAGVSAEDH +TGGLDNLRSRLAGVGGRLDVSCV-DGRFT-LGARWEADEEESV------------- +>GCF_005280335_PROKKA_01001 +MTPPSPLAPEPVPDRAPAQDPGSGHAPSPASAALPPGHRPTGALPVAPGFDRDLHRLWWY +TAAGLLSAVVVVAGF-LVFVMARRLAVAEGPDASPLAVTVLVAGIAAAVAAAVGQTLATL +RLRRAWEEEREPLRRTAVAAL-----LPALLVALTPLAVPSLSAWPVLSLWLSVCLIAPQ +AAAHVRTAVLTSGAAATLGLTALALVRTPAGPAD-SAVGVLLWWAMVLLVVLPTVWVWRV +AVRLEEAR-----AQAGELAVARERLRFAADLHDVQGHHLQVIALQAELAGRLLEKGRTD +QAGAALRDVREQAAEALGETRALVRGLRQVSVASEIENAREVLAATGAVVEVDVDPAAAR +LAREAARLVGLAVREATTNALRHAEPRRVRLALGPADGAAGGVRLTVTNDGARPPAA-PP +GTGLAGLAARAAEVSGRLSAGPDDDGGFR-LELTVPSSSGATTR-TDPTTTTGEDA +>GCF_005280335_PROKKA_02588 +MTS------EPTSE------------------------------------TRRLRS---- +-----RTSFVLLAVF-GVAAIVALLTSA----VEPWPPLVLAPGL-----------IAGL +WLLSQWHREVAAPTRWAVLALGTLTWALSALWELTPLGALAFALAGALEVMWS-----RH +ARAVVTLLVLTVGAAA----GALVFVTDP--PALWVYVGMGALLTGVACVTIPVSRTSFD +LMRLQDQR----AEQERAASLDAERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTD-TD +AARRELDEAQQTLRQTMAETKALAQDGHTLTLRGELANSVALLEAAGITVTTDDDGDPRR +--EEFEHVAGVVIREGTTNILRHSDARRVEISLAPG-------HVVISNDGVAGAPAEDH +TGGLDNLRSRLAGVGGRLDVSCG-DGRFT-LEARWEADEEETV------------- +>GCF_020097155_PROKKA_01178 +MSP-------------------AGGPPAPARPTVGTAEHDPAVLP--------LHL--WP +STMGFAGVWLISFGFVLVELLRRAFTPGDGRGEAILGVAAIAVFILVYLAA-----FVVP +RPVRAWPAWANTVLTWFVLAG-----CVAVLTRIL----------GVHALLYSPFLVATW +IFPHRLRVGLTGAGATMAAALATGLLFFPGDPA----LPVVLGNLAVLLVVL-------V +GMRLAIARDDRVVEMTHELDLAGQRERLGRDLHDILGHSLTTINVKTQLVHRLIDTD-PA +RAKEEAAEVIALSRTALAEARAAVAELAAPELGGQLSLSVGALRDAGMAVEAPPPGAVTE +VPQRRRALAAWIVREAVTNVLRHAGARRVRISLDAH-------HVAVLDDGAGLPAAVVA +GVGPRTLAERAAAEGARLEVGPGLGGAGTGVAVHWGGTTPEAARGVLPATEGRMDA +>GCF_023573625_PROKKA_00381 +MTS------EHTSE------------------------------------TRRLRS---- +-----RTSFVLLAVF-GVAAIVALLTSA----VEPWPPLVLAPGL-----------IAGL +WLLSQWHREVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWS-----RH +ARAVVTLLVLTVGSAA----GALVFVTDP--QALWVYVGMGALLTGVACVTIPVSRISFD +LMRLQDQR----AEQERAASLDAERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTD-TD +AAQRELDEAQQTLRQTMAETKALAQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRG +--EEFEHVAGVVIREGTTNILRHSDARRVEISLAPG-------HVVISNDGAAGVSAEDH +TGGLDNLRSRLAGVGGRLDVSCV-DGRFT-LGARWEADEEESV------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000421.fa new file mode 100644 index 0000000000000000000000000000000000000000..00ea436ef5a9f5bd7bae7a16f4d6ce20a094e257 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000421.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00379 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG +>GCF_003691675_PROKKA_00103 +MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE +GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>GCF_005280335_PROKKA_02576 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>GCF_020097155_PROKKA_02448 +MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK +RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE +HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG +MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA +SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA +AAVTYLLGLLVGGSIG +>GCF_023573625_PROKKA_00385 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000422.fa new file mode 100644 index 0000000000000000000000000000000000000000..6821e6b3a985b101fba87d8ac3fdf7fe5da39d09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000422.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00380 +MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLLAAVVLPRG +>GCF_003691675_PROKKA_00104 +MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLMLAVVLPRG +>GCF_005280335_PROKKA_02575 +MDAAETPEGPEATAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVALSTVLLVLAALLAVGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLMLAVVLPRG +>GCF_020097155_PROKKA_02447 +MDAAETPDGPEAAAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVALSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLMLAVVLPRG +>GCF_023573625_PROKKA_00386 +MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLLAAVVLPRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000423.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2cfc21d88f9bb3efd54741724b22501e39f1624 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000423.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00381 +MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA +>GCF_003691675_PROKKA_00105 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA +>GCF_005280335_PROKKA_02574 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA +>GCF_020097155_PROKKA_02446 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA +>GCF_023573625_PROKKA_00387 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000424.fa new file mode 100644 index 0000000000000000000000000000000000000000..c33fafd9020c01b24224b1913135b88e55645eb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000424.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00382 +-----------------------MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG +VILKIVATNICGSDLHIYRGSFPAPEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNV +ACGRCRNCRAGRTEICETANPDQACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQ +AMEKILDLTVLSDILPTAFHGLVEAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG +DQDASRLELVRKHGCETIDLSTTENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEM +QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA +PVMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR +>GCF_003691675_PROKKA_00106 +-----------------------MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG +VILKIVATNICGSDLHIYRGSFPAPEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNV +ACGRCRNCRAGRTEVCETTNPEQACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQ +AMEKILDLAVLSDILPTAFHGLMEAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG +DQDASRLELVRKHGCETIDLSTTENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEM +QPIAAVNQVLDVTRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA +PIMRYNRQLMMSILWDRMPYLTELVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR +>GCF_005280335_PROKKA_02573 +MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG +VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV +ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ +AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG +DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM +QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA +PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR +>GCF_020097155_PROKKA_02445 +-----------------------MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG +VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV +ACGRCRNCRAGHTEICETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ +AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG +DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM +QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA +PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR +>GCF_023573625_PROKKA_00388 +-----------------------MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG +VILKIVATNICGSDLHIYRGSFPAPEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNV +ACGRCRNCRAGRTEICETANPEQACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQ +AMEKILDLAVLSDILPTAFHGLMEAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG +DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEM +QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA +PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000428.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000428.fa new file mode 100644 index 0000000000000000000000000000000000000000..91eb3dc2d6731df235002c1b6b516203db41f958 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000428.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00388 +MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA +VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR +RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQ-TD +>GCF_003691675_PROKKA_00112 +MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLRRVRHARLGLA +VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR +RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQ-TD +>GCF_005280335_PROKKA_02568 +MTPQHHDTADAPSMQRPDPVAEPGDHLMFEHPDGEPVLVLDEDQVWRLLRRVRHARLGLA +VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR +RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGTHPERNESQ-TD +>GCF_020097155_PROKKA_02439 +MTEH-----TTPSMQRPDPAVGPGS--MFPHPEGEPVLKLTDEQIWKLMRGVRHARLGLA +VGGEPDIVPVNVRAVDGVVWFRTAPGSKLAELTVNPRVVVQADGILSDQAWSVLLHGTAR +RADTAEEIAEAESMGIRPWVPTIKDFYVKVEVDSATGRHFLLGEQPERDGAEPTD +>GCF_023573625_PROKKA_00394 +MTQQHHDTDDAPSMQRPDPVAEPGDHLMFEHPDGEAVLVLDEDQVWRLLGRVGHARLGLA +VDGRPDIVPVNVRAHDGAIYFRTAPGSKLAELTVNPRVVVQADGILADQAWSVLVHGTAR +RLDTEAEIAEAESLGIEPWVPTLKDFYVRVDVQRVSGRHFVFGPHPERNESQ-TD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000430.fa new file mode 100644 index 0000000000000000000000000000000000000000..238655f89ebcf57296eb965e41dde0a36913acea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000430.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00391 +MPAASDAPTPA----PRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMA +FTGYGSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGD +LRTTVRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDD +TVVVTSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQT +LTRFLGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQH +DPEIYAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRRSTPGIPWCYGPDGATLSNQ +LEDLGILPVEFVDVQPEAWREDILGDDEAPATLD-------AAAQRDDRSTD--EEAAR- +-------------------------- +>GCF_003691675_PROKKA_00115 +MPAASDAPTPA----PRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMA +FTGYGSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGD +LRTTVRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDD +TVVVTSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQT +LTRFLGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQH +DPEIYAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQ +LEDLGILPVEFVDVQPEAWREDILGDDEAPATLD-------APGQRDGRPAD--EEAAR- +-------------------------- +>GCF_005280335_PROKKA_02565 +MSAVSDAAPVS----PRRTRLAALGDPTPVENVATHLQEGWNRWHRSRALRAGHVPTIMA +FTGYGSTSWVRILSRVVIAPDEEFLNGRRISKVVADGVRGWRNFVAPPMAYAEVEVEVGG +TRTTVRTDRMGVVDAVLDVEMEPGWRTATLHV-GDDEHVTMDLYICHPDARIGLVSDIDD +TVVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRVAELEPKAPVLYLSTGAWNVAQT +LTRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKKTQLERLAEQFPDIKWILVGDDGQH +DPEIYADFAQRHPDRVAAIVIRQLTPSEALLAGGRAEDTRRSTPGIPWCYGPDGASLSNQ +LEDLGILPVGFVDVQPEGWKEDILGDDEVLSAAE-------HGAAALGDEADAPDTAAEP +RVPAGEAAVGDGAADEAEAAEAGGSR +>GCF_020097155_PROKKA_02436 +MPASESASIAAQNDPARRQRLAAAGGPTPAENVATHLQEQWNRWHRSRALRRGFVPTVMA +FTGYGTTSWVRVLSRVVLAKDEDFLNGRRLSKVVADGVHGWRNFVAPPMAYAEVEVEVGD +LVTTVRADRMGVVDVVLDVELEPGWRTAVLRV-GDEEEVTTDLYIASPDAKVGLVSDIDD +TVVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRIAAAEPMAPVLYLSTGAWNVAQT +LTRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKVTQLERLAQQFPDLQWILVGDDGQH +DPEIYADFATKHPDKVKAIVIRQLTPSEALLAGGRAEATRHSTPGIPWCYGPDGAALSNQ +LEDLGILPVDFVDVHPEGWLEDILGEDEASAAGRDGDEHGVHGGRADQDEARDVDVSAQ- +----------D--------------- +>GCF_023573625_PROKKA_00397 +MPAASDAPTPA----PRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMA +FTGYGSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGD +LRTTVRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDD +TVVVTSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQT +LTRFLGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQH +DPEIYAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQ +LEDLGILPVEFVDVQPEAWREDILGDDEAPATLD-------AAAQRDGRSAD--EEAAR- +-------------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000432.fa new file mode 100644 index 0000000000000000000000000000000000000000..3abb4bca877cbb491bbb62ac4791b9a1c3aaf0f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000432.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00393 +--------MTLLSDHSRALLPGRGPLLCAADPHDGAARRRLERAWTRGVLVRLCPRVYIS +VSDWAALRPWDRTVVSAVALSIARPETVFTGLTAARLHGLGPAVEPPALELRAPSPGHHG +AGPLTRRPFAPSLMAHDRRPPGLP--------------------RRRPRWGLP--EADPA +APQR---VEAVLSDGQSLGTVLADPLPTVLLVLGAATPFRDAVATLDALVRARPEEAARW +ARQAESRLGSAAALRRFERAWHFADARAESAGESYSRAIVHELGFVPPTALQHRHRDANG +REVARTDFWWEQVRVYGEFDGLGKYDLSFFDGDDTARRASIRREKEREVALQLVTRAGAH +WTWGDLLRPDRLARILTAAGVPRSV----------------- +>GCF_003691675_PROKKA_00117 +--------MTPLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLSPRVYIS +VSDWAALRPWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPALELRAPSPGHHG +CGPLTRRPLAPSLVAHDRRLPVPP--------------------RRRPRWGLP--EAAPT +GPQP---VEAVLSDGQSLGTVLADPLPTVLLVLGAATPFRDAVAPLDALVRAWPEEAARW +ARQAESRLGSAAALRRFERAWHFADARAESAGESYSRAIIHELGFVPPTALQHRHRDANG +RGVARTDFWWEQVRVYGEFDGLGKYDLSFFDGDDTARRASIRREKEREVALQLVTRAGAH +WTWGDLLRPDRLARILTAAGVPRSV----------------- +>GCF_005280335_PROKKA_00172 +MDDAPDPRLAPLRHDGH-LLPGHGPLLRAAPGAPTRARKALARLWAQGVLVRLGAGLYVP +LAHWCALAPWDRYTLACAGYALLHPAARFTGTTAAHLHGLPLAQTPPEIRLRSPAPGHRA +RRPLAASAFSDLADARGRRLPAPPAVRWTWNGVQAPADDGGELRRRRLASGGPEGEAPPP +GPLPPVTVEAALSDGTLLGPVTVDALPTVQLALGSGPVFREAVVPLDGLRRRLPGPSAAW +AERHADRLPTRAARERFERAWGFSDPRAESAGESLSRALIHELGFAAP-HLQRTVFGRDG +RAIGRTDFWWEEVDVVGEFDGIGKYDVDLH-ASAAERRQAITREKEREVALRRVCRDVAR +WTWADLREPAGLEAELVRAGVPR-----------------RR +>GCF_005280335_PROKKA_02563 +--------MTALADVAD-LRPGTGPLLHVARREDLAARRRLERAWTRGDLVRLAAGVYLP +APTWTALSPWDRSTASAAALALARPATVFTGLTAARLRGLPVALELPALDLRATSPGHRG +AAPLTSRPFSPALLATGGRLPRPP--------------------RRRPRWGLP--QAPGM +APEP---VEIRLSDGTGLGWGLADASATLLLVLGAATPFRNAVAPLDVLLATHP-EAQSW +AQAAEEALPTRAARERFERTWSFAAAGSESAGESYSRALMHELGFASPTALQHRHRDATG +REVARTDFWWADARVAGEFDGIGKYDLGLHRGDDAARRASIRREKEREVALQLVTRAVAH +WTWEDLRAPERLARILTAAGVPRTVCPEPTDAQRHHRRAERR +>GCF_023573625_PROKKA_00399 +--------MTLLSDHSRALLPGRGPLLSAADPHDGAARRRLERAWTRGVLVRLCPRVYIS +VSDWAALRPWDRAVVSAVALSIARPATVFTGLTAARLHGLGPAVEPPVLELRAPSPGHHG +AGPLTRRPLAPSVVAHDRRLPVPP--------------------RRRPRWGLP--EAAPA +APQP---VEAILSDGQSLGTVLADPLPTVLLVLGAATPFRDAVAPLDALVRARPEEAARW +ARQAESRLKSAAALRRFERAWHFADARAESAGESYSRASIHELGFVPPTALQHRHRDANG +REVARTDFWWEQVRVYGEFDGLGKYDLSFFDGDDTARRASIRREKEREVALQLVTRAGAH +WTWGDLLRPDRLARILTAAGVPRSV----------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000434.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000434.fa new file mode 100644 index 0000000000000000000000000000000000000000..31d0d77eae8dbefb1b308826c05fae8d493029de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000434.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00396 +MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE +VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR +RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR +LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG +RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVF---G +>GCF_003691675_PROKKA_00120 +MRVVVVAESFLPHMNGVTNSLLQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE +VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR +RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR +LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG +RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVF---G +>GCF_005280335_PROKKA_02561 +----MVAESFLPHMNGVTHSILQVLRHLRERGDEAIVIAPAASWSAGWTQRAGEGQAPRE +VEGFPVHALPSVPLSGYSSVRVAAGTVGRLRGILTAFGPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNTATLTLAPSSFTVRQLHAAGLR +RVHLWGRGVDTRRFHPVKRDDALRAELAPHGERLIGFVGRLAHEKQVEDLRVLSDLPGTR +LVVIGSGPLREQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDPSRTGWLYPPGELDELRRHVADLAHDDVKRSAFAQAAWASVQG +RTWPVLCEQLVGCYEKAVAVQDRRRRELARRLLAMPSQLTARVF---G +>GCF_020097155_PROKKA_02432 +MRVAVIAESFLPHMNGVTNSILQVLKHLRSRGDEAVVIAPAASWSAGWTQRAGAGQAPSE +VEGFPVITLPSMPLSGYASVRVAAGTVLRLRSLLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPRYAAKYGAPWLEDVLWNHVTRLHNTATLTLAPSSFTLRQLHHVGVR +RVHLWGRGVDSTRFHPAKRDEALRAELAPNGERLIGFVGRLAHEKQVADLRVLADLPDTR +LVIIGSGPLRDQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDSSRTGWIYQPGDLGELRARVADLAYDDAKRAAFAEAAWASMQG +RTWPVLCEQLVGYYEKAIHVQRRRRGELSRRLLGAPGAVASRAYRVFG +>GCF_023573625_PROKKA_00402 +MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE +VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR +RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR +LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG +RTWPVLCEQLVGYYEKAIAVQERRRVELARRLLTAPSLLAARVF---G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000435.fa new file mode 100644 index 0000000000000000000000000000000000000000..087bec951ebd121e0d7ae64c23874306c0343147 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000435.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00397 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQVGGVLWLALHAVPVTVTTAM +PTAPDHLITGTAWLVPWGLTLLPLALSWRAGRRLARASYRDQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALL +PALLFGVAALAGARREAGTWAHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGGGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPALPALGALPGTWSPWQLLLLA +VPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLSTLALAVLTGLLTGLLLLVPLALTSGTLGLGALTDLGSHVWA +VSAAVAGWVALGCAAGYLTALAVA-----GHRDGTTTVPRSGDRA-SGLRDRPSPRR----------------------- +-------------------------------------------ARD +>GCF_003691675_PROKKA_00121 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQVGGVLWLALHAVPVTVATAM +PTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYRDQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALL +PALLFGVAALAGARREAGTWAHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAQAIGGGPLGGLLVALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPALPALGALPGTWSPWQLLLLA +VPISAGVVAGVWLLREGENHLDDWLHTRHGSRAVSLTLSTLALAVLTGLLAGLLLLVPLALTSGTLGLGTLTDIGPHVWA +VCAAVAGWVALGCAAGYLTALAVA-----GHRDGTTTVPRSGDRA-SGLRDRPSPRR----------------------- +-------------------------------------------ARD +>GCF_005280335_PROKKA_02560 +---------------------------MTALLSLLAVMIPTLVVWATGGFQRPTIEGALQVGGTLWLALHAVPVTVATVL +PTAEGHVLSGTAWLVPWGLTLIPLLLSWRAGRRLARASYRDQAWQAFAGAVVGYALAGLTVAFLPGTPELRVSPWAAALL +PALLFGIAALAGARREAGTWAHLIGLDLTERIARRSQYERWAGSYAWSVVRAAVVALLVLAALSALLVAVRLAVEWPAVV +TLAQAIDAGPFGGLLLAVLQIGWLPTLTGWAIAWTAGPGFSVGSDSLYSVFGATPAAAPALPALGALPAAWAPWHPLFLA +VPIAAGVAAGVWLLREGENHLDDWLDARTGHRAVSLALSTLALAVLTGLLAGLLLLVPLALTSGTLGVGTLTDIGANVWA +VCAAVAGWVALGCAAGYLVALALA-----GRR----FIPPA--EA-AVAAERPRPRR----------------------- +-------------------------------------------SRD +>GCF_020097155_PROKKA_02431 +MS--PRVPSLLRPVPLPLWLQGVVEALVTALTSLALVLVPTLAVWITGGFSSTRIEDVLQTGGALWLGLHAVPLAVTTVV +AQADTPTVTGTVWLVPWALTALPVWLSWRAGRRLARASYREQAWQALAGAVAAYAVVALACALLPGEGRITVHPLPSVLL +PCLLFTTSAVAGARREAGTWAHLIGLDLTERIARRSQYERWAGTYAWSVLRGAGVGLAALAGLHALLVTVAVLVRWPRII +EVQQMVGAGPVGGLMLALLEIGWLPTFTAWAVAWTAGPGFAVGADGHYSVFGTTPAPVPALPLLEALPAPWAPWHPAFLL +VPVLAGAVAGWWLLREGENHLDDWIDSRITARWASLTLSTLALALLLGLVSGVAVLVPLALTNGTLGVGSMREIGSNAPL +VALAVAGWMALGCALGYLVALAVVDRPVRGRRRISLPLPGSAPRAVTGRARRLPPRRLPRGVADAEADEPEVAAPAAARE +EIPGRETPAQETPSEEPPAAARPAPRRAGAPRVPRVPRPAPRRARD +>GCF_023573625_PROKKA_00403 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQVGGVLWLALHAVPVTVATAM +PTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYRDQAWQAFVGAVGAYALVGLAVAFLPGTDELTVHPAPAALL +PALLFGVAALAGARREAGTWAHLIGLDLTERISRRSQYERWAGSYAWSVVRAAVLAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGAGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPALPALGALPGTWSPWQLLLLA +VPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLSTLALAVLTGLLTGLLLLVPLALTSGTLGLGTLTDIGSHVWA +VCAAVAGWVALGCAAGYLTALAVA-----GHRDGTTTVPRSGDRA-SGPRDRPSPRR----------------------- +-------------------------------------------ARD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000436.fa new file mode 100644 index 0000000000000000000000000000000000000000..956ba2f0169708f585bece9d7ab35b630ad1eb09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000436.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00398 +MSA--PVPSSPP--RPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALG +LVALVLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGAS +ALTVRAQQACADEFTRQVEERTGVPQLRP +>GCF_003691675_PROKKA_00122 +MSA--PVPSSPP--RPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALG +LVALVLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGAS +ALTVRAQQACADEFTRQVEERTGVPQLRP +>GCF_005280335_PROKKA_02559 +-----------------------------------------MVLSLSLVLPWKLAALVLG +LVALVLGVRVWLTSRGERRAGLPRAVAAGGMALALFGTTTAALPLLAWDATVELERCTSS +ALTVRAQQACADAFTRAVEERTGVPQLRP +>GCF_020097155_PROKKA_02430 +MSALPPVPPSAPDRRPADAA---ARARVGRLLVAQSAALLAMLGAFTLVLPFKVLTLAAA +LAALVLGVLVFTASRRTAQSLVPRAAAGAGMALALMGLTVGVFPLLLWNETAGFERCTAS +AVTVRAQQTCADDFTATVERRTGVAQLGG +>GCF_023573625_PROKKA_00404 +MSA--PVPSSPP--RPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALG +LVALVLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCSAS +ALTVRAQQACADEFTRQVEERTGVPQLRP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000438.fa new file mode 100644 index 0000000000000000000000000000000000000000..8df95436e95e7536414cdb2bcdc0a7c2129c4c51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000438.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00400 +MSSATPPRPSADGAHPGPAPDVVAPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD +AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL +AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW +WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR +AVIDRMVAATGAPRRPYTMPPAEPARSSGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY +IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA +LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD +>GCF_003691675_PROKKA_00124 +MSSATPPRPSADGAHPGPTPDVVSPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD +AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL +AIFSVFTIAGALTDSLLWFALFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW +WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR +AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY +IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA +LTVWLASVLDVPAAVLPLVLAFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD +>GCF_005280335_PROKKA_02557 +--------------------------------------------MQGRIFLIGGLGFMFD +AWDVALNGVMIPLLREEWALAPADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL +AIFSVFTLAGALTDSLLWFAVFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW +WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAEAR +KVIDRMVEATGAERREYVMPPVEQERAGGVLAQLAAVWRFSPRITAVTWALFVAIMVVYY +IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATVLIEVTGRRWLLGVSAVVASA +LLVWLASVLGVPSAVLPLVLAFGFVVQIAIPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLFFVGTLVPAMGLPAAFAVTGGLVLLACVAMLALAPETRGRALEVSAD +>GCF_020097155_PROKKA_02427 +MP-----------------PTGSHAASAAPTGEQVVQELPWRWPVQGRIFLIGGLGFMFD +AWDVTLNGVMIPLLTEEWGLSKADAAWIGTANLIGMAVGAFLWGTVADQIGRKAAFTWTL +LIFSVFTLAGALTDSLLWFAVFRFMAGIGLGGTVPVDYALVGEFTPRRLRGHVLTAMDGW +WPIGAALCGVVSAWLVGTWSDWRLPLLAMVLPALLVFLVRLGIPESPLYLMSRGREREAR +AVIDRMVERTGAEPRPYVMPAADSRAHGGLLAQLAAVWRFSPRITATAWLLFVAVMLIYY +IALQWLPTFLIEAGFAQSRAFITTSGMAAAGLVGVAVSAVLVEATGRRRLLAVSGVVASG +LLVWLASVLGVPGAALPLVLAYGFVIQIAVPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLFFVGTLVPALGLPGAFGVTAGLVVVAVLVMFAWAPETRGRALEVAED +>GCF_023573625_PROKKA_00406 +MSSATPPHPSADGAHPGPTSDVVAPDATLPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD +AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL +AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW +WPVGAALCGLVSAWLVGTWGDWRLPLMAMVLPALLVFVVRLGIPESPLFLMSRGRETQAR +AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY +IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA +LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000444.fa new file mode 100644 index 0000000000000000000000000000000000000000..6133554e46f35cd0172e903044befb08b446ddb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000444.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_00410 +MVPMPTP-------VDPVTVP---SALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPPALAVRLA +DHG-----GGRVLVTQPRRVAVRAAWRRLRTAVLAAAADSHPGADPDARARLADAAVGYAVRGDAVGGGASAVEFVTPGL +LLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGE-APLPVVSTP +AVLHPLREEHAPFRGHRLTAEGRVDRAFLDHVAATAARAHAKALEADPTVDALVFLPGVAEVETVAGRVAALAPDTEVRV +LHGRQEPADQDAALAGRTDPAVPRVVVATAVAESSLTVPGVRLVVDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR +AARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLGAVDADG +RITPHGAVLAELPLDPPLGHALLRAAPLTGPRPAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWHREADRLERL +ARRHAHHAPETREPDEPGPEA-ATAPRHSAGLVAALAFPAWIARRAGEEGAYLLASGTRAALPRDAV-GGLAGQEWLAVA +EVARVAGDAAGTGAAIRAAAPIDRSLVERAGAGLRRTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRDA +LAADGLARFDPRGRAERLRRRVHLLHRVLGAPWPDLSDTALPDLDTLVDGLAADLAAGRPLARLDAEALLRGALPWPEAG +RLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG +PYAQVRAENRGRYPKHPWPEDPAVAEPTARTNRRAL +>GCF_003691675_PROKKA_00130 +MDPMPTP-------VDPVAVP---SALSTALGRLSAGLTFAAALPELGSALDARGAAVVEAPPGTGKTTVVPPALAVRLA +DHG-----GGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDARARLADAAVGYAVRGDAAGGGASAVEFVTPGL +LLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGE-APLPVVSTP +AVLHPLREEHAPFRGHRLTAEGRVDRAFLDHVAATAARAHAEALEADPTVDALVFLPGVAEVEAVAGRVAALAPDTEVRV +LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR +AARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVALAFTAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADG +RITPHGAVLAELPLDPPLGHALLRAALWTGPRPAAEATAALALDLRAPGADLEALVASVRDGRHPEAGRWRREADRLERL +ARRHAHHSLETRAPGEPGPEATAAARRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALPRDAAGGGLAGQEWLAVA +EVARVAGDAAGTGAAIRATAPIDRTLAELAGAGLRRTEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAA +LAADGLARFDPSGRTERLRRRVHLLHRVLGAPWPDLSDAALPGLDALVDGLAADLAAGRSLARLDAEALLRGALPWPEAG +RLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG +PYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR +>GCF_005280335_PROKKA_02549 +M-PAPSPHSSRPASVDTAVAP----ALSAALERLGSGLTFVAALPDLEAALDARGAAVVEAPPGTGKTTVVPPALAVRLA +DHG-----GGRVLVTQPRRVAVRAAWRRLRSAVLDAADRT---SAPDA---LADAAVGYAVRGDAVGGGASAVEFVTPGL +LLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGEEAPLPVVSTP +AVLHPLREEHAPFRGRRLTAEGRVDRAFLDHVAATAARAHAAALDADPTVDALVFVPGVAEVEAVAGRVAARAPDTEVRV +LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR +AARLGPGTVVRCHTAAALGAAPAAPTPALAVVDLAPVALAFAAWGAPGGRGLTLPKDPPADAMAAAERTLASLGAVDTDG +RITPHGAVLAELPLDPPLGHALLRAAPLTGPRPAAEATAALALDLRASGADLEALVAALRDGRHPESRRWRREADRLERL +ARRHAHRAPETREPDGPGPEA-ATARRHPAGLVAALASPAWIARRAGEAGAYLLASGTRAALPRNAVVGGLAGQEWLAVA +EVARAAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRTEDTADWRGDRLTGRRVDRMGALVLAETPAPVAPDAAAQAVRAA +LAADGLARFDPSGRAERLRRRVHLLHRVLGAPWPDLSDTALPGLDALVDGLAADLAAGRSLAHVDAEALLRGALPWPEAG +RLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGRELVVLHLLSPAGRPLAVTADLPSFWAG +PYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRVR +>GCF_020097155_PROKKA_02417 +---MSTS-------SASHSTPDLRAALAAASARLGADLAFSASLPALEAALDARAGAVVHAPPGTGKTTAVPPAVALWLA +RRAESGGEGGRVLVTQPRRVAVRAAWRRLHGAVADALG---PESGPDT-GRLPDAVVGYAVRGDAVGRGASAVEFVTPGL +LLRRLLGDPGLEGVGAVVLDEVHERDLDTDVLFALLADLRQLRPELALTAMSATLDADALAARWATGMGE-DPVPVVRTP +SVQHPLTVEHAPFGGPRTTADGRVDRDFLDHVAATAARAHAEALDADPTVDALVFVPGVAEVEAVAGRVAALAPDTEVRV +LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGITGLATVQASRAAADQRAGR +AARLGPGTAVRCHTAAALGAAPAAPTPALAVADLASVVLAFAVWGAPGGDGLVLPEDPPADAMAAAERTLASLDAVDTDG +RITPHGTVLAELPLDPPLGHALLRAAPLTGPRSAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWRREADRLERL +ARRHAHRAPETREPDEPGPAATATARRHPAGLVAALAFPAWIARRAGEEGAYLLASGTRAALPRDAVGGGLAGQEWLAVA +EVARVAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRVA +LAADGLARFDPSGRAERLRRRVHLLHRVLGAPWPDLSDATLPGLDALVDGLAADLAAGRSLTRLDAEALLRGALPWPEAG +RLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG +PYAQVRAENRGRYPKHPWPEDPAAAEPTDRTNRRAR +>GCF_023573625_PROKKA_00413 +---MPTP-------VDPVSVP---SALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPPALAVRLA +DHG-----GGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDAQARLGDAAVGYAVRGDAAGGGASAVEFVTPGL +LLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGEDAPLPVVSTP +AVLHPLREEHTPFRGHRLTAEGRVDRAFLDHVAATAARAHAEALDADPTVDALVFLPGVAEVEAVAGRVAALAPDTEVRV +LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR +AARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADG +RITPHGAVLAELPLDPPLGHALLRAAPWTGPRPAAEATAALALDLRAPGADLEALVAAVRDGRHPEAGRWRREADRLERL +ARRHAHHA-----PGEPGPEAAATVRRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALPRDAAGGDLTGQEWLAVA +EVARVAGDAAGTGAAIRAAAPIDRTLAELAGAGLRRTEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAA +LAADGLARFDPSGRTERLRRRVHLLHRVLGAPWPDLSDAGLPGLDALVDGLAADLAAGRPLTRLDAEALLRGALPWPEAG +RLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG +PYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000445.fa new file mode 100644 index 0000000000000000000000000000000000000000..22b413e7ba7a4c08308b2f02af53c26ddba5fa5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000445.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00411 +-----------------MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA +GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPEDLPEDIGWAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQ +QRYAPPSGVSESTPAETDDFIQEVLRGERLL +>GCF_003691675_PROKKA_00131 +-----------------MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA +GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPEDLPEDIGWAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQ +QRYAPPSGVSESTPAETDDFIQEVLRGERLL +>GCF_005280335_PROKKA_02548 +-----------------MRHDTRARQRRRATLAGAVVAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA +GLDMSQPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDEV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGNNGSFMVNWPFVWPATL +GSVEEGSLPEDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGEKSEYQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ +QRYAPPSGVSESTPAETDDFIQEVLRGERLL +>GCF_020097155_PROKKA_02416 +MGDDGRHIRLASNEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA +GLDMSKPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDQV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPKDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ +QRYAPPSGVSESTPAETDDFIQEVLRGERLL +>GCF_023573625_PROKKA_00414 +MRDDGRHIRLASIEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDEIVTVPFWANTQLLWYRKSVAEAA +GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPEDLPEDIGWAVYPRTVEGKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLDLGAPRPQTPYYNEVSTAIQ +QRYAPPSGVTESTPAETDDFIQEVLRGERLL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000448.fa new file mode 100644 index 0000000000000000000000000000000000000000..6f8b2e995eaf2e23219a6629f0618a39c26c69fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000448.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00416 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDA----VAG- +>GCF_003691675_PROKKA_00136 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDA----VAG- +>GCF_005280335_PROKKA_02544 +MAHIITVAGAGPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGERTNLQ +DNVVLHADKGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKVNAATYLELSAAHREA----TAER +>GCF_020097155_PROKKA_02412 +MGHLVTVLGRTPRVDPSAFVARTAVLSGDVELGPRASAFYGVSARGDSAAIRVGEGSNLQ +DNVVLHADAGFPCTLGAGVSVGHAAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +VVLEGTQVPPGSLVAGVPAKVRRGLTEEERASLTVNARTYLDLAAAHRAAEEAEQAGV +>GCF_023573625_PROKKA_00419 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAEHSSAFYGASARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDA----VAG- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000450.fa new file mode 100644 index 0000000000000000000000000000000000000000..7552b7a5fddf17edc0b2e9376d6badec878a2cc9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000450.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00419 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERRPHAKGSGAFGEFEVTEDVSK +YTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFALRFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDS +GLRDATMQWDFWTNNPESAHQVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVGTLTLNRNPENHFAQIESAAF +SPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLPVNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDE +TGPVDDGWEADGTLTREAQALRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>GCF_003691675_PROKKA_00140 +MTEYQKKTPHATGSTRQNGAPAISDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERRPHAKGSGAFGEFEVTEDVSK +YTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFALRFYTEEGNYDIVGNNTPIFFLRDPMKFTHFIRSQKRLPDS +GLRDATMQWDFWTNNPESAHQVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVGTLTLNRNPENHFAQIESAAF +SPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLPVNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDE +TGPVDDGWEADGTLTREAQALRADDDDFGQAGTLVREVFSDQERDDFVETVSGALKGVRQDVQARAFEYWKNVDATIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>GCF_005280335_PROKKA_02540 +MTENQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLVETHQHFNRMNIPERRPHAKGSGAFGEFEVTEDVSK +YTKALVFQPGAKTETLLRFSTVAGELGSPDTWRDVRGFALRFYTDEGNLDVVGNNTPVFFLRDPMKFTHFIRSQKRLPDS +GLRDATMQWDFWTNTPESAHQVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNFSNEEAEAMA +GKNADYHRQDLFESIAKGDYPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVGTLTLNRNPENHFAQIESAAF +NPGNMVPGVGLSPDRMLLGRSFAYHDAQLYRVGAHVNQLPVNRPKNEVHNYAFDGQMWYDHTGSRSTYAPNSNGDSWSDE +TGPVDDGWEADGTLTREAQALRKDDDDFGQAGTLVREVFTDAERDAFVETVAGALDGVREDVQARAFQYWKNVDATIGQR +IEDEVNKGQGDDIPGAAGGGEARI +>GCF_020097155_PROKKA_02409 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERRPHAKGSGAFGEFEVTEDVSK +YTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFALRFYSEEGNYDIVGNNTPVFFLRDPMKFTHFIRSQKRLPDS +GLRDATMQWDFWTNNPESAHQVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVGTLTLNRNPENHFAQIESAAF +SPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLPVNRPKNAVNNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDE +TGPVDDGWEADGTLTREAQALRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>GCF_023573625_PROKKA_00422 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERRPHAKGSGAFGEFEVTEDVSK +YTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFALRFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDS +GLRDATMQWDFWTNNPESAHQVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVGTLTLNRNPENHFAQIESAAF +SPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLPVNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDE +TGPVDDGWEADGTLTREAQALRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR +IEDEVKRHEGDGIPGVEAGGEARI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000454.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ae74a8ec9f2438ee863d380aeab1ede1d8038b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000454.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00424 +M----------------------------TPRPPHP-ADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESG +LDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQV +IGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVHGLP +-PAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSF +TIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVL +ALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAG +AAGESAGPPSAAAYAHAASTAMGMVAVCWALTAAVAALDVVRRRRAARAA +>GCF_003691675_PROKKA_00145 +M----------------------------TPRPPHP-ADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESG +LDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQV +IGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVHGLP +-PAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSF +TIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVL +ALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAG +AAAESAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA +>GCF_005280335_PROKKA_02533 +MGGPVAATARRPANRRAGPVVVRAYPEAVTPRPRSADGDAAPAAFTPEQRRILTALLMPLFLALMSVSVVNVALPAIESG +LHATSADLQWVLAGYTLTFGTVLVASGRAGDLWGRKSLFLVGIGLYVAGALVSGFAADPLMLNAGRLVTGVGAGVFNPQV +VGFIQSNFSGRARGRAYGLFGTVIGLGVAVGPMLGGLLLGALGPEWGWRSTFLMNAPVGLAAIVMGVLWLPAPTRVHGLP +-AAPGPRGIAALDPVGALLLGLGAVCLMVPFIVPGTAGLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRLSF +TIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVL +ALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAG +AAAEGAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA +>GCF_020097155_PROKKA_02403 +M---------------------------TLPSP----AAAESGAFTADQRRILTVLLIPLFLALMSVSVVNVALPSIEGG +LGASSADLQWVLSGYTLTFGMVLVAAGRAGDLWGRRPLFLAGIALYVLGSLLSGLAPDPLWLNAGRLLTGLGAGVFNPQT +IGFIQSHFTGRARGRAYGLFGMVVGLGVAVGPLLGGLLLGALGPDWGWRSTFLMNVPVGVLAIVMATAWLSPDTRVKGAA +GRSGGPRGIAALDPVGALLLGGASLCLMVPFIAPGTWALLAGAAVLGVGWWLWELRVKRRAAATGVEPMVDPALFRRASF +SIGAAESTIFLSSMPAVFAVTAVFLQQGMGFSPLASGLATLPGAVVQAVASPWAGSKVPSQGARMVFGGGVVGLASLAIL +ALAFERSAAGAWSPWIVGAALAVMAVSQALILTTTQVLMMEDVAGHEAGAAGGVAQTAQRMGTALGLSVVMGAFYAALAG +AAGPG-GAPSAAGFAHAASAAVLMVGACWLVTTAIAAADLVRRRRTAR-- +>GCF_023573625_PROKKA_00427 +---------------------------------------------------------MPLFLALMSVSVVNVALPAIESG +LDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKSLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQV +IGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVHGLP +-PAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVKARAWATGVQPMVDPALFRRPSF +TIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVL +ALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAG +AAAESAGSPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAARAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000457.fa new file mode 100644 index 0000000000000000000000000000000000000000..03a577c8df1035345e22b753afdc5ba1a9e988b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000457.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00427 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR +>GCF_003691675_PROKKA_00148 +MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR +>GCF_005280335_PROKKA_02530 +--MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDD +FEAFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDP +KRTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKV +DVADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR +>GCF_020097155_PROKKA_02400 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV +AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR +>GCF_023573625_PROKKA_00430 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000458.fa new file mode 100644 index 0000000000000000000000000000000000000000..1f07fb6bd524a75ab67b3d5aaf9ce82b4d88f07d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000458.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00428 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA +DERVG---TERDGARA +>GCF_003691675_PROKKA_00149 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA +DERVG---TERDGARA +>GCF_005280335_PROKKA_02529 +MHT-VQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSG +SGKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVL +ENTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPT +VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVD +E-------TTTAGAQA +>GCF_020097155_PROKKA_02399 +MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG +SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL +ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT +VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA +AEGAGRAVAAGTGARA +>GCF_023573625_PROKKA_00431 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID +DERVG---TEQDGARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000459.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5849803f560ae477162a88caae6cbb630b8815e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000459.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00429 +MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG +ELTVMKQQDMSSAGAASGSPQEYAEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR +VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEA--GAAEIVMPESWVEDLGAGD +AEDLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGL +PESQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGF +ALIALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGI +GLGVAVGLIANQVLTT-GPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAAR +KDPIEALRHE +>GCF_003691675_PROKKA_00150 +MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG +ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR +VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEA--GAAEIVMPESWVEDLGAGD +AEDLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQAIYDITTEGL +PESQRNTYFQATAIVEDPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGF +ALIALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGI +GLGVAVGLIANQVLTT-GPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAAR +KDPIEALRHE +>GCF_005280335_PROKKA_02528 +MKATDLAGTALANTMRAKLRTFLTVVAIVIGAFTLTLTSGLGAGINKFVDNMVEGFGSPD +QLTVMKQVDPTSF-AAGGAPQEYEPDEAAAGEMFGLPLLTAADLDRIRDTEHVTEVETAR +LVEPEYIEGEDGRQWQVPFMGSSFEIGALSLAAGREPAA--DAAEVTVPQDWVEALGGQT +PEDVLGQTVTLVAADPLGKQDGVEAEVVGVTEPMASGSGSGPVPSGEVETRLHEIQTAGL +PEAQRDTFFSASVTVADMAANEAAVKAALAEEGYSAQTLEDQLGPIRGIIDAVTWVLNGF +ALIALLAASFGIINTLLMAVQERTREIGLMKALGMTGRKIFGLFTMEAVVIGLLGSLIGV +GLGVAVGVVANQVLTE-GALSGVTGLVLYAVEPLSLALIVLLIVAIAFLAGTLPAARAAR +KDPIEALRYE +>GCF_020097155_PROKKA_02398 +MKAPDLIRTALGNTARAKLRTFLTVIAIMIGAFTLTLTSGLGAGINKYVDNMVAGFGAPD +ELTVSKPAGNQMAGMTGGAPTEY-EDSAAAGEMYGMPLLTQEDLDRIGATEHVTGVETVR +IVEVQDLRGADGRRWSVPMMGGTYEIGKLSVKAGREPAADGGAMELTVPTEWVESLGGTA +PEDVLGQEVTLTTKTPLQQERTVQAEVVGVTERLPSGVGANPVPSAALEQGLHDIQTEGL +PEEQRNTYFQATAIVEGMPGNEAAVKAALSEQGYQAQTLEDQLGSIRGIISAVTWVLNGF +ALIALLAASFGIINTLLMAVQERTREIGLMKALGMTSGRIFGLFTLEAVVIGLLGSLLGV +GLGVAVGVGVNAWLTTGGPLEDVAGLVLYAVDPLALLLIVLLIVAIAFVAGTLPAARAAR +KDPIEALRHE +>GCF_023573625_PROKKA_00432 +MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG +ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR +VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEA--GAAEIVMPESWVEDLGAGD +AEDLIGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGL +PESQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGF +ALIALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLIGI +GLGVAVGLIANQVLTT-GPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAAR +KDPIEALRHE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000460.fa new file mode 100644 index 0000000000000000000000000000000000000000..9faddcf154691fe882d3273ec98902ea2df6f8cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000460.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00430 +MTTDRP---NPDPNPEQP-------A---------------------------------- +---VGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLALYVLSSLPALFGG +EESIE-RMRDSLRQSGLTPEQVEEI---APVVGASVTVGTIIVLLIGVALYALVYFNLRG +AKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWLVKAFNPQ +VAAYTRQGRRA-- +>GCF_003691675_PROKKA_00151 +MTTDRP---N--PNPEQP-------A---------------------------------- +---AGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALYVLSSLPALFGG +EESIE-RMRDSLRQSGLTPEQVEEI---APVVGASVTVGTIIVLLIGVALYALVYFNLRG +AKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWLVKAFNPQ +VAAYTRQGRRA-- +>GCF_005280335_PROKKA_02527 +MSNQNPDFTNPAYNPANPPFEGESGQAGQ-APQQGQPGQAAQYGQPGPYGQAPQYGQPGQ +YPATGTRYGTQPYGVDGR-------YGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTM +DDMMDVVMRDAASQPGVTAEDMEMV---SSFMRTAGITSIVISLIIGLGLYALVYFNLRG +VKNWARILGIVFAILGALAIFSGI-GFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSD +VAEWFRQGRPAAA +>GCF_020097155_PROKKA_02397 +MTDQNT------PYPQNP-------QGGQPAPQYGQPGQA-----------APQYGQPG- +---EGSRFGTQAYGAPGL--QYGAP---LAEPAKFRTLLKLTLASAVVYVLSALPGLFVD +QDAL---VRDQLRAQGMSAEQIDQAMQNAGMFSAMAGIGAVVGLLIALGLYALVYFGLRA +GKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMIASLVLSVLFIAVNVLWLVNAFNKD +VAAYTKQGRLPAA +>GCF_023573625_PROKKA_00433 +MTTDRP---NPDPNPEQP-------AAGGPGPYPGQ---------------NPAYGQPT- +---AGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLALYVLSSLPALFGG +EESIE-RMRDSLRQSGLTPEQVEEI---APVVGASVTVGTIIVLLIGVALYALVYFNLRG +AKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWLVKAFNPQ +VAAYTRQGRRA-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000477.fa new file mode 100644 index 0000000000000000000000000000000000000000..5054faa9d8d59eaf249f888fb2982dc00f4b7d1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000477.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00449 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL +HSVQERRQAGHHGHLDGHPDADRADTAP----AAPASPSAPPRRTAPARPAGRRTRPAPR +RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA +REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDT +EAEDTPAARADEVVNTRLPWAEGLWDSAVRAGLE---------------- +>GCF_003691675_PROKKA_00170 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL +QSIQERRQA-------GHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR +GAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA +REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET +--EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE---------------- +>GCF_005280335_PROKKA_02507 +------------------------------------------------------------ +------------------------------------------------------------ +-------MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAA +EEEIAAMQAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPR---- +--DPRPEAPAGEPVNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP +>GCF_020097155_PROKKA_02379 +MSARRPRVPRVAVPDTAPER-ATPAVVEPVVVEPAPVAPA-APEAPAP-PAPPGPQVIDL +QEAAQRRR----------------------HEATRPSPRPDAERAAAQRVA--RLREERR +RATVREHAAARRRVPLPEPVPARQLTGRSLVVLAVLIIAAVLVAPTARLMLNQQLEISAA +QQDIAEQQRRKAEYEEQIRRWDDPGYVAQQARQRLELVMPGETLYTVTGLPDESGA---- +--VPADSVP-QEKVNDRLPWVEGLWDSAVRAATE---------------- +>GCF_023573625_PROKKA_00452 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL +QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR +RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA +REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET +--EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE---------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000479.fa new file mode 100644 index 0000000000000000000000000000000000000000..e76283821dd9200dd62558fd938facec62921475 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000479.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00451 +MSLTPELSPKPRLLIVGGGYAGFQLAKELQTKVKDRGGVVTVVDPLPYMTYQPFLPEVVG +GHIVGRNVVVDLATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFELPYQDIAMTAGAT +TRVFPIKGLGEHGIGLKTVEEAVTLRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG +IETVGEMEHLIRTAVARNPRLSQSEVRIVLVEAMGRIMPEVGEDQAVGVVEHLKDRGIEV +LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANAVAKQTDFPVEERGRIEV +TPTLQVKDGENGVFEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYMAVR +HGEGEVQEYVHKSLGAVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI +LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG +>GCF_003691675_PROKKA_00172 +MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG +GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV +TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG +IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVEHLKDRGIEV +LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA +TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR +HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI +LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG +>GCF_005280335_PROKKA_02505 +MSLTPELSPKPRLLIVGGGYAGFHIAKELQKKVKDAGGVVTVVDPLPYMTYQPFLPEVVG +GHIDGRNVVVDHATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFEVPYQDVVMTAGAT +TRVFPIAGLGEHGIGLKTVEEAEALRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG +VETVGEMEHLIRTAVSRDPRVSQSEVRIALVEAMGRIMPEVSEDQAAGVVEHLKDRGIEV +LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANSVAKQTDFPVEERGRIEV +TATLQVKDGQGGVLEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYLAVR +HGEGEVQEYVHKSLGTVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI +FAGWVAETLFGRDSTSVEGQDRPFNAFRRAAGVELEPGRFERKRALESSKG +>GCF_020097155_PROKKA_02377 +MSITPDLSPKPRLLVVGGGYAGFHIAQTLQSKVKDRGGVVTVVDPRPYMTYQPFLPEVVG +GHIEGRHVIVDLQTHLKDTEVVRGAVTKVEHARKVAVVRGEDGAEFEVPYQDIVMTAGAN +TRVFPIPGLAEQGIGLKTVEEAVALRNQILERLDAAALMTDAEQRRAALTFVVVGGGFAG +IEAIAEMENLIRTAVSRNENLSQTEVRIVLVEAMGRIMPEVSEDQAQAVVAHLKGRGIEV +LLNTSLGDATGGVMKLVNMADKSEADSFRADTLVWTAGVAANGVAKQTDFPVEDRGRIEV +TPTLQIKDGE-GVLEGAWACGDVAAVPDLTGAGPGGFCVPNAQHAGRQAAQLAKNYMAVR +HGEGEVQEYVHKSLGAVAGLGFLKGVGNPMGVKLFGVPAFLAHRGYHAYAMPTLERRFRI +VSGWIAETLFGRDSTSVDGQETPFNAFRVAAGAEPVPSTLEKKRAGELAAK +>GCF_023573625_PROKKA_00454 +MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG +GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV +TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG +IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVGHLKDRGIEV +LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA +TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR +HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI +LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000482.fa new file mode 100644 index 0000000000000000000000000000000000000000..b56eccba5d2667671bf6a11aaec89c3a6c52a0d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000482.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00458 +MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD +AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTP----- +--EELTERTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA-------- +----- +>GCF_003691675_PROKKA_00176 +MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD +TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTP----- +--EELTERTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA-------- +----- +>GCF_005280335_PROKKA_02489 +MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA +TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG +AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF +FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL +GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPP----- +--EQLTDRSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGT-SGDLR-------- +----- +>GCF_020097155_PROKKA_02373 +MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA +VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH +LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF +FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL +GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL +LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL +PGEKVFRPSDEVIA--AARRDAKLDPKLDPTSFDD-------DSGP-DGDVEDGRTGSTR +TELKP +>GCF_023573625_PROKKA_00458 +MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD +AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTP----- +--EELTERTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA-------- +----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000485.fa new file mode 100644 index 0000000000000000000000000000000000000000..d46a4bfdbba633fe18079ca8e426f26f66e49005 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000485.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00461 +MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL +EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG +>GCF_003691675_PROKKA_00179 +MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL +EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG +>GCF_005280335_PROKKA_02486 +MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL +EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG +>GCF_020097155_PROKKA_02370 +MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL +EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA +>GCF_023573625_PROKKA_00461 +MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL +EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000487.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a82ed153f4ac10739461cddcf392a7767a86220 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000487.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00464 +MTPLSGLPLVLTALAAAS----PAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMA +IIVLRVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRA-GGEHLDADSEDRLRRLQEKY +PGYLQEPAPEPQAPDTGRD-- +>GCF_003691675_PROKKA_00182 +MTPLSGLPLVLTALAAAS----PAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMA +IIVLRVMVRSVRRVQQRSPEAEAMLVERHQQHLPDEVRA-GGEHLDADSEDRLRRLQEKY +PGYLQAPAPEPQAPDTGRD-- +>GCF_005280335_PROKKA_02483 +MSPLSGLPLVLTALAAAS----PAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMA +IIVLRVMVRSVRRVQQRSPEAEAMLVDRHQQHLPEDVRELAPEDEERDAQDRLRHLQEKY +PGYLQEPAPRPQSPDDGRS-- +>GCF_020097155_PROKKA_02367 +---MSLAPLALSAVSLAASVSPSAPMPAVPEPTLKPGLDKQDISPGIEGFLFTALMVVMA +IIVFRLMVRSVRRVQQRSPEAEAMLVDRHQQHLPEEVRE-GGERLDGDAHDRIERLRRRY +PGYLQDPTPEPESPDTGREPR +>GCF_023573625_PROKKA_00464 +MTPLSGLPLVLNALAAAS----PAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMA +IIVFRVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRA-GGEHLDADSEDRLRRLQEKY +PGYLQEPAPEPQAPDTGRD-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000488.fa new file mode 100644 index 0000000000000000000000000000000000000000..96b9ad12f208a2df3f0ec27a3463f3aae60602de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000488.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00465 +---------MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVL +IVLAPTATLRWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYT +PLSLALLAPDRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFF +AADAAAGWLIVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRA +VLVVA +>GCF_003691675_PROKKA_00183 +---------MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVL +IVLAPTATLRWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYT +PLSLALLAPDRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFF +AADAAAGWLIVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRA +VLVVT +>GCF_005280335_PROKKA_02482 +------MDPLTPAREPEAARRLRWRIERIRDPEHPLFKPRLRGWIHAAMAPLTLAAGIVL +IVLAPTATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYT +PLSLALLPPGKAHLLLTLVWAGAVAGVAFRLLWTDAPRWLYTPVYVVLGLAALLYIGDFF +AADVAAGWLIVAGGAAYIVGAVFYALRAPTIHREWFGFHELFHVFTVGGFVCHAVAIYRA +VLVVA +>GCF_020097155_PROKKA_02366 +MWEHGGMVTRAPSVENRTGRPLKWRIERIRDPEHPLYKPRLRGWVHAVMAPLVLVAGIVL +IVLAPGATLTWACVVYVVTGLLLFGVSATYHLVQWNETVSRVLKRLDHTNIMLVIAGTYT +PLSLAMLPADKAWTLVTAVWVGAALGVAFRLLWTDAPRWLYTPVYVALGLAAVVYLGDFF +AASVPAAVLICAGGAAYIVGAVFYALKAPTIHREWFGFHELFHVFTVGGFVCHYIAVMMA +VLAA- +>GCF_023573625_PROKKA_00465 +---------MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVL +IVLAPTATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYT +PLSLALLAPDRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFF +AADAAAGWLIVAGGVAYITGAVFYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRA +VLVVA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000492.fa new file mode 100644 index 0000000000000000000000000000000000000000..d25b52ae3021be085ded19225dea63777920fad5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000492.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00469 +MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT +GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA---- +>GCF_003691675_PROKKA_00187 +MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT +GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA---- +>GCF_005280335_PROKKA_02478 +MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA +GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV +VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG +>GCF_020097155_PROKKA_02362 +MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG +GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV +LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA---- +>GCF_023573625_PROKKA_00469 +MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT +GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000499.fa new file mode 100644 index 0000000000000000000000000000000000000000..249fb2063231b432f18b8e4b200c5ce0936614af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000499.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00477 +---------MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRALQEAGV +AVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHGWPMILKTARGGYDGKGVLKLDDADDARASAA +DGTLAAWLGAGITPLLAEALVPFSRELSAQVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLA +EELDVTGMLAVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAGVVMKNVLGGAR +EDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAVRTAESAAALLRD----DAPTTGTETEARP-- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_003691675_PROKKA_00195 +---------MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRALQEAGV +AVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHGWPMILKTARGGYDGKGVLTLDDADDARASAA +DGTLAAWLGAGIAPLLAEALVPFSRELSAQVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLA +EELDVTGMLAVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAGVVMKNVLGGAR +EDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAVRTAESAAALLRD----DAPTTGTETEARP-- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_005280335_PROKKA_02470 +---------MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRVLQEVGV +AVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHGWPMILKTPRGGYDGKGVLKLDDADDARASAS +DGTLGTWLGAGIAPLLAEALVPFTRELSAQVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLA +EELDVTGMLAVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAGVVMKNLLGGAR +EDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAVRAAESAAAVLRDGAAPDAVDASPSSPATPHP +AGGPPMTATPQNPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVI +VAGAGGAAHLPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARILASADTEEGERL +RAALTEHAAELNAQAQAKGARLRERMAADR +>GCF_020097155_PROKKA_02354 +MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVVTFDHEHVPTEHLRTLEAAGV +AVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEEVIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAA +DGTLGTWLGAGIAPLLAEAMVPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA +EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPLGGTAPRGDGTVMKNVLGGAH +EDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAEHGLSLADAERIAESTAAVLRDA---TAPSAPTPKA----- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_023573625_PROKKA_00477 +---------MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRALQEAGV +AVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHGWPMILKTARGGYDGKGVLKLDDADDARASAA +DGTLAAWLGAGITPLLAEALVPFSRELSAQVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLA +EELDVTGMLAVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAGVVMKNVLGGAR +EDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAVRTAESAAALLRD----DAPTTGTETEARP-- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000501.fa new file mode 100644 index 0000000000000000000000000000000000000000..64bd333ba9d033ec7d89cf9c751155cee935a344 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000501.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00479 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDE-----PGAVDQRIELSGRVTVNWAAK +FAGLLGAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEG----------DSPAAV +LTDRPEAWPDPSVAVFAVALPRGLEPEF-DGPAVDPAVVDVAAEIRAQPDALPGPVDHVR +PASIPAG----------ADVAPDDDGP---------RPRLTWAGVRAALEAWDAGRAVTV +RP +>GCF_003691675_PROKKA_00197 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDE-----PGAVDQRIELSGRVTVNWAAK +FTGLLGAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEG----------DSPAAV +LTDRPEAWPDPSVAVFAVALPRGLEPEF-DGPATDPAVVDVAAEIRAQPDALPGPVDHVR +PASIPAG----------TDVAPDDDGP---------RPRLTWAGVRAALEAWDAGRAVTV +RP +>GCF_005280335_PROKKA_02468 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPGE-----HGAVDQRIELSGRVTVNWAAK +TAGLLADEGLGPGDPVALDLPAHWLSHALALGVLCAGAEPADDG----------AAPAAV +LTDRPERWTDPATAVFAVALPRGLELPT-GGAVADPSVVDVAAEILGQPDALPGPVDHVR +PEALPAADVAAADGDARTDEDQDDDGP---------RPRLTWAGMRAVLQAWDAGRAVQV +RP +>GCF_020097155_PROKKA_02352 +MVSLSAPRPDGPLVTRLASSPRPALVQEPAPAGEAAGAAHGAVDQRIELSGSVTVNWAAK +AAGLLLDEGVAPGDAVLLDLPDHWLSRALALGVLCAGARPAFVAGPADRAQEAPDDAAAV +LTDRPEHWDDPVLTVVAVRLPRGIEPDFGDDDAGDPSVVDLAAEIRAQPDALPGRVDHVT +VDAVPADPADAA-------------GPLTEGGVGVGRARLDAPALRASLEAWDAGRAAHV +PA +>GCF_023573625_PROKKA_00479 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDE-----PGAVDQRIELSGRVTVNWAAK +FAGLLGAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEG----------DSPAAV +LTDRPEAWPDPSVAVFAVALPRGLEPEF-DGPAVDPAVVDVAAEIRAQPDALPGPVDHVR +PASIPAG----------ADVAPDDDGP---------RPRLTWAGVRAALEAWDAGRAVTV +RP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000505.fa new file mode 100644 index 0000000000000000000000000000000000000000..76e0bf543fa90c19f9eb925fe292513ac4a47fa2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000505.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00483 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGEAQPLKGARIAGSLHMT +VQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPER +GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP +ICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV +HEWTLGGGTEAERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY +>GCF_003691675_PROKKA_00201 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGEAQPLKGARIAGSLHMT +VQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPER +GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP +ICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV +HEWTLDGGTEAERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPFKADHYRY +>GCF_005280335_PROKKA_02464 +MTETPAESRTPDVDPAYANRATVPGAAFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGESQPLAGARIAGSLHMT +VQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNETLEDYWWTASQILTWPGAAEDPER +GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP +ICALQAAMDGYQVARLEDVVGQGDLFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV +HEWTLDAGTDSERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKSQAEYLGVDVAGPYKADHYRY +>GCF_020097155_PROKKA_02348 +MTETSSARPTPDVDPAFANRSTVPGATFDFAVRDLSLAEAGRHQIRLAEHEMPGLMALREEYGESQPLKGARIAGSLHMT +VQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAIVVGSGTPDAPAGVPVFAWKGESLEEYWWTASQILTWPGAAEDPDR +GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ +LAQEGTLLFPAINVNDSVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP +ICALQAAMDGYQVARLEDVVEQGDLFVTTTGGKDIIMAEDMLRMKDKAIVGNVGHFDNEIDMAGLGRVDGVVKTEIKPQV +HEWTFDTGTEDERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELYDGSTGQGALTGEHYEKQVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY +>GCF_023573625_PROKKA_00483 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGEAQPLKGARIAGSLHMT +VQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPER +GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP +ICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV +HEWTLDGGTEAERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000516.fa new file mode 100644 index 0000000000000000000000000000000000000000..45a582ee519babf1a95b3c16eb15a41daf28136d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000516.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00500 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGVA +>GCF_003691675_PROKKA_00221 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGVA +>GCF_005280335_PROKKA_02449 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGDA +>GCF_020097155_PROKKA_02333 +MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD +VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS +IAPLIARAIREVFEDGSVTSLFDGDA +>GCF_023573625_PROKKA_00499 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGVA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000517.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c573ef7b125a819d52171507fcd5b7cbb181ccf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000517.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00501 +MAERVE--PAHGE--DG------------GAVAAP-QPHRPRLPFWASLLLNVVVALAVV +AVVQALWVKVYSVPSGSMENTLEVGDRMLVNRTAYPDGAADAQDVVVFTANEDWA-HPMP +PEGAVENAVRTFGDLTGIGRSHEQALVKRVIGTAGQTVECCTAEGAVTVDGEPLDEPYIH +NDLPFIRDELDCESEVMSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDC +ARFVTREDIVGEVFVTVWPPTHWGGH +>GCF_003691675_PROKKA_00222 +MAERVE--PAHGE--DG------------GAVAAP-QPHRPRLPFWASLLLNVVVALAVV +AVVQALWVKVYSVPSGSMENTLEVGDRMLVNRTAYPDGMADAQDVVVFTANEDWA-HPMP +PEGAVENAVRTFGDLTGIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPVDEPYIH +NDLPFIRDELDCESEVMSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDC +ARFVTREDIVGEVFVTVWPPTHWGGH +>GCF_005280335_PROKKA_02448 +MAERVE--PVRGEDGDD------------GSVAAP-ERRRSRLPGWASVLLNVVVAIAVV +AVVQALWVKVYSVPSGSMEQTLEVGDRMLVNRTAYPDGMAASQDVVVFNANEDWA-QPLP +PEGPVENAVRTFGDITGIGRSHDQALVKRVVGTEGQTVECCTSEGRVTVDGQPLDEPYLH +NDLPFAPGRLDCESDVMSARCFGPITVPEDSMLVLGDHRSNSADSVIGCRGLPAEQAEGC +ARFVTREDVVGEVFVTIWPPSNWGGH +>GCF_020097155_PROKKA_02332 +MAHTPDAVPARDEAACDEAVRDDAAPAPASSAAAPGRRRRVQLPFWASVLLNVAVALLVV +SVVQALWVKVYSVPSGSMEQTLQVGDRMLVNRTAYPDGVAERQDIVVFDANETWGVDTVG +EEGPVEGAVRTFGDLTGIGRSHENALVKRVIGLPGETVECCTSQGAVTVGGTPLEEDYLY +EDLPFVPGTLDCTTTPRSSRCFGPVTVPERSMLVMGDHRSNSADSVYQCRGLTAEQAGDC +AHFVRDEDVVGRVFSTVWPPSNWSGH +>GCF_023573625_PROKKA_00500 +MAERVE--PAHGDDVDG------------GAVAAP-QPHRPRLPFWASLLLNVVVALAVV +AVVQALWVKVYSVPSGSMENTLEVGDRMLVNRTAYPDGAADSQDVVVFTANEDWA-HPMP +PEGAVENAVRTFGDLTGIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPLDEPYIH +NDLPFIRDELDCESEVMSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQVGDC +ARFVTREDIVGEVFVTVWPPTHWGGH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000519.fa new file mode 100644 index 0000000000000000000000000000000000000000..8048ab658da97a8aa9725550b3e2d2de855164f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000519.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00504 +MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPR- +-LTVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSP +QVVNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDW +VMGAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSD +PLRRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEH +ALVWKGQRR +>GCF_003691675_PROKKA_00224 +MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPR- +-LTVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSP +QVVNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDW +VMGAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSD +PLRRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEH +ALVWKGKRR +>GCF_005280335_PROKKA_02446 +MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPR- +-LTVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSP +QVVNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDW +VMGAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSD +PLRRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEH +ALIWKGTRR +>GCF_020097155_PROKKA_02330 +MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE +GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP +QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW +VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD +PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER +DLIWKGTRR +>GCF_023573625_PROKKA_00503 +MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPR- +-LTVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSP +QVVNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDW +VMGAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSD +PLRRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEH +ALVWKGRRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000521.fa new file mode 100644 index 0000000000000000000000000000000000000000..32432231eb8fba08b3d2ed39f28b0fb3509e21e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000521.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00506 +M-----TDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRR---STG +DDAPRLLLPAGDVHTLVALESFGPTQLAALASPVAALATAR--------PEAAAGVGWVL +PA----GDAPALPGAVGHREHAATADVVTDRLPGLRRVLVAGEYLPSGRAAVRWARQRGA +RVGVVQHGLLAVSTPPVPRDATLYAFTSADADWWTQGRADVEAVAVGSALLEQARRAA-- +--PAPSDTAGDGPGVFLGQLHGAELPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQH +AAWRRAGVRIDDAGAPLVATRGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRY +GMTRWRPGRTPEPTPPLASPTADPAAAIAEHVWKESA +>GCF_003691675_PROKKA_00226 +M-----TDAPLFWRSGDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALARRG---STG +DDVPRLLLPPGDVHTLVALESFGPTQLAALASPVAALATAR--------PEAAAGVGWVL +PA----GDAPALPGAAGHREHAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGA +RVGVVQHGLLAVSTPPVPQDATLYAFTSADADWWTQGRADVEAVPVGSALLEQARRTA-- +--PALSGAGDDGPGVFLGQLHGAELPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQH +AAWRRAGVRIDDAGAPLVATRGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRY +GMTRWRPGRVPEPTPPLASPTTDPAAAIAEHVWKESA +>GCF_005280335_PROKKA_02444 +MSGVGSGDVPLFWRPEDLPAWQRWQRAQWPASRRLADTARRLARAGRGALAAGRGAAPAP +ESGLRLVLPAGDVHTLVGVESAAPTQRAALVEPVRALAEGRAGHAAADAARTAAGVGWVV +PADVVAAQLPDLPGSDALSVHAVDDVMVAERLGGLRCVLVAGEYLPAGRAAVRWARERGA +RVGVVQHGLLAVSTPPVPRDVALYAFTDHDAHWWTQGRTDVQAVAVGSALLEAARRMASH +A-VADAVPRAAGPGVFLGQLHGAELPRTDFARAAQEYVRATGAAYRPHPAERDRLSLAQH +EAWRKAGMRIDATAGPLASTAGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWERY +GMTRWRPGVETEPTPPLASPSADPAAAIAAHLWKETA +>GCF_020097155_PROKKA_02328 +MTR-AVAQPPLFWRAEQLDAWRRWQRTQWPLARRAADLVRGGVARSRGAV-------QAP +DAGLRLLLPAGDVHTLIAVESAGPTQRAALVEPTRALAEGRTGLDAAARTRLLGGVAWVV +PADVAGALLPDLPAAAQLTGHAADPDTVGTRLAGLERVLVAGEYLPAGRAAVRWAHERGA +SVHVVQHGLLAVSTPPVPRDATLYAFTARDADWWTQGRADVRAVPVGSALLEAARRGAAS +ADPTATGSTGPGPGLFLGQLHGAELPRAQFAAAAEQYVRTTGAVYRPHPAERDRLSRAQH +ARWEGAGIAVDRSGAPLTQTAGPVAAVFSTGILEAAQTGRPAWAVHPDPPRWLVEFWDRY +GITRWMPGADPTPTPALVAPTADPAAAIARDLWKEHA +>GCF_023573625_PROKKA_00505 +M-----TDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRR---STG +DDAPRLYLPAGDVHTLVALESFGPTQLAALASPVAALATAR--------PEAAAGVGWVL +PA----GDAPALPGAVGHREHAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGA +RIGVVQHGLLAVSTPPVPQDATLYAFTSADADWWTQGRADVEAVPVGSVLLEQARRTA-- +--PALSGAGDDGPGVFLGQLHGAELPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQH +AAWRRAGVRIDDAGAPLVATRGPVAAVFSTGILEAAQAGRPAWAVHPEPPAWLEGFWRRY +GMTRWRPGRTPEPTPPLASPTADPAAAIAEHVWKESA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000524.fa new file mode 100644 index 0000000000000000000000000000000000000000..3f5c3cc42d3bf78d6c5220949c4a9fca3cab8109 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000524.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00511 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRL +GGPGRLGYLRALRAWDRGRGKDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLAPSRFAADRIRGARVLHNWVPAPT----TPQAGRARDADEPLTVGFLGRL +SEDKGIVTLLEAAALLRKTDPGAFVFRVAGESRFVADDEAERLATALKAAGEDVQVLGWQ +DTAEFLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSEHPFVFPQRD +AAALADRLQAVRAVDLGAVAHSQQRRWESLFSPEAGRAAVAELLDDLSL +>GCF_003691675_PROKKA_00231 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV +GGPGRLGYMRALRVWDRGRGGDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLVPSRFAADRIHGARVLHNWVPGPT----TPQAGRARGTDEPVTVGFLGRL +SEGKGIVTLLEAAALLRRTDPGAFVFRIAGESRFVAEDEAERLATALKAAGEDVQVLGWQ +DTGEFLTSVDVLAVPSQWAESFGLVAAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRD +AAALANCLRAVRAVDLGEVAHSQRHRWASLFSPEAGRAAVAELLDDLSL +>GCF_005280335_PROKKA_02440 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAANGFDVVRV +GGPGRLGYLRALRAWDRDRGNDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLAPSRFAADRIRGARVLHNWVPGPT----TPPARRARDADEPVTVGFLGRL +SEDKGIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEAERLATALKAAGEDVQVLGWQ +DTAEFLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGNDHPFVFPQRD +AAALADRLQAVRAGDLGAVAHSQRRRWASLFSPEAGRAAVAELLDDLSL +>GCF_020097155_PROKKA_02323 +MTRRIWIAANQGEVGGGEVMLHHLATALHELGRDIAVVAPAAPSATAARLEADGFTVDRV +GGPGRAGYMRALRRWHNGH-REDVVWCNGLLPATALAGRPRRIVHLHQWLIRPRDRVLGT +LAMRGALAVIAPSESVAREIPGCRVLHNWVPRPLPLSGAAPARRRPGEGGALRVGYLGRL +SFDKGFHLLMDVAEELHREQPDEWRFFVAGEPRFTTGDDAREIRERL-AASRAVTALGWQ +APGDFLPTVDVLVVPSLAPESFGLVAAEAMAAGVPVAVSDSGALPEVAGDDHPLLFECDD +HEELAAALRRARQIDLAPLVAAQHRRWEALFSPEAGRAGVAALLEELHV +>GCF_023573625_PROKKA_00510 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV +GGPGRLGYLRALRAWDRGRDGDDVAWCNGLLPATALAGRPRRIVHLHQVPEKPVLRVFSA +LARPGALAVLVPSRFAANRIRGARVLHNWVPAPT----APQTRPARGADDPVTVGFLGRL +SEDKGIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEADRLATALKAAGEDVQVLGWQ +DSGEFLATVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRD +AAALANCLRAVRAIDLGAVAHSQRHRWESLFSPEAGRAAVAELLDDLSL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000531.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c14eab5684dd321589fa04f71a8a01b2ec22e3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000531.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00529 +MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGALRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG +>GCF_003691675_PROKKA_00250 +MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGSLRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVDRQARALSSWLERDGGAARS +>GCF_005280335_PROKKA_02423 +MAFSAQQSIPHPPAAVAAALASEEFHRSVVEQLGGSLVSFRVEGSPEGPMTVTTVRSAPA +DRL----PEMARKFIGSSLQVEQVERWEAPAADGSRVGTTTITVPAAKATAEGAQRLTAA +GEGSQYSVDGTVTCKIPLVGSKLAAKAEPMVGKVVNRQARALTSWIGRDGGAAGA +>GCF_020097155_PROKKA_02305 +MAFSAQQTIPHPPAAVAEALFSEDFHRSVAESLGGGLVSFARQDQADGGVELTIVRSGPT +DRL----PDMVRKVVGENLNIEQVERWSAPAADGSRTGTTTIRVPKAKATAEGTLRLAAA +PAGTEYGVNGDLQVKIPLVGSKMAQMAEPMVGKVVARAGREVSAWIDRGG---RG +>GCF_023573625_PROKKA_00529 +MAFSAQQPIPHPPSAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRTGTTTITVPSAKATADGSLRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000534.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a9a8063f403873f2342342ad9e3a1a3ab65f4f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000534.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00532 +-----------MTVETTEGWTLAPNIAWARTAGGQAAVMTLEAGQPLLLGASGDVIWDVL +VGGRTPEDDLVADPPASLSTTDVTVQVAEAFGLAPADVAADVHAFLEMLEAHGVLVRVRT +A---- +>GCF_003691675_PROKKA_00253 +-----------MTVETTEGWALAPDIAWARTAGGQTAVMTLEAGQPLLLSASGDVIWDVL +VGGRTPADDLVADPPAPLSTTDVTVQVAKAFGLYPADVAADVHAFLEMLEAHGVLVRVRT +A---- +>GCF_005280335_PROKKA_02420 +MAADRLPAPFGMTSERGSAWAVAPGVAWALTDGGDAAVMHLEHGVPLLLSPTGHAVWDVL +VGGRTPEDDLTAAPPIPLPEEAVAAETAAAFGLAPEDVAADVGAFLAMLEQHGVVVRVGG +VLPRP +>GCF_020097155_PROKKA_02302 +M-SDAEHPPF-AQAPAARAWRVAPTTAWVRSGEHQVTVMDLDEGNPQVLSPTGSAVWELL +LDGRTPEDDLAADPPKPVEEEALCGAVAEAFGVDVEVVAADTRAFLGMLAGHRLVVP--A +VLP-- +>GCF_023573625_PROKKA_00532 +-----------MTVETTEGWALAPDIAWARTAGGQAAVMTLEAGQPLLLSASGDVIWDVL +VGGRTPEDDLIADPPVPLSTTDVTVQVAEAFGLDPADVAADVHAFLEMLEAHGILVRVRT +A---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000540.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bb7ab9a8f953ed318cd64121511deddb20a664a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000540.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00539 +MTDQ-TSIPSPDS--PLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLI +GDEVAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTV +RTAAAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRL +RAIAREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVF +GISLVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL +>GCF_003691675_PROKKA_00263 +MTDQ-TSIPSPDS--PLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLI +GEEVAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTV +RTAAAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLAGATFVDLTDLYSPRL +RAIAREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVF +GISLVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL +>GCF_005280335_PROKKA_02410 +MSEQ-TFSPSPAS--PLAGDHPGFDQARAAAAVIADATGVAEHRIAVVLGSGWGEAAGLI +GEEVAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTV +RTAAAAGAKTVVLTNGCGGLDPEIAPGTPVLISDHLNLTGATPLVGATFVDLTDLYSPRI +RQIAREVDPSLREGVYVQFSGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVF +GMSLVTNLGAGISETALSHGEVVEAGQAAGPRISRLLADIVWRL +>GCF_020097155_PROKKA_02292 +MSEQSTPTPTPASLARLAGDHPGFAEARAAAEAIAEATGCAEHRIAVVLGSGWGEAAELI +GVERARIDLADVPGFHAPKVPGHNAVIRSVELADGSRALVFGSRTHFYESRDAQAVAHTV +RTAAAAGAATVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDVYSPRI +RAIAQEVDPTLTEGVYVQFSGPQYETPAEVRMATALGGDLVGMSTALDAIAARHAGLEVF +GISLVTNHGAGIQETPLSHQEVVEAGQAAGPRISRLLAEIVGRL +>GCF_023573625_PROKKA_00542 +MTDQ-TSIPSPDS--PLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLI +GDEVAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTV +RTAAAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRL +RAIAREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVF +GISLVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000541.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000541.fa new file mode 100644 index 0000000000000000000000000000000000000000..97ce7995084677eb537a95db4bbba94a0cd1fbd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000541.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00540 +MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGADVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI +>GCF_003691675_PROKKA_00264 +MEPVTEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGVGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGAEAHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLSGSGHVLVDGVSRTSVPSIYAAGDCTGTLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI +>GCF_005280335_PROKKA_02409 +----------------------------MVAAKLGARVTLVERQGVGGAAVLTDVVPSKT +LIATADSMRRVGLAEDLGVDLGDAEPRADMRQVDRRILDLAGEQSRDIRAALERRGVRVI +DGVARVVGPNEVSVRTLQDAD--AEPEVITSDAILVAVGASPRELPTAVPDGERIFNWKQ +LYAMTELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFQ +DNGLTVVARSRAEAVERTETGVRVELSGEGAADTPYVEGSHALVAVGGIPNTAGLGLEDV +GVELTESGHVKVDGVSRTTVPSIYAAGDCTGNLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFATNPRAKMSGVQEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI +>GCF_020097155_PROKKA_02291 +MN-VTEENTTFLPSLTIIGGGPGGYEAALVAAKLGARVTVVERAGMGGSAVLTDVVPSKT +LIATADSMRRVMAASGLGVDLGEAQPHADMHAVDRRILELAGQQSSDIHRALEKRGVRVV +IGDAVVTGPHEVTVRR-RGIEEGEEPEVITSDAILVAVGASPRELPTARPDSERIFNWKQ +VYALQDLPEHLIVVGSGVTGAEFASAYNQLGAAVTLVSSRDRVLPGEDPDAAELLEDVFA +QNGLDVAGRCRAESVERTETGVRVHLSGEGADGRPYIDGSHCLLAVGGVPNTAGLGLEEV +GVELTESGHVKVDGVSRTTVPSIYAAGDCTGQLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVIRLDFATNPRAKMQGVSTGFVKIFARQG +SGTVIGGVVVAPRASDLIYSLALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRV +>GCF_023573625_PROKKA_00543 +MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGGDVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRAI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000542.fa new file mode 100644 index 0000000000000000000000000000000000000000..74ecf4490a05f170b929439cf254069c739bdbe6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000542.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00541 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAA-R +>GCF_003691675_PROKKA_00265 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAA-R +>GCF_005280335_PROKKA_02408 +MSRTT------TPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPL +IFFPGDDQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLI +GLLPTAFQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAP +IGFFLANGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETP +VFQRAIANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGM +LGVPYAEFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAE +RMGTGAGVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGA +ALTPFLAAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV +>GCF_020097155_PROKKA_02290 +MSHTT----------ARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPL +IFFPGDDPTTALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLI +GLLPTAFQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAP +IGFLLANGLFLILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALEDDTRVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGM +LGVKYADFLVLQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPA +AMGQGDALNVPSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFLAGWLVKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR +>GCF_023573625_PROKKA_00544 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAA-R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000544.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b17b8cffa939a3753494a505831ffc04e1d0a35 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000544.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00544 +MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARADDELNARLLEDLAALELQDE +TDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAVFDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAG +HVAAVRQVDIVVEQARAHGAAGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI +EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPERTLKGTEALRTWMQRLSDDA +VEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAM +MNRENLNLWRRSFCWTSGHGEGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLKAFHTRALRLGGMGLDTLREA +LA +>GCF_003691675_PROKKA_00269 +MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARADDELNARLLEDLAALEPQDE +TDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAVFDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAG +HVAAVRQVDIVVEQARAHGAAGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI +DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPERTLKGTEALRTWMQRLSDDA +VEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAM +MNRENLNLWRRSFCWTSGHGEGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLKAFHTRALRLGGMGLDTLREA +LA +>GCF_005280335_PROKKA_02403 +MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRADDELNARLLADLEALEPQDE +TDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAVFDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAG +HVAAVRQVDIVIEQARAHGAAGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI +ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPERTLNGTAALQAWMQRLSDEA +VQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAM +MNRENLNLWRRSFCWTSGHGEGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLKAFHTRALRLGGMGLDTLRAA +LA +>GCF_020097155_PROKKA_02286 +MTQTTS--APEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALDELNRTTLEELAGLEPADD +VDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFDLMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAG +HVAAVRQVEIVVEQARAHGAEGGFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGI +EHYRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPARTLTGTKALQEWMQRLSDEA +VEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPGRMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAM +MNRGTLNLWRRNFAWTSGHGEGWALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTP +EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAFHTRALRVGGMGLDTLREA +LA +>GCF_023573625_PROKKA_00547 +MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARADDELNARLLEDLAALEPQDE +TDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAVFDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAG +HVAAVRQVDIVVEQARAHGGAGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI +DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPERTLKGTEALRTWMQRLSDDA +VEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAM +MNRENLNLWRRSFCWTSGHGEGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP +EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLKAFHTRALRLGGMGLDTLREA +LA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000546.fa new file mode 100644 index 0000000000000000000000000000000000000000..8b211a88b035fbd4a638196bffc5a49005547a64 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000546.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00546 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD +GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL +ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIVDEGHLLQLQELYAPNVITGL +ARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV +PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL +>GCF_003691675_PROKKA_00271 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD +GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL +ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIVDEGHLLQLQELYAPNVITGL +ARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV +PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL +>GCF_005280335_PROKKA_02401 +MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD +GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL +ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIVDEGHLLQLQELYAPNVITGL +ARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAFNIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV +PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL +>GCF_020097155_PROKKA_02284 +MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELDALATHRTTAFGMDAKHPAGD +GVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVM +ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE +DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALVDDGHLLQLQEMYAPNVITGL +ARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV +PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN +PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL +>GCF_023573625_PROKKA_00549 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD +GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL +ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIVDEGHLLQLQELYAPNVITGL +ARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV +PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000550.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a078dbc2016ead0cf840b4bc071e853a392b0d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000550.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00552 +M----------SARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSS +GSDWVTDYDRRAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVR +GLPQFCTSVAVTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADA +TTAGVDLPDRDAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRI +GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAG +DVDGSALAAMTGERA +>GCF_003691675_PROKKA_00277 +M----------SARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSS +GSDWVTDYDRRAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVR +GLPQFCTSVAVTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADA +TTAGVDLPDRDAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRI +GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAG +DVDGSALAAMTGERA +>GCF_005280335_PROKKA_02393 +MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS +GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR +GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA +TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI +GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG +DVDEAALAAAQEETA +>GCF_020097155_PROKKA_02278 +M------SAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSS +GSDWVTDYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIR +GLPQFGTSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADA +TTAGVAVPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRI +GSAALDLCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAG +DVDAAALAAAKEATA +>GCF_023573625_PROKKA_00555 +M----------SARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSS +GSDWVTDYDRRAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVR +GLPQFCTSVAVTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADA +TTAGVDLPDRDAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRI +GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAG +DVDGSALAAVTGERA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000551.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c6d4ee150f4632a783f8bc5cca030fc54da9e8b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000551.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00553 +MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA +GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD +GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQ----HAGG-------DA +>GCF_003691675_PROKKA_00278 +MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA +GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD +GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQ----HAGG-------DA +>GCF_005280335_PROKKA_02392 +MRRLVGDPWFWPVLFGSAGLVFLVWGTLRRDVVVLVAALAMLWMLRRHLPQLRVRSRPLA +GAQAHVQDGGVVVFWRPGCQYCQALLRDLDPAQRDAVYWVNIWTDKDAVPVLRRLHAGRD +GHAHEAVPTVWARRKDFVAADEASRSRLKDMLRDAR--PAGGPRTREEGPR +>GCF_020097155_PROKKA_02277 +MRRLVGDPWFWPVLFGAAGVVFLVWGTVRRDVIAIVAGVAMLWMVWQYLPALRVRSCPMA +GAQAHVDAGGVVVFWRPACRYCLALIKDLDPAQRAAVYWVNIWTDPDAVPVLHRLHATRD +GHAHEAVPTVWSRRRDFVVKDEATRRRLTDMLGAVRHIPESG--------R +>GCF_023573625_PROKKA_00556 +MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA +GAQAHVERGGVVVFWRPGCSFTRRLVTELTAQERERAYWVNIWQEPAAATFLAGLHEARD +GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQ----HAGG-------DA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000561.fa new file mode 100644 index 0000000000000000000000000000000000000000..b73a3c09b6e0c4e22ded8c7a7a805ccd6193a966 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000561.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00564 +MPLARLAGVNANPTPAVEP---VVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPE +HVTVAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTV +SLLGFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKV +FWGRGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPR +G +>GCF_003691675_PROKKA_00289 +--------MNANPTPAVEP---VVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPE +HFTVAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTV +SLLGFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKV +FWGRGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPR +G +>GCF_005280335_PROKKA_02379 +M-----NNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPE +RFTVAAVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTV +SLLGFSQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKV +FWGRGQDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR-- +- +>GCF_020097155_PROKKA_02263 +M------NDTTPRDPA----PFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPE +AFTALAVRAPMDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTV +SLLGFSQGMAMATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKV +FWGRGQEDPIISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL-- +- +>GCF_023573625_PROKKA_00567 +MPLARLAGVNANPTPAVEP---VVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPE +HVTVAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTV +SLLGFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKV +FWGRGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPR +G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000562.fa new file mode 100644 index 0000000000000000000000000000000000000000..afc5a4ab42219a6480f011ef5a3e11fb92374032 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000562.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00565 +----MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR +GAQLHDGDVVEFAGEAFVVQAEQA- +>GCF_003691675_PROKKA_00290 +MMDTMTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR +GAQLHDGDVVEFNGEAFVVQAGQA- +>GCF_005280335_PROKKA_02378 +MMDTMTETNPADARPLPIRDASIRLGQALKLAALVEDGAMARDVVQDGLVTVNGAVETRR +GAQLKDGDVVEFHGEAVVIEAGSAD +>GCF_020097155_PROKKA_02262 +M------TSSSDVQPLPIRDESIRLGQALKLASLVEDGAMARDVVQDGMVSVNGEVETRR +GRQLHDGDVVEFNGEEIVVEAGQS- +>GCF_023573625_PROKKA_00568 +----MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR +GAQLHDGDVVEFAGEAFVVQAEQA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000563.fa new file mode 100644 index 0000000000000000000000000000000000000000..f46e3748b68566ec8afb47b6ec35f427c711d9dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000563.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00566 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAGQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPTTQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK +>GCF_003691675_PROKKA_00291 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPAEDRAHYSDGTIDLEYDFGFTGGDGWGELMGIANRTDYDLGQHTTH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQSLAAELRGLWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK +>GCF_005280335_PROKKA_02377 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHKRHRQDHLLEAFEAKKGRPSASMD +EIVCPDCGTKGAWTEPQMFSGLVKTFLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDTWVEACWDWFID +LGIDPENLRRLDVPEEERAHYSDGTIDLEYRFGFGGGDGWGELMGVANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGTDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQALAAELRALWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMSQERVALSQVKSYLLERLVK +>GCF_020097155_PROKKA_02261 +MAAKSPLDNVINLAKRRGFVFQAGDIYGGSRSAWDYGPLGVELKENIKAEWWRTFVRSRE +DMVGLDSSIILPRQVWEASGHVATFTDPLVECQQCHRRHRQDHLLEAFEAKKGRAAAGME +EITCPDCGTTGKWTEPQMFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKEHFDTWVEACWDWFID +LGIDPANLRKFDVPEEERAHYSDGTIDLEYRFGFAGGDGWGELMGVANRTDYDLTSHANA +SGAKLQYFDQANDVHYTPYVIEPSFGLTRSMMAFLVDAYTEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKLELQEPSQRLAAELRAHWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQSVTIRERDTMSQERVALAQVRAYLAERLTK +>GCF_023573625_PROKKA_00569 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPYCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000570.fa new file mode 100644 index 0000000000000000000000000000000000000000..878e742f0c71b2c8b13e4aee0d9bc7585bed1108 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000570.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00580 +MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALPDPAEARWSVAGDGLDVLGEE +QGRVPSPGPRLVRHDDPADPDRAWAGLAAAAAPRPVVGGEGLPLRGGLVGWLGYELGLADLGVTPPSRRAEDPAPLPAQF +WVRPSRYVVADHAAGVLHCCVVSLDPTTAEAGADRWAADVRRALAAARRALETAAGDAVVPPPQDAVPGPRADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAALLEHGTGSRRWAVVSASPERF +LSGREGRYSTKPIKGTAARLADPAGDAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYASVHQL +VSTVTGTARAGIEPVDVVRSLFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVL------ +AGGRWSVGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGLPTTAPDIA- +>GCF_003691675_PROKKA_00313 +MPTAPAPSVAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALPDPAEARWSVAGDGLDVLGEE +QGRTPSPGPRLVRHDDPADPDRAWADLAAAAAPRPVVGGEGLPLRGGLVGWLGYELGLADLGVTPPSPRPGDPASLPAQF +WVRPSRYVVADHAAGVLHCCVVSLAPTAAETGADRWAADVRRALAAARRALETASGDVVVPPPRDAGPGPQADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAALLEHGTGARRWAVVSASPERF +LAGRAGRYSTKPIKGTAARLADPVADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQL +VSTVTGTARAGVEPVDVVRSLFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVL------ +AGGRWSVGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDVA- +>GCF_005280335_PROKKA_02353 +-------------------------------------MAAVYAHAVQRGAGSFWLDSALPDPAEARWSVAGDGLDVLGEE +QGRVPSPGPRLVRHADPADPERAWSDLAAAAAPRRVVGGEGLPLRGGLVGWLGYELGLADLGVRPPSRRAGDPAALPAQF +WVRPSRYAVADHAAGTLSCCVVALDAAAAEAAADRWAADVRRALDAARRATQAAADDAAASEVRADVAPEAGTGEAAGAW +REDRAAYDEHIARCHAALHAGDSYELCLTTRFDADPALRVDPLALFLELAAHQPAPYAALMEHGTGPRGWAVVSASPERF +LAGRDGRYSTKPIKGTAARLPDPAADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYATVHQL +VSTVTGTARAGVAPVDVVRSLFPGGSMTGAPKRRSVELLAQWEDSPRGVYSGALGLLGADGAVSLSIVIRTAVL------ +AAGRWGIGAGGAIVADSTAEAEHEEVLLKARGLRRALARADGTARTTTAPPRSR +>GCF_020097155_PROKKA_02247 +MPTAPGRPDASPAPLHVAVRTLDIATLAAVGHTAATAAGAVYAHAVQRGTASFWLDSALPDGGEARWSMVGDGVDVLGEE +EGRIPSPGLRLIRHGDPADPDRAWADLAAAAAPREVHGGEGLPLRGGLVGWLGYELGLADLGVTPPPPRPGDPAALPAQF +WVRPSRYAVADHVAGALSCCVVSLDADAAEAAADRWEADVRRALEAARTSTEEVEVDVDAP-------------EAPGVW +REDGAAYAEQIARCRAALHAGDSYELCLTTRFDADPALRVDPLALFRDLAAHQPAPYAALMEHGTGAERWAVVSASPERF +LSGRDGRYSTKPIKGTAARLPDPTEDAAAAAALAADPKTRAENLMIVDLLRNDLSRVCEPGTVQVPALMAVESYATVHQL +VSTVTGVARAGVAPVDVVRSLFPGGSMTGAPKRRTVELLAAWEGSPRGVYSGALGMLGADGTVELSIVIRTAVLSPTTPD +APARWSVGAGGAIVADSDAHAEHEEVLLKARGLRRALTRAAGTA---------- +>GCF_023573625_PROKKA_00581 +MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALPDPAEARWSVAGDGLDVLGEE +QGRVPSPGPRLVRHDDPADPDRAWADLGAAAAPRSVVGGEGLPLRGGLVGWLGYELGMADLGVSPPSRRPEDPAPLPAQF +WVRPSRYAVADHAAGVLHCCVVSLDPTAAEAGADRWAADVRRALAAARRDLETAAGDAVVPPPEDAGPEPRADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVNPLVLFHELAAHQPAPYAALLEHGTGARRWAVVSASPERF +LAGREGRYSTKPIKGTAARLPDPAADAAAARALADDPKTRAENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQL +VSTVTGTARAGVEPVEVVRSLFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVL------ +AGGRWSVGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDIA- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000571.fa new file mode 100644 index 0000000000000000000000000000000000000000..6671ab2921b1579b4809ca0cb343f0a84295d074 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000571.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00583 +---MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTYHCFGCGAHGDVISFLME +LEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFEANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQ +FGLGYAPQGWSHLLDHLRQRGFRDEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTP +ETPLYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVARRLISDDGTGGEVIFTF +DGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKGDEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGA +LRHAVPIVAGIKDAVLRPGYERELAGWLGLDPNAVHRAVAAAGRA------------PRRGPEPEARP----APADDGQA +IGPQGRHGEAAAPAPRIVVPVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGATP +QRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELLGRLQRLGPEGDPAEFTRLNSE +LMELEARRRALRADD +>GCF_003691675_PROKKA_00316 +---MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTYHCFGCGAHGDVISFLME +LEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFEANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQ +FGLGYAPQGWSHLLDHLRQRGFRDEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTP +ETPLYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVARRLISDDGTGGEVIFTF +DGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKGDEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGA +LRHAAPIVAGIKDAVLRPGYERELAGWLGLDPNAVHRAVAAAGRA------------PRRGPEPEARP----APADDGQA +IGPTGRHGEAAAPAPKIVVPVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGATP +QRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELLGRLQRLGPEGDPAEFTRLNSE +LMELEARRRALRADD +>GCF_005280335_PROKKA_02351 +---MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTYHCFGCGEHGDVISFLME +LEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLEANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQ +FGLGYAPQGWSHLLDHLRQKGFRDEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTP +ETPLYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMARRLISDDGTGGEVIFTF +DGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQGDEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGA +LRHAAPIVAGIKDAVLRPGYERELAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPS +VGPQGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQYAAVHHGVKVAGSSGATP +QRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSE +LMELEARRRALRADD +>GCF_020097155_PROKKA_02246 +MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTYHCFGCGEHGDVISFLME +MEHTTFTETVERLAARAGVELHYED-GQGPDRAETSRRRRLLEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQ +FGLGYAPQGWSALLDHLRQQGFRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTP +ETPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIKIARRLISDDGTGGEVIFTF +DGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQQGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGA +LRHAAPIVAGIKDSVLRPGYERELAGWLGMDPNVVSRAVAQELRGRRRGGPSGG--SAERTPAPERAP----EGANAGQA +PGE-----EPAAPRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKVAGTAGATP +SRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIVHRKEELLGQLQRLGPEGDHDEFMRLNAE +LMELETRRRALRADD +>GCF_023573625_PROKKA_00584 +---MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTYHCFGCGAHGDVISFLME +LEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFEANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQ +FGLGYAPQGWSHLLDHLRQRGFRDEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTP +ETPLYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVARRLISDDGTGGEVIFTF +DGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKGDEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGA +LRHAAPIVAGIKDAVLRPGYERELAGWLGLGPNAVHRAVAAAGRA------------PRRGPEPEARP----TPASDGQA +VGPTGRHGEAAAPAPRIVVPVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGATP +QRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELLGRLQRLGPEGDPAEFTRLNSE +LMELEARRRALRADD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000575.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e26e344d65b818026aa96cab685e64049277dc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000575.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00634 +MK----------RTMTLTALALASALTLTACGTGAQDENAGAEASATAASSAPAATPAAT +ATATPSTT------ATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAE +VAAFAQKVIDAQGPEIKRMNSMLTAWGQDPVDTD-GMDGME-----------GMDHGGMS +GMMSEEDMTALDQAQGTEAARLYLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIAD +QEAEITEMQQMLDKL +>GCF_005280335_PROKKA_00406 +MK----------RTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAAT +ATATPSTT------ATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAE +VAAFAQKVIDAQGPEIKRMNSMLTAWGQDPVDTD-GMDGME-----------GMDHGGMS +GMMSEEDMTALDQAQGTEAARLYLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIAD +QEAEITEMQQMLDKL +>GCF_005280335_PROKKA_00753 +MSTETSAAGRAGHSVRLVVLATVIVLILGAAGW------ALGRLTAPVTSFPSAASPEAG +--------------------------------FARDMQVHHLQAVEMSFLVRDRTEDP-E +IRQLAYDIARTQQHQAGQMYGWLSIWGLPQASPEPAMAWMDEDAGHSSPHDTGQQSTAMP +GMATAAQLEALTDAEGSEAEQLYLELMISHHQAGTTMAQAVLDRTDNEAVRALAQSIATS +QQTEIRYLEQLLRTR +>GCF_020097155_PROKKA_02195 +MK----------RTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAAT +ATATPSTT------ATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAE +VAAFAQKVIDAQGPEIKRMNSMLTAWGQDPVDTD-GMDGME-----------GMDHGGMS +GMMSEEDMTALDQAQGTEAARLYLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIAD +QEAEITEMQQMLDKL +>GCF_023573625_PROKKA_00597 +MK----------RTMTLTALTLASALTLTACGTGAQDENAGAEASATATGSAPAATPAAT +DTATPSATESATSSATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAE +VAAFAQKVIDAQGPEIERMNAMLTAWGQDPVDTD-GMDGME-----------GMDHGGMS +GMMSEEDMTALDQAQGTEAARLYLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIAD +QEAEITEMQQMLDKL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000577.fa new file mode 100644 index 0000000000000000000000000000000000000000..e976bf3b7ea4f5650287b28954a76cb1d022da25 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000577.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00637 +MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL +NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA +CRRCEQACADLLVTLG +>GCF_005280335_PROKKA_01994 +MTHHVNAMLDTHPKDLGGIDRQKLAECIEACFACAQTCTACADACLSEDMVAELRQCIRL +NLDCADVCAATGAVLTRQTGEDASTVRALLEACRAACRSCGEECASHAGMHEHCAVCAEA +CRRCEQACADLLAALG +>GCF_020097155_PROKKA_02191 +MTHHVSAMLETYPKEVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL +NLDCAEVCAATGRVLSRQTGTNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA +CRRCEQACADLLVTLG +>GCF_023573625_PROKKA_00594 +MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL +NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA +CRRCEQACADLLVTLG +>GCF_023573625_PROKKA_00894 +MTHHVSAMLETHPKDLGGVDRRKLAECIEACLACAQTCTACADACLSDDMVAEMRRCIRL +NLDCADVCGATAAVLTRQTGEDASTVRALLEACRTACRACGDECASHAEMHEHCKVCAES +CRRCEQACADLLASLG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000578.fa new file mode 100644 index 0000000000000000000000000000000000000000..3359eb8f9d0f46f14416a7eafca2fcd6a60e1198 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000578.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00641 +------------------------------------------------------------ +---MDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET +EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA +ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR +LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT +CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS +ARWDLHVLQHRGALRGLSGPR +>GCF_003691675_PROKKA_00378 +------------------------------------------------------------ +---MDTTRFDDDLRAMLDEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET +EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA +ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR +LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLT +CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLATWSPRLDEQGNSRRGIGLFEGLS +ARWDLHVLQHRGALRGLSGPR +>GCF_005280335_PROKKA_02321 +------------------------------------------------------------ +---MDTTRLDDDLRAMLAEVESDRRGEPSDYLEDVAGQHVDGLAAAVCTVDGHQAAAGET +DHAFALQSVSKALTYAVVLQEVGLDAVLERVGVEPSGEAFNHLSLHDDGRPYNPLINAGA +IMAHALLPAGDHEERVALLVRRYSALAGAELEVSQDVLDAELTRADRNLGLAHLLADAGQ +LPVSAREAVAGYLAQCSVTVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT +CGMYDATGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDERGNSRRGIGIFEGLS +ARWDLHVLQHRGALRGLRASR +>GCF_020097155_PROKKA_02184 +MGIGSLIATMLPSSIAFLPACTGMVIGWRWLGLPLGPNARSSAHRDRPGARPRPGRPSTT +VTGMDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET +EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA +ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR +LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT +CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS +SRWDLHVLQHRGALRGLSGPR +>GCF_023573625_PROKKA_00611 +------------------------------------------------------------ +---MDTTRFDDDLRAMLDEVESDRRGEPSDYREDVAGQHVDGLAAAVCTVDGHQAAAGET +EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA +ILVHALLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR +LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLT +CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDEQGNSRRGIGLFEGLS +ARWDLHVLQHRGALRGLSGPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000581.fa new file mode 100644 index 0000000000000000000000000000000000000000..a8fd01d4e6c9d4f4a6be9028b51572f29b65248b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000581.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00645 +MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK +GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG +LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK +VEKEENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF +AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL +AGRLRRR-- +>GCF_003691675_PROKKA_00382 +MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK +GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG +LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK +VEKKENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF +AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL +AGRLRRR-- +>GCF_005280335_PROKKA_02318 +MSHQAPPADALKAGAPRPAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVVAK +GKKAGIGAGVTVVGLFFLALVVVALVVALIGAFADPTFWFPALMVAAAFLVLGAIFAGIG +LFMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAKRAEERRK +VEKEENKKARKNGEAAPHPDRDEASEAEIRRRADLRRRHLGDIRSGLEEKTSVKGQLAAF +AAQRKGRGVTPQTAHATDQTAPFTGAARAGEKAAEAEDYVKDNWQPLALLGASSAAFLAL +AGRLRRR-- +>GCF_020097155_PROKKA_02177 +MSHAAPTA---APRAPRPTTPVTPQTRASSLTDLLAAVVRLLPLQLKDELALAKGQAAAK +GKKAGIGAALAVVGLFFLALMTIALVVALIGAFANPPFWFPALMVALVFLVLGLVLAGVG +AMQIKGAMPLVPQETVRNLEYDLGYLKEGNDFDPAEYDRLKAERAEAKRLEKQREAERKK +VEKEENKQARKDGLAAPHPAKDDASEDEVRRRAELRRRHLGDIRSGLDEKTSVKGQVAAF +TAQRKLRGTTPDTAHATEQTAPFTTAARAGEQTAAAEDYVKERWQPLALLGASGTAFAVL +ASRLRGRKG +>GCF_023573625_PROKKA_00615 +MSHQAPPADASKARAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVAAK +GKKAGIGAGVAVVGLFFLALMVVALVVTLIGAFADPSFWFPALMVALAFLVLGLIFAGVG +LVMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK +VEKEENKKARKNGEAAPHPDRDDATEAEIRRRADLRRRHLGDIRSGLDEKTNVKGQLAAF +AAQRKGRGVTPETTHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL +AGRLRRR-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000582.fa new file mode 100644 index 0000000000000000000000000000000000000000..033705b15951d6bc38e19b67bcefe11415d7647b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000582.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00647 +MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT +VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI +NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA +AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL +DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL +>GCF_003691675_PROKKA_00384 +MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT +VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKTSFRRIYREVQPDVVHAQCHYMIGEAAI +NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA +AQAMAEHAGLDNVLPISNGIDASAYELQPGEKVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGAADRVLLRGHVSEEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERIARIL +DLSDAERAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRALL +>GCF_005280335_PROKKA_02316 +MSDRPGTAADRPLKVLIAADTYPPHVNGAATFCHRLATALHARGHEVHVVMPRGEAGPDT +VEERPEATVHLLRAIPAPTHEYYRLVMPWHAKAAFRRIYREVQPDVVHVQCHYMVGEAAI +NEAERRRIRMVSTNHFMPENLEPFLPFPQWFLDIVSRVSWRDMGRLMGKGAAVTTPTALA +ARAMAEHAGLDNVLPVSNGIDAAAYELQPGETVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARVRPDLDVHAEIVGDGEQRDRIRAAVESEGVADRVLLRGHVSDEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALAERVARIL +DLPEAERAAMGEASHAKAMHHSAQKTVDVFERLYRGATPAEVRELL +>GCF_020097155_PROKKA_02175 +MTSSARPAQERPLTVVIAADTYPPDVNGAAVFCFRLASALHERGHRVHVIAARNEPGPDT +VEERPEATVHRLESHRAFTHEYYRLVFPWHASRSIDRILAEVRPDVVHAQCHYMIGEAAI +NVADRRRIRTVSTNHFMPENLEPFLPFPQWFLNIVSKNSWRDMGRLMGKGAAVTTPTALA +AAAMAEHAGLDRVLPISNGIDASAYELAPGEVVERAAHPTVLFVGRLAVEKHVDVLVRAV +AHLARTRPDLDVHAEIVGDGEQRTALDAVIAEEGVADRVRRLGHVSDAELHTAYLRADVF +CQPGTAELQSLVSLEAMSASTPVVLADALALPHLVDDGVNGWLFPPGDHVALAERIARVL +DLPEAGRAAMGEASHAKAVRHSQAKTVDLFERLYRGATPAEIRAAL +>GCF_023573625_PROKKA_00617 +MSDRPGIAADRPLKVLIAADTYPPHVNGAATFGHRLATALHARGHEVHVVMPRSDAGPDT +VEHRPEATVHLLRSLPAPTHEYYRVVLPRHAKISFRRIYREVQPDVVHAQCHYMIGEAAI +NEAERRRIRIVSTNHFMPENLEPFLPFPQWFLDIVSRVSWKDMGRLMGKGAVVTTPTALA +AQAMAEHAGLDNVLPVSNGIDASAYELQPGERVDHPGHPVVLFVGRLAVEKNVEVLIRAI +AHLARTRPDLDVHAEIVGDGEQRDRIRATVDEEGVADRVLLRGHVSEEELRAAYLRADVF +CQPGTAELQSLVTLEALSASTPVVLADALALPHLVDEGVNGHLFPPGDHVALADRIARIL +DLSDADRAAMGEASHAKALHHSAQKTVDIFERLYRGATAAEVRAML + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000583.fa new file mode 100644 index 0000000000000000000000000000000000000000..55c6dc7eed8e6a4c4dacd4a9ce502eaba9e627f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000583.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00649 +MSVTSSHAAVRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETAYTVRSGDGWWII +AQRTGVSMSRLQSLNGMTAATVLHPGMVLKTSGTATPTPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASILQSINGMSSSTMLHPGMVLKTTSVSTSSAPAVAPAPAP----ASKQAAV +DYVRSAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQ +AQPGDLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY +>GCF_003691675_PROKKA_00386 +MSVTSSHAASRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII +AQRTGVSMSTLQSLNGMTAATVLHPGMVLETSGTATPAPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASILQSINGMTSSTMLHPGMVLKTTSVSTSSAPALAPASAP----ASKQAAV +DYVRAAVRNPSSYYAWGGNGPSGFDCSGLTQQAMAQAGISIPRRAGDQYLAAKSYVPISQ +AQPGDLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY +>GCF_005280335_PROKKA_02314 +MSVTSSRAASRRAPRTAAASLALALGAGALAGVGSVTAAETAQAVETTYTVRAGDGWWVI +SQRTGVSMSTLQSLNGMTSATMLHPGMVLKTSGTAAPAPAPAP--SASTYTVLAGDGWWI +ISYRTGVSASVLQSINGMTSSTVLHPGMVLK-TSVVASSAPAPAPAPVT----NGKQAAV +DFVRSTVQNPSSYYLWGGNGPYGFDCSGLTQQAMAKAGISIPRRAGDQYNAAKSYVPISQ +AQPGDLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLLFTSTTIMKSDMLAVAARY +>GCF_020097155_PROKKA_02171 +MPEALLTPA--RRPRAAAASLALALGAGAGVTAGAAVIAPQAVAAE-TYTVQAGDGWWII +SQRTGVSMATLMQLNGMTSADMLHPGMVLKTSGTVTAA--------AGTYTVKAGDGWYA +ISRATGVPVSTLTSLNGMTITSMLYPGMVLKTTGTPASTAPAPAPAPAPVVRQSSKQAAI +DFAVAKVNDPNTYYAWGGNGPYGYDCSGLTKAAFAAAGITIPRVSHDQYVNAPAYAPLSQ +AQPGDLVFWANQSTGRVYHVAVYIGNGKVAHALNTTDDLVITSTDVMTSNRLAVVGRY +>GCF_023573625_PROKKA_00619 +MSVTSPHAAARRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII +AQRTGVSMSTLQSLNGMTAATVLHPGMVLKTSGTATPAPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASVLQSINGMTSSTMLHPGMVLKTTSVSTSSAP--APAPAP----ASKQAAV +DYVRSAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQ +AQPGDLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000584.fa new file mode 100644 index 0000000000000000000000000000000000000000..42a166e7871b6a9471ee85ef24bfe1c01423f90a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000584.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00651 +MTPRTHLPRPLPRPHIAG----CVAAALLA----WLVLASGVGGLDAVPRATSAPSG--R +DALLLVAASPAGPGSTAAPVAWHAPVAGAAPDDVLRAFVAPERPWGRGHRGVDLAVPSGA +AIRAPAAGRVVFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAP +PHCTRACVHWGVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP----- +>GCF_003691675_PROKKA_00388 +MTPRTLLPRPLPRPRIAG----CVAAALLA----WLVLALEMGDLGPASRATPAPST--R +DALLLVAASPAGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGA +PIQAPAAGRVVFAGVVVDRPVLTLEHADGTRSSLEPVEADVAVGAVVDAGDPVGRLAGAP +PHCPRACVHWGVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP----- +>GCF_005280335_PROKKA_02312 +MTARSPAP---RRARPAASPHRLLAVLLLCVLGLALAFALGPGIGAATPSSIRAEDGPTA +DARLAVAATPAR--------AWTAPAAGVRPGDVLRPFAAPERPWGRGHRGVDLAVSPGA +AVLAPAAGTVVFAGTVVDRPVVTLEHADGTRSSLEPVEAAAPVGARLERGAPLGTVADAP +AHCAVPCVHWGVRVPDGWRFGDATFDRYLDPLVLIGWSGPSVLWPHAAPPPAGPAPARE +>GCF_020097155_PROKKA_02169 +MNEASTPP---PRLRAAA----VLAVALLA-----------------TASAARAEDA--- +---------PAAPPVTG---ALLAPTPGAGPSDVLRGFAGPERPWSRGHRGVDLATSSG- +LVTAPAAGTVRFVGSVAGRGVLTLAHPDGTLSSFEPVTSDLTAGQAVAAGQEVARVQEGA +AHCPVRCVHWGVRREDAWAVGAARFDRYLDPLLLLGWSGPSVLWPVGDAG--------- +>GCF_023573625_PROKKA_00621 +MTPRTLLPRPLPRPRIAG----CVAAALLA----WLVLALGMGDLGPVSRATPAPST--R +DALLLVAASPAGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGA +PIQAPAAGRVVFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAP +PHCTRACVHWGVREPDGWRVGEAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000586.fa new file mode 100644 index 0000000000000000000000000000000000000000..c86dce0b0344e73a79c22b1c13fcc2c04f279d75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000586.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00653 +MANYTAADIKALRERTGAGMMDVKKALDEADGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASEHEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAYVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA +AHDIAVHVAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN +>GCF_003691675_PROKKA_00390 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN +>GCF_005280335_PROKKA_02310 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKAEKFITLGDVVLRAAVASGAADVESLLASEHEGRT +LGDHVIEEGALLGEKVAVRRLARVEGALVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA +AHDIAVHTAAYSPTYLSREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLEDQPFAKDPKQTVGKVASDAGTKVTGFARFRVGN +>GCF_020097155_PROKKA_02167 +MANYTAADIKALRERTGAGMMDVKKALDEANGDADKAVEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFISLGDVVLKAAVASGAADVDSLLASDHEGRT +LGDYVTEEGALLGEKVAVRRVARVEGAHVDAYLHKTSKDLPAQVGVLLAVDADSDAAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIAEESARAEGKPEQALAKIVEGRLTGFFK +EGVLVDQPFAKDPKTTVGKVASEAGTAVTGYARFRVGN +>GCF_023573625_PROKKA_00623 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000590.fa new file mode 100644 index 0000000000000000000000000000000000000000..89dfbda3d628a3761c7cc38a386451d4a08e3df6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000590.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00658 +MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY +FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH +QELERQRREHALYLQQFGDEEAGA +>GCF_003691675_PROKKA_00395 +MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY +FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH +QELERQRREHALYLQQFDDEEAGA +>GCF_005280335_PROKKA_02305 +MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY +FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH +QELERQRREHALYLQQFDDEEAGA +>GCF_020097155_PROKKA_02161 +MT--DVHLP---EQDA--PPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLH +RELTLVRRLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLL +RGVEAGELLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVC +FGDGATSEGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPAL +RVDGNDVLAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWAR +RDPLERLTAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPH +QELARQQRDLQLHLDGLDAGEEQA +>GCF_023573625_PROKKA_00628 +MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY +FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH +QELERQRREHALYLQQFDDEEAGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000591.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a03757180061f305fcef6703e0ae09d4352f705 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000591.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00659 +MSERMTFGRAINRGLQRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD +KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEET-R +>GCF_003691675_PROKKA_00396 +MSERMTFSRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD +KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEET-R +>GCF_005280335_PROKKA_02304 +MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQDEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTPGLRVVSPSSPQEGHDLIRAAIASDDPVVYLEPKRRYHD +KGEVDLDADIPPMSTAKILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGVDRALGRPNSLDSVDAFAAPETAEQFLAAQTAGEET-R +>GCF_020097155_PROKKA_02160 +MSEQMTFGRALNRGLHRALADDPKVLLMGEDIGRLGGVFRITDGLQEEFGVDRVVDTPLA +EAGIVGTAIGLALRGYRPVVEIQFDGFLYPAFDQIVANLAKLRARTRGRVAVPVTIRIPY +GGGIGSPEHHCESPEAYFLHTPGLRVVSPSSPQAGYEMIRAAIASDDPVVFFEPKRRYHD +KGPVDLDAAPGPLSVGRVLRPGADVTLVAYGPLVKTALQAAEVAEQEGVSVELIDLRSLS +PLDTGLVEASVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLESPPVRVTGLDIPYP +PATLEHLHLPDLDRILEGVDRALGRPNPQDAVDAFAPPQTAEDFLSARADSSEVPA +>GCF_023573625_PROKKA_00629 +MSERMTFGRAINRGLHRALADDPKVLLMGEDIGALGGVFRITDGLQAEFGEDRVLDTPLA +ESGIVGTAIGLAMRGYRPVVEIQFDGFVYPAFDQIVANLAKLRARTRGAVPMPVTIRIPF +GGGIGSPEHHSESPEAYFLHTAGLRVVSPSSPQEGYDLIRAAIASEDPVVYLEPKRRYHD +KGDVDLDVAIPPMSPARILREGRDATLVAYGPLVKTALQAAEVAAEEGVEVEVVDLRSLS +PLDTGLVESSVRRTGRLVVAHEASRTGGLGAELVATVAERAFHWLEAPPVRVTGMDVPYP +PSKLEHLHLPDLDRILDGLDRALGRPNSLDSVDAFAAPETAEQFLAAQNAGEET-R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000593.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000593.fa new file mode 100644 index 0000000000000000000000000000000000000000..3800a392be880c0eb12288bf9cd952e3201da64b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000593.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00661 +MAGTRDGDAVEPRPERSTAVLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD +YHWAHLLGDEDTVVRTIEHEGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFL +EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAA-D +>GCF_003691675_PROKKA_00398 +-------------------MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD +YHWAHLLGDEDTVVRTIEHEGRAVGALVCIQQDGVGELSFWTAQDYWGLGLTTAAVDRFL +EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAA-D +>GCF_005280335_PROKKA_02302 +-------------------MLLRDVRPEDLDEFFLHQQDEQASLMSAFAPRNPRDRGVFD +YHWSSLLAAETAVVRTIEHEGRAVGAIVCTEHDGVGELSFWTAQDYWGLGLTTAAVDAFL +REHTRRPLRAHVPEDNAGSVKVLSRRGFETVGQEKVFSNARAEVITELVMELPAGAE +>GCF_020097155_PROKKA_02158 +-------------------MPLRDVRPDDLDAFFLHQQDERANLMSAFAPRNPSDRGVFD +YHWAHLLGDDATEVRTIEHEGRPVGALVCTRVDGVDELSFWVAREFWGQGLTTSAVDEFL +STHRERPVRAHVPEDNLGSVKVLTRRGFREVGREKVFSNARAEVVEELVLELPGA-- +>GCF_023573625_PROKKA_00631 +-------------------MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD +YHWAHLLGDEDTVVRTIEHEGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFL +EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAA-D + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000594.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000594.fa new file mode 100644 index 0000000000000000000000000000000000000000..f1bd5fb94d6f414375565b78ab9741f76c722eca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000594.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00662 +MP-AADPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISG +PAIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDV +IRVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPREDQATAVFRAQAVLGLLNST +PRSVRRTAADRAARRATLVAMAWAAATAPGPLSGE-----D +>GCF_003691675_PROKKA_00399 +MP-AVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISG +PAIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDV +IRVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNST +PRSVRRTAADRAARRATLVAMAWAAATAPGPLSGE-----D +>GCF_005280335_PROKKA_02301 +MPAAVDPSAPAASAAAPTSRVAAKARRREDLLAAAARLFAARGFDAVRLEDIGAEVGISG +PAIYRHFAGKAAVLVAILATASQDLLEGALATEREHDAGEDALRALIAFQTDFALAQRDV +IRVQDRDMSALPEDERAAVTGTQRAYIDVWARQLRVVHPSEDQATAVFRAQAVLGLINST +PRSVRRTAADRAARRATLVAMAWAAATAPGPAADR-----P +>GCF_020097155_PROKKA_02157 +MPHAPDTAAPGPTGTP---RERAKARRRAELLAAAARLFAAHGYEATRLEDIGAAAGISG +PGIYRHFAGKAAVLVEILSSASLFLLDGAEAVAARGLSGAEAVHDLIAFHTDFALANRDV +IRVQGRDMSSLPPADGAEITRVQRRYIDLWGAQLRRLHPGEDHATARFRTQALLGLINST +PFSVRRSRADRGARRDALIGMAWAAARTPGGTARPEPPVVP +>GCF_023573625_PROKKA_00632 +MP-AVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISG +PAIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDV +IRVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNST +PRSVRRTAADRAARRATLVAMAWAAATAPGPLPGG-----D + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000595.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000595.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6fd9b517ca402c453319c4bc0bce332f4b3a20a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000595.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00664 +M--TENHAQGTPLFDTVLLANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVRLGPAPARESYLDIDAVVD +AARRTGAQAVHPGYG--FLSENADFARALEAAGIVFVGPPVGSLDAM---ADKIRAKETVAAYDVPVVPGIQDPTLTDAQ +ITAEAEHVGFPLLIKPSAGGGGKGMVAVRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVH +LGEREC----SLQRRHQKVIEEAPAPLL-----------------TGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFL +VSDENPDEFFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGEPLGFAQEDVSLDGAAVEARVYAEDPANGFLP +STGPVLRWREPAGEGVRVDTLLLPSQ-GEERAFGTVLTIRDDEGALWEGLAAPDGAQPEITGFYDPMIAKLI---TRGAD +RTEAL-----ERLDAALADTVLFGVRSNLGWLRELAARTDVRTGRLTTELI-----DGLEAWTAPAL-PEDLAALAAEAL +ADVSEDAAAAEQRAAGTAWARADGWRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGALAGVNLLAGDPRDPRSAWL +HRDGAAWQVRRLTRAEVVEAARAAAAARRAPAGAASPEARTPMPGTVVAVSVATGDTVAAGQELAVVEAMKMEHPVTAAV +AGVVTVHVAEGDPVAAQALIAVVEPAENAAPEENA +>GCF_003691675_PROKKA_00401 +M--TENHAQGTPLFDTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVRLGPAPARESYLDIDAVVD +AARRTGAQAVHPGYG--FLSENADFARALEAAGIVFVGPPVASLDAM---ADKIRAKETVAAYDVPVVPGIQDPTLTDEQ +ITAEAERVGFPLLIKPSAGGGGKGMVAVRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVH +LGEREC----SLQRRHQKVIEEAPAPLL-----------------TGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFL +VSDENPDEFFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGGPLGFAQEDVTLDGAAVEARVYAEDPANGFLP +STGPVLRWREPAGEGVRVDTLLLPSRPAEERAFGSGPQTGPAAGAV--DPVDVDGAQPEITGFYDPMIAKLI---ARGAD +RAEAL-----DRLDAALADTVLFGVRSNLGWLRELAAREDVRTGRLTTELI-----DGLEAWTAPAL-PEDLAALAAEAL +ADVSEDAAAAEHRAAGTAWARADGWRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGGLAGVNLLAGDPRDPRSAWL +HRDGAAWQVRRLTRAEVVEAARAAAAARRAPASAASPEARTPMPGTVVAVSVATGDTVAAGQELAVVEAMKMEHPVTAAV +AGVVTVHVAEGDAVAAQALIAVVEPTEHAAPAENT +>GCF_005280335_PROKKA_01220 +MDLDARPLAGRKL----LLLDGSRKSIEIVDEAHRLGVHVIVTDYNTPEQSPAKLAADQHFQV-------STSDVDAVVD +LIRREGVDGVLAGFSDRWLATYAEICAAAQV-------PCYATVDQIRLFTDKKRYKAMLEQFGVPTITGYSVDDATSGA +IPEEA----FPLIVKPADGSGSRGISVVASQSELQNGLDVALNYSWT----QDLVIERFLPGQEATVYWVFQDGDCRVSL +MWHRHMHDFGPQDRYRLPVAYSSPSSLLPTYLADVAPSVQAMLRSAGVRDGIMFMQGLIHEGVFHTYDIGYRVTPTQEYR +VVEE-------------LCGYNPLS---------------MLIHYALTGTMG--------------------------QP +DLAAVAEPRHP-GYGFNVSTLIRPGT----------------VGAV--------------TGLDDVAALRGILSTTAAID +AGETLPEEGWGQLRQVAVRTV--GVADSLDLLRQTMRQVD--------ELIDVRDVDGASMVIHPDMPPQDLDAYVL--- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------- +>GCF_005280335_PROKKA_02299 +M--TENPTQGAPLFHTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADAQARHVLEADEAVRLGPAPARESYLDIEAVVE +AARRTGAQAVHPGYG--FLSENADFARALEAAGIVFVGPPMASLDAM---ADKIRAKETVAAYDVPVVPGVADPTLDDAA +LAAEAQRVGFPLLIKPSAGGGGKGMVAVHAADELPAALASARRTARSAFGDDTLLLERLIAAPRHIEVQVFADAHGTTVH +LGEREC----SLQRRHQKVIEEAPAPLL-----------------TGLAHGAELRERLGKAAVDAAVSVGYRGAGTVEFL +VSDEDPDAFFFMEMNTRLQVEHPVSEEVVRVRGQRQDFVELQLRIAAGEPLGFAQDDIALEGAAVEARVYAEDPANGFLP +STGPVLRWREPQGEGVRVDTLLLPAA-----------------DAA--DPAAVDGGQPEVTGFYDPMVAKVI---TRGAD +RAEAL-----DRLDAALADTVLFGVRSNLGWLRELAAREDVRAGRLTTELI-----DGMEAWNAPTL-PEDLAALAAEAL +EEASDDAAAAERHAAGSAWARADGWRGAGAPQPGMRVRVGDEDRVLHGPAADAETEEDESALAGLNLLAGDPRDPRSAWL +HRDGAAWQVRRLTRAEVVEAARAAAAARRAPGRAQRP----PRPA----------------------------RPCRAPS +S-------------PSRWPPGTPWPSARSWPWSRP +>GCF_023573625_PROKKA_00634 +M--TENHAQGTPLFDTVLVANRGEIAVRVIRTLRRLGIRSVAVHSDADADARHVREADTAVRLGPAPARESYLDIDAVVD +AARRTGAQAVHPGYG--FLSENADFARALEAAGIVFVGPPVASLDAM---ADKIRAKETVAAYDVPVVPGIQDPTLTDEQ +ITAEAERVGFPLLIKPSAGGGGKGMVAVRAAEELPGALASARRTARSAFGDDTLLLERLITAPRHVEVQVFADAHGATVH +LGEREC----SLQRRHQKVIEEAPAPLL-----------------TGLAHGAELRERLGRAAVDAAVSVGYRGAGTVEFL +VSDENPDEFFFMEMNTRLQVEHPVSEEVVRVRGQRLDFVELQLRIAAGGPLGFAQEDVTLDGAAVEARVYAEDPANGFLP +STGPVLRWREPAGEGVRVDTLLLPSRPAEERAFGSGPQTGPAAGAV--DPVDVDGAQPEITGFYDPMIAKLI---ARGAD +RAEAL-----DRLDAALADTVLFGVRSNLGWLRELAAREDVRTGRLTTELI-----DGLEAWTAPAL-PEDLAALAAEAL +ADVSEDAAAAEHRAAGTAWARADGWRGAGAPQPGMRVRVGDEDRILTAPAADAEVDEDAGALAGVNLLAGDPRDPRSAWL +HRDGAAWQVRRLTRAEVVEAARAAAAARRAPAGAASPEARTPMPGTVVAVSVATGDTVAAGQELAVVEAMKMEHPVTAAV +AGVVTVHVAEGDAVAAQALIAVVEPTEHAAPAENT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000598.fa new file mode 100644 index 0000000000000000000000000000000000000000..fa9d863afb494db57fb733f43bdccbd3741d75af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000598.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00670 +MTHGSLTDYTLPAP-AP----AHDGGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVAL +AGGANTTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLG-RPAPRPVLFTGPRAAE +QIAAWPGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVP +VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVV +TTNSASLVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRL +PIALGLCWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAA +NEESVDAFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWAR +RAARARW +>GCF_003691675_PROKKA_00407 +MTHGSLTDYTLPAP-AP----ADDDGAPRAVALIGSTGSIGTQGLDVIAQDPTRLRAVAL +AGGANTTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLG-RPSPRPVLFTGPCAAE +QIAAWPGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP +VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVV +TTNSASLVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRL +PIALGLCWPRRLSGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAA +NEESVDAFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWAR +RAARARW +>GCF_005280335_PROKKA_02292 +MTHGSLTDYTLPAAGAPSASNAHDDGAPRAVALIGSTGSIGTQGLDVIAQDPARFRAVAL +SGGANTGLLAEQAVRFEVQAVGSATATEDELRAAIADAAARLGLKPAPRPALFTGPTAAE +RIAAWKGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP +VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALAEVTPAQALAHPTWDMGRVV +TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHPQSVVHSMVEFTDGSTLAQASPPDMRL +PIALGLAWPARVPGAAAGCDWTRAATWAFEPLDEDAFPAVRAAKEAAAASPTHMAVFNAV +NEEAVDAFHDGRIRFDAIVDTVRAVVGEYEPARVLGAAGHGHVAQDLTVEAVLAAEDWAR +TAARARW +>GCF_020097155_PROKKA_02154 +MTHGSLTDYTFPADHGP----GASDGACRAVALVGSTGSIGTQGLDVIAQAPERFRAVAL +SGGANTALLAEQAVAHGVEAVGSAAASEEELRAALADAAARLR-RPDPRPALFTGPEAAA +RIAAWEGADTVLNGITGSIGLAPTLAALRAGHRLALANKESLIVGGALVKAAAAPGQLVP +VDSEHSALAQALRGGTAGEVRRLVLTASGGPFRGFSAAQLAEVTPAQALAHPTWDMGRVV +TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHSQSVVHSMVEFTDGSTLAQASPPDMRL +PIALGIGWPHRVLGAAAGCDWTQAAQWTFEPLDEAAFPAVSLAKEAAASSDTHMAVFNAA +NEEAVDAFHGGRIRFDQIVETVRAVLGEYRPDGVLAAAGADP--DELTVEAVLAAEDWAR +AAARGRW +>GCF_023573625_PROKKA_00640 +MTHGSLTDYTLPAP-AP----ADDDGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVAL +AGGANTTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLG-RPAPRPVLFTGPRAAE +QIAAWPGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVP +VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVV +TTNSASLVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRL +PIALGLCWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAA +NEESVDAFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWAR +RAARARW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000601.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e8cfe345d1394ed5b4940b9d74f3a0b8e60092a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000601.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00673 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAA-GTLFLGI------DD-DAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGD +AEALGAAAAALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLG-TAGGIDP +NPHVVQAQPHDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGP-- +-RDAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLY +VNAYNTPALRTYERVGFERRGTFATVLY +>GCF_003691675_PROKKA_00410 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAA-GTLFLGI------DD-DAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGD +AEALGAAAAALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLG-TAGGIDP +NPHVVQAQPHDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGP-- +-RDAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLY +VNAYNTPALRTYERVGFERRGTFATVLY +>GCF_005280335_PROKKA_02289 +MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAA-GTLFLGIDAGEGRDD-DGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGD +AEALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLG-ADGAAET +SPHVVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGP-- +-ADAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLY +VNAYNTPALRTYERVGFERRGTFATVLY +>GCF_020097155_PROKKA_02151 +M---------------DLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRL +AGPRGGRADGTLFLGV------EDPDRP--GALRSACWVGSTVVPLAGHD--------DD +VPALAASVAALRRRFASVYGPAVTVLAVGRTLRDAGHRPRAVREEQPLMVHARTPGDLVP +DPAVRAAAPGEWESVVPASAAMFEEELGFSPFLTGAAQYRDRVRRLVADGRVFTAPGEPV +VDDPTSGVRFKADIGLLSASCVQVQGVWLHPSRRGRGEAAPAMAAAVALMARRAPAVSLY +VNGFNTPALRTYERVGFERVGTFATVLY +>GCF_023573625_PROKKA_00643 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAA-GTLFLGI------DD-DAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGD +AEALGAAAAALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLG-TAGGIDP +NPSVVQAQPRDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGP-- +-RDAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLY +VNAYNTPALRTYERVGFERRGTFATVLY + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000604.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec23b8ef7b76d3c60abe6264f35bb29788706a53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000604.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00676 +MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV +ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA +APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD +ADAAAGEDTAEHTEA +>GCF_003691675_PROKKA_00413 +MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV +ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA +APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD +ADAAAGEDTAEHTEA +>GCF_005280335_PROKKA_02286 +MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL +AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG +EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD +A-AAAGEQTAEHTEA +>GCF_020097155_PROKKA_02148 +METVP-----AALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEV +AELSGLVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAA +LPVTARVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTA----- +AEQSGAEQTAEQTEA +>GCF_023573625_PROKKA_00646 +MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV +ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA +APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD +ADAAAGEDTAEHTEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000610.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000610.fa new file mode 100644 index 0000000000000000000000000000000000000000..9eb43a07c6ba35f2ad9c120fd0a698778ba59a03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000610.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00683 +MA----------PSDGAPA---RNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVA +YTLSAVAAVVYIVATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVW +SRFGAGYGYVPLVLPVVGLIWLLTHRPARPAEAG-AL +>GCF_003691675_PROKKA_00420 +MA----------PSDGAPA---RNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVA +YTLSAVAAVVYIVATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVW +SRFGAGYGYVPLVLPVVGLIWLLTHRPARPAEAG-AL +>GCF_005280335_PROKKA_02280 +MARTRTASGAARPGAAAPA---RNQGLGRIIVMVYAVFALSATARSLFQILTDVEAAPVA +YSLSAFAATVYIVATLALARSGARAWAVALGAVLVELIGVVGVGLWTVLDPGLFAEETVW +SRFGAGYGYVPLVLPVVGLAWLLAHRPSRPTAEEMAR +>GCF_020097155_PROKKA_02141 +MVEQHP---VA--DDGAPARPRRNQGLGRIIVMVYAVFALSASARSLFQILDHFWVAPFA +YVLSAFAAVVYIVATLALARSGPTAWKVAVAAVGVELAGVVGVGLLTVLDPQLFADATVW +SRFGAGYGYVPLVLPMVGLAWLLSHRPSREGRV---R +>GCF_023573625_PROKKA_00653 +MA----------PSDGAPA---RNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVA +YTLSAVAAVVYIVATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVW +SRFGAGYGYVPLVLPVVGLIWLLTHRPARPAEAG-AL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000616.fa new file mode 100644 index 0000000000000000000000000000000000000000..78509089b8f83fb0c558295e025d49f3491a8003 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000616.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00689 +---MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR +DESPEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL +PMAVEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP +IGGTPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQG +ALPAPRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG +GGMSSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMA +EADVTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAG +QVRAVAARLAAGDRARVVVAPA +>GCF_003691675_PROKKA_00426 +---MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR +DESPEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL +PMAVEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP +IGGTPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQG +ALPAPRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG +GGMSSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMA +EADVTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAG +QVRAVAARLAAGDRARVVVAPA +>GCF_005280335_PROKKA_02266 +MAGMSIHREIPLDFTGVLADEGHGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR +DESPEGYGSTHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL +PMAVEVLTDMLTSSLLDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP +IGGTPETIRAVTREHVAGHYARWYRPDELVVTAAGNLDHDEVCRLVLAALQASGWELAPG +ALPAPRRAVDTEGAAASRVLTGTHTVAKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG +GGMSSRLFQEVRERRGLAYSTYSFSAGYSDAGYWGLYAGCQPDRVDEVSALMEAELDRMA +AEVVTEEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLERVRAVDAA +QVRAVAARLAAGERARVVVAPA +>GCF_020097155_PROKKA_02135 +MAGMTVQREIPLDFSGVLA-EDRGAVVCRSVLPGGVRVLTESMPDQRSVTVGYWVAVGSR +DESPEGYGSTHFLEHLLFKGTPTRTAMDIASAFDRVGGESNAGTAKESTVYHAHVLDEDL +PMAVEVLTDMVTSSLIDADELETERGVILEELAMDADDPVDVAHERLAAVLMDGHPLGRP +IGGTPETIRAVTREHVVAHYRHWYRPQELVITAAGNLDHDDVCRLVLDALERSGWDLAEG +AAPAPRRTADAAGAGA--VLAGTHTVAKQVEQANVIVGGQSLSTTDPDRFALGVMMSVLG +GGMSSRLFQEIRERRGLAYSTYSFSAGYSDGGYFGLYAGCQPERVDEVAALMEAELERMA +AAEVTAEELDRAHGQICGGTVLGMESTGARMSRLGRAELVTGEFVDLSASLARVRAVDAG +RVRAVAARLAAGERARVVVAPA +>GCF_023573625_PROKKA_00659 +---MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR +DESPEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL +PMAVEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP +IGGTPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTPG +ALPAPRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG +GGMSSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMA +EADVTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAG +QVRAVAARLAAGDRARVVVAPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000618.fa new file mode 100644 index 0000000000000000000000000000000000000000..77b5d8fd5824a45cf9d30e5c6c6c8f137fc8fda9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000618.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00691 +MDWTDTWTLAEPSRTPDDGAVG-PPAPAVRARRSTVMSKVWVGFVCLLVLLFAGFALNAS +VALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRS +PGGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRL-HR +AG +>GCF_003691675_PROKKA_00428 +--------MAEPSRTPDDGAVG-PTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNAS +VALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRS +PGGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRL-HR +AG +>GCF_005280335_PROKKA_02264 +--------MADRAPRPAEQTVADPAEHAARARRSTLMSKLWVGFVSLLVLFFASFAVYVA +VAFIRAPQLLAKGIGVGVIFVVLVTVAVLAREVWFGQQTERLADLLEAEGGLPEDDLPRS +PGGRIDRAAADAQFEVYRVEAEAAPRDWRTRYRLALAYDASGDRRRAREAAREAVRL-HR +QG +>GCF_020097155_PROKKA_02132 +--------MASTDPRPGVDR-----EQAPRAGSST-GAKLWVLFVAALTLFFAFFVVRAA +VVFIAAGGVLPAVIGVAVILVVLVGLGLLGREMLFGLQTERLARTLEAEGGLPADDLPRS +PGGRIDRDAADAAFADAADEVRAAPEDWRARYRLSLAYDAAGDRRRAREAARQAISLASR +RG +>GCF_023573625_PROKKA_00661 +--------MAEPSRTPDDGAVG-PTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNAS +VALVRAPQPLAKAIGVGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRS +PGGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRL-HR +AG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000622.fa new file mode 100644 index 0000000000000000000000000000000000000000..df064909bf555fe9c01e7dd8366d81c8e7f35b26 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000622.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00696 +MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRGA-- +>GCF_003691675_PROKKA_00433 +MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRGA-- +>GCF_005280335_PROKKA_02258 +MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV +LTGLEYVKDAWILRRDALAAPRGA-- +>GCF_020097155_PROKKA_02129 +M--NAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMY +TDKLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGIT +AMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTV +VTGVEYVRDAVRLRADWLASHPEARR +>GCF_023573625_PROKKA_00666 +MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRAA-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000623.fa new file mode 100644 index 0000000000000000000000000000000000000000..466203ad01cf663802d29e17514b959f0ee0d22f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000623.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00697 +--------------MAGAQDVVHALAHAGRTVATGESLTAGLLAARLADVPGASAVLHGG +VVAYQNAVKTGLLGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQ +GQPVGTVWLGLAVPDADANALDVLGGERDG-----------------AATAILLRLDGDR +AAIREATVAAALQALTRLLAVRGH--------------- +>GCF_003691675_PROKKA_00434 +--------------MAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGG +VVAYQNAVKTGLLGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQ +GQPVGTVWLGLAVPDADASALDVFGGERDG-----------------AATAILLRLDGDR +AAIREATVAAALQALTRLLAGRGH--------------- +>GCF_005280335_PROKKA_02257 +---------------MAAQETVRALAGAGLTVATAESLTAGLVAARLADVPGASAVLQGG +VVAYQNSVKAGLLGVPADLLERVGAVDPEVARRMAEGARAGLGADVGVATTGVAGPEPHQ +GRPVGTVWLGVAVPERLTAALDGLGGERRG-----------------AATAIPLALDGDR +RAIREATVAAALAALTRLGAPVGERATGEGAAGEPCAGA +>GCF_020097155_PROKKA_02128 +MSTGVGAVAAEGEAADPARAAVRALTTAGLTVATAESLTAGLVAARLADVPGASAALQGG +VVAYQNHVKAGLLGVDAGLLTARGAVDPEVARQMACGARRAAGADVGVATTGVAGPEPHQ +GKPVGTVFVGVAVPAELAPALAGLDGEPGAGEAAPGEAGSGGSEAGVAAAAFALTLPGNR +AEIRAATVETVLDLLAALG------TTGRGMPDEAPALS +>GCF_023573625_PROKKA_00667 +MT------------TAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGG +VVAYQNAVKTGLLGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQ +GQPVGTVWLGLAVPDADASALDVLGGERDG-----------------AATAILLRLDGDR +AAIREATVAAALQALTHLLAGPGH--------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000624.fa new file mode 100644 index 0000000000000000000000000000000000000000..626f120b318060677ceec308af6658bb7aa030f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000624.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00699 +--------------------------------MPLLRHEIGDVLRDVRQLQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICQALDIPLSYLLREVSDRLVEQEGMVVPDTLPD +DLT---DPSLGSLAGR +>GCF_003691675_PROKKA_00436 +--------------------------------MPLLRHEIGDVLRDVRQLQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICQALDIPLSYLLREVSDRLVEQEGMVVPDTLPD +DLT---DPSLGSLAGR +>GCF_005280335_PROKKA_02255 +MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE +DLTDAADPSLGTLAGR +>GCF_020097155_PROKKA_02127 +MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA +DMAEDGAADVAPLAVR +>GCF_023573625_PROKKA_00669 +--------------------------------MPLLRHEIGDVLRDVRQLQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICQALDIPLSYLLREVSDRLVEQEGMVVPDTLPD +DLT---DPSLGSLAGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000628.fa new file mode 100644 index 0000000000000000000000000000000000000000..d23797d6f9b9bd5f715d766d0dfefcfe60eb3c2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000628.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00706 +MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAEDAQADLVVFNTCAVRENADNR +LYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPST +LPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRSAKFLRILEKVRERIPHA +AITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATL +VGTRQELLVTADSGSKAAERGRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD +AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS +>GCF_003691675_PROKKA_00440 +MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAEDAQADLVVFNTCAVRENADNR +LYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPST +LPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDRVLKDMRRSYRSAKFLRILEKVRERIPHA +AITTDIIVGFPGETAEDFAETMRVVEASRFSSAFTFQYSIRPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATL +VGTRQELLVTADSGSKAAERGRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD +AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS +>GCF_005280335_PROKKA_02251 +------------------------------------MNVHDSERISGLLESTGYAPVPQDAQADLVVFNTCAVRENADNR +LYGNLGNLRAVKDARPGMQIAVGGCLAQKDQATIQRKAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPST +LPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGQIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDTVLKAMRRSYRSKRFLGILEKVRERIPHA +AITTDIIVGFPGETEEDFQDTMRVVEASRFSSAFTFQYSIRPGTPAGEMADQVPKAVVQERFERLVALQDRISAEEMATL +VGTRQELLVTADSGTKASERGRLSGRARDNRLVHFSVPAGAPTPRPGDFVTVTVTEAHPFFAVADPAPEDYSLRRSRAGD +AWDRAQAESCGVPTPGASGGAGATSLGMPTLRPRS +>GCF_020097155_PROKKA_02123 +MTLTDP---TTHLPALGTAPDAHAGLTYEVRTFGCQMNVHDSERISGLLESTGYTPAEDGTQPDLVVFNTCAVRENADNR +LYGNLGNLRPVKDAHPGMQIAVGGCLAQKDQATIQEKAPWVDVVFGTHNIGSLPALLERSRHNAEAEMEILESLEVFPST +LPTKRESTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGEIDGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRSAKFLRILEKVRERIPHA +AITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATL +VGTRQELLVTADSGSKATERGRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD +AWDRAQAESCGAPAPGAAGGSGATSLGMPTLRPRF +>GCF_023573625_PROKKA_00673 +MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAEDAQADLVVFNTCAVRENADNR +LYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPST +LPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRSAKFLRILEKVRERIPHA +AITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATL +VGTRQELLVTADSGSKAAERGRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD +AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000632.fa new file mode 100644 index 0000000000000000000000000000000000000000..35f69709cf1324775ac83d4e2c406269b33b0db1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000632.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00710 +MG---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +-RTQ----------------------WPLT-------------------DEFAGQRVVIV +GMGVSATQLLAEISTVADTLWVTRREPRWQDSAAPGALAESVRGVDERTRAGLPPGSVVG +ATGMHRSSWVREAESRGVLVRHPMFTAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLA +PLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG +>GCF_003691675_PROKKA_00444 +MGVECTG---RRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQA +GLSAAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVN +HIHELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFF +VRTDGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIV +GMGVSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVG +ATGMHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLA +PLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG +>GCF_005280335_PROKKA_02245 +MRTILAADRRRR-------HPSPVGEHAPAVPTLGRMTPHPDR-----HVTVLVVGAGQA +GLSAAHHLRRRGFQPVGPG-EAPRPAPEGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVN +HIHELPGHPVPPADPAARANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFR +VHTD--AGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTHDYRDPEEFARRRVVVV +GMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVS +ATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLA +PLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA +>GCF_020097155_PROKKA_02118 +------------------------------------MTPHPDR-----HVTVLVVGAGQA +GLSAAHHLRRRGFLPVGPG-EAPGPAPGGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVN +HIHELPGHPVPPADPDAQANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFR +VHTD--TGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTHDYRGPQEFAGRRVVVV +GMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVS +ATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLA +PLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA +>GCF_023573625_PROKKA_00677 +MGVECTG---RRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQA +GLSAAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVN +HIHELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFF +VRTDGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIV +GMGVSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVG +ATGMHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLA +PLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000639.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ff2e92336f9a33967225e22014c17b4e7414db8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000639.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00720 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>GCF_003691675_PROKKA_00451 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>GCF_005280335_PROKKA_02238 +MARPTSVPGVRPSVAVLDYGSGNVHSAVRALERAGADVELTRDPEAVQSADGLLVPGVGA +FASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERAEGMGEWPGVVEA +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLRWEFDQTISAMRPPQVTWAH +HGADFVAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>GCF_020097155_PROKKA_02110 +MASPTSVPGVRPTVAVLDYGSGNVHSAVRAVEHAGARVELTKDPDAVLGADGLVVPGVGA +FASVMEALRSSGGTRWIGRRVAGGRPVLGICVGHQVLFEAGVEHGVRTEGMGEWPGVVEP +LPAATVPHMGWNTVRPAEGSALFAGIEDERFYFVHSYAVQSWEFDQGNEAMRPPQVTWSH +HGADFIAAVENGPLSATQFHPEKSGDAGQALLRNWLETL +>GCF_023573625_PROKKA_00684 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPAEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000640.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000640.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6a00e4b9d2b63d9c83c591ce103cbde23cb9b00 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000640.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_00721 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA +>GCF_003691675_PROKKA_00452 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA +>GCF_005280335_PROKKA_02237 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR +>GCF_020097155_PROKKA_02109 +MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV-- +>GCF_023573625_PROKKA_00685 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000641.fa new file mode 100644 index 0000000000000000000000000000000000000000..29ebf8c78dd16939bd78905a8485bbe9f59f73fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000641.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00722 +MTPN--APALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDL +DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWT +ARVIERFGDRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTL +KGPNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ +ALAVAGGATVEQARSEQPGPVAP +>GCF_003691675_PROKKA_00453 +MTPN--APALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDL +DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWT +ARVIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTL +KGPNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ +ALAVAGGATVEQARSEQPGPVAP +>GCF_005280335_PROKKA_02236 +MTPNPAAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQRAGAEWIHLVDL +DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPAWT +ARVIERFGDKVAVGLDVRGTTLAARGWTQEGGDLWEVLARLEDAGCSRYVVTDVTKDGTL +KGPNTELLAQVCARTDKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ +ALAVAGGATVEQARAEQPGPVAE +>GCF_020097155_PROKKA_02108 +MTET--TPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQDAGAEWIHLVDL +DAAFGRGDNRDVLRRVVDEIGVKIELSGGIRDDASLENALAMGAARVNLGTAALEDPAWT +ARAIERFGNRVAVGLDVRGTTLAARGWTQDGGDLWEVLARLEEAGCARYVVTDVTKDGTL +RGPNRELLARMCAATDKPVVASGGISSLEDIAALAAMVPQGVEGAIMGKALYAGRFSLEQ +ALAVAAGATVERAREQHPFQAAP +>GCF_023573625_PROKKA_00686 +MTPN--APALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDL +DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWT +ARVIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTL +KGPNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ +ALAVAGGATVEQARSEQPGPVAP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000644.fa new file mode 100644 index 0000000000000000000000000000000000000000..2395ad03499fa9953101f9586361cf33836bdcb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000644.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00725 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR +LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL +C-------------------- +>GCF_003691675_PROKKA_00456 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR +LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL +C-------------------- +>GCF_005280335_PROKKA_02233 +MNSSSTPTPEPS------------------------ETARHAWRAYFEATQMLSEMLERG +LKKDSGMSLADYNLLLLLYEAPEGRLRMGELASGMVFSPSRITYQVKTLVARGLIERRAA +ECDRRGFEAVLTDEGRTAFRRAAAGHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGL +C-------------------- +>GCF_020097155_PROKKA_02105 +MTSSSTPAAEPTGP----------------------RAARHAWRAYFESTQMLQDQLERG +LKAECGITLADYNLLLLLVESDGGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRV +ECDRRGFEAVLTDAGRTAFRRAAVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESR +CAGRAAPSEPCGAQASNSADA +>GCF_023573625_PROKKA_00689 +MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR +LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV +ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL +C-------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000649.fa new file mode 100644 index 0000000000000000000000000000000000000000..00089cc44373b795b4782afe028f256508dad305 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000649.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00730 +MAQIVLFHHALGLTDGVRALAEQI-ASGGHTVHTPDLYDGRTFATVDEGVAHAQHL-GFE +EIGRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQP +HTALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDAD +LTAVLVRRIHELLA +>GCF_003691675_PROKKA_00461 +MAQIVLFHHALGLTDGVRALAEQI-AGGGHTVHTPDLYDGRTFATVDEGVAHAQHI-GFE +EIGRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQP +HTALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDAD +LTAVLVRRIHELLA +>GCF_005280335_PROKKA_02223 +MAQILLFHHALGLTDGVRALAAQI-EAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFD +VIAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQP +HTALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPA +LTEVLVRRIHELLA +>GCF_020097155_PROKKA_02099 +MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQI-GQD +EVMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQP +HTSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDAR +HTEVMVERIRELLA +>GCF_023573625_PROKKA_00694 +MAQIVLFHHALGLTDGVRALAEQI-ASGGHTVHTPDLYDGRTFATVDEGVAHAQHL-GFE +EIGRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQP +HTALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDAD +LTAVLVRRIHELLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000650.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb2bf24ec84f0d693010a4b1964db5a113e1228b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000650.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00732 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR +>GCF_003691675_PROKKA_00463 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR +>GCF_005280335_PROKKA_02221 +MDAVRILEDEIREVVRRQGIDPQREHARVIALIQDAAADYESRAEVSALPDLEDPAAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARAGRSELTGIVLTEEEVHDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFISRARRLEDLVRSGSLT +PTAARFLDAAVDVGMNVLVSGATQAGKTTLLNCLASSIGARERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRSFVVPTVATCIDVVVHCERDWDGRRRVLEVLTVGA +RVEDGVIETSTLFQRDSAGDLRLNEAASLEFDAFARRGVDVHELVGLR +>GCF_020097155_PROKKA_02097 +MDAVRMLEDELRELVRRRGVDPRVEGHRIRTMIAEATLDYESRSLVSSLPPLEDPEAARQ +ELFDRIAGLGPLQRLMDDPTVEEIWLNAPDQVYCARAGRSELTGIVLSEEQVRDLVELML +KSSGRRLDLSMPFVDASLPDGSRLHVAIPDITRRHWAVNIRKFISRAHRLDDLVRSESLT +TPAARFLDAAVDAGMNILVSGATQAGKTTMLNCLSASIGARERVITVEEIFELQIPVRDV +VGLQCRQPNLEGTGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSASDALTKLCTLPLLAGENISRNFVVPTVATCIDVVVHCERDREGRRRVREILTVGS +RVEGGVIETSTLFRRDAHGDLVLNPSADLEFEAFARRGLDPRDLVEVR +>GCF_023573625_PROKKA_00696 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDTGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000653.fa new file mode 100644 index 0000000000000000000000000000000000000000..e5c5a7c3765916aa3dc41b4ad59c373e307c4e6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000653.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00735 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA +ISQVSQGG- +>GCF_003691675_PROKKA_00466 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA +ISQVSQGG- +>GCF_005280335_PROKKA_02195 +MLHHHVISILTALRGLLHDDVRDDRGDVPGWVMITLMSAVLVAALLTLALPALTDLFDQA +ISQVTQGE- +>GCF_020097155_PROKKA_02094 +MLTNAYLTVVSALTSLLHDDARDERGDVPGWVMITLMSAALVVALLGLAMPALKAMFDQA +ITQVNNAAG +>GCF_023573625_PROKKA_00699 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALEGLFNQA +ISQVSQGG- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000664.fa new file mode 100644 index 0000000000000000000000000000000000000000..5bc26116ce80ed6f2718e9c4863767167d0be028 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000664.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00751 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE +RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED +>GCF_003691675_PROKKA_00481 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED +>GCF_005280335_PROKKA_02179 +MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL +DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED +SASSED +>GCF_020097155_PROKKA_02074 +MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA +PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV +VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL +DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR +ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF +EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNR-TTAEAGG +SASSED +>GCF_023573625_PROKKA_00715 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000668.fa new file mode 100644 index 0000000000000000000000000000000000000000..723c3947cbb33f1800f78d56217bda1a9661e11f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000668.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00755 +MHNRRIRIAAVGDQLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER +WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT +PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA +>GCF_003691675_PROKKA_00485 +MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER +WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT +PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA +>GCF_005280335_PROKKA_02175 +MNDRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPGVELENYVLAVPHETTEDLNER +WWGEASRRYSEDTENRLVVALSDADLDLEASSTARSRLNLANVLDTASQRGIPVLVVGPT +PTLDEERNARLAELNAAYLDVADRRSHVYVDTFTPLQGHEQWRADLAAGEGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA +>GCF_020097155_PROKKA_02070 +MQNRRIRIAAVGDHILAGAGDPRSIGWWGRVLARTAAPEVTLENYVLAVPHETTEQLNER +WWGEASRRFSESAENRLVVALSDADLDLEASSSARSRLNLANVLDTASQRGITALVVGPV +PTLDEARNDRLADLNTAYQDVAARRGHLYVDAFTPLRTHEQWRADLAAGDGVPGQAGHGL +IAWLVLHRGWYQWLGVPEPTA +>GCF_023573625_PROKKA_00719 +MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER +WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT +PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000669.fa new file mode 100644 index 0000000000000000000000000000000000000000..17e691408c05585be48def3d1cc547bc78fb6b6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000669.fa @@ -0,0 +1,85 @@ +>GCF_002008305_PROKKA_00756 +--------MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAE---AEPKAAAKTEPKTAAK +AEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADTATTTA-DEKQEKATVLKGMAKAVATNMDA +SLSMPTATTVRDLPAKVLIDNRVVINSHLARTRGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGL +AIDLPRPDGTRALVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRLSQGQAAII +GVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQ +DVQVNPEEQIGKVARIQQLIHAYRDRGHLLANVDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILG +VLRDAYCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLEGGESLIPL +LDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGASGSGDVKYHMGTEGTFVSDAGNSTRVYL +AANPSHLEAVDPVLEGVVRAKQDRLDLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQV +GFTTPPTQARSAVYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDDPSMTQPRM +YNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETH--EDAPASGGEGLRPAEDRDAAPEAPASTAIS +AETLRAIGQAHIDVPEGFTVHPKLAALLERRAKMAVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFH +DRITGDTWAPLRHLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSADQKWSQT +SSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHAYARPRRPLIVFTPKQLLRLKAAANSV +EDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYYDLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQ +DEPANQGPWPFMALNLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR +>GCF_003691675_PROKKA_00486 +--------MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAE---AEPKAAAKTEPKTAAK +AEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADTATTTA-DEKQEKATVLKGMAKAVATNMDA +SLSVPTATTVRDLPAKVLIDNRVVINSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGL +AIDLPRPDGTRALVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRLSQGQAAII +GVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQ +DVQVNPEEQIGKVARIQQLIHAYRDRGHLLANVDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILG +VLRDAYCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLEGGESLIPL +LDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGASGSGDVKYHMGTEGTFVSDAGNSTRVYL +AANPSHLEAVDPVLEGVVRAKQDRLDLGGQRPDSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQV +GFTTPPTQARSAVYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDDPSMTQPRM +YNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETH--EDAPASGGEGLRPAEDRDAAPEAPASTAIS +AETLRAIGQAHIDVPEGFTVHPKLAALLERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFH +DRITDETWAPLKHLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSADQKWSQT +SSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQAYARPRRPLVVFTPKQLLRLKAAANSV +EDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYYDLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQ +DEPANQGPWPFMALNLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR +>GCF_005280335_PROKKA_02174 +MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAPA---E--KAPAQAAAKAAPK +AEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVPSEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDA +SLSMPTATTVRDVPAKVLIDNRVVINSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGL +AIDLPRPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRLSKGQAAII +GVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQ +DLQVNPEEQVGKVARVQQLIHAYRDRGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILG +VLRDAYCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLEGGESLIPL +LDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFEGATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYL +AANPSHLEAVDPVLEGVVRAKQDRLDLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQV +GFTTPPTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRRGHNEGDDPSMTQPRM +YNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETH--EGSASSGGEGIRPAEDRDQAPEAPETTAIS +AETLRAIGQAHIDVPEGFTVHPKLAALLERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFH +DRITGDEWAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIIDEFISSAEQKWAQT +SSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHFHLLREQAYARPRRPLVVFTPKQLLRLKAAANSV +EDFTEGRFQPVIPDAGVDPKKVTRVQLVSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQ +DEPANQGPWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR +>GCF_020097155_PROKKA_02069 +--------MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPKATSSATAEPAPA +VKPAVKRGAATPADPQAAAKKSGPTDVS---APAQRKRSVSEAVPSEPARDAAAGA-SEKQDKATVLKGMAKAVATNMDA +SLSMPTATTVRDLPAKLLIDNRTVINSHLARTRGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGL +AIDLPKPDGTRALVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRLSKGQAAII +GVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIHGYLLGEDGFYDDVFHDLRIPYEPVRWAQ +DVQVNPEEQIGKVARIQQLIHAYRDRGHLLANVDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILG +VLRDAYCRTVGVEYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLEGGESLIPL +LDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGASGSGDVKYHMGTEGTFVSDAGNSTRVYL +AANPSHLEAVDPVLEGVARAKQDRLEAAGESGAAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQV +GFTTSPAEGRSSVYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDDPSMTQPRM +YTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAETGQAVATTGLEPARDRDAARPAPSTTAIS +PDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFH +DRVTDETWTPLNHLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISSAEQKWSQN +SSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLREQAYSRPRRPLVVFTPKQLLRLKAAADPV +EAFTQGGFRKVIGDASVDAAQVERVILVSGRLYYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQ +DEPANQGPWPFMALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA +>GCF_023573625_PROKKA_00720 +--------MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAAAAE---AEPKAAAEAEPKAAAR +AEPKATAKVTEPKAATAPARGAQPKETSVSTGPKAKKTPAAQAVPSEPADTATTTA-DEKQEKATVLKGMAKAVATNMDA +SLSMPTATTVRDLPAKVLIDNRVVINSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGL +AIDLPRPDGTRALVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRLSQGQAAII +GVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQ +DVQVNPEEQIGKVARIQQLIHAYRDRGHLLANVDPLEYSMAYHPDLDIREHGLTLWDLDREWPTGGFGGASSLTLRKILG +VLRDAYCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLEGGESLIPL +LDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGASGSGDVKYHMGTEGTFVSDAGNSTRVYL +AANPSHLEAVDPVLEGVVRAKQDRLDLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQV +GFTTPPTQARSAVYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDDPSMTQPRM +YNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERAFAETH--EDAPTSGDEGIRPAEDRDAAPKAPASTAIS +AEMLRAIGQAHLDVPEGFTVHPKLAALLERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFH +DRITGDTWAPLKHLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSADQKWSQT +SSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHAYARPRRPLIVFTPKQLLRLKAAANSV +EDFTEGRFQPVIPDAGVDAKDATRVLLVSGRLYYDLLARRQKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQ +DEPANQGPWPFMALNLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000673.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b9a820c1175dc11a75d4fa5a4152c4e81bf60c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000673.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00760 +ML---RRRRLPALTGALAALTLSLAACGGTSGDSAGAQAAGASADSGSGSAAGAPVAVAT +TTQLGSVLDRVVACADARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGME +SALANAEADGATVVEVAPQLDPLPFGGHD----------------HA-EEGA--GHEGHD +HGSEDPHVWMDVARMARAAELMGDTLAQERGDERFAECGATVRGELEQTDAQVREILAGV +PEDRRTLVTDHDAYGYFSDAYDFTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVI +TSVGARNSLVDTVAEE-AGNLPVIEVYESGVGPKDTPEADYAEAMLANARTLADALEG +>GCF_003691675_PROKKA_00490 +ML---RRRRLPALTGALTALTLSLAACGGTSGDSAGEQAAGASAAAGSGSAAGAPVAVAT +TTQLGSVLDRVVACADARSVTVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGME +SALANAEADGATVVEVAPQLDPLPFGGHD----------------HA-EEGA--GHEGHD +HGSEDPHVWMDVARMARAAELMGDTLAQERGDERFAECGATVRGELEQTDTQVREILAGV +PEDRRTLVTDHDAYGYFSEAYDFTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVI +TSVGARNSLVDTVAEE-AGDLPVIEVYEGGVGPKDTPEADYAEAMLLNARTLADALEG +>GCF_005280335_PROKKA_02170 +MHRTPRRRAAAALT---LASALALAGCG---ADSGGDGQAG----------SGEPAAVAT +TTQLGSVLGDVARCAGATTATVMGPGDDPHDFAPSSQQVAQMARAGLVFANGFGLEAGMA +SALENAAQDGAQVLEVAPRLDPLPFGAGEGAADGHAGETADEHAAHA-EEGSAGAHDGHD +HGSQDPHVWMDVARMARAAEVMGDALAEHTGEDRFADCGRQVRGELEATDAEVREILAAV +PEDRRRLIADHDAYGYFAAAYGFEVAGVVVPGGSTDGEPSSQRIAELTQAVAEAGADALV +TSAGGGAPTVETIAADGGGSTPVVELYEGGVGPADGEPAGYAEAMLHNARVLADALGE +>GCF_020097155_PROKKA_02065 +MS---RSSPTPRLAAPAVVAALGVALAGCSVADSSSPSAAEEGAVTASSSAAGPVVAVAT +TTQLASVADRVARCGGGSVVSVMGPGDDPHDVAASSDQVAQMVHSGLVFTNGLGLEGGMD +SALDNARQDGAVVVEVAPRLDPLPFGEHDAD--------------HAGHEGA-DAHAGHE +HGSQDPHVWMDVARMAAAARVVGDELAAETGEQKYAECGATVEGELEETDRQVREILAAV +PQERRTLVTDHDAYGYFSAAYGFTIEGVVVPGGSTDAEPSSRELAALTQQVKDHGAAALL +TSTGTPNGLVETVARE-AGGLPVVQLYEGGVGPVGTPEADYAQAMLHNARTLADALKG +>GCF_023573625_PROKKA_00724 +ML---RRRRLPALTGALTALTLSLAACGGTSGDSSGAQAAGASADAGSGSAVGEPVAVAT +TTQLGSVLDRVVACAGARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGME +SALANAEADGATVVEVAPQLDPLPFGGHD----------------HA-EEGA--GHEGHD +HGSEDPHVWMDVARMARAAELMGDTLAQERGDEQFAECGATVRGELEQTDTQVREILAGV +PEDRRTLVTDHDAYGYFSEAYDFTVSGVVVPGGSTDGEPSSQELAELARSIRDGGADAVI +TSVGARNSLVDTVAEE-AGDLPVIEVYEGGVGPKDTPEADYAEAMLVNARTLADALEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000674.fa new file mode 100644 index 0000000000000000000000000000000000000000..88d2974a353fb5d8b378d8c04e109faf117666d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000674.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00761 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQRERETP-----------V +VALPGAEVAR- +>GCF_003691675_PROKKA_00491 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAP-----------V +VALPGAEAPR- +>GCF_005280335_PROKKA_02169 +MDWLIEPFLLGFQQRALVGGLIAAALCAVVGTWLVLRGMSFFGDAFVHGVMPGIALSVVL +GFDAHLGAALAALVMLAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISLSDSYTGSLT +AILFGDALGVTWEGIVRQAVIAALVLVLALVLYRPLMALSFSPAKARSLGMRPRLTHALL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALAVLLGAAGVTIGLVLS +YHLGTAASATMALVPIAMFFVVLAGRAGLRALRSRRVRADRRRA---------------V +VETPSRRSVSP +>GCF_020097155_PROKKA_02064 +MDWLIDPFLLGFQQRALLGGLIAALMCSAVGTWLVLRGMSFFGDAFVHGVLPGIALAVLL +GGSPHLGAALAAVLMMGGISLVHRTTTLKEDTAIGLLFVGMMALGVVIISLSSSYTGSLT +AILFGDALGVTPENLLVQAAIGVVVVVLALVLYRPLLALSFSEAKSQALGMRPRLTHTLL +LVLIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALSAGIGALSVVAGLVLS +YHWGTAASATMALVPVVLFFVVLLGRSAVQAAAGRRRRTRGAASAPTPAGDDDAESRRET +EGSPAR----- +>GCF_023573625_PROKKA_00725 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAP-----------V +VALPGAEAAR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000676.fa new file mode 100644 index 0000000000000000000000000000000000000000..b217e540ab364733b43499459ccd0df29cef5ae9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000676.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00764 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQARVVPAPTAAPSSSHDAGGDPDA----D +TDGVDPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPEGPAYAQPGRCRPNRVILLDVRFR +ATA-GGPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEG +DTIVVYDDDHGLSAARAWWLLRHAGLRDSMLLDGGLEAWRAAGLPLQPGEVIPVPGTARP +SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAED +GRLRPAAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWV +QDPSNAVAVGPEPDGASGRD +>GCF_003691675_PROKKA_00494 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDA----D +IDGVDPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFR +ATG-GGPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEG +DTIVVYDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARP +SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAED +GRLRPAAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWV +QDPSNAVAVGPEPDGASGRD +>GCF_005280335_PROKKA_02165 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------MWGIDDG +DTVVVYDDDRGLSAARAWWLLRHAGLRDSMLLDGGLAAWRAGGLPLQPGEVIPMPGSART +SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGETEPIDPVTGHIPGARSLPTAGSLAED +GRLRPAEELAARFDAVGVDDETPVAVYCGSGVTAAHAVLTLAVAGRPGVALYPGSWSAWI +QDPSNAVAVGPDPHGEPGRD +>GCF_020097155_PROKKA_02061 +MK--------------------------DSTEGR-PPSPASSPAADAPTDQTPLAELAED +ATAPDPAAAEPPSLVDVGVLAGWLGLTPAEPVPAPPPGPVFDR--RVDPGRVILLDVRYA +VAGAGGSGHDAYLRGHLPGAVFVSLPNQLAGHAGPRQGRHPLPDPVQFAHSLRMWGIDDG +DTVVVYDDDRSLAAARAWWLLRHAGLRDSVLLDGGLGAWRAAGLPLQPGEVIPQPGSVHP +SWGRMPVVDTDGAEAIAAGGLLLDARSAERYRGEEEPLDPVAGHIPGARSLPTSGNVAAD +GRLLDPAALAARFEDAGLSDEVPAAVYCGSGVTAAHQVLALAVAGRHGVALYPGSWSAWI +QDPDRPVATGPRPEG----D +>GCF_023573625_PROKKA_00728 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDA----D +IDGVDPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFR +ATG-GGPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEG +DTIVVYDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARP +SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNAPTAESIAED +GRLRPAAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWV +QDPSNAVAVGPEPYGASGRE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000677.fa new file mode 100644 index 0000000000000000000000000000000000000000..36b2ab73f7026de58839a14dbaf7f52c36b9cfe2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000677.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00765 +MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL +TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD +DAAARLRAALRDLGHGEVVPQD +>GCF_003691675_PROKKA_00495 +MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL +TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD +DAAARLRAALRDLGHGEVVPQD +>GCF_005280335_PROKKA_02164 +MASVFSRIIAGELPARFVWQDETCVAFLSTGPLNPGHALVVPREEVDAWVDADPALVMHL +MTVAQQLGKAQVRAFSAQRAGLMVAGYEILHLHVHVWPSNSLADFDLNRVDNSPDPAEMD +DAAARLRAALRELGHGEVVPQD +>GCF_020097155_PROKKA_02060 +MATVFSRIIAGELPARFVWQDEQCVAFLSLGPLAQGHTLVVPREEVDQWVDADPDLLAHL +TRVAQAIGRVQVRAFGAQRAGLMVAGYEIPHLHVHVWPSNSMNDYDMARVDNAPEPESLD +EAAAAIRAGLREDGHGDVVPQD +>GCF_023573625_PROKKA_00729 +MATVFSRIVAGELPARFVWQDQTCVAFLSAAPLQPGHTLVVPRAEVDEWVEVDPALVTHL +TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD +DAAARLRAALRDLGHGEVVPQD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000678.fa new file mode 100644 index 0000000000000000000000000000000000000000..c51e7e0615ef385679aaf6e2047069cfaaa57b46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000678.fa @@ -0,0 +1,95 @@ +>GCF_002008305_PROKKA_00766 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGSIGH +TQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKATRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNID +FLLGYLRNLLPQRPDLKVIITSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVVAGTTRLAGTEILPLFGRLSM +AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDG +IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGAL------- +--------EAGG---ARA---GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAAD +ELHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQLAKDVGLTVEAGPVDPVGR +HEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGH +LVKRAYNEPHWSRRAGSVVAREKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA +LETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTADAEDLDTDAFPTTFSYPMPG +GDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADL +EAHADPLRDELPEALSAAVRRVRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARL +AGTDDPASARPGP------------------RGTGRGGRAQADARAGAEGRRRPE------GPGRSG-ATPAFEERHRLT +SWSIGTVPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN +REKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGS +VSLALAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAH +RARFAGTPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA +>GCF_003691675_PROKKA_00496 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGSIGH +TQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKATRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNID +FLLGYLRNLLPQRPDLKVIITSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVVAGTTRLAGTEILPLFGRLSM +AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDG +IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGAL------- +--------EAGG---ARA---GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAAD +ELHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQLAKDVGLTVEAGPVDPVGR +HEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGH +LVKRAYNEPHWSRRAGSVVAREKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA +LETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTADAEDLDTDAFPTTFAYPMPG +GDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADL +EAHADPLRDELPDALSAAVRRVRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARL +AGTDDPASARPGP------------------RGTGRGGRAPADARAGAEGHRRPE------GPGRSG-ATPVFEERHGLT +SWSIGTVPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN +REKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDS +VSLALAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAH +RARFAGTPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA +>GCF_005280335_PROKKA_02163 +MTETPTP--PAAASSAP-----AIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGVIGH +TQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMTDGILLAEIPHDPQLRRYSVVIVDEAHERSLNID +FLLGYLRTLLPQRPDLKVIITSATIDPERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTG +EPSPDDPEDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLAGTEVLPLFGRLSM +AEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSPG +IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSG +AKDGHDGGRGRG---GRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRERPVEQREAAD +ELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLAKDVGVAVHAGPVDPVGQ +HEAVHRSLLTGLLSQIGSYDERRREYAGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGG +LVKRTYNEPHWSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA +LETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLLDLDVAALLTADAEDLDTDAFPTVFPYPLSG +GDVDLDLEYTFDPTGASGTDGVTVSVPVLLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADL +DAHADPLADELTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAKANRSAIAARL +AGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGR-----GRDGTGRPEAG----AQGAGG-AAAAFAERHGLT +SWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAAGLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN +REKLTFTQNPHGSVDSLVADCSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS +VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDGQHMAVVQRLEDEFDAAVQAH +RARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALAQAARA +>GCF_020097155_PROKKA_02059 +MTDFPQP--PAAAP--------VITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLALGLGGAGVVGH +TQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGILLAEIPHDPDLRKYSAIIVDEAHERSLNID +FLLGYLKRLLPRRPDLKVIITSATIDPERFARHFGT-----EDE-------------PAPIIEVSGRTYPVEIRYRPLTE +EPSPDDPDDDADDHAETRDPIDAVGDAVLELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSM +AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASANQRSGRSGRTSDG +IAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMDFPFVQPPDSRQVTDGAATLTELGALHADAPT- +----RGGGRGRGKGAGNRSAAGTITDIGRRLARLPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAAD +ELHARFADDRSDFSAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPGPVDPVGK +HDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAAELVETSRLWARAVARIEPEWIEEVAGD +LVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVPERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDE +LETRLRRRDLRVGDEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTAFRYPLPG +GDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTALIKALPKAVRKNLVPAPDVARLLVEDL +DAHADPLRDELPAALSSAVRRVRGAVVEPELWRLDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARL +AGTDDPRNARPG-------------------QGAGR-GRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLT +SWTVGEVPRQITTAPGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRYVLDHLDN +KEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLIDTVFAVTALVEQVLSRAAEVRRRLKGG +VSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQLQHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAH +RSRFPGTPVPAELERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG +>GCF_023573625_PROKKA_00730 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGSIGH +TQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTTQTSKATRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNID +FLLGYLRNLLPQRPDLKVIITSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVVAGTTRLAGTEILPLFGRLSM +AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDG +IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGAL------- +--------EAGG---ARA---GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAAD +ELHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQLAKDVGLTVEAGPVDPVGR +HEAVHKSLLTGLLSQIGAYDERRREYVGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGH +LVKRTYNEPHWSRRAGSVVAREKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA +LETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTADAEDLDTDAFPTTFTYPMPG +GDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADL +EAHADPLRDELPDALSAAVRRVRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARL +AGTDDPASARPGP------------------RRTGRGGRAQADGRAGAEGRRRPE------GPGRSG-ATPAFEERHGLT +SWSIGTVPRTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSADDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN +REKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGS +VSLALAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAH +RARFAGTPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000682.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bea5c2d4662eac196ae44c693f47904682573e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000682.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00772 +MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI +IVMLVVTWIVERSTVRRRAARAARA +>GCF_003691675_PROKKA_00503 +MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI +IVMLIVTWIVERTTVRRRAARAARA +>GCF_005280335_PROKKA_02158 +MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG +TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI +MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW +GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA +GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT +AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI +IVMLIITWIAERTLVRRRAARAARA +>GCF_020097155_PROKKA_02053 +MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI +MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW +GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA +GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT +AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI +VAMLIATWILDRTLVRRRAARADRA +>GCF_023573625_PROKKA_00739 +MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI +IVMLVVTWIVERSTVRRRAARAARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000684.fa new file mode 100644 index 0000000000000000000000000000000000000000..1825902d7adba109cfbd27f4834bdd9710e46751 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000684.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00775 +MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA +AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL +ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART +LRAGLPG +>GCF_003691675_PROKKA_00506 +MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA +AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL +ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART +LRAGLPG +>GCF_005280335_PROKKA_02155 +MHSPDPLLMAAAGRDDGDTGPGTGRRARLAASRLYVCTDLQRFLRPDGTLDTVAFADFCA +AAFRGGVDLIQVRDKAVDVAVELAAFAVLVPLARAHEALSAANDRADVAALAGVDVFHTG +QTDLTTVQCRALLGPDVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL +ELPSHAARLDAEDPAGARPWFAIGGVDADRLTEVRAAGADRIVVVRAVTQAEDPEAAART +LRAGLPG +>GCF_020097155_PROKKA_02050 +MHSPDPLLMTAAGRDDGDTGPGAGRRARLAASRLYVCTDLQRFLRPDGTLDTAAFGGFCA +AAFRGGVDLIQVRDKAVDVAVELAAFAVLIPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPNVVLGRSCHTPDHVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL +GLPTLAARLDAEDPAGARPWFAIGGVDAERLPEVRAAGAGRIVVVRAVTQAADPEAAARE +LRAGLPA +>GCF_023573625_PROKKA_00742 +MHSPDPLLMAAAGRDDGGTGPGAGRRARLAASRLYVCTGLQRFLRPDGTLDTAAFADFCA +AAFRGGVDVIQVRDKAVDVALELAAFAVLVPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPNVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL +GLPSLAARLDAEDPAGARPWFAIGGVDADRLPEVRTAGAERIVVVRAVTQAEDPEAAART +LRAGLPG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000687.fa new file mode 100644 index 0000000000000000000000000000000000000000..8d4fbe3d3ea370be2d144a276fdea6c4e93eeacc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000687.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00778 +MAEH------RTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTV +ALRRWSADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIAD +ERTLLPDVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGI +LNRAHLELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR +LALEAGFHARRAGRIPRREHALASSPMAGRVTAEEDER +>GCF_003691675_PROKKA_00509 +MAEH------RTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTV +ALRRWSADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIAD +ERTLLPDVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGI +LNRAHLELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR +LALEAGFHARRAGRIPRREHALASSPMAGRVTAEEDER +>GCF_005280335_PROKKA_02152 +MAEH------RTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTV +ALRRWSADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIAD +ERTLLPDVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGI +LNRAHLELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR +LALEAGFHARRAGRIPRREHALASSPMAGRVTAEEDER +>GCF_020097155_PROKKA_02047 +MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV +ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD +DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI +LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR +LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA +>GCF_023573625_PROKKA_00745 +MAEH------RTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTV +ALRRWSADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIAD +ERTLLPDVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGI +LNRAHLELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR +LALEAGFHARRAGRIPRREHALASSPMAGRVTAEEDER + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000691.fa new file mode 100644 index 0000000000000000000000000000000000000000..b6a6d24161d87a96b2872b3ce0c2c7939a958bd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000691.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00782 +M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV +RDTGATRDWQADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKA +LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFIL +DRMDSEGADFDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVA +GITAITAEDNAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAF +NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDP +AEAHTSFMVVLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRAR +QRDLDATVEALAALDVVHEVASVLRVEGN +>GCF_003691675_PROKKA_00513 +M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV +RDTGATRDWQADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKA +LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFIL +DRMDSEGADFDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVA +GITAITAEDNAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAF +NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDP +AEAHTSFMVVLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRAR +QRDLDATVEALAALDVVHEVASVLRVEGN +>GCF_005280335_PROKKA_02148 +M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV +RNTGATRDWQADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKA +LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYIL +DKMDSEGAGFDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVS +GITAITAEDNEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAF +NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDP +AEAVTSCLVVLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRAR +QRDLDATVEALAALDAVHEVASVLRVEGN +>GCF_020097155_PROKKA_02042 +MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV +RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA +LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL +DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE +GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY +NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV +SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGA-DDAAGASLRLITHRAR +QRDLDDVVAELTTLDAVHEVASVLRVEGN +>GCF_023573625_PROKKA_00749 +M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV +RDTGATRDWQADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKA +LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFIL +DRMDSEGADFDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVA +GITAITAEDNAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAF +NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDP +AEAHTSFMVVLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRAR +QRDLDATVEALAALDVVHEVASVLRVEGN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000692.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a9b24b509f973e1709045aba2c04ad44354bb37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000692.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00783 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI +VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF +VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV +VTVAQALGLS +>GCF_003691675_PROKKA_00514 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI +VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF +VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV +VTVAQALGLS +>GCF_005280335_PROKKA_02147 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI +VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF +VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV +VTVAQALGLA +>GCF_020097155_PROKKA_02041 +MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS +FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP +DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL +VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF +VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV +VTVAEALGLT +>GCF_023573625_PROKKA_00750 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI +VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF +VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV +VTVAQALGLS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000693.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000693.fa new file mode 100644 index 0000000000000000000000000000000000000000..81617058d90cb0333f5d7f257bf0df15f669cded --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000693.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00784 +MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA +TLPRDGAHLILRLAREQLRGRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATVRLRLHERVVPVV +AIPDTELSTHVARGVLPADVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA +VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL +VPCVAVDGVRVESLHHG +>GCF_003691675_PROKKA_00515 +MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVEGEGEA +TLPRDGAHLILRLAREHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV +AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLLAATRDWLHQEPRA +VAMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAASWRVL +VPCVAVDGVRVESLHHG +>GCF_005280335_PROKKA_02146 +MPAPRTLAAGTAVVVAVPATSANLGPGFDSMGLALELRDEVSLTVVDGPDVAEVTGEGAD +VLPRDGSHLILRLAHEHLRARGVRAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAADRRPPEALLEAATDFEGHPDNVAPALVGGATVSWTRDDDARPATAPLRLHERIVPVV +AIPDTELSTHAARGVLPESVPHAVAAAQAGRAALLVHALAERPELLMAGTRDWLHQGPRA +AAMPASAALVAGLRVRGHAAVVSGAGPTVLALCDGAEAAEQAAAAARALTADDVLAWRVL +VPAVAADGVRVEPLHHG +>GCF_020097155_PROKKA_02040 +MRELRDLTPGTGARVLAPATSANLGPGFDALGLALELRDEVTLTVVDGPDTAVVTGEGAA +ELPTDGEHLVLRLAHAHLTRRRFRAPGLALTAVNRIPHARGLGSSAAAVVTAVLAAEALL +PADERLSAAELLDVTARREGHPDNVAPALSGGASVSWHRDGGPGWATAAVALHPQITPVI +GIPDVTLSTHAARAALPESVPHAVAAEQAGRAALLTLALASRPDLLLPATRDWLHQDARA +SAMPPSAALVRGLREQGHAAVVSGAGPTVLVLAPTPADAERAAEAMRALAPETGAAWRVL +VPGVAAEGARVEPLHHG +>GCF_023573625_PROKKA_00751 +MAAPQPLAPGTAASVSVPATSANLGPGFDSMGLALELRDEVTLTVVAGPDVAEVVGEGEA +TLPRDGAHLILRLAHEHLRDRGFTAPGLHLRAVNRIPHARGLGSSAAAVVAAYAAAEALL +PAALRRAPADLLEAATRFEGHPDNVAPALVGGATVSWTRDDVPGPATARLRLHERVVPVV +AIPDTELSTHVARGVLPAEVPHAVAAAQAGRAALLVHALAEDPALLPAATRDWLHQEPRA +VTMPASAALVAGLRERGHAAVVSGAGPTVLALCDGVQAAEHAAEAARALTADGAAAWRVL +VPCVAVDGVRVESLHHG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000694.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ee11f3778f50a4c2d03cac410894a16cb51dcf4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000694.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00785 +MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADRDAAERAAQAPAAPAAEAAPA +A-ASSQDAAPAAERPARRRSRRADADTSAPA-AAQDGQPQAEAREDQTEQAPRETASDQDRSEGSETRDEGEGRPQSERR +S-RG-RRAGDDDAQ-----QGQDRRSDGA-----QGEDG--ADRRGDREDRDDNGRENGRGRNGRNGRDRDNGR----DR +ENGRENNRDRENG----RDGSREQ---RGDKSEDGGRGDGGRGDR------SRRDDRDDEGGRNRRNRRNRNERGRNRRG +RGGPEVDETELTEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDGEKQQHHG +GGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIGPRVIDLVSPIGKGQRGLIVSPPKAGKT +MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD +SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL +SRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDLLTNKIKDTASNAEFLMLVSKTTLGSKG +DD +>GCF_003691675_PROKKA_00516 +MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADRDAAERAAQAPAAPAAEAAPA +A-ASSQDAAPAAERPARRRSRRADADTSAPAAAAQDGQPQAEAREDQTEQAPRETASDQDRSGGSEARDEGEDRPQSERR +S-RNRRRAGDDDAQ-----QGQDRRSDGA-----QGEDG--ADRRGDREDRDDNGRENGRGRNGRNGRDRENGR----DR +ENGRENNRDRENG----RDGSREQ---RGDKSEDGGRGDGGRGDR------SRRDDRDDEGGRNRRNRRNRNERGRNRRG +RGGPEVDETELTEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDGEKQQHHG +GGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIGPRVIDLVSPIGKGQRGLIVSPPKAGKT +MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD +SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL +SRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLDQQQALDLLTNKIKDTASNAEFLMLVSKTTLGSKG +DD +>GCF_005280335_PROKKA_02145 +MTESTEQTTPTTGGGLAALKLAQLQALASQLGIPGGSRMRKADLVTAISDHQRGGSVADRAAAERAAKAAAAPAAEAAPA +ADKAAEQPAEAAERPARRRSRRADADTSAAAQSAESGKDQAERRAEQPAEG-RDAEGSQD--SGDRAQDSGD-RTQGERR +S-RGRRRAGDDDAR-----GQDRRRQDGEDAGQDQAHDS--AEDRGG--DREDGGRENGRGNRGRNG--RDNGR----DR +ENG--NGRDRDNGNGRDRDGSREQ---KQDKSEDGGR-DGGRNDR------NRRDDRDDEGGRGRRNRRNRNERGRNRRG +RGGPDVDETELTEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKHGLRKGDAVVGAIRAPREGEKPQHQG +GGSNRQKFNALVKISSVNGQPAVEHPERVEFAKLVPLYPQERLRLETDPKQVGPRVIDLVSPIGKGQRGLIVSPPKAGKT +MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD +SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL +SRHLAERRIFPAVDVNASGTRREEALLSPEEVKIMWKLRRVLSGLEQQQALELLTNKIKDTGSNAEFLMLVSKTTLGAKG +ED +>GCF_020097155_PROKKA_02039 +MTESPDQTTA--GGGLASLKLAQLQALASQLGITGGSRMRKSDLVAAISDHQRGGSVADRDA---AAQAAAAPAAQAEAA +E-APAAEQAPR----SRRRSRRADSDGAVAA-------DQPAEATQAPADE-QPAAETED--APARAEASAE-SGAQEAG +SGRSRRRRGDRAARDEQQDGAQDEKQESG-----RG-----AGEETRREQDGDEERAEGRSRSRRGRGDRDRGERQNADR +QNGERANGERANG----QGEDRSQGGRREDREEESGRGQGGDGQKRSDRGNGRREDR-DEDGRRGRNRRNRNDRGRNRRS +R-GPEVDDVEVTEDDVLQPVAGILDVLDNYAFVRTSGYLPGEKDVYVSLAMVKKFGLRKGDAVVGAIRAPREGEKP--HS +GGGRNQKFNALVKVTTVNGQPAEENPQRVEFGKLVPLYPTERLRLESDHKLVGPRVIDLISPIGKGQRGLIVSPPKAGKT +MILQSIANAITRNNPEVHLMMVLVDERPEEVTDMQRSVAGEVIASTFDRPAEDHTTVAELAIERAKRLVEMGRDVVVLLD +SMTRLGRAYNLAAPASGRILSGGVDSAALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL +SRQLAERRIFPAVDVNASGTRREEVLLSPEEVKIMWKLRRVLSGLDTQQALELLTNKIKDTASNAEFLMLVSKTTLGSKG +DD +>GCF_023573625_PROKKA_00752 +MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADRDAAERAAQAPAAPAAEAVPA +A-ASSQDAAPAAERPARRRSRRADADTSAPAAVAQDGQPQAEAREAQTEQGPRETASDQDRSGGSETRDEGEDRPQSERR +S-RGRRRAGDDDAQ-----QGQDRRSDGA-----QGEDGADADRRGDREDRDDNGRENGRGRNGRNGRDRDNGR----DR +DNG----RDRENG----RDGSREQ---RGDKSEDGGRGDGGRGDR------SRRDDRDDEGGRNRRNRRNRNERGRNRRG +RGGPEVDETELTEDDVLQPAAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDGEKQQHHG +GGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIGPRVIDLVSPIGKGQRGLIVSPPKAGKT +MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD +SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL +SRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDLLTNKIKDTASNAEFLMLVSKTTLGSKG +DD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000695.fa new file mode 100644 index 0000000000000000000000000000000000000000..a4a44929ae7a9ce85d23a9430ebc9f695f8390ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000695.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00786 +MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA +AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV +YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER +RLAALGGDA- +>GCF_003691675_PROKKA_00517 +MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA +AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV +YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER +RLAALGGDA- +>GCF_005280335_PROKKA_02144 +MFDSEERREAVDRLLAEHRELTARLSDPAVHQDPVLARRLNRRFAELGAVVTAHAAWREA +AAELADARELAAAGDDDAAAFAAEVPCLEEAETAAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAIRAGATDPAEGV +FARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVRIDPNEVKTDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAAMRVLRSRLLERRRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVVASCLALDEER +RLAALGGDA- +>GCF_020097155_PROKKA_02038 +MF------ESVERLLAEHRELAGQLSDPALHADAARARRVGRRYAELGAVVAAHREWEQA +VADRDDARELAAAPGEDAAAFAAEVPALEAAADEAAERLRRLLIPRDPDDGRDVILEIKG +GEGGEEAALFAGDLLRMYLRYAESRGWRTEVLSATHSDLGGFKDVHVAVRGSAQDPAEGV +YARLKHEGGVHRVQRVPVTESAGRIHTSAAGVLVLPEADAPDEVQIDPNDLKTDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAERDAEDS +AARSAQVRTMDRSERIRTYNFPENRIADHRTGFKAHNLDAVLDGALDPVIDSCVALDEQR +RLARLGEEAR +>GCF_023573625_PROKKA_00753 +MFDSDQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA +AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV +YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER +RLAALGGDA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000697.fa new file mode 100644 index 0000000000000000000000000000000000000000..912807b234f5478b6f893c30c1ad7be031faf656 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000697.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00789 +MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG +FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL +GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV +AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH +HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE +RRRADRNDA--AAHPDERGDA +>GCF_003691675_PROKKA_00520 +MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG +FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL +GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV +AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH +HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE +RRRADRNDA--AAHPDERGDA +>GCF_005280335_PROKKA_02142 +MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG +LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL +GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV +AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH +HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR +RRRAGAPAAGPALDPEE--GA +>GCF_020097155_PROKKA_02035 +MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG +LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL +GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY +SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV +AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH +HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPL-- +RARAARPASRPDAQPKD--QP +>GCF_023573625_PROKKA_00756 +MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG +FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL +GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV +AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH +HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE +RRRAVRNDA--AAHPDERGDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000698.fa new file mode 100644 index 0000000000000000000000000000000000000000..66a1c88b9c87673bb28dcfe3c8fd9d1e95fb5308 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000698.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00790 +MTG------------AGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGE +AAGSALLGGGAVLALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPG +WVRADAAAIAALVTILVWQAAEVLVFARTRRGIYAD +>GCF_003691675_PROKKA_00521 +MTG------------AGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGE +AAGSALLGGGAVLALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPG +WVRADAAAIAALVTILVWQAAEVLVFARTRRGIYAD +>GCF_005280335_PROKKA_02141 +MSPRTAPDAAPRSARARRRPRRRRWENRRGWWGILAWSLAATAAAVAVVCAVALAAGGPD +AAASALLGGGAVLVLSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGTVPRPD +WILPDAAAIAALVAILVWQGVEVLVFARTRRGIYAD +>GCF_020097155_PROKKA_02034 +MT-------------ASARPARRRWENRAGWWGILRWCCAATAVGVLACGAVAAVLHGGP +AGLSALTGGGAVLVLSALTGATTAVAWDRARAAALPLSVGAFVVKLVLYALLLATLRMPE +WMSGTAVAVGALVGVVVWQAVEVLVFARTRRGIYAD +>GCF_023573625_PROKKA_00757 +MTG------------AGGRRRRRRWENRRGWWGILGWSLAAAGAALAITCAAWLLSAGGE +AAGSALLGGGAVLALSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPG +WVRADAAAIAALVTILVWQAAEVLVFARTRRGIYAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000699.fa new file mode 100644 index 0000000000000000000000000000000000000000..157f2321ea7cbc33e27e1131789093830c74390f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000699.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00791 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>GCF_003691675_PROKKA_00522 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>GCF_005280335_PROKKA_02140 +MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL +PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>GCF_020097155_PROKKA_02033 +MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP +KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM +PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI +VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL +LMYLQAFVFTLLTALYIQGAIDANDH +>GCF_023573625_PROKKA_00758 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000701.fa new file mode 100644 index 0000000000000000000000000000000000000000..8633048a5daa3ae684b95c831dc2ab976c511e54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000701.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00793 +MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG +LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE +QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA +GVAE +>GCF_003691675_PROKKA_00524 +MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG +LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE +QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA +GVAE +>GCF_005280335_PROKKA_02138 +MISNGLILAA--GANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG +LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAESTRISE +QAQAQIAAERQQAASQLKGEVGTLATTLASKIVGESLEDDARSQRVVDRFLADLDRHQSA +GVAE +>GCF_020097155_PROKKA_02031 +MISNGLILASAEGANPLVPNPWEILVTTVGFAVLMFIVVKFVVPALEKSYTDRVEAIEGG +LEKAEKAQAEANKMMADYEGQLADARQEANRIREEARTEGAQIVAEARERAAAEAARITE +QAQTQIAAERTQAAAQLKGEVGTLATTLASKIVGESLDDDARSQRVVDRFLADLDRHQSA +GVSE +>GCF_023573625_PROKKA_00760 +MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG +LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEATRISE +QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA +GVAE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000702.fa new file mode 100644 index 0000000000000000000000000000000000000000..c8155e2f7c8e06c4cf8412fe5aabccc74a265e13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000702.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00794 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL +LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAIRKAADAVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG +>GCF_003691675_PROKKA_00525 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL +LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAIRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG +>GCF_005280335_PROKKA_02137 +MMTGASRDSLTASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVIKDLAGRRWSAERDLGDALETVAAHAAAAEAGRGGHAGLAAL +SGELLAFNRTVEDSHEVQRALTDQHAPVEARAALARRLLGESASPAGQLLVERAVAAPRG +VKPAAAVRQAADVVAERQRQWIAEVTVARPLGAEQQERLALGLRRAFERDLVMDVTVDPH +VVGGIRVQVGDDVVDGSMASRLNDLQRRMAG +>GCF_020097155_PROKKA_02030 +MMTGASGDSLTASLESVRTVLDEGGVALARELFAALDVVDQQGALRRALTDPAWSTERRH +GVLDSLFGGRVSPGALQVLKDLAGRRWSAERDFGDALEAVAADAAAGEAARGGHAGLAAL +SGELLGFQRVFQDSHEVERALTDQRAPRESRSGLARRLLGAQASPAAVLLVERAVTDGRG +VKPATALRSYADVVATRQRQWIAEVTVARPLEDGQRERLAAGLRRAFGRDLVLDVNVDPT +VVGGIRVQVGDDVIDGSMASRLNDLQRRMAA +>GCF_023573625_PROKKA_00761 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAAHAAAAEAARGGHAGLAAL +SGELLAFNRTVEDSHEVQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAVRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGIRVQVGDDVVDGSMASRLHDLQRRMAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000707.fa new file mode 100644 index 0000000000000000000000000000000000000000..b77dcf08240b58dec74613ef91bb99ee33d6c220 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000707.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00799 +MQGPVLIASATVAAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL +RLTGRWRLSRERWSADRSRLQIDRLPADEAGRTVLELSAGAR----PVRVVVDPDDAGAL +RAWSEAGPSAASSFWRR----- +>GCF_003691675_PROKKA_00530 +----MLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL +RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGAR----PVRVVVDPDDAGAL +RAWSEAGPSAASSFWRR----- +>GCF_005280335_PROKKA_02132 +----MLIALAGVLAVFALSASALAVRRRALLRTSAAFPAVLQGHGRPRERVIGVYDETRL +LFTGRWMIRRERWSVGRCDLQIDRLPVAEDGRAVLELDGGRG----SVTVVVDPDDAGAL +RAWSEAGPSAASSFWRR----- +>GCF_020097155_PROKKA_02025 +MRGPVLL-LSGALAVFALLALAGWARHRALVRGPGRFAGVLVTDGGRRCRVVGCFRSHEL +VLSHHLLPERRLWSAERWRLEVDRLPAAEAGHTRLRITDASGRSDDAVDLEVEDDVAGAV +RAWTEAGPSQAGQSWWRPPGAA +>GCF_023573625_PROKKA_00766 +MEGPVLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL +RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGTR----PVRVVVDPDDAGAL +RAWSEAGPSAASSFWRR----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000708.fa new file mode 100644 index 0000000000000000000000000000000000000000..46e9d6f4b4ac2c70b09cce6b6aaacf22fca30536 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000708.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00800 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>GCF_003691675_PROKKA_00531 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>GCF_005280335_PROKKA_02130 +MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA +PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA +EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>GCF_020097155_PROKKA_02023 +MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA +EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN +RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF +>GCF_023573625_PROKKA_00767 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000710.fa new file mode 100644 index 0000000000000000000000000000000000000000..25154406963a6aed39b5eb27754ba3e508c8074a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000710.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00802 +------------------------MEEKEPASGPDAPSVADVRAPAEPEGAEQQPVGGIP +VEPAGAAAAP-PSHGPTPAGRRRRLR---LGSVLRRRRP-FLEEDRVD--PEPDPADGAE +DPAVAAVALESPVLTGFLLAVGVTLAIGIVSVLRTNGQLIVWIAAALFIALGLDPLVRRV +ESWGAPRWVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMRAEWFVQL +DEEFHLQEAVRAQTERLAADGVAITDLFGGLLGLGQTVLNAVFSVLVVVVLTLYFLSSLP +HMKYWAYRLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAV +LLAAIAAFMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMA +RAVPVPAAVAVIAVIAGGALLGVLGALMAIPLAAALALLVREVFIPRQDAR +>GCF_003691675_PROKKA_00533 +MSLGPTVASRARRGQAGALTYAERVEEKETASGPDVAGVADVRGPAEPEGAEQPPVAGVP +VEPVGVAAAP-PSHGPTPAGRRRLPR---LGSVLRRRRP-FLEEDRVD--PESVPVDGAE +DPAVAAVALESPVLTGFLLAVGVALAIGVVSVLRTNGQLIVWIAAALFIALGLDPLVRRV +ESWGAPRWVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQL +DEEFHLQEAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLP +HMKYWAYRLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAV +LLAAIAAFMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMA +RAVSVPAAVAVIAVIAGGALLGVLGALMAIPLAVALLLLVREVFIPRQDAR +>GCF_005280335_PROKKA_02128 +ME------------------------------------------PVDPTAA--------- +--PASAAPAPLPASGRVPRRRRRRGRLIPLRGVLRRRRPVFLAEDRVDPDPEHPEPEPTG +EPPVTAVTVESPVATGFLLTVGVALALAVVWVLRTNGQLLVWIAAALFIALGLDPLVRRV +ESWGAPRWAGVLTAALGLAAVASAFVALLVPTVVEQSRQLVEGLPGTIEDVMTSAWFIEL +DQEFHIQEAVRAQTDRLTTDGAAVTDLFGGLLGIGQTVLNAFFSVFVVVVLTLYFLASLP +HMKYWAYRLAPRSRRPQVERLSEKITSSVGHYVMGQSFVAALNGTVAFTALAVAGTPFAV +LLAAFAAFMAFIPLVGAVIGGTVLTLLSLLTSWQTAAVFAAIYFVYLQIEAYVVSPRVMA +RAVAVPAAVAVIAVIAGGALLGVLGALMAIPLAAALSMLVREVFIPRQDAR +>GCF_020097155_PROKKA_02021 +MD------------------------------------------HIED------------ +--------SP-APSGPSRGA--RRLR---LGSLVRRREA-FLPNERVDPLPPGSPDAAPA +EPEVPELALRAPVAAGFLLTMGVCLAAVLVWVVLENTQLLVWIAAALFIALGLDPVVRLV +ERWGAPRWVGVLLAALGLAAVAGAVVGMLVPAVVQQSTQLITGLPDTITQIMATPWFREV +DRQLQIQHAVQSWLDGLTKDGAAVTQLFGGLVGIGQTVMNAVFSTIVVVVLALYFLASLP +HLKYWGYRLAPRSKRLRVEALGEEITLSVGHYVMGQTVVAVLNGTVAFIALSVAGGPFPV +LLAFVAAVMAFIPLVGALIGGTILTAVCLLESWQAAALFAAIYFVYLQIEAYVVSPRVMA +RAVAVPAAVGVIAVIAGGTLLGVLGALMAIPTAAAVLLIVREVLIPRQDAR +>GCF_023573625_PROKKA_00769 +MSLRPTVASPARRGQAGALTYAERVEEKETASGPDAAGVADVRAPAEPEGTEQPPVAGIP +VEPVGVAAAP-PSHGPTPAGRRRLPR---LGSVLRRRRP-FLEEDRVD--PESVPVDGAE +DPAVAAVALESPVLTGFLLAVGVALAIGVVSVLRTNGHLIVWIAAALFIALGLDPLVRRV +ESWGAPRWVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQL +DEEFHLQEAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLP +HMKYWAYRLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAV +LLAAIAAFMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMA +RAVSVPAAVAVIAVIAGGALLGVLGALMAIPLAAALLLLVREVFIPRQDAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000712.fa new file mode 100644 index 0000000000000000000000000000000000000000..70813405ac505dde17796f00dabb721583753a1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000712.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00804 +M----------------TPH---ASEPAPTHL-AAATRRRAVDAPDPDLALVTRGLTQRF +GDKLALDALDLDVPAGSFFGVVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLE +AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVA +DYSAGMTKKVSLAAAMVHAPDLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHV +MDLVQRMCTHVAVIAAGTLRAAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL +>GCF_003691675_PROKKA_00535 +M----------------TPH---APEPAPAHL-AAAARRRAADAPDPDLALVTRGLTQRF +GDKLALDALDLDVPAGSFFGVVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLE +AKRRVGVLADGVRTFDRLTGTQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVA +DYSAGMTKKVSLAAAMVHAPDLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHV +MDLVQRMCTHVAVIAAGTLRAAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL +>GCF_005280335_PROKKA_02126 +MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF +GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE +AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV +DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV +MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL +>GCF_020097155_PROKKA_02019 +M--------------------------------------RAQDAPDPNLALVTRGLAKRF +GEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATGMLRPDAGRVWIHGVDVWEQPLE +AKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTVDVRTADLLRVMDLEEAGRKLVV +DYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV +MDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERFVDLVGGRHTGEGLAWL +>GCF_023573625_PROKKA_00771 +M----------------TPH---APEPAPAHL-AAAARRRAVDAPDPDLAFVTRGLTQRF +GDKLALDALDLDVPAGSFFGVVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLE +AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVA +DYSAGMTKKVSLAAAMVHAPDLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHV +MDLVQRMCTHVAVIAAGTLRAADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000719.fa new file mode 100644 index 0000000000000000000000000000000000000000..28e97f5a515e4d30280597ce2724d4761a334e78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000719.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00812 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEAD--PAEAPAA--- +-EDGVDTPEDPPAAPPSVSAAQDAGPVAGLDAS---DAAFWGLVSGLHLSQDPEPQRSAP +TDPAVARLLPDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAP +AFGRALNDVRLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMT +EMLSELPEGADESAPGAGDAEDEQ +>GCF_003691675_PROKKA_00544 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEAD--PAEAPAA--- +-EDGVDTPEDPPAAPPSVSAAQDAGPVAGLDAS---DAAFWGLVSGLHLSQDPEPQRSAP +TDPAVARLLPDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAP +AFGRALNDVRLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMT +EMLSELPEGSDESAPGAGDAEGEQ +>GCF_005280335_PROKKA_02118 +MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVL-SEADDLPADAPGAPEP +SADVAPVPQGPEAG---------AGPAAGLDEA---DAAFWELVSGLHLSQDRVPHRAAP +ADPAVARLLPEAMPQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAP +AFGRALNDVRLVLAARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMT +EMLSELPEGADEDAPGADEAGDDA +>GCF_020097155_PROKKA_02009 +MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSD--AG-------- +------TAEDAPEAGAEPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAP +EDPAVARLLPDAMPHAEPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAV +SFGRALNDVRLVLAARLGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMA +EMLSELPL---EGAAGPDEEE-RA +>GCF_023573625_PROKKA_00781 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEAD--PAEAPAA--- +-EDGVDTPEDPPAAPPSVSAAQDAGPVAGLDAS---DAAFWGLVSGLHLSQDPEPQRSAP +TDPAVARLLPDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAP +AFGRALNDVRLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMT +EMLSELPEGSDESAPGAGDAEGEQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000720.fa new file mode 100644 index 0000000000000000000000000000000000000000..46c731f1cf7421ebca002a62e363eef1ccd40540 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000720.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00813 +MSG----QRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIA +EVRALALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAV +AATRTGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETA +REYTAPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLE +HPHSAAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRS +TAFVPLGAEQEGVT-- +>GCF_003691675_PROKKA_00545 +MSG----QRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIA +EVRALALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAV +AATRTGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETA +REYTAPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLE +HPHSAAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRS +AASVRPGPEQEGVT-- +>GCF_005280335_PROKKA_02117 +MSAPPQ-ARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIA +QVRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAV +AATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATA +QEYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLE +HPHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTP +DLIARLGAEQERET-- +>GCF_020097155_PROKKA_02008 +MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA +QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV +AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA +EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE +HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP +DVLARLRAEMEEDGAR +>GCF_023573625_PROKKA_00782 +MSG----QRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIA +EVRALALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAV +AATRTGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETA +REYTAPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLE +HPHSAAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRS +AASVRPGPEQEGVT-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000724.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7ca10205754121c659a9e07c89cf19711910758 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000724.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00817 +MSGGRVPV--PGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRF +DPRNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDV +PGLEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLG +APPADADVLPGLTDAPAG-RG------VDRLMRAQGLGVSVLAPRAAGAGAESKATRQAR +RTEGVFDARVPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQR +AKTRAAAHGAQTANRVGAATTMLVVGDGFEAADL----------HRPRAEDGAPQAVTT- +-ALAHRKTRDALRRRDRG------------------------ +>GCF_003691675_PROKKA_00549 +MSGGRAPV--PGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRF +DPRNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDV +PGLEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLG +APPADAEILPGLTDAPAG-RG------VDRLMRAQGLGVSVLAPRAAGSGAESKATRQAR +RTEGVFDARVPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQS +AKTRAAAHGAQTANRVGAATTMLVVGDGFEAADL----------HRPRAEDGAPQAVTT- +-ALAHRKTRDALRRRDRGQAIALVSEGEFLQMLDGNWPDAAR +>GCF_005280335_PROKKA_02113 +MSGVLAPV--PGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRF +DPRNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDV +PRLDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLG +TEAGD-----GAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQAR +RAQGVFDARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQT +AKVRAARLGAQTANRVGAATTMLVVGDGFEAADL----------DRPAPAPGTREAVTT- +-ALAHRKTRDALRRRERGQHISLVSEGEFLQMLDGNWPDAAR +>GCF_020097155_PROKKA_02004 +MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF +DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV +PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRV-- +CPPGEAT--------------------VDALLASQGLRRSRLTARAAGTGRESRATRQAR +TMPGLFDATIPLADDRTLPDLMRWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQE +AKNRAAQRGAATANRVNGRTTMLVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPG +GAVTHRKTREALQRRAKGQAIALVSEAEFLQMVDGAWPAGAR +>GCF_023573625_PROKKA_00786 +MSGGRVPV--PGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRF +DPRNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDV +PGLEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLG +APPADAEILPGLTDAPAG-RG------VDRLMRAQGLSVSVLAPRAAGSGAESKATRQAR +RTEGVFDARVPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQS +AKTRAAAHGAQTANRVGAATTMLVVGDGFEAADL----------HRPRAEDGAPQAVTT- +-ALAHRKTRDALRRRDRGQAIALVSEGEFLQMLDGNWPDAAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000725.fa new file mode 100644 index 0000000000000000000000000000000000000000..983fbeb9d77d1b57723ed4442dc7c3bc56a8cc17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000725.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00818 +MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT +DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ +D-GALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVM +RSAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHA +RAWLDTLG-EEAEETRAAVTAAVDLAG---TVDADPGAPGALPTALGEGWVAEEALAIAL +YAALTAQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADR +AAAEASVPGWIAEREVVLEAARRWSAATT +>GCF_003691675_PROKKA_00550 +MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT +DAADLLAQQGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ +D-GALPEGAPPAPPRWIDAHAELKVRRAPGTACLSGLAEPGMGLPGDPHNPGSKGCGTVM +RSAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHA +RAWLDTLG-EEAEETRAAVTAAVDLAG---TVDADPGAPGALPTALGEGWVAEEALAIAL +YAALTAQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADR +AAAEASVPGWIAEREVVLEAARRWSAATT +>GCF_005280335_PROKKA_02112 +MTETPAAPS------LPGPEHATRVAALLAAGAAGDALGYTVEFDADAAVRARHGAEGLT +TGEAALAVVGGEALPISDDTQMTLYVLDGLLEWIEWQNDGQAADPAACVWLACLRWWATQ +HGGALPDGAPPVPPRWLEDHPELRARRAPGNACLSGLDSAAMGLPGDPRNPDSKGCGTVM +RSAPYGMVPGLEDVHVVSFARQGAVLTHGHPTAWVAAAAYSLMIAALLRGAGLEDAVAHA +RVWVDSLDPAEGGETAAALASAVELAA---SPADDAGRPGTLPAALGEGWVAEEALAIAV +HAALVAQARH-EDPADMLALALRIGANHAGDSDSTASLAGQLLGAAHGPAVFGADAAADG +PA--GLVPAWVAEREVVAEAARRWSAATT +>GCF_020097155_PROKKA_02003 +MTDAAPSPRTDVS-------YPSRVLGLLAAGAAGDALGYAVEFDSVDRILGRLGAAGVT +DGPALAAVSGVSALPVSGDTQMTLYVLDGMLEWIEWQNAGQASDPAACVWLACLRWLRTQ +D-GALPDGAPPAQDRWIDAHTELHAQRAPGMACLSGLRSSGMGVVPDPKNPDSKGCGAVM +RSAPYGMVPGLEDHHVASFARQGAVLTHGHPTGWTAAAAFALTVSALFDGAELRGALEHP +RTWLDSTG-EDGAETRAALDGALAEAARAVEAGDDVGAPGTLPASLGEGWVAEEALAIAA +YAALVAEARA-EDPAAALGLALRIGANHDGDSDSTAALAGQLVGARHGMAVFGS-----R +GQDADSVPAWITEREVVAEAARRWIAATT +>GCF_023573625_PROKKA_00787 +MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT +DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ +D-GALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVM +RSAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAGAYALVIAALLRGLDLAAAVAHA +RAWLDGLG-EEAAETRAAVTAAVDLAG---TVDADPGAPGALPTALGEGWVAEEALAIAL +YAALTAQAVHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGVAHGTAVFGAHDPADR +AAAEASVPGWVAEREVVLEAARRWSAATT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000727.fa new file mode 100644 index 0000000000000000000000000000000000000000..325251c619478bec2425184cf6abec5b39c7d8d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000727.fa @@ -0,0 +1,70 @@ +>GCF_002008305_PROKKA_00820 +MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGRSAESLVTTLREPGAVIPEVQ +VEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVSLRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLL +PQGQFAQFLTAKSDERRALLRRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +D--TDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRRDHDAEAETAAARRRAVDA +HERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAAAWLAAARADGA-----------ADAPA-SRQALGEAER +AAEAVARAVQDRARMGELEQEAAAAAERRAEIGRDRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAAR +RTAAEAAAARAVEAETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAATADTAVT +EADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERAEAERAALDQAAKDLAADRRRLTAAEK +TLAGADETAAALAAEDGRLAEAAAHRAARLTELRDAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADE +TDQALTAALAEQHFDDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQTRAAAE +ALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLLDLVRGGGENLLKMPLTSYVLAGRLEE +VAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLELVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIEL +DTLFVDEGFGSLDADTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA +>GCF_003691675_PROKKA_00552 +MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGRSAESLVTTLREPGAVIPEVQ +VEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVSLRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLL +PQGQFAQFLTAKSDERRVLLRRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +D--TDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRRDHDAEAETAAARRRAVDA +HERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAAAWLAAARADGA-----------ADAPA-SRQALGEAER +AAEAVARAVRDRDRMRELEQEAAAAAERRAEIDRDRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAAR +RTAAEAAAARAVEVETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAATADTAVT +EADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERAETERAALDQAAKDLAADRRRLTAAEK +TLAGADETAAALAAEDGRLAEAAAHRAARLTELRDAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADE +TGQALTATLAEQRFDDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQTRAAAE +ALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLLDLVRGGGENLLKMPLTSYVLAGRLEE +VAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLELVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIEL +DTLFVDEGFGSLDADTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA +>GCF_005280335_PROKKA_02110 +MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGRSPESLVTTLRPPGAVVPEVL +VEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVSLREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVML +PQGRFAEFLTARSDERQRLLRRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP +A--TDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERERAHREGAEAAAGDRTAVAA +HERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSAGWLEQARRDAAETPADDAAETSADAAALPRDAVALAER +AVEEVVRAVRDRAAAERLEETERTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQG +LAAAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAVCGSPEHPDPAPRVGTAVT +EADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGRTPAQAEEALAAARTEHAELAAVRKALAADRRRLRALET +ERDEAAAAETARTAEDARLQEAARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAAD +ADRALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGRELQDQQATAPTPEDLEAAAA +RLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAALLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEE +VAAAATERLLAMTDGRYSIEYSDDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVEL +DTLFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSLAVHVDA +>GCF_020097155_PROKKA_02001 +MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGRTPESLVTTLRPPGAVVPQVL +VEFTVQGRRFEVLRSPRHARPKKR----GGGTTATQASVSLRERVDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSL +PQGRFAEFLTARSDDRQRLLRRLFGTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAP +EEGEDERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREHRQAADHVAADRSAVAL +HERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAWLDEA----------------EDADA-ARR---RADR +ETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGKRRAAQIAELHDTVDAAAARLGAEDEVARRLAEATER +AAAAGQAAERAVAQERARAARDERRDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVT +EADVAAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAARTALATDRRALARRES +EQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDAADLDARTAHVRTATRALSALVEAGDAAARAAAVAED +AAQALAGALAEQDFADVAAARAAALPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQE +TLREATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENRLKMPLASYVLAGRLEE +VAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVEL +DTLFVDEGFGSLDADTLDDVLDVVDGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG +>GCF_023573625_PROKKA_00789 +MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGRSAESLVTTLREPGAVIPEVQ +VEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVSLRERVDGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLL +PQGQFAQFLTAKSDERRVLLRRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +D--TDDRLLGLAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRRDHDAEAETAAARRRAVDA +HERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAAAWLAAARADGA-----------ADAPA-SRQALGEAER +AAEAVARAVQDRARMGELEQEAAAAAERRAEIGRDRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAAR +RTAAEAAAARAVEAETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAATADTTVT +EADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERAEAERAALDQAAKDLAADRRRLTAAEK +TLAGADETAAALAAEDGRLAEAAAHRAARLTELRDAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADE +TDQALTAALAEQHFDDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQTRAAAE +ALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLLDLVRGGGENLLKMPLTSYVLAGRLEE +VAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLELVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIEL +DTLFVDEGFGSLDADTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000728.fa new file mode 100644 index 0000000000000000000000000000000000000000..37ba958e161dc6bbcd31e4231bda2b2e3e3eeeb9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000728.fa @@ -0,0 +1,80 @@ +>GCF_002008305_PROKKA_00821 +MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVVDAQVGEPLETALQAVEGLES +SRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQLPEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVL +APRLQKIDGVRGADVLGGTDENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR +GIVVAPS---------------------------------------GDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLS +VSVTATPDADLVAVSQAVRDALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLVT +AVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRRTAILDGTREVATAITASTLVS +VAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTIVPVLCWWFLRSPRR--------GAETTAAPAVPGD------ +RPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALALLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERI +ERVLLDTDGVETVQWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQGPSGGQD +IEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAAARLGLTEEAVAGQAAAALQAVPVGDVR +FGFESFAVQLGDPEPVESLDALRQVPVETAEGPVPLADLAEVSRVSVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQ +AVAELDLPEGVTAAVGGAAEQQAQTFRDLGLALLAAVATVYVVLVATFNSLRQPLVLLVSIPFAATGVFLALLATGTPLG +LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMPLDEAIEVGALNRVRPVVMTALATVLAMTPMALGVTGHAGFISQPL +AVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERRLQEER-RVAAAW--EAQRVAAER---AAKQERRAEQG---------S +AAPSEL-----DAGR----LGRLRQRLR---RRWRRA-- +>GCF_003691675_PROKKA_00553 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+LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVMTALATILAMTPMALGITGHAGFISQPL +AVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERRLQEER-RVAAER--EAQRVAAER---AAEQARRAEER---------W +AAPSEL-----DAGR----LGRLRQRLR---RRWRRA-- +>GCF_005280335_PROKKA_02109 +MGALARFSLRRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVVDSLVGEPLETALQAVEGLES +SGSTSQASFNSIQLQFAYGTDLNRARSQVDRVVSNLASQLPEEAETSSFAGSVSDFPVVFLALSGDEDLNELRRRAEAVL +APRLQKLEGVRGADVLGGTEEHVSVVPDPEALAAAGLSTQDITTALEENAGLFPVGQVTEGESTYPVQAGAAVEDLEGLR +GIVVTPAEGGQGAAPQDRTADGGPVGGGGGPPADAEATPAAPAEPAGDGEPRTLGEVAEVSLQAAEPTSVTRTDGADTLS +VSVTATPDADLVAVSEAVREALPELESVVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSLRSTLVT +AVSIPLSLLAALIGVAVFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLDLGADRRTAILIGTREVATAITASTLVS +VAVFLPIAFVGGLAGELFRPFAVTATIALLASLVVALTIVPVLCWWFLRTPRRPAGDESPADAAEGGAPAVPAGEHGHDA +HPSAAGGWLARAYRPVLRWTQRHTVATLAGAVAVLAGTAALVPLIPTNLIGDTGQNSFVVTADQEPGTSLEATAAAAGVI +ERTLLETEGVETVQWTAGTAGGPAGAFGGSSADRARFTVVTDENADQTALQDGVRADLAALEGVGEVSVSTQQGPGGGQD +IEVSVSAPDPQALATAADEVAGALRGVEGAREVTTPAADVRPTFQVDVDTEAAARLGLTEEAVAGQAAAALQAVPVGDVR +FGFEQFQVRLGDPDPVESLEALRQVAVQTGSGPVPLEELASVERVDVPARVTSSNGERTAVVTVTPDDQDLGAVSRRVTE +AVDGLALPEGVTATVGGAAEQQAATFRELGLALLAAIATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTALG +LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMGLDEAIEVGALNRVRPVVMTALATILAMVPMALGLTGHSGFISQPL +AVAVVGGLLSSTLLTLVLVPVLYRLTEARGERRIQAER-AEQARRDEEARRRAAEAEQAAAEQAESARAGLLARRRTGGA +PAASAAAGMADDGGRRPGPLGRLRARLGGLVGRARRA-- +>GCF_020097155_PROKKA_02000 +MGALARFSLSRRALVALVTAFIAVFGVLSAGLLKRELIPSLELPVISVSTTYPGASPEVVDAEIGQPLEQALQAVEGLDS +SASTSATSFNSVQLRFRYGTDLTRARSQVDRVISNLASQLPEEAQTTSFAGSVSDFPVVFLALSGDEDLNALKRRAEDVL +VPRLQRIDGVRGAQVLGGTEEYVSVVPDAAKLAAAGLTTQDVTTALEENAGLFPIGQATSGTVTYPVQAGAPVGSVADLE +QVTVTPG-GGQSSTG---AADQGAGAGAGGGPGAA------------TGTPARLGDVAAVSMQAADPTSVTRTDGAPTLS +LSVTATPDADLVAVSHAVADALPELESLAGSGAKLTVVFDQAPFIEQSIRTLFVEGLLGLAMAILVIAVFLLSARSTMVT +AVSIPLSLLTALIGVAVFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADKRTAILEGTREVATAITASTLVS +VAVFLPIAFVDGLAGELFRPFAVTTSIALLASLVVALTIVPVLCWWFLRAPRA--------AAAPGGAEGVSSP-----V +EDAAQDTWLARAYRPVLRWTQRHAVATLAGAAALLAGTVALAPLIPTNLLGDSGQNSFVVTAQQAPGTSLEATTAIAGRI +EAALRDTPGVRTVQFTAGSAGGAMGAFGRGSADRATFTVVTDPDADQTALQDEVRGRLAGLGDVGEVDVSAQQGPAGGQD +ITVSVTAPDPEALADGIDRVAEALRGLDGVLQASTPSSDVRPTFQVDVDTLAAAERGLTEKAVSGQVAAALQAVPAGTVR +FGFQEFTVRLGDPDPVESLGALRAVPISTPSGPVPLSELADVRRADVPAQVTSSNGQRTAEVTVTPDPADLGGVSRRVSD +ALEGVALPDGVEATVGGAATEQAKTFRDLGLALLAAIAAVYVVMVATFNSLRQPFVLLVSIPFAATGVVLALLASGTALG +VATMIGLLMLVGIVVTNAIVLIDLINQYRRRHGMALDEAIERGALHRVRPVVMTALATVLAMTPMALGITGHAGFISQPL +AVAVVGGLASSTVLTLVLVPVLYRLTEARGERRIQAERAAREAEERELAEREARERELAEREAAARAVAG---------- +PAAAA----------HPAPAGRL-SRRRGWRGWIRRATS +>GCF_023573625_PROKKA_00790 +MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVVDAQVGEPLETALQAVEGLES +SRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQLPEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVL +APRLQKIDGVRGADVLGGTDENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR +GIVVAPS---------------------------------------GDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLS +VSVTATPDADLVAVSQAVRDALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLVT +AVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRRTAILDGTREVATAITASTLVS +VAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTIVPVLCWWFLRAPRR--------GAETTAAPAVPGD------ +RPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALALLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERI +ERVLLDTDGVETVQWTAGTTAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQGPSGGQD +IEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAAARLGLTEEAVAGQAAAALQAVPVGDVR +FGFESFAVQLGDPEPVESLDALRQVPVETAEGPVPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQ +AVAELDLPEGVTAAVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTPLG +LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVMTALATILAMTPMALGITGHAGFISQPL +AVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERRLQEER-RVAAER--EAQRVAAER---AAEQARRAEER---------W +AAPSEL-----DAGR----LGRLRQRLR---RRWRRA-- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000731.fa new file mode 100644 index 0000000000000000000000000000000000000000..7baacd5ba3a85a934ef382bf3f864b4232b3b86b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000731.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00825 +MTDTTQ--HRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDF +RDSLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYG +RTFEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA +>GCF_003691675_PROKKA_00557 +MTDTTQ--HRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDF +RDSLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYG +RTFEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA +>GCF_005280335_PROKKA_02097 +MSDTTQ--NRLQPGDIAPSFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF +RDSLASLTAAGYVVLGVSPDPIGKIIRFAQKEGLTFSLLSDEDHAVAEAYGAWGEKKNYG +RTYEGLIRSTVVVGPDGRVTHAQYNVKATGHVARLRRTLGLDEA +>GCF_020097155_PROKKA_01996 +MTENTAAPARLSPGDVAPEFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF +RDSLASLTAAGYRVLGISPDPIGKIIRFAQNEGLTFSLLSDEDHAVAAAYGAWGEKKNYG +RTSEGLIRSTVVVGPDGKVTLAQYNVKATGHVARLRRELGLDD- +>GCF_023573625_PROKKA_00794 +MTDTTQ--HRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDF +RDSLASLTAAGYVVLGISPDPIGRIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYG +RTFEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000732.fa new file mode 100644 index 0000000000000000000000000000000000000000..f43234ed0674291fc2ceace76394821e8ee7d376 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000732.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00827 +MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE +MLLCPFDPTSTPDDHDRRAPG--VAEDDPHGPVTEASADRADVVEVGLANVATVADTGSG +YQVETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYAT +PETDATDVTPPDLH----GV +>GCF_003691675_PROKKA_00559 +------------MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE +MLLCPFDPTSTPDDHDRRAPG--VAEDDPHGPVTEASADRADVVEVGLANVATVADTGSG +YQVETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYAT +PETDATDVTPPDLH----GV +>GCF_005280335_PROKKA_02095 +------------MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE +MLLCPFDPTSTPDDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSG +YQVETVTGFRTWFDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAA +PEAGGTDVTGPDLH----AR +>GCF_020097155_PROKKA_01994 +------------MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLE +MLLCPLDP-------------------------VEAVAAVPE--EVALANVATVADTGSG +YQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADDAADFHAFMTAFMDELDRLYAE +P-------ADPDLHPPQKSV +>GCF_023573625_PROKKA_00796 +------------MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE +MLLCPFDPTSTPDDHDRRAPG--VAEDDPHGPVTEASADRADVVEVGLANVATVADTGSG +YQVETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYAT +PETDATDVTPPDLR----GV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000733.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7fa7ed59658b9556722df991ac9de5d5971ac7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000733.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00828 +MLTRLRGMDSAAS--TPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIGIASSWNEITPCNLSLDRL +AQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL +DLASVFVYAGSIMPGVARLTDGTERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALG +MSLPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS +DFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDA +MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITG +AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLLVDEAELAARRESWEPVEP +KFTTGVLGKYAKLVHSAAEGAYLG +>GCF_003691675_PROKKA_00560 +MLTRLRGMDSAAS--TPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIGIASSWNEITPCNLSLDRL +AQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL +DLASVFVYAGSIMPGVARLTDGTERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALG +MSLPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS +DFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDA +MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITG +AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLLVDEAELAARRESWEPVEP +KFTTGVLGKYAKLVHSAAEGAYLG +>GCF_005280335_PROKKA_02094 +-------MDTAAS--TPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNEITPCNLSLDRL +AQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL +DLASVFVYAGSTMPGHARLSDGTEKQVTIIDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALG +MSLPGSATPPSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLSLE +DFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDALTVTGRTVAENLAELAPDPVDGDVIRTMDRP +MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITG +AIKGAGLGKDVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELEARRREWTPVPP +KFTTGVLGKYAKLVHSAAEGAYLG +>GCF_020097155_PROKKA_01993 +-------MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSWNEITPCNLSLDRL +AQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL +DLASVFVYAGSIMPGVARLTDGTEKQVTIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALG +MSLPGSAAAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS +DFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGTVIRTMENA +LHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITG +AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAELEARRTSWQPVPP +KFTTGVLGKYAKLVHSAAEGAYLG +>GCF_023573625_PROKKA_00797 +MLTRLRGMDSAAS--TPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIGIASSWNEITPCNLSLDRL +AQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL +DLASVFVYAGSIMPGVARLTDGTERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALG +MSLPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS +DFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDA +MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITG +AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLLVDEAELAARRESWKPVEP +KFTTGVLGKYAKLVHSAAEGAYLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000736.fa new file mode 100644 index 0000000000000000000000000000000000000000..ce152b7e476ba1d45f9ea9ed3654aeec70adff23 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000736.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00832 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>GCF_003691675_PROKKA_00564 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>GCF_005280335_PROKKA_02092 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>GCF_020097155_PROKKA_01991 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTQVPGISRMTVVVDADAHLLEQ +VTKQLNKLINVIKVVELAGDSSVQRDHLLVKVRADASTRGQVVQAADLFRAHVVDVAPDS +LTFEATGTREKLEAFLEMMEPHGIRELVRSGTLALARGPRSMTDRALAR +>GCF_023573625_PROKKA_00802 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRAVAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000737.fa new file mode 100644 index 0000000000000000000000000000000000000000..119cae77a1e2796f1d25eecd4f10f5880d1c252b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000737.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00833 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQKGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR +>GCF_003691675_PROKKA_00565 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR +>GCF_005280335_PROKKA_02091 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA +PEFKELRAKGEAHPIEKTGRELREMFSWLKDADDDYTEGTAAR +>GCF_020097155_PROKKA_01990 +MTAQKFYDDDADLSIIQGRTVAVIGYGSQGHAHSLSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDEHIAPNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEQDASGQAEALALSYAKAIGGTRAGV +IKTTFTEETESDLFGEQAVLCGGASQLIQYGFEVLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEFGDYVSGPRVITPEVKDHMKEVLADIQNGAFAKHFMDDQKAGA +PEFTELRAKGESHPIEKTGRELRQMFSWLKDTDDDYTEGTAAR +>GCF_023573625_PROKKA_00803 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSRSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000739.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b35deb4c62d1c1d0d389a34bd3032f8c4b384e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000739.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00847 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKMEQTAQQQGVSALELATRNAAV +FKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGDIYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEV +TWTEEESYFFRLSKYQQPLLDHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH +VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLELPRRVMIHGFLNNNGAKMSKS +LGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAVVSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEA +DRAVLAQVDALLERSRSAYAVQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM +PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAED +>GCF_003691675_PROKKA_00569 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKMEQTAQQQGVSALELATRNAAV +FKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGDIYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEV +TWTEEESYFFRLSKYQQPLLDHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH +VTYVWVDALTNYLTGAGWPADDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLELPRRVMIHGFLNNNGAKMSKS +LGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAVVSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEA +DRAVLAQVDALLERSRSAYAVQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM +PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAED +>GCF_005280335_PROKKA_02088 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIATDAMARFQRLDGRDVRFLTGTDEHGQKMEQTAQREGVTALELATRNAAV +FKEMDDEVLDISYDRFIRTTDADHAEAVQEIWRRMEANGDVYLGSYAGWYSVRDERYFGEDETAVGEDGVRRAVETGTEV +TWTEEESYFFRLSKYQEPLLEHYRRNPEFAAPRYRFNEVIRFVEDGLEDLSISRTSFDWGVPLPAPVDPDAEVADRRADH +VTYVWVDALTNYLTGAGWPGRDPEAFGRYWPADLHVIGKDISRFHCIFWPAFLMSAGIELPKRVMIHGFLNNNGAKMSKS +LGNVVHPRDWVARYGLDAIRFFLLREFPFGADGSYSHEAVVGRKNADLANNLGNLAQRSLSMVAKNCEAAVPQPGPLTAE +DEAVLAQVDALLERSRTAYAVQDFHDALEETWRVLGEVNAYFADQAPWVLRKTDEARMRTVLYVTLQAVRRVALLVQPVM +PASASRLLDLLGVPAEGDAGRTGASGQGPRSFAAFHEDLVPGTALPKPEGVFPRHEEPAEA +>GCF_020097155_PROKKA_01988 +MTDTRAPYYVTTAIHYPNGEPHIGHAYEVVGADALARFMRLDGRDVFFLTGTDEHGQKMAQTAERLGVTPMELATRNSAA +FKAMDDEVLGVSYDRFIRTTDEDHHRASQEIWRRMEANGDVYLDRYAGWYSVRDERFFDEDETEVREDGQRYAAETGTEV +TWTEEESWFFRLSKYQEPLLALYRDDPEFAAPRSRFNEVIRFVEGGLEDLSISRTSFDWGIDVPAPADGAASD----AHH +VMYVWVDALTNYLTGVGFPDESSESFRRFWPADVHVIGKDISRFHCVFWPAFLMSAGIELPKRVMIHGFLNNNGEKMSKS +LGNVVAPRDWVARYGLDAVRFFLLREFPFGADGSYSHEAVVGRKNADLANNLGNLAQRSLSMVAKNCGGGVPEPGSLTEA +DTAVLAQVDALLEHSRAAYTVQDFHGALEETWRVLGEVNAYFADQAPWVLKKTDEPRMRTVLYVTLQAVRRVALLVQPVM +PASSSRLLDLLGVPAEGDAGATAASNAGPRSFAAFGEDLMPGTALPRPEGVFPRHEDPAEG +>GCF_023573625_PROKKA_00806 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKMEQTAQQQGVSALELATRNAAV +FKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGDIYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEV +TWTEEESYFFRLSKYQQPLLDHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH +VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLELPRRVMIHGFLNNNGAKMSKS +LGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAVVSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEA +DRAVLAQVDALLERSRSAYAVQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM +PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000745.fa new file mode 100644 index 0000000000000000000000000000000000000000..b42a2537d9fdc93db7d18c0ba201da278f4803a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000745.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00853 +M---TDATAPVSENAPAPFADVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGGTLVFRIEDTDAKRDSEE +SYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIEKLKAGGYIYPSYSSPEETEARHRAAGRDPKLGYDGHD +RDLTDEQIAAFEAEGRAPVWRLRMPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE +DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEGLLNYLGLLGWSLSADED +IFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVADFRDRLVPYLHAAGLVGEHLTEREMQILTAAAPLVQER +VQLLGEAVEMLAFLFTADRDVRTAEGALKGMPADLGAAVAAAREALAALPEDEFTTERIEAALRAALIDGLGLKPRQAFG +PVRVAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGRPTDA +>GCF_003691675_PROKKA_00575 +M---TDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGGTLVFRIEDTDAKRDSEE +SYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIEKLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHD +RDLTDEQIAAFEAEGRAPVWRLRMPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE +DLLSSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEGLLNYLGLLGWSLSADED +IFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVADFRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQER +VQLLGEAVEMLAFLFTADRDVRTAEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFG +PVRVAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA +>GCF_005280335_PROKKA_02081 +------------------------MDAETPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEE +SYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGFD +RDLTDEQVAAFEAEGRAPVWRLRMPDTDITFTDLVRGEITFKAGTVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE +DLLSSTPRQIALYRALHAVGVAAYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHREHGFIREGLLNYLALLGWSLSADED +IFTPEQFVEHFDVHKVLANPARFDEKKAIAINGSHVRMLDADDFRERLVPYLHAAGLVDAEPTEREREILAAAAPLVQER +VQLLGEAVEMLAFLFTADADVATSEGALKGMPADLGAAVAAARDALAALPEDGFTTERIEEALRAALIDGLGLKPRQAFG +PVRVAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGLPTDA +>GCF_020097155_PROKKA_01976 +MTEPTTASDTAAENAPAVFADVPQVDADTPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEE +SYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSTPEETEARHRAAGRDPKLGYDGAD +RDLSAEQVEAYEAEGRRPVWRLRMPDADITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE +DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQSNLFLHRDRGFIPEGLLNYLALLGWSLSADED +IFTPEQFVEHFDIHKVLANPARFDEKKATAINGTHVRMLEPADFRARLVPYLQAAGLVGERLTEREERILDAAAPLVHER +VALLGEAVDMLAFLFTPDAEIATAEGALKGMPADLPTAVAAAREALAGIDEAEFTTAAVEEALRAALIDGLELKPRQAFG +PVRVAVTGKKVSPPLFESLEILGKESALARLDRFAAEQAA-------A +>GCF_023573625_PROKKA_00812 +M---TDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGGTLVFRIEDTDAKRDSEE +SYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIEKLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHD +RDLTDEQIAAFEAEGRAPVWRLRMPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE +DLLSSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEGLLNYLGLLGWSLSADED +IFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVADFRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQER +VQLLGEAVEMLAFLFTADRDVRTAEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFG +PVRVAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000746.fa new file mode 100644 index 0000000000000000000000000000000000000000..8b7f6c3871224c8e8a2b32a6d697226f21a18010 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000746.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00859 +MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGATGSGKSSLFNALTGRDLARV +AATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAAALLDWLGVRRRHLLDEAPVLDDGRPGFLGFGRRDGADATG +LILLDLPDIDSVERGNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS +LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAAASGEGEPAGVGPGDEQRLGR +ELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQ +RAVVDGAVRTLAAAAGAGASEPWAAAIRRAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW +LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRHARRRLEEATTDVGRRLVVDPVR +AEVDRFRAFRDALARASGAPVR-RGRR +>GCF_003691675_PROKKA_00581 +MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGATGSGKSSLFNALTGRDLARV +AATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAAALLDWLGVRRRHLLDEAPVLDDGRPGFLGLGRRDGADATG +LILLDLPDIDSVERGNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS +LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAAASGEGEPAGVGPGDEQRLGR +ELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLMPASTAPRRDRDEVARDPALHRTSLPERSGTQ +RAVVDGAVRTLAAAAGTGASEPWAAAIRRAGREHAEDLPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW +LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRARRRLEEATTDVGRRLVVDPVR +AEVERFHAFRDALARASGVPVR-RGRR +>GCF_005280335_PROKKA_02076 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------MELSNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDTVLAS +LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQIAAIVERRGAAAERLGADVAARARDLDAASGEGEPAGVGPGDEQRLGR +DLATAGGVPAVVRAVEGSYRLRSAKQTSWPVLRWMHSFRADPLRRLHLMPDRPAVRRDRDEVGRDPALHRTSLPERTGTQ +KAVVDGAVRTLVTAAAAGAPEPWAASVRRAGRAHAEQVPDAVDQAIAATDLGAGRGSWWHPVLNVLQWLALLTAVVGAGW +LGVLALAAYLQFPLPPAPVVEGFPIPTLLLVGGLALGVLLALLAIPLTRITAASRGRRARRRLEEGTTDVGRRLVVDPVR +AEVDRFHAFRDAVARAAGATAR-RGRR +>GCF_020097155_PROKKA_01970 +MSRPAAPTLAQRLDALGTAAELARDRLPDAVVADAQAAVRAAEERQSLSAEHTVVGFFGATGSGKSSLFNALTGRELAGV +AATRPTTSEPLAAVWGVGRGENLD---------GEGGGAAALLDWLGVRRRHLLDDAPVLDGGRPVFLGLGHREGADATG +LILLDLPDIDSVQRSHRDVTARLAGHVDVLVWVVDPEKYADAVIHRDFLATMASHAAVTLVLLNQVDRLTVTDRDAVLAS +LRRMLSGHGMGDVRVLPVSARTGEGLEEVGRQIAAIVSRRGAAAERLGADVSARARALDEASGPGEPAGAGDDDAVRLGR +DLAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLLPERAVARRDRDPVDRDPALHRTSLPERTQTQ +RAVVEGAVRTLVTSASAGASEPWAASVRRAGREHLDELPAAVDHAIAGTDVEAGRGSWWWPVLDVLQWLALAVAVAGAGW +LGAYALAAWLQFPLPPAPTTQGFPIPTLLLIGGLALGLLLALLAVPLTRLTAASRGRRARRRLEEAAVRVGRELVVDPVN +AEAARHREFRSALAAAQGSGVRSRSRR +>GCF_023573625_PROKKA_00818 +MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAAVRAAGERQALSAEHTVVGFFGATGSGKSSLFNALTGRDLARV +AATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAAALLDWLGVRRRHLLDEAPVLDDGRPGFLGVGRRDGADATG +LILLDLPDIDSVERGNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS +LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAAASGEGEPAGVGPGDEQRLGR +ELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQ +RAVVDGAVRTLAAAAGAGASEPWAAAIRHAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDMLQWLALLTAVVGAGW +LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRARRRLEEATTDVGRRLVVDPVR +AEVDRFHAFRDALARASGVPVR-RGRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000747.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7b01f96a68d2f9ab7f38b03a000e667f1f74296 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000747.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00860 +M------TVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVP +APRGGTLISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTAL +TLPPTTPVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLC +RTPAAADRDRVLAEGADLVHAQAVPDGPRAA----------APPGPGWAAAGLAVLLTDR +AELERRADALPAADRPSPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDA +HRMAAATGGA----GPAPAPWLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLG +LAWPETELPRGFTRIGRLVPAGARAPAGHRPLPGSGWDPFA---G +>GCF_003691675_PROKKA_00582 +M------TVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVP +APRGGTLISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTAL +TLPPTTPVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLC +RTPAAADRDRVLVEGADLVHAQAVPDGPRAA----------APPGPGWAAAGLTLLLTDR +AELERRADALPAADRPSPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDA +HRMAAATGGA----GPAPAPWLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLG +LAWPETELPRGFTRIGRLVPAGARPPAGHRPLSESGWDPFA---G +>GCF_005280335_PROKKA_02075 +M------TPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVP +APRGGTLVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTAL +TLPPTTPLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLR +RAPAPAARERVLAEGADLVHAQDAPGSSGAARSGALRPSA-ARPGPGWAAAGLALLLTDR +DELARRAAALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDA +HRMAAATGAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLG +LAWPETALPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFG---G +>GCF_020097155_PROKKA_01969 +MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP +APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL +ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR +RAAGGERGARIARRGADLVLAA---GSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDR +AVLTRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDG +HRLARASSAP----GAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLG +LAEPGLALPSGFRRVGRLAPAG-ETPDGHVRLPEAGWDHFDAGRG +>GCF_023573625_PROKKA_00819 +M------TMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVP +APRGGTLISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTAL +TLPPTTPVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLR +RTPAAADRDRVLAEGADLVHAQAVPDGPRAA----------APSGPGWAAAGLTLLLTDR +AELERRADALPAADRPSPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDA +HRMAAATGGA----GPAPAPWLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLG +LAWPETELPRGFTRIGRLVPAGARPPAGHRPLSESGWDPFA---G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000748.fa new file mode 100644 index 0000000000000000000000000000000000000000..ced755daa681f40fa8066162933661e386ad7605 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000748.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_00861 +MTETTAPAAPAEQEAA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR +GEVPFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVD +AAVASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGF +AVRDTLTPDRLVIGMHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASG-PAPTPASVQVLN +GTRIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDS +LEAAVDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLG +HRFDPERLLRA-------A +>GCF_003691675_PROKKA_00583 +MTETTAPAAPAEQEAA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR +GEVPFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVD +AAVASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGF +AVRDTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASG-PAPTPASVQVLN +GTRIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDS +LEAAVDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLG +HRFDPERLLRA-------A +>GCF_005280335_PROKKA_02074 +M---THPSAPAEQDRA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPEKIARLSR +GEVPFHEPGLPELLRTHVESGRLRFTTDVAEAARWADVHFVGVGTPQKVGESGADLRYVD +AAVASLAAAIDRDALIVGKSTVPVGTARRLAAMVRRVRAEAGLPGEVELAWNPEFLREGF +AVKDTLTPDRLVIGTDGPRAEQVLRRVYARQLAADTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITEAVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDAGRGEAAAYG-GKTTASGVEVLR +GARIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVHDPEGNANAAARFPRLDYVDS +LEEAVEGAELTLLLTEWQAFREMDPAAVGALVDARLLIDGRNVLDLAAWAEHGWTVVGLG +HRFDPAALG---------A +>GCF_020097155_PROKKA_01968 +MTETAVVPAAAESEEAPARPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR +GEVPFHEPGLPELLRAHVASGRLRFTTDVAEAASWADVHFIGVGTPQKVGEAAADLTYVD +AAVESLARAIDRDALIVGKSTVPVGTARRLAARVAEIRAAEGLPGEVELAWNPEFLREGY +AVKDTLTPDRLVIGTHGPRAELLLRTVYATPLAAGTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITETVGGDIGTLADAIGHDGRIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARQGVVRSAPGGARTAPTPAGVQVLN +GTRIAVLGVTFKPYSDDVRDSPALDVANRLFTAGAEVAVYDPEGNANAAARFPRLGYVDS +LDAALQGAELVLLLTEWDEFRQMDPAAAGELVAQRILIDGRNVLDVDAWGEHGWTVLGLG +HRFDPAALNGGRPGDDAQA +>GCF_023573625_PROKKA_00820 +MTETTAPAAPAEQEAA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR +GEVPFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVD +AAVASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGF +AVRDTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRVRRADASG-TAPTPASVQVLN +GTRIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDS +LEAAVDGAELTLLLTEWRQFREMDPDAVGARVASRLLIDGRNVLDAAAWREHGWDVIGLG +HRFDPERLLRA-------A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000749.fa new file mode 100644 index 0000000000000000000000000000000000000000..5295201584cdba50d0d9970f7c8b9345827ebc43 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000749.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00862 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA +>GCF_003691675_PROKKA_00584 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA +>GCF_005280335_PROKKA_02073 +MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL +HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD +AVVAAATRLTELIRAGEA +>GCF_020097155_PROKKA_01967 +MTTTPLPDAGAD--IGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL +HRLAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAG +SVVAAADRLTELIRAGEA +>GCF_023573625_PROKKA_00821 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000750.fa new file mode 100644 index 0000000000000000000000000000000000000000..37e7d2f52a4b7e25aa5b1574cca6172850f8f219 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000750.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_00863 +--MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLA +GRPVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGI +VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA +VTVDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAG +ARAGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF +VTWGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSC +TNSRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC +SMCLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA +LTPQEA +>GCF_003691675_PROKKA_00585 +--MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLA +GRPVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGI +VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA +VTVDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAG +ARAGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF +VTWGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSC +TNSRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC +SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA +LTLQEA +>GCF_005280335_PROKKA_02072 +--MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLA +GRPVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGI +VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA +ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAG +ARAGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPF +VTWGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSC +TNSRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC +SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA +LTPQEA +>GCF_020097155_PROKKA_01966 +MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA +DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI +VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA +ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG +ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF +VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC +TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC +SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA +LENQEA +>GCF_023573625_PROKKA_00822 +--MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLA +GRPVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGI +VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA +VTVDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAG +ARAGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF +VTWGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSC +TNSRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC +SMCLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA +LTPQEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000755.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000755.fa new file mode 100644 index 0000000000000000000000000000000000000000..1049eb4e4b393d6d5814f812132d0b054f8902bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000755.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00868 +MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLDLALERGVGLH +>GCF_003691675_PROKKA_00590 +MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGAAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGSTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLDLALERGVGLH +>GCF_005280335_PROKKA_02067 +----------------MLLLFGGRSSEHPISCVTAAGVLHAADPQRWDVVPVGVARSGLW +SHDELDVAAFRLDGETLPEVPEPEAPVSLRTLPDGTVELTAEDGSSLGRVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITDRDWARD +PEAALARAGALAFPLFVKPARGGSSFGITRVSDPADLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGSDAPRASLPGEIVVKHDEGDLQFYDFQAKYQDDDAAQLSCPAELPEEQT +RRLRELAVRAFEAVDGSGLGRCDFFHTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DALISELLDLALERGVGLH +>GCF_020097155_PROKKA_01961 +--MTQPPETAPGRRPRVLLLFGGRSSEHPISCVTAAGVLHAADRERWDVVPVGVAHSGLW +SHGEVDAAAYALGDGELPSVPEPERPVSLRARADDAVELVGADGEDLGVVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAGGLEVGPWETITDRQWRND +PEAALERAGALDYPLFVKPARGGSSFGITKVDAPEDLRAAVEEARRFDPKVVVEAGILGR +EIECAVLDGHGAESPRASLPGEIVVKGAESGHQFYDFEAKYQDASAAQLSCPAELPEEAI +ERLREQAVRAFEAVDGAGLGRCDFFYTPDGRWVVNEINTMPGFTSISMYPAMWERTGLPY +GELISELLDLALERGVGLH +>GCF_023573625_PROKKA_00827 +MTAIPAPEAAAGARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGGALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLYLALERGVGLH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000756.fa new file mode 100644 index 0000000000000000000000000000000000000000..4d4cdb9a0dd8490185b9c6a1c2bc9a28ff3cbb0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000756.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00869 +MES---RRLRR---LVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGD +LDLRPTDSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGR +DPAVEVLFGKDQASSDTVMVGLSSAVAQIEPSGGCVGVQDATPVG +>GCF_003691675_PROKKA_00591 +MES---RRLRR---LVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGD +LDLRPTDSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGR +DPAVEVLFGKDQASSDTVMVGLSSAVAQIEPSGGCVSVQDATPVG +>GCF_005280335_PROKKA_02066 +MESRPLRPLRR---LVPLLTAIALGATACSGRVATVEAAPDAANPECAPAMVAMPDALGD +AALRPTDSQATAVWGDPAAVVLRCGAPVPGPTTDRCISVDGVDWVIRDEDENWRIVTYGR +DPAVEVLFGKDKASSDTVMVGLASAVAQIDADGGCVNLQDATPVG +>GCF_020097155_PROKKA_01960 +M-----PRLPRPVILAPALAAAALGLTACSGPVVSVEAAPGAADPACAPAMVAVPDVLGG +QDRRETDSQATAAWGEPAAVVLRCGVPTPGPTTDRCVSVDDIDWVVRDEDDHWRITTYGR +TPAVEAVFGKSEVSSDSVMTGLGSAVAQIPSQRRCVNIEDATPVG +>GCF_023573625_PROKKA_00828 +MES---RRLRR---LVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGD +LDLRPTDSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVIRDEDENWRITTYGR +DPAVEVLFGKDQASSDTVMVGLSSAVAQIESSGGCVSVQDATPVG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000758.fa new file mode 100644 index 0000000000000000000000000000000000000000..e10f93dc6288f476e8967646689b0621463c435d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000758.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00871 +---------------------MGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC +PAQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADR +AARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTLMLADCV +QAVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGAHAA +EAEPAA-AAEAPAEGAVEVMGTLALTPLAAAELRRRLTEVGDAVILAPLGTARDGQGRVP +WRVHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSH--------GDDA--APDGCHGR +>GCF_003691675_PROKKA_00593 +-MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC +PAQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADR +AARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCV +QAVEETESLLAPLTGAQVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAA +EGEPAA-AAEAPAEGAVEVMGTLTLTPLAAAELRRRLADVGDAVILAPLGTARDGQGRVP +WRVHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSH--------GDDA--APDGCHGR +>GCF_005280335_PROKKA_02064 +-MSTPPRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC +PAQDDAGAVLARAGAAALDLARGNSGTLLAVALAGMAEPLRGRARADAFALAAAFGAADR +AARQALSDPREGTILTVLSAASRSLARSATQAPDSPAVAADVDPAVRLGPAVTAMMADCL +RAVEQTESQLAPLAQARVVDAGAVGLLWVLEALRAAVTDTAPDEELATALHGYVEGVRPG +P-EPA-------GEDAVEVMGTLALTPLAAADLRRRLAETGDSVILAPVGTERDEHGRVP +WRVHVHVPRAADAVELMRAAGEVQGLAVTELSGDAA--------GPDA----DGCHGR +>GCF_020097155_PROKKA_01958 +MIRARLRGALA--WLRGAEAALAQAAPRLDALNLFPVPDADTGSNMLATVRAARQAAER- +SAGTDMSAVLRDAGAAALDSARGNSGTLLAVALVGLAAPLTPDAPLTTAELAAGARAADR +AARAALSDPREGTILTVLREAATVL---------EAAAAGGREPAEALGSVVEA----AR +RAVEDTEGQLAPLTRARVVDAGAVGLLLVLEALRAEVTRTPFDEGVVAALHGWADGPGAA +GEDPQADGREAP---GVEVMCSIDLTPVDAAGLRRGLEEAGDSVILAPLSRAVDGAGRLR +WRVHVHVARAEDAVALLEAAGAPEEVAVTDLWDPAHRHPDDPAEGDAASPAPDG-HGR +>GCF_023573625_PROKKA_00830 +-MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC +PAQDDVGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADR +AARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCV +QAVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAA +EGEPAA-AAETPAEGAVEVMGTLALTPLAAAELRRRLADVGDAVILAPVGTARDGQGRVP +WRVHVHVPRAEDAIGPLRAAGDVEGLAVTDLAGPSH--------G-DA--APDGCHGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000763.fa new file mode 100644 index 0000000000000000000000000000000000000000..0651a5f98ecf43aa6b9634f09671490b2bf97e07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000763.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00876 +M----TVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAG +LADVLMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALG +LGHAVNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSA +YGVAAVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGG +EIQLTDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAW +LREFTAGL +>GCF_003691675_PROKKA_00598 +M----TVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAG +LADVLMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALG +LGHAVNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSA +YGVAAVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGG +EIQLTDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAW +LREFTAGL +>GCF_005280335_PROKKA_02059 +M----TV--PSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAG +LQDVLMITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALG +LGHAVNCARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSA +YGVAAVEAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGG +EIQLTDALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAW +LKAFAAGL +>GCF_020097155_PROKKA_01953 +MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG +LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG +LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA +YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG +EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW +LKGFAAGL +>GCF_023573625_PROKKA_00835 +M----TVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAG +LADVLMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALG +LGHAVNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSA +YGVAAVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGG +EIQLTDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAW +LREFTAGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000766.fa new file mode 100644 index 0000000000000000000000000000000000000000..68a62b3d200338e2892f58d7625e16fa341f9fe1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000766.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00879 +------------------------MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDS +VLGYVVTDHIFTVYPDLAEGDLARRRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGA +DKDSILADTLEALIGAVYVDHGAVAAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASR +HGLGAVRYAIEGQGPAHDPRYRATLVVGEREYGSAVASSKKQAERDAAAASWPALEADLP +AAGR +>GCF_003691675_PROKKA_00601 +------------------------MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDS +VLGYVVTDHIFTVYPDLAEGDLARRRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGA +DKDSILADTLEALIGAVYVDHGAVAAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASR +HGLGAVRYAIEGQGPAHDPRYRATLVVGEREYGSAVASSKKQAERDAAAASWPALEAGLP +AAGR +>GCF_005280335_PROKKA_02056 +------------------------MHVTAETLERALTHRSYAYEQGGLPTNERLEFLGDS +VLGYVVTDHIFTVHPDLAEGDLARRRAAVVSTRALAKVARRIGIGPFVRLGTGEGRTGGA +DKDSILADTLEALIGAVHVDHGLVAASALVHRHVVPLLDEPDLVRESTDWKTVVAEAANR +HGLGAVRYAIEGQGPAHDPRYRATLVVGEREYGSAVASSKKQAERDAAAASWPALEADLP +AAGR +>GCF_020097155_PROKKA_01950 +MASPQTRTGSVPVPESSALLERLGVHITAGTLERALTHRSYAYEHGGLPTNERLEFLGDS +VLGFVVTDHLFTAFPDLPEGDLARRRAAIVSTRALAKVARRIGVGPHVRLGTGETRTGGA +DKDSILADTFEALIGAVYRDHGAVAAAALVHRHVVPLLDEPGLLRESTDWKTVVAEAASR +HGLGEVRYDIEGQGPAHDPRFRATLTVGGRAFGSAVASSKKQAERDAAAEGWPELSATLP +AAGS +>GCF_023573625_PROKKA_00838 +------------------------MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDS +VLGYVVTDHIFTVYPDLAEGDLARRRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGA +DKDSILADTLEALIGAVYVDHGAVAAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASR +HGLGAVRYAIEGQGPAHDPRYRATLVVGEREYGSAVASSKKQAERDAAAASWPALEAGLP +AAGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000768.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000768.fa new file mode 100644 index 0000000000000000000000000000000000000000..39e54df6281e16dbf7c796f786e32d033adb6710 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000768.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00881 +MSHPPAASWTP--------EPL-----PRPEPPRDDAPPVARRR-----------RRWPW +VVGLLAVLLAALLGLGAWYTSSLGRTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREG +EGEQDMGQRSDTMMLVHIPADRRQVYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVD +TVELLLGVSIHHVLEVDFQGFRGVTNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTA +ALRYVRERHAFDDGDVTRVENQQRYLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDE +GLTSGVIASLAWQLRDVRGEDVEMFTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDD +VQRYVDEHEPTK-------EKKAQAAGG-PAPVLTLLTGTTPA---PVLGEDPCDD +>GCF_003691675_PROKKA_00603 +MSHPPAASWTP--------EPL-----PRPEPPRDDAPPVARRR-----------RRWPW +VVGLLAVLLAALLGLGAWYAGSLGRTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREG +EGEQDMGQRSDTMMLVHIPADRRQVYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVD +TVELLLGVPIHHVLEVDFQGFRGVTNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTA +ALRYVRERHAFDDGDVTRVKNQQRYLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDE +GLTSGVIASLAWQLRDVRGEDVEMFTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDD +VQRYVDEHEPEK-------EKKAQAAGG-PAPVLTLLTGTTPA---PALGENPCDD +>GCF_005280335_PROKKA_02054 +MSQPPAASWTP--------EPL-----PRP--ARSPEPPRPARR-----------RRWPW +VLGVLAAVLVVLLALGAWYAVSLARTFDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGG +EGEEDMGERSDAMMLVHLPADRSQVFVMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVD +TVEQLLGVPVHHVVEMDFQGFRGVTNALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTA +ALRYVRERHAFDDGDVSRVQNQQRYLAGAVERFLSPQILGNPARTTEVVATFSDHLGVDA +GLTSGVVASLAWQLRGVRAGDVEMFTVPRAGFGYSPDGDSIVELDEAKLADLRSALKDDD +VQRYVAEHESED-------GQDASAAGADPAPVLALLAQPAPT---PAVGEDPCAD +>GCF_020097155_PROKKA_01948 +MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA +VLGVLALLLVVALGA---YGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAA +EDSAETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAA +MLDKLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTA +ALRYVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDE +GLDSATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDD +VESYLRAHDPEALAAGEDVQPALAAAPG-ATPLLTELAAAPPAGEGTLLGEDPCGG +>GCF_023573625_PROKKA_00840 +MSHPPAASWTP--------EPL-----PRPESPRDDASSVARRR-----------RRWPW +VVGVLAVLLAALLGLGAWYAGSLGRTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREG +EGEQDMGQRSDTMMLVHIPADRRQVYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVD +TVELLLGVPIHHVLEVDFQGFRGVTNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTA +ALRYVRERHAFDDGDVTRVKNQQRYLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDE +GLTSGVIASLAWQLRDVRGEDVEMFTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDD +VQRYVDEHEPTK-------EKKAQAAGG-PAPVLTLLTGTTPA---PALGEDPCDD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000772.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c2d78d279dc58ea58235c5d357b13f0a04de5cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000772.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00896 +MSDTG-DPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANS +VNALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSR +SISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIP +LLALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFA-DFPPMMTA +MHLNPLFCVLDIARQSLLYASDADPMRWVVLAAWTAALLVVGTVVFWRAEETYGEE--R +>GCF_003691675_PROKKA_00618 +MADTG-DPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANS +VNALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSR +SISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIP +LLALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFA-DIPPLMTA +MHLNPLFCVLDIARQSLLYASDADPMRWIVLAAWTAALLVVGTVVFWRAEETYGEE--R +>GCF_005280335_PROKKA_02043 +MSGTGMAASGPVNTVV--VDAAPLGVVGARPSLRDYVLSLFRYRSFILFDSRSRISGANA +VNTLGRLWMVLNPILDGGAYFLVFGVLLGTGRGIPNFIAYLIIGVFFFRYSSQAITAGSK +AVSSNLTLVRAFRFPRATLVLATNLRALLEFVPTLAVMVVLILAIPPLEVFTWRWLLLVP +LLILQTLFNVGLSLVLARFVAHWPDLANMIAFGMRIWLYLSAVFFSVERFD-GQPIVQTA +MHLNPLYCVLDIARQSLLYGQDAEPHRWLVLAGWAALVAVVGLVVFWRAEETYGEE--R +>GCF_020097155_PROKKA_01941 +MTDRV-EATSPP--VELRVDESRLERVGRRPSLGDYVTRLWRLRHYVRYDAVAAVQAQNR +RHRLGNVWLLLNPILNGATYFLVFGVLLRTSLGVENFIGYLTVGVFMFTFTTRAVTALSR +SLTARNNVADAFQLPRAVLPLTALAREVLAYGFTLAAMLLAVLILPPHAQVTWWWLLFPV +VVALQLMLVAGVGLLLARAVSRVRDLSQIVGFGIRLWMYGSAVFYSFDRFV-SQPNVLAV +LQLNPMYQVLDISRDLLLYGRSPSPVAWGILAAWSVGLLVVGVVVFWLGEERYAKDLNR +>GCF_023573625_PROKKA_00847 +------------------------------------------------------------ +-------------MLDAIFYWLIFGLLLRFDHGMDNFVAFVIVGVFMFQMTSAALTSGTR +TIASNLSLTRAFRFPRMALPLADLVYDVLQRLPAIAVMFILVIAIPPHETPEWSWLVFPG +VLGLHVILNFGIMLLLARLSTLLPDVSRMVPFVSRLLMYGSGVIFPITRFTDNHPALHAI +IQLNPLYVLITMYRQVIIEGVTPPASSWAMLAAYAVCLTIVGGIVFWLGEESYGRDQYR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000773.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b4a90cac5cff4bdc29dbe4318949f42dfbd5dbf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000773.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00897 +MP-KVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL +NIIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA +GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALL +EAVGHQVPFEDERLAELEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE +VTFVLPAHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP +SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGD +GRAAERTVSAIAELLGVGERLPAFDGGDPA +>GCF_003691675_PROKKA_00619 +MP-KVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL +NIIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA +GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALL +EAVSHQVPFEDERLAGLEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE +VTFVLPAHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP +SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGD +GRAAERTVSAIAELLGVGERMPEFAPDDRG +>GCF_005280335_PROKKA_02044 +M--KVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL +NIIQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA +GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALL +EAVGHQVPFEDERLAELEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE +VTFVLPAHRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP +SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGD +GRAAERTVSAIAELLGVGERLPAFDGA--- +>GCF_020097155_PROKKA_01942 +MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL +DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA +GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL +ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN +LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP +SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD +GRAGLRTVAAIAQLLGVGDRLDEFGA---- +>GCF_023573625_PROKKA_00848 +-----MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL +NIIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA +GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALL +EAVSHQVPFEDERLAELEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE +VTFVLPAHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP +SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGD +GRAAERTVSAIAELLGVGERLPAFDGA--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000774.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000774.fa new file mode 100644 index 0000000000000000000000000000000000000000..eeea17b128cfdd5aaa2743cf699d2ceffbfc25a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000774.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00900 +---MPSSPP-AARVPLPTEIKVMVAAAFVIAIGFGIIAPLLPQYAEMFASDFANPATAVA +AVVSAFGLTRLLFAPVSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQDYTQLLLYRALG +GVGSTLFTVSAMAFLASKSPPTIRGRVSGAYASAFLIGNIVGPIVGSVLAVFGFRVPFLI +YGTSLVIAAGIVFVMLRDTRLQDRARGETRPVMPLRAALGHRSYRAALTSMFANGWATFG +VRNAITPLFAASAFTGTALLGWGITEENRQLMAGLALSVFAAGNVLAVASSSRLSDLHGR +KPLILVGLAVMAVFTGAIGWLESPLLFLVSCALAGAGTGTLNAPQQAAVADLVGQDRKAG +PVMSAAQMSGDLGAILGPLLVGLVVDAAGYGWGFVVTGAVIAVGALAWARAPETNLPVAP +GGPRTGSLPKVDP-DVDPCRMEGRELG +>GCF_003691675_PROKKA_00620 +MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQY----AATFDASAVGVA +AVVSAFGLTRLLFAPVSGKLTNRLGETPVYMTGVLIVAASMFLVAFAQTFPQLLLFRALG +GVGSTLFTVSAMAFLARKSPPTMRGRISGAYASAFLIGNIVGPIVGSALSVFGYRAPFLI +YGSSLVVAAALVFFLLKDTRLADRAVRDVRPAMPVREALSNPSYRAALVSFFANGWATFG +VRNSVMPLFAATAFAGTGLLGWQV---DGAMMAGLALSVFALGNVVAVSFSSRLSDVHGR +KPLILTGLLVMAVTTGAIGWVGTPSLFLIACLVSGAGTGILNAPQQAAIADVVGQDRRSG +SVMSSAQMSADLGAIVGPLAAGLVVDVAGYGWAFVVTGAVILLGAIAWWRAPETNLPVVP +GGPRTGALPKIEPEDA---RPPHREDG +>GCF_005280335_PROKKA_02041 +---MPSSSSRTARAPLPREIKVLVAAAFIIAIGFGIIAPLLPQY----AASFNASATAVA +AVVSVFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFAQLLAFRAIG +GVGSTLFTVSAMAFLARKAPPSMRGRVSGAYASAFLIGNIVGPIVGSALAVFGYRAPFLI +YGTSLVIAAALVFFMLKDTRLADRAARDARPAMPVKEALENPSYRAALVSFFANGWATFG +VRNSVMPLFAASAFAGSGLLGWQV---DGALMAGLALSVFALGNVVAVTFSSRLSDMHGR +KPLILTGLLVMAVTTGVLGWMQSPLLFLLACLVSGAGTGVLNAPQQAAIADVVGQGRRSG +AVMSSAQMSADLGAIIGPLLAGLVVDAAGYGWAFVLTGGVILLGALAWWRAPETNLPIVP +GGPRTGSLPLVRPEDA---RVTPREDG +>GCF_020097155_PROKKA_01939 +---MPTTPS-AARAPLPREIKVLVAAAFVIAIGFGIIAPLLPQYAERFASDFANPATAVA +AVVSAFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMYLIAFAQDYTQLLVFRGLG +GVGSTLFTVSAMAFLASKSPPSMRGRVSGAYASAFLIGNIVGPIVGSVLSVFGYRVPFLI +YGTSLVIAAAIVFFMLKDTRLHDRAAADSRPVMRLREALDHPSYRAALVSMFANGWATFG +VRNAVTPLFAASAFTGTALLGWTVTQENQALMAGLALSVFAAGNVAAVTFSSRLSDVRGR +KPLILLGLAVMAVCTGVIGWMTSPLLFLVACLLAGAGTGTLNAPQQAAVSDLVGQGRKAG +PVMSVAQMAADLGAISGPMLVGLVVDGAGYGWAFAVTGAVLAVGFLAWLRAPETNLPIVP +GGPRTGSLPKIAPEDVAP---PHHREA +>GCF_023573625_PROKKA_00849 +MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQY----ASSFNASATAVA +AVVSAFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFEQLLLFRALG +GVGSTLFTVSAMAFLAAKSPPTMRGRVSGAYASAFLIGNIVGPIVGSALAVFGFRAPFLI +YGTSLVIAAGMVFVLLRDTRRADRGTGDPRPTMPLKEAFGLPSYRAALASFFANGWATFG +VRNSVMPLFAATAFAGTGLLGWQV---DGAFMAGLALSVFALGNVVAVTFSSRLSDVHGR +KPLILTGLLTMAATTGVIGWMSSPALFLLACLLAGAGTGTLNAPQQAAIADVVGQGRRSG +AVMSAAQMSADLGAISGPLLAGLVVDTAGYGWAFVLTGGVILLGALAWWRAPETNLPIVP +GGPRTGSLPLVRPEDA---RVTPREDG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000778.fa new file mode 100644 index 0000000000000000000000000000000000000000..07181149dde8bcf110fc494ee61a0f7ca458ffad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000778.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00905 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAP---A--AEAPAEDAEKSE +>GCF_003691675_PROKKA_00624 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAEEA--AEAPAEDAEKSE +>GCF_005280335_PROKKA_02037 +MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL +SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE +PKAKESAEAETPAEEA--PEAPAEDAEKSE +>GCF_020097155_PROKKA_01935 +MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE +APAESAE-AEAPVEEAADAEAPAEDAEKAE +>GCF_023573625_PROKKA_00853 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAEEA--AEAPAEDAEKSE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000780.fa new file mode 100644 index 0000000000000000000000000000000000000000..36987436040b845efb64ab042ea6e56053528d04 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000780.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00907 +MSPAAQ----DDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAE +LTVTRARWNKQILVVGFEESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVD +GERVGVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLEL +ATGE-----DEGAADGPTDADA--ED +>GCF_003691675_PROKKA_00626 +MSPAAQ----DDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAE +LTVTRARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAVPEESDEWYEEDLVDLEVRVE +GERVGVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLEL +ATGE-----DEGAVDGPADADA--ED +>GCF_005280335_PROKKA_02035 +MSPAPQ----DGLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGATLTVRDGGPSLPAE +LTVTRARWNKQILVVGFEQSPDRNTAETLRGAQLFAAPAAPEESDEWYEDDLVDLEVRVD +GRRVGVVTALTTGAVQDLLHVALDGVDEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLEL +ASGEAEQDDDAAASDAEADADAGREG +>GCF_020097155_PROKKA_01933 +MSPAPQPAETEGQVRVARIGKPHGIRGEVTVQLFTDDPEARFAADSRLEVRQGPPGAPAA +LTVTRARWNKAILVVGFAEVPDRNAAEALRGAQLYAAPLEKVEDDAWYEDDLLDLEVHVD +GARVGVVTGLLTGTVQDLLQVRLDATGDDALVPFVEEIVPEVDQEAGVVVVAPPPGLLEL +ASET-----TAG------------EG +>GCF_023573625_PROKKA_00855 +MSPAAQ----DDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAE +LTVTRARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVE +GERVGVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLEL +ATGE-----DEDAADGPADADA--ED + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000782.fa new file mode 100644 index 0000000000000000000000000000000000000000..17e43f9cba066a0949c8bd69a190e390e019a5c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000782.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00909 +MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV +RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK +>GCF_003691675_PROKKA_00628 +MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV +RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRADAK +>GCF_005280335_PROKKA_02033 +MHILDSLDSNSLRSDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRNGYGVRETFRV +RKVSFGVGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK +>GCF_020097155_PROKKA_01931 +MHILDSFDKASLREDIPAFGPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV +RKVSFGVGVERVFPVHSPVIDKIEVLTKGDVRRAKLYYMRDRHGKAARIREKRADAK +>GCF_023573625_PROKKA_00857 +MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV +RKVSFGIGVERVFPVHSPIIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000783.fa new file mode 100644 index 0000000000000000000000000000000000000000..54788354d76cb650902b4cfb74e92018a3bd6099 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000783.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00910 +MRTSEPRDPRRSRGSVAS---GAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRA +LTGPVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLER +GLEDVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEP +AAAGTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRG +TVDAPSGDT-----P +>GCF_003691675_PROKKA_00629 +MRTSEPRDPRRSRGSVAS---GAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRA +LTGPVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLER +GLEDVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEP +AAAGTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRG +TMDAPSGDT-----P +>GCF_005280335_PROKKA_02032 +MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA +LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER +GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP +AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG +PVDASAPEAAPGAAP +>GCF_020097155_PROKKA_01930 +MRAQEPRDRNRSRGSRAS---GEAGRP------------WWALVLLTLAGAVVAAALLRA +FTGPVYLVPSGSMEPTLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDR +GLEDVAAFWGVGAAQDVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAP +ASRSTWAFEVPEGRMVVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRG +DVPAGAQDGSRG--- +>GCF_023573625_PROKKA_00858 +MRTSEPRDPRRSRGSVAS---GAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRA +LTGPVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLER +GLEDVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEP +AAAGTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRG +TVDAPSGDT-----P + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000787.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ee09187f61632704bae0bef48b17969e5e987f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000787.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00914 +M----TGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGEL +DIVAHHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVR--AHAADR--RGT +PWRVDAVAVLVPRTGGIRFDLLQDVRP +>GCF_003691675_PROKKA_00633 +M----TGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGEL +DIVAHHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVR--AHAADR--RGT +PWRVDAVAVLVPRTGGIRFDLLQDVRP +>GCF_005280335_PROKKA_02028 +M----TGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGEL +DLVAHHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVR--AHGEGR--RAE +RWRVDAVAVLVPRTGGIRFDLLQDVRP +>GCF_020097155_PROKKA_01926 +MVPLDTTTT------TPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGEL +DLVARHGPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQ +QWRVDAVAVLVPRTGGVHFDLVQDVRP +>GCF_023573625_PROKKA_00862 +M----TGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGEL +DIVAHHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVR--AHAADR--RGT +PWRVDAVAVLVPRTGGIRFDLLQDVRP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000788.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000788.fa new file mode 100644 index 0000000000000000000000000000000000000000..2839f4ddd50476cec2c678d26658cf137031e7c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000788.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00915 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLPLTRRHLTVNLLPAGVHKRGA +CHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPETVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHL +HDVIRAFGGEPDG-----EPPH-RPARRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTML +AERLPGILPPLDRRTALECAALRSLRGGDARVRR---RGGTSQGFDGEIDRTPPFEAPHHSASRSALVGGGSGLARPGAA +SLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQLVLAANPCPCGKGGGTGVECRCSVPERRRYA +QRLSGPLLDRVDLQVTVRPVEARQLTGAPASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGP +YAVPRAARRPADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA +>GCF_003691675_PROKKA_00634 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLPLTRRHLTVNLLPAGVHKRGA +CHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPETVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHL +HDVIRAFGGEPDG-----EPPH-RPARRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTML +AERLPGILPPLDRRTALECAALRSLRGGDARVRR---RGGTAQGFDGDIDRTPPFEAPHHSASRSALVGGGSGLARPGAA +SLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQLVLAANPCPCGKGGGTGVECRCSVPERRRYA +QRLSGPLLDRVDLQVTVRPVEARQLTGAPASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGP +YAVPRAARRPADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA +>GCF_005280335_PROKKA_02027 +MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLPLTRRHLTVNLLPAGVHKRGA +GHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPETVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHL +HDVILAFGGEPEG-----EAPQRRPVRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTML +AERLPGILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMAALVGGGANLARPGAV +SLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYPARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYG +QRLSGPLLDRVDLQVTVRPVQARQLAGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGP +YAVPRAARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET +>GCF_020097155_PROKKA_01925 +MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLPLTRRHLTVNLLPAGVHKRGA +AHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPETVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHL +HEAILAFGGRPDASVARPSGPS-GTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTML +AERLPGILPPLDDRTALETAALRSLRGLEPSAR--------------GLRRTPPFEAPHHSASMAALVGGGTGLGRPGAV +SLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAANPCPCGFGSGTGAHCRCTSLQRRKYA +ARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSRAVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGR +FAVPPEARATADRAVDRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR +>GCF_023573625_PROKKA_00863 +MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLPLTRRHLTVNLLPAGVHKRGA +CHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPETVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHL +HDVIRAFGGEPDG-----EPPH-RPARRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTML +AERLPGILPPLDRRTALECAALRSLRGGDARVRR---RGGTSQGFDGEIDRTPPFEAPHHSASRSALVGGGSGLARPGAA +SLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQLVLAANPCPCGKGGGTGVECRCSVPERRRYA +QRLSGPLLDRVDLQVTVRPVEARQLTGAPASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGP +YAVPRAARRPADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000790.fa new file mode 100644 index 0000000000000000000000000000000000000000..ebac45db412777e8d90763516c08dd80764cee87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000790.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00917 +M-APSSSVRPAPAPR-AP-SPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDYVA +GTAATAGTPPVDDDAPARHGPSAPDVLPELDIEDLRGWLAAMSGSGLARATLARRVAAVR +TFTAWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAA +HALALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRA +LQAWERLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHT +AATHLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA +>GCF_003691675_PROKKA_00636 +M-APSSSARPAPAPR-AP-SPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLRALIDHVA +GTAGTSGSPAADDDAPARHVPSAPDVLAELDIEDLRGWLAAMSGAGLARATLARRVAAVR +TFTAWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQDRVDAAAAGDDPAA +HALALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRA +LQAWQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHT +AATHLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA +>GCF_005280335_PROKKA_02024 +MASSSSSARPAAARAFAP-SPRDAAWLEAFEEHLRHERNRSPQTVRAYATDLRDLVAHVA +SGTWGGHPGTATSEAAVEADAVAPDVFAEVDVEDLRGWLAAMTDAGLARTTLARRVAAVR +TFTGWLRREGLREDDPALRLRSPRPAATLPHVLQEQQAERLLAGAQARVAEAAVGDDPAA +HALALRDAALLELLYATGARVAELSALDVDDLEPGRAVARLTGKGDRQRTVPYGAPAARA +LDAWLRLGRPRLARDGSGPAVFLGVRGGRLGVRQVRAVVDRALEGLGDTAARGPHALRHT +AATHLLDGGADLRSVQEVLGHSSLRTTQVYTHVSIDRLREGYRQAHPRA +>GCF_020097155_PROKKA_01923 +M-HPPHAHHAPGAPL-PPASARDEAWLEAFAEHLLHERGRRPRTVRAYLADLRHLAAHVT +-----------DDGA---------DAFAEVDLEDLRRWLARMRDQGLSRATVARRVAAAR +TFLGWLHRSGLRPDDPTLRLRAPAPDSRLPQVLQAEQAQRLLQAAEERVHEARRADDLHG +AALAARDVALFELLYATGARVAEVAALDVDDLDLDRRTARLTGKGDRQRTVPFGAPAAAA +VERWLRVARPVLATEHSGVALLLGARGGRADVRVLRGAVDRALERLGDTAARGPHALRHT +AATHLLDGGADLRSVQELLGHSSLQTTQRYTHVSVDRLRDGYRRAHPRA +>GCF_023573625_PROKKA_00865 +M-TPSSSARPAPVPR-DP-SPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDHVA +GTAGTSDTPAVDDDAPARHASSAPDVLAELDIEDLRGWLADMSGSGLARATLARRVAAVR +TFTAWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAA +HALALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRA +LQAWQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHT +AATHLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000792.fa new file mode 100644 index 0000000000000000000000000000000000000000..8dfb6da942b1a24099bfecb8789b94ef2cb2b529 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000792.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00919 +MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS +EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD +TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS +GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH +VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV +>GCF_003691675_PROKKA_00638 +MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS +EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD +TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS +GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +IESEEHAKARGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADIAPEDVCH +VNAHATSTPKGDAPEYLAMRAVFGEHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV +>GCF_005280335_PROKKA_02022 +MTRTAVITGLGATTPIGGDVPTFWSNALKGVSGARTMEHEWVEELGLPVTFAAELAVPTA +DVLSKVEQKRQDPGTQMATVAAREAWRDAGLEGVELDGDRLAVAFGTGIGGVWTLLDGWD +ILRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLIRS +GQADVVICGASEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +VESEEHARARGARVYAELAGTGVTSDSHHITAPEPEGLGATRAMRAALKAADLTPEDVCH +VNAHATSTPKGDAPEYLAMKAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLENQDPEIPLNVVTGSPAQLPEGPRVAVKNSFGFGGHNAVAVFRSV +>GCF_020097155_PROKKA_01921 +MTRTALITGLGATTPIGGDVPTFWANAQKGVSGAATMQHEWVEQYDLPVTFAAELAVPTS +EVLSKVELKRQDPSTQMATVAAREAWADAGLADADVDPERLAVAMGTGIGGVWTILDAWD +ALRERGPRRVMPMTVPMLMPNGAAGALSLEFGARAGARTVVAACAAGTEALDTALTLIRT +GQADVVLCGATEAAVHPMPMAAFAAMQALSKRNDDPQSASRPYDVDRDGFVLGEGAGVMV +VESEEHAAARGARVYARLAGTGVTSDSHHITAPEPEGLGATRAMRRALADAGLRPEDVGH +VNAHATSTPKGDAPEYLAMKAVFGTGLDDVLVSATKSQTGHLLGASGAIESILSVLAVHH +GVAPVTINLENQDPEIPLNVVTGTPAALPADRRVVVKNSFGFGGHNAVAVFTGV +>GCF_023573625_PROKKA_00867 +MTRTAVITGLGATTPIGGDVPTFWSHALQGVSGARTMEHDWVEKYELPVTFAAELAVPTS +EVLSKVEQKRQDPATQMATVAAREAWKDAGLEGAEVDGDRLAVAFGTGIGGVWTLLDGWD +TLRERGPRRVLPMTVPMLMPNGAAGALSLEFGARAGARTVVSACAAGTEALETALLLVRS +GQADVVICGAAEAAVHPLPMAAFAAMQALSKRNDDPQAASRPYDVDRDGFVLGEGAGVMV +IESEEHAKTRGARVYAELAGAGVSSDSHHITAPEPEGLGATRAMRAALRSADITPEDVCH +VNAHATSTPKGDAPEYLAMRAVFGDHLDQVQVSATKSQTGHLLGASGAIESILSVLAVHH +GQAPVTINLDHQDPEIPLNVVTGSPARLPEGPRVAVKNSFGFGGHNAVAVFRSV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000793.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000793.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a14853933ccd817757d68ae1d75479ee00923eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000793.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00920 +MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA +>GCF_003691675_PROKKA_00639 +MASKEEILAGLAEIVNEETGLDAAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA +>GCF_005280335_PROKKA_02021 +MASKEEILAGLAEIVNEETGLDTADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDNAQA +>GCF_020097155_PROKKA_01920 +MASKEEILAGLAEIVNEETGLETADVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDQAQA +>GCF_023573625_PROKKA_00868 +MASKEEILAGLAEIVNEETGLDTAEVQPEKSFTDDLDIDSISMMTIVVNAEDKFGVKIPD +EEVKNLKTVQDAVDFIDGAQA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000795.fa new file mode 100644 index 0000000000000000000000000000000000000000..5fb1dc116f0d03fcf3fcb3a5e9a75a181b47d68e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000795.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00922 +MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR +ARVIPLKVAGAFHTEHMRPAVDDLATHVAGLSPSDPRLPLLSNRDGETVESGTDVLARIV +DQVTRPVRWDLCMATMAARQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHSA +>GCF_003691675_PROKKA_00641 +MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIDAAGLTPANVNGAGQIVAAGTAEALGALAESAPAR +ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV +DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHSA +>GCF_005280335_PROKKA_02019 +MLAIVCPGQGSQTPGFLSPWLELDGTRALLESLSDAAGVDLVRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPASTLVAGHSVGEITAAAVTGVLSPADALALVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIEAADLAPANVNGAGQIVAAGTAEALAALGESAPAR +ARVIPLKVAGAFHTEHMRPAVEELAAHVAGLSPADPRLTLLSNRDGQAVDAGAEVLSRIV +DQVTRPVRWDLCMEAMAEREVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHTA +>GCF_020097155_PROKKA_01918 +MLAIVCPGQGSQTPGFLAPWRELEGVPSLLDRLSAAAGVDLTAHGTVSDEETIKDTAVAQ +PLIVAAGLVAADVLGLDALAPDRVLAAGHSVGEITAAAVAGVLSPEDALALVRVRATGMA +EAAAATPTGMAAVVGGDQDEVLAAVEAAGLTPANVNGGGQIVAAGTQDALDALAAQPPAR +ARVIPLKVAGAFHTEHMRPAVDALAAHVTGLSPADPRLTLLSNREGAAVASGTEVLERIV +NQVTRPVRWDLCMEAMAERGVTGIMEVLPGGTLAGLAKRGLKGVPSLAVKAPDDLDAARA +FIAEHTA +>GCF_023573625_PROKKA_00870 +MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR +ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV +DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHSA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000796.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000796.fa new file mode 100644 index 0000000000000000000000000000000000000000..932d170fbd11615d8304706832eb0dd1e57a9715 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000796.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00923 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERP-TSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAE +RDQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRA +TALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDA +RAVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPE +RALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRL +KRVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD +>GCF_003691675_PROKKA_00642 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERP-TSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAE +RDQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRA +TALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDA +RAVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPE +RALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRL +KRVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD +>GCF_005280335_PROKKA_02018 +MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA +LQGFISWFDRP-KTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAE +RDQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRA +TALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDA +QVVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPE +RALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRL +KRVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA +>GCF_020097155_PROKKA_01917 +MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA +LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE +ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA +TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP +DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE +RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL +RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL----- +>GCF_023573625_PROKKA_00871 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERP-TSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAE +RDQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRA +TALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDA +RAVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPE +RALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRL +KRVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000801.fa new file mode 100644 index 0000000000000000000000000000000000000000..b923cb15a31cc53d14ce1dc36d16525e1cb4904c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000801.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00929 +M----TGAAYLVAAAVVAGLVTFCLRAVPFALLQPLRESVLAARLAVWMPAGVLTILALV +MLLDAAALAPGEPVDGTRVAHALFAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA- +>GCF_003691675_PROKKA_00648 +M----TGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALV +MLLDAAALAPGEPVDGTRVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA- +>GCF_005280335_PROKKA_02011 +M----TDAAYLVAVAVVAGAVTFALRALPFALLRPLRESVLAARLAVWMPAGVLTILAVV +MLLDAAALAPGAPVDPRRVAHALIAAVVTVAVHLLGGRRTLLSIAAGTLAYVLLVNLA- +>GCF_020097155_PROKKA_01910 +MIDGVVHPGYIVAAALVAGGVTFLLRALPFVLLRPLRESRLVARLAVWMPAGILTILAVV +MVLDSAALAPGDPVDWPRVGCTLAAGAVTVLVHLLGGRRTLLSIGAGTLAYVLLVNLAL +>GCF_023573625_PROKKA_00877 +M----TGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALV +MLLDAAALAPGEPVDGARVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000802.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba424ca65a7994b6e29925b11b8c361688e05f83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000802.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00930 +MGLLRDLLTRRS--ARDRSSDPPATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGG +RNVFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAER +GLHLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAASRA +WAERLGEPAPPPVRPG-------------------------------------------- +-------------------- +>GCF_003691675_PROKKA_00649 +MGLLRDLLTRRS--ARDRSSDPTATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGG +RNVFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGEKSNGVGPAQITWPPYFAQAAER +GLHLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAATRA +WAERLGESAPPPVRPG-------------------------------------------- +-------------------- +>GCF_005280335_PROKKA_02010 +MATTPS-VGRMSWFPRRRAASAPRALAARLENADAIAAAARRADVPLPVAAALAQLESGG +RNVFGHDAGGVHAAPRGTDVPVTRELFEELEARVAAGETSNGVGPAQITWPPYFAQARRR +GLRLWEPEDNMAFGLEILRGHLGGDLTEEGIARAGTLYNAGTLQGGVTDYGRRLARASRD +WARRLGEPAPPSSSPGRGAGRDGDRGRARSGAPGRTHVIEPGDTLWAIARANGTDVATLR +RLNPDLVPEALAVGAPVRLP +>GCF_020097155_PROKKA_01908 +M-------------------DPVTVLSASLAHPEAIVAAAGRARVPVSVAAALAELESGG +RNVFGNDVGGVFSSPGAPDVEVTPERVAELRRRVADGERSNGVGPAQITWPPLFDRADAE +GLDLADPEDNMTLGLSLLRDSARGDFSVAGLERAGTLYNAGTLAGGVTDYGRRLAAAAAA +WERRL-------TARG-------------------------------------------- +-------------------- +>GCF_023573625_PROKKA_00878 +MGLLRDLLTRRS--ARDRPSDPTATLGRHLDNAATIVAAARRADVPLPVAAALAELESGG +RNVFGHDAGGVHSAPRGTDVPVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAER +GFRLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLTHGVTAYGRRLAAATRV +WAERLGELAPPPVRPG-------------------------------------------- +-------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000803.fa new file mode 100644 index 0000000000000000000000000000000000000000..62af50d3f559419bbeaf612bbebb8de23d849c53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000803.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00931 +MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQ-WSILALFQDELAGKAAAR +TLDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILP +ATDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG------- +>GCF_003691675_PROKKA_00650 +MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQ-WSILALFQDELAGKAAAR +TLDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILP +ATDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG------- +>GCF_005280335_PROKKA_02009 +---------------------------------MLFLQDGQ-WSILGLFQDELAGKATAR +TLDALLQSVTCLRMGGRDVLDGADTPRPGVEWAGYDREFEEADVAESRDVEPHGRIWILP +ATDGATVGLKLPGHRRYHDAVAQFADVDAARAAVAAIDELLGVGPRG------- +>GCF_020097155_PROKKA_01907 +MPATPHGFWKLPAPSDAGPRHLAVITGGEAEQTMLFLQDAAGWHVLALFQDELAGRTTAR +TLDRLLQSVTYLRMGGADLMDGADTERPGVEWAGYDREFEEQDAADETAADPAARLWILP +ATDGASVGLKLPGHPRYADAVAQFVDAGTARAAVDAVDALIGARRPGAARPAAD +>GCF_023573625_PROKKA_00880 +MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQ-WSILALFQDELAGKAAAR +TLDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILP +ATDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000812.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e20f00f7509839021e07d01ac39a95e25da6eb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000812.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00940 +MLILLPPSEGKTAPRSGAPLDLDALALADDAAVTGARADLLTRLAAVSAAPDALAALGVG +ASLTGEVEANTRLASAPAAPGHRVFTGVLFDALDHASLSAAAKRRARASVLVFSALFGAT +ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGD- +---GHGWEVELARPSGAKPGALRVILPEG +>GCF_003691675_PROKKA_00659 +MLILLPPSEGKTAPRSGAPLDLDSLALADDAAVTGARADLLTRLAAVSAAPDALTTLGVG +ASLAGEVEANTRLAVAPAAPGHRVFTGVLFDALDHASLSAAAKRRARLSVLVFSALFGAT +ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAEQTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLDRVADVVARAGD- +---GPGWEVELARPSGGKPGALRVILPEG +>GCF_005280335_PROKKA_01999 +MLILLPPSEGKTAPRSGAPLRLEDLALAEHDAVTAARRDLLARLAEASAAPDALETLGVG +ASLAGEVAANTSLATAPAAPGHRVFTGVLFDALDHASLSPGAKRRARDAVLVFSALFGAT +SLADRIPAHRLSVGARLPGLPGLAAHWRPVLAPALDAVAQADGGPIVDCRSGGYAAMWKA +PAERTATVDVFQLRGGEPTVVSHFAKHTRGLVARALLEAGARATGALDRAAEVVAAAGAG +DVEGRRWDVELVAPSGAKPGSLRVVLPEA +>GCF_020097155_PROKKA_01896 +MLILLPPSEGKTGPRSGRPLDLSSLTLADDDAVTAARAELLPRLAEASARPDALDILGVG +ASLADEVAANTRLATAPSAPARKVYTGVLFEALDLTSLSPAAKRRAASDVLVFSALFGAT +TPGDRIPAYRLPVGARLPGMPGLAAWWRPRLAPALDGYAEARGGVVVDCRSGGYAAQWKA +PAERSLAVDVFQLRAGRRTVVSHFAKHTRGLVARALLEAGSRAAGTPATAADVVARAGDG +GVPGQRWEVELVPPTGRKAGSLQVILPEE +>GCF_023573625_PROKKA_00889 +MLILLPPSEGKTAPRSGAPLDLESLALADDAAVTGARADLLTRLAAVSAAPDALTALGVG +ASLAGEVEANTCLASAPAAPGHRVFTGVLFDALDHVSLSSAAKRRARASVLVFSALFGAT +ALADRIPAFRLSVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGD- +---GHGWEVELARPSGAKPGALRVILPEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000817.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000817.fa new file mode 100644 index 0000000000000000000000000000000000000000..babda17d423bfdbdb6a4bd83f47e1e2e18dba7c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000817.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00956 +MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAEVVSGAQA +>GCF_003691675_PROKKA_00669 +MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAEVVSGAQA +>GCF_005280335_PROKKA_01931 +MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA +LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF +LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY +RAAVMAPSPGPTSEEAQAIARVVAEAQA +>GCF_020097155_PROKKA_01883 +MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA +LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF +LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY +REAVMVPAPGPTSEEARAIAEVVSGAQA +>GCF_023573625_PROKKA_00902 +MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAQVVSGAQA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000819.fa new file mode 100644 index 0000000000000000000000000000000000000000..004e50f1999b6e532cb5468a08c5f45d7acbfb8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000819.fa @@ -0,0 +1,75 @@ +>GCF_002008305_PROKKA_00959 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------TSHPR--------------SPA-----PSRPSGRWVGLLVGLTVVAAAVGVLTKQ +WCRVNGWAAPGVHAHMCYSDFAQLFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDV +NAIGVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGRPTLAGLLIGLGTATKLY +PLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTAFDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTT +LQNGLFLVCCVGIAYLALAARHRPRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGV +WMESARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGAPEIAPGVAEDPHAGVFT +GARDRLLLPPAGLGLQPL-GESAGR +>GCF_003691675_PROKKA_00672 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------TSHPR--------------SPA-----PSRPSGRWVGLLVGLTVVAAAVGVLTKQ +WCRVNGWAAPGVHAHMCYSDFAQLFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDV +NAIGVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGRPTLAGLLIGLGTATKLY +PLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTAFDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTT +LQNGLFLVCCVGIAYLALAARHRPRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGV +WMESARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGAPEIAPGVAEDPHAGVFT +GAPDRLLLPPAGRGLQPL-GGSADR +>GCF_005280335_PROKKA_01929 +MRRAGLAPTPAPPGLPERETAPPEPAVAVRQGTWAAVLIMVGSWGVGWLPMTPDSVFSGSTLLNPLRVNLPGVLASTLLL +ASGSLLLVRAWLVLGRSLRGRWEGHGRLVSRAAWQWSAPLMLALPIFSRDVFSYLQQGRLFALGLDPYTQGVSALPGWFM +QGADSIWAESPSPYGPLFLLCAEAIWRVTGGQIELSVTAFRLLALAGLALCLWAVPRLAEAAGRCGAWAAWVCVANPLFL +LYMIAGVHNDALMSGLMLAGIVLMVRVPRRRLHALWGIVLIALSVAIKPLTALVLPFVGLLLPTGWDRFRRADPGLRRRD +RLGPWITTAAIALAVLTILGAGSRLWFGWVPAMLTSGDAAFPYAPVGVLGLLLGAAADGLAGLPARAVAGGFYTLMTLAA +LGFGAWLALRRRAPEPVSAAAAVLFVAVVTAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV +DQISVAQWLPVAAVRALTAVVVLAGIAWIVVRDPATAPLFPGRRRPPREVVEPREAVGPREPGAPPGPPTAAPDAEFPPD +ALAADPDRRRRPAPDRRPARPGETVTSQPRRPADTRTGSAAAPPSPA-----ALRPGPRWIGILVGLTAVAAVVGLLTKQ +WCRVNGWAAPGVHVHMCYSDFAQLFPTRGLSDGYFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPDSGDLHERTVMYFDV +NALGVVLCWVVLVIATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAHRPTLAGLLIGLGTALKLY +PLFFFGAILVLALRTGRWRGLITSLAAGVAAWLAVNVPFMLTAFDQWSRFYTFSGDRAVSFSSTWLSLAWTGWSGETFST +LQNGMFALFCAGIAWLGLSARHRPRMAQLCFLIVASFLLWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGV +WMESARITSGGAFADGAWWITAWYASGIVAHIVALVWLMVTVVKDILDPSRDPVRRTALAQGAPTIAPGVAEDPHAGVYA +GAPDRLVLPPAGRGLQPAEGATSGS +>GCF_020097155_PROKKA_01880 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------SSHPR--------AADAAPRPAAGLRPAGRPSPRWIGVLIAVTAAAAVVGLLTKQ +WCRLNGWATPGVHVHMCYSDFAQLFPTRGLSDGYFPFYTPLPEEQWMEYPALLAVVAGASSWLVPSTGTLAERTVTYFDV +NAAGVVLCWMAVVVATAFTARGRSKDALLVAVAPGIILTSMLNWDLWAVMLAALALWAWSEDRPVLSGLLLGLGAAMKLY +PLFFFGALLVLALRTGRWRGFLGALAAGAAAWLAVNVPFMLTAFDQWSRFYTFSGDREVSFSSMWLAFTWTGLSGSAFSV +ISNGLFALCCVGVAYLGLSSRHRPRLAQLCLLIVAAFLLLGKVYSPQFVMWLIPLVVLATPRRKQFWIWQAAEFFHWAGV +WMESARITSGGEFGGT--WVTVWYASGIVLHMATLIWICVTVIRDIRDPERDPVRRSALEQGVEPLAPGVAEDPNAGVFT +GAADRFLLPPAGHGLQPT------R +>GCF_023573625_PROKKA_00905 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------TSHPR--------------SPA-----PTRPSARWVGLLVGLTVVAAAVGVLTKQ +WCRVNGWAAPGVHAHMCYSDFAQLFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWFVPASGDLHERTVTYFDV +NAIGVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGRPTLAGMLIGLGTATKLY +PLFFFGAIFVLALRTGRWAGFVKAAVAGAAAWLAVNLPFMLTAFDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTT +LQNGLFLVCCVGIAYLALAARHRPRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGV +WMESARITSDGAFAGGAWWITAWYASGIVAHVVALVWLMTTVVKDVLDPVRDPVRRTALDQGAPEIAPGVAEDPHAGVFT +GARDRLLLPPAGRGLQPL-GESAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000824.fa new file mode 100644 index 0000000000000000000000000000000000000000..a53855ed7575a04b286de0a97dc09e0471076251 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000824.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00966 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVAVEP--VRPEALPTGAPTLPDHSARLGAPLAVLRP +RVAKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATP------------ +GTP------AAPGQAASFYDAVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRR +LLMFLEQYWGGPRTYSEERGHPRLRMRHAPYRIDPAARNAWLRHMRAAVDTLELSPLHEA +ELWDYLERAAHSLQNSA +>GCF_003691675_PROKKA_00679 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVAVEP--VRPEALPTGTSTLPDHSARLGAPLAVLRP +RVAKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPTGATP------------ +GTP------AVPGQATSFYDAVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRR +LLMFLEQYWGGPRTYSEERGHPRLRMRHAPYRIDPAARDAWLRHMRAAVDTLELSPLHEA +ELWDYLERAAHSLQNSA +>GCF_005280335_PROKKA_01921 +MKHTFALRTEWTGNRGTGTSGVRDYDRSVVIQDAAVGEIHASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGLVVTGMACAAEGVLEVDGDGAGRFAAVTLRPEVALQDEAD +RERADALHAEAHRLCFIANSLSAPVSVEPAVAGSGAAASGGPALPDHSSRLGAPLAVLRP +RVAKRPSQVTGLAERPTEVEPVMKAGAPAPVDQMQARDAAAGRA-ASP------------ +ATPAPAAETAAPGQAASFYEAVGGRETFDRLTAEFYARVREDELLSPMYPQDDFEGAQRR +LLMFLEQYWGGPRTYSEERGHPRLRMRHAPYRIDPAARDAWLTHMRAAVDTLGLSPLHEA +ELWDYLERAAHSLQNSA +>GCF_020097155_PROKKA_01869 +MKHTFSLRAEWTGDRGTGTTGVRDFDRSVVIQESEVGEIHASAARPFRGDAAKWNPETLL +LGALAECHVLSYLHAAATGGLVVTGMTCAAEGTLEVDSDGAGRFASITLRPEVALRDEAD +RARADELHAEAHRMCFIANSISAPITVEA-GPGSSPTRGDGAALPDHSARLGAPLAVLRP +RVANRPTRVTGLADRPTEAEPVVRADAPSGAEQARARDEATARG-ERPPSATPIATPAPG +ATPAASPATAAPGQATSFYEAVGGHPTFEKLVHVFYQGVREDPLLAPMYPHQDWDGAEER +LRMFLEQYWGGPRTYSERRGHPRLRMRHMPFTVDPAARDAWLRHMRAAVDAVELSPLHEA +ELWDYLERAAHSLQNSA +>GCF_023573625_PROKKA_00912 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFIAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVTVEP--VRPEALPTGTPTLPDHSARLGAPLAVLRP +RVAKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATP------------ +GTP------AAPGQATSFYDAVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRR +LLMFLEQYWGGPRTYSEERGHPRLRMRHASYRIDPAARDAWLRHMRAAVDTLELSPLHEA +ELWDYLERAAHSLQNSA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000827.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000827.fa new file mode 100644 index 0000000000000000000000000000000000000000..2be1001e78635289f2b6889ce83048da989943b6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000827.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00974 +MMHGS---RPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVW +DLDLQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLE +DATEEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKH +AAVGFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLD +AVEAGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRR---------SR +LFAGRETAR +>GCF_003691675_PROKKA_00688 +-MHGS---RPALRRAASALAGRRPLPLHGATVLVTGGASGIGRLIALGAAHRGAGRVVVW +DLDLQGVEAVAAEIRSQGADARAERVDVTDAAAVEAAAAGAGEVDVAVNNAGVVTGAPLE +DATEEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKH +AAVGFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPHHVAQEVLD +AVEAGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRR---------SR +LFAGRETAR +>GCF_005280335_PROKKA_01916 +-MPRSRTPRPALRALAGALPRRRRLPLRGTAVLITGGASGIGRLMALGAARRGAARVVVW +DLDLSAAEAVAAEARALGAEAVAERVDVTDAAAVEAAAARAGAVDVAVNNAGVVTGARLE +DATEEGIRRTFEVNALAPYWLTRAVLPGMKARDRGAVVVIASAAGLVGVARQTDYSATKH +AAVGFAESLSAELRKDGSAVTALAVCPFYIDTGMFDGVRSRIPWLLPVLRQEEVAEQVLD +AVEAGRTRLPLPRAVGLLAPLRALPTPVFDRAMDVMGVNDTMDGFTGRRPAVDVPAPDPR +VFAPDGAAR +>GCF_020097155_PROKKA_01863 +-M------TPILNR----LRGRRPLPLAGRAVLITGAGSGIGRLMALEAARRGAAVVHVW +DRDDAAARTVAAEVAALGARGEAACVDVTDTAAVEAAAARAEAVDVLVNNAGVVTGTPLL +ETTEEGIRRTFEVNALAGYWTTRALLPGMLERGRGAVVTVASAAGLVGVARQTDYSASKH +AAVGFAESLRAELRRADAPVTSLVVCPFYISTGMFAGVRTKVPALLPILEPEAVAAQVVD +AVEAGRERLVLPPAVQLIAPLRALPVPAFDRVMDVLGVNRAMDGFTGRR----------- +--------- +>GCF_023573625_PROKKA_00917 +MMHGS---RPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVW +DLDLQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLE +DATEEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKH +AAVGFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLD +AVEAGRTRLLLPRAVGLIAPLRALPAPVFDLAMDVLGVNATMDGFTGRR---------SR +LFAGRETAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000832.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a96e9f672987a6ab4b211580589b513fdaeb0fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000832.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00980 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHD-A +DILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIF +DGAVALADFPYFYEIKRARTTDPQFD +>GCF_003691675_PROKKA_00694 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHD-A +DILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIF +DGAVALADFPYFYEIKRARTTDPQFD +>GCF_005280335_PROKKA_01910 +MSENT-QPVVDFYFDPTCPFAWITSRWILEVEKVRDIQVKFHQMSLYMLNEGRDLPEDYR +RSTDRGLIPGRGTQHVGAEH-PERLAEWYTALGTRIHNEGQKDYEAALTGAAVDLGLDPA +PILAATETDAEDERLREKQRAAEELVGNDVGTPVVSFNGTAFFGPVLTRIPRGEEAGRIF +DGAVALAEYPYFYEIKRARTTDPQFD +>GCF_020097155_PROKKA_01857 +MSENT-APVVDFYFDPTCPFAWITSRWILEVEKVRDLSVTFHQMSLYMLNEGRELPEDYR +RHTDRGLMPGRATLHVGEHH-PELLSDWYTAVGTRIHNEGNQDYEAVVTGAAAELGLDAA +PILEATRTDAADDDLRAKQRAAEELVGNDVGTPVVSFDGTAFFGPVMTRIPRGEEAGEIF +DAAVRLAQFPYFYEIKRARTTDPQFD +>GCF_023573625_PROKKA_00923 +MTDTTQQPTVDFYFDATCPFAWITSRWILEVQKVRDVRVVFKIMSLAVLNEGRDLDPDYL +ARLEKAWLPARAAVQVRERHGAEALGPWYTAVGTRIHEQGRTDYEAVVAEALEELGHD-A +DILDAARTDVADEQLRASQKEAEDLVGNDVGTPVVAFNGTAFFGPVMTRIPRGEEAGRIF +DGAVALADFPYFYEIKRARTTDPQFD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000833.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0688fe6652250e4339aea7df0e7ea22c66d2593 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000833.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00981 +MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARS +>GCF_003691675_PROKKA_00695 +MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARS +>GCF_005280335_PROKKA_01908 +MRRASAPRTDTAGATGTGARRMAAALAGMGVLHFARPKPFDGLIPPALPGPARAWTVGSG +VAELAVAGMLAAPRTRRAGGRAAQALFLGVWPGNAWMAWRWRGRSWPWRALALGRLPLQV +PMIRAAGRIARG +>GCF_020097155_PROKKA_01856 +MKPTPDPAPAGRRASDGSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPHTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARR +>GCF_023573625_PROKKA_00924 +MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000836.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea51e8e70fdc4ce44a9deb0461049292d94f789d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000836.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00984 +MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER +VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD +AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE +APRGAAGGR +>GCF_003691675_PROKKA_00698 +MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER +VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD +AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE +APRGAAGGR +>GCF_005280335_PROKKA_01905 +MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER +VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD +AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE +APRGAAGGR +>GCF_020097155_PROKKA_01852 +MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER +VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD +AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE +APRGAAGGR +>GCF_023573625_PROKKA_00927 +MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER +VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD +AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE +APRGAAGGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000837.fa new file mode 100644 index 0000000000000000000000000000000000000000..be2c742a545f2c4ceea8f9b9aa8b88c7d7e6c41c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000837.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00985 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEGFDSIPSDDLHGRFRWWGLYT +QRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQLRVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRL +ESVGLSTTEACGDVPRVILGSPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNKARMKYLLEDWGPERFRTVLE +EEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAPVVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVER +DRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDYVERVVRRYDEQREPGETFAR +WAHRVDEEALR +>GCF_003691675_PROKKA_00699 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTTPLNHNEEFKQQDDGLNVRERIEQVYAREGFDSIPSDDLHGRFRWWGLYT +QRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQLRVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRL +ESVGLSTTEACGDVPRVILGSPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNKARMKYLLEDWGPERFRTVLE +EEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAPVVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVER +DRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFAR +WAHRVDEEALR +>GCF_005280335_PROKKA_01904 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------MVLDVEG +DRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQIHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFAR +WAHRVDEEALR +>GCF_020097155_PROKKA_01851 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAREGFDSIPSDDLHGRFRWWGLYT +QRKQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQLRVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRL +ESVGLSTTEACGDVPRVILGSPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNKARMKYLLEDWGPERFRTVLE +EEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAPVVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVER +DRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFAR +WAHRVDEEALR +>GCF_023573625_PROKKA_00928 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEGFDSIPSDDLHGRFRWWGLYT +QRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQLRVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRL +ESVGLSTTEACGDVPRVILGSPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNKARMKYLLEDWGPERFRTVLE +EEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAPVVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVER +DRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDYVERVVRRYDEQREPGETFAR +WAHRVDEEALR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000838.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000838.fa new file mode 100644 index 0000000000000000000000000000000000000000..6afa8be66a625ac6cdda20d35493fb7895373950 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000838.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00986 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>GCF_003691675_PROKKA_00700 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSLDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>GCF_005280335_PROKKA_01903 +MSTVPPTRPTEELERLQALAESGAAELGWDAPAAAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWTGTAKTECGIH +V +>GCF_020097155_PROKKA_01850 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>GCF_023573625_PROKKA_00929 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHSMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000840.fa new file mode 100644 index 0000000000000000000000000000000000000000..6562bccec925c49a4e52f39e91fb5d0cf7f75bc3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000840.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00988 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPHDGATLAAGMVRGGDEA +>GCF_003691675_PROKKA_00702 +MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPHDGATLAAGMVRGGDEA +>GCF_005280335_PROKKA_01901 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPQDGATLAAGMVRGGDEA +>GCF_020097155_PROKKA_01848 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPQDGATLAAGMVRGGDEA +>GCF_023573625_PROKKA_00931 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPHDGATLAAGMVRGGDEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000845.fa new file mode 100644 index 0000000000000000000000000000000000000000..1222dba13f8ff28875d31ad1f3e29844ee219065 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000845.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_00995 +M-----RGDAPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTSTARMVEAVLRAYGLRT +GRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAELEAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVG +LGGVTDATNVADAVVSVVTPISLDHTDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAAQAADVPFRFEGVE +FGVLERSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLREGLSQVTSPGRLEVLR +TAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAPGMLAALYRAFGDDVEDLAVTQSSSARAIPAGELAR +MAVDAGWPEDDVYATESVPDALEWAVGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLD +PADL----------------LDAVGLADADEDDLDPEILELLEDRDDAGARRRPEED----------------------- +-------------------------------------------------------------------------------- +------------------------------------------------R +>GCF_003691675_PROKKA_00709 +M-----RGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTSTARMVEAVLRAYGLRT +GRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAELEAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVG +LGGVTDATNVADAVVSVVTPISLDHTDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAARAADVPFRFEGVE +FGVLERSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLREGLSQVTSPGRLEVLR +TAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAPGMLAALYRAFGDDVEDLAVTQSSSARAIPAGELAR +MAVDAGWPEDDVYATESVPDALEWAVGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLD +PADL----------------LDAVGLADADEDDLDPEILELLEDRDDAGARRRPEED----------------------- +-------------------------------------------------------------------------------- +------------------------------------------------R +>GCF_005280335_PROKKA_01894 +MSGAP----APQTVEQVYADLLARAPENAMEPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTSTARMIEAVLRSYGLRT +GRYTSPHLQSVTERISIDGAPVSDETFVRVWGEILPIVQAVDAELEAEGRPRLTYFEAVTTLGFAVFADEPVEVVVLEVG +LGGITDATNVADGAVSVVTPISLDHTDLLGETEAEIAEEKAGIVKPGGALVSAVQERDAAQVLLEAARAADVPFRFEGVE +FGVLERSLAVGGQQVSVRGLAAEYRDLFLPLHGEHQAQNLAVAVAALEMFLGGGDRPLDEELLREGLAQVASPGRLEVLR +TAPTLIVDAAHNPDGVRATARAVQEAFGFTRLALVVGILREKDAPAMLEALFRAFGDDVEDLALTQSSSPRAIPAGDLAR +MAVDAGWPEADVFAAESVPDALEWAVGRAEALETSADELASGTGGGVLVLGSVTLAAEVRALVGEPRHAGPVTVAARGLD +PADLPRRRRPGRGGRGRPGPRDPRAARGPRRRRLPPPHRGGPMSTPQPGTGRTPEEDERFGDESWRPERETRAQRAWRPG +TRRRRRSVRALFTSTVLMLEAVVIFFLGMMLFGMNRDQPGAVWFIAGYTLLAAVAVLTCALVRRPVGIAIGWAIQAVLVL +SGFWEYSMFVVGALFALTWAYAVIKGGGMDVENAERDRLQAEWEAEHGQ +>GCF_020097155_PROKKA_01841 +M-SAPAEGRVPGTVEEVYADLLARAPEHRMEPRLDPVRRVLALLGDPQHAAPVIHLTGTNGKTSTARMIEAVLRAYGLRT +GRYTSPHLERVTERISVDGEPVADEDFVRVWGEILPMVHTVDAELEAAGEPRLTYFEAVTVLGFAVFADAPVEVVVLEVG +LGGITDATNVADGAVSVVTPISLDHTDLLGDTEAEIAEEKAGIIKPGGFLVSAAQDADAAQVLLEAARAADVPFRFEGVE +FGVLERRLAVGGQQVDVRGLADEYRELFLPLHGAHQAENLAVAVAALEAFLGGGQRPLDVELLREGLAQVTSPGRLEVLR +TAPTVVVDAAHNPDGVAVTARAVQEVFSFTRLALVVGVLQEKDARTMLEVLHREFGDLISDVALTQSASPRAIPAGDLAA +LAVDAGWPEDDLFITESVPDALEWAVGRAEAVETSADALASGTAGGVLVLGSITLAAEVRSLLGAPAHAGPVTVAARGMD +PADL----------------LAAVGLEDDDADAVDPEVLELLDDREE--------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------HTR +>GCF_023573625_PROKKA_00938 +M-----RGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTSTARMVEAVLRAYGLRT +GRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAELEAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVG +LGGVTDATNVADAVVSVVTPISLDHTDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQALLEAARAADVPFRFEGVE +FGVLERSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLREGLSQVTSPGRLEVLR +TAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAPAMLAALYRAFGDDVEDLAVTQSSSARAIPAGELVR +MAVDAGWPEDDVYATESVPDALEWAVGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLD +PADL----------------LDAVGLADADEDDLDPEILELLEDRDDAGARRRPEED----------------------- +-------------------------------------------------------------------------------- +------------------------------------------------R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000847.fa new file mode 100644 index 0000000000000000000000000000000000000000..947dc918566097f333064951012ab8c738445145 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000847.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00998 +--------MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIII +IVERTLLTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLL +AGARFARWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN +LQTGTLPAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID +>GCF_003691675_PROKKA_00712 +--------MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIII +IVERTLLTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLL +AGARFARWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN +LQTGTLPAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID +>GCF_005280335_PROKKA_01892 +--------MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVI +IVERSILAADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLF +AGARFARWYWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN +IQTGTLPASPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD +>GCF_020097155_PROKKA_01838 +MDVTETAENPPAP-----RAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIII +IVERSILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLF +AGARFARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRN +LQTGALPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR +>GCF_023573625_PROKKA_00941 +MS------MPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVI +IVERALLTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLL +AGARFARWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN +LQTGTLPAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000848.fa new file mode 100644 index 0000000000000000000000000000000000000000..81495f1543923a66df874ced3749eaeacabbf4aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000848.fa @@ -0,0 +1,85 @@ +>GCF_002008305_PROKKA_00999 +MAANNEDTTRADERVEETAEQ----------------------AVTQTAADTADGA-EPERTAASDDAAD---------- +-PAEEPSAPTLQVDPTDPFAVPANLIEVLRTETTSRQRSED--------------------------------------- +-------EDAGESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKR +QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT +GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIK +TVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRT +KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGILIQDTPVERGRSGGEQRGEAEGRRR-RRRRG--DGEGEHA +HAAAATTT-GAEHADSEDERQRRERAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAE +AGQPAGT-------DEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAA +APEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAE-----QDDRPRRSRRRRGGRGRSRRGGEAASTEADADAE------ +-----DHGA--ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPV---PAEDAPAPRRRRSRRASS------DGVVR +PAAGAD-ASAERTADRTDAAPVEAT------------------------EPSPEESTDATEVHEQPAAPAAVEEAVMVEP +AATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQ +GAAPVMLGVGVKAADLARRGR +>GCF_003691675_PROKKA_00713 +MAANNEDTTRADERVEETAEQ----------------------AVTQTAADTADGA-EPERTAASDDAAD---------- +-PAEEPSAPTLQVDPTDPFAVPANLIEVLRTETTSRQRSED--------------------------------------- +-------EDAGESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKR +QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT +GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIK +TVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRT +KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGILIQDTPVERGRSGGEQRGEAEGRRR-RRRRG--DGEGEHA +HAAAATTT-GAEHADSEDERQRRERAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAE +AGQPAGT-------DEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAA +APEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAE-----QDDRPRRSRRRRGGRGRSRRGGEAASTEADADAE------ +-----DHGA--ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPV---PAEDAPAPRRRRSRRASS------DGVVR +PAAGAD-ASAERTADRTDAAPVEAT------------------------EPSPEESTDATEVHEQPAAPAAVEEAVMVEP +AATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQ +GAAPVMLGVGVKAADLARRGR +>GCF_005280335_PROKKA_01891 +M-AANEDTTGAEERAEQTEQTTAETSAAVAGQAAAESPVEDGGTVTQAQADAAEGADAPERTAEAADIEDEAETDTAAEP +EPDEAPGAPALQFDPTDPFAVPANVMEILRTEKSERRPARDERPARGAEDEEEAPGRSRRRRRPSRDRDQAETEAGAEDE +AVETAEGEQDAETAERGEGAVVSRRRRRRRRGDVDMELDGGEDGDPENTVTRVRAPRQALSTGSDAVQGVKGSTRLEAKR +QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSLIGNVYVGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPKKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT +GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASSTKVLAPELLYAEPDLTIK +TVRDVFNEDFSAVLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPQDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFIDMVLEANQDLVLRRLVECLGRDRT +KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGILIHDTPVERGRSGGEPRGEGEGRRR-RRRKG--AGEGEQA +QPAESTTTAGGEEVDAEDERQRRERAEAARAALHSIAKASGKVSEDEDPAEQAAPAEQAADAAEDQAAEAVEAARQDAAE +ETGEAGAQDGEGAEDEDEAPRRRRRRGRRRGRGRSEEAAE--AAEAASEDGSRDADAAP---AGQAPAADEEEA-PAA-- +-----DPVAQAEAAVTAVAEAEADAESGGEEREAEPAGDEEGARPRRARRRRGGRGRSRRGADREASTADADDEAAQPAQ +EPAQADAGAAGDRARASRAGRVGAARAARVRPGRGRGGRRAASRPAPP---PF----APRFERRCRAPGRGPGRRPGVVR +PGDPVPRGGGRRRGDRAHRGAVHGRHRGARAPGRPRPGGGGRDGRAGGGRPRPGRAGRA-----RPAARPELRARRPPSP +GAVGPVARCPRTACACRSRTPPGRHGADASRRPPPSPRPPPSRA-------------------------------PRRP- +--------------------- +>GCF_020097155_PROKKA_01819 +M----------------AADE----------------------STTQDTHETAEGSTTP---VEATEEETAAEVAESPAG +EAAEATAAPDVRFDPTNPFAVPEGLLPLIEAETVE-----------------------RRRRRPAAD----PVPEGAADD +AHADDEDDEDR--------PAVSRRRRRRRRGTVDMELAGGEDGDPEDTVTRVRAPRRALSTGPEAVQGVKGSTRLEAKR +QRRRESRSGGRRRTVITEAEFLARRESVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVDWDAAQLDGKAKKIENALKSGDTVLVQVTKDPVGHKGARLTSQISLPGRYLVYVPGGTMT +GISRKLPDVERARLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRVQWEGIQEKASSTKTLAPELLYAEPDLTIK +TVRDVFNEDFSAMLVQGEATWDSIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFIDMVLESNQDLVLRRLVECLGRDRT +KHQVAEVTSLGLVQMTRKRMGTGLVEVFSEVCEHCGGRGILIQDTPVERNRWGHEHRAEPEARRRNKRRRGTESGEGGPA +EPTAAELT--------EEERLRAERAAAARTALMSIAKASGKAADEE-------PSEEAAPRAEDAPEEAADEVRPSPAG +DAEEQG--------ESESGGRRRKRRGRRRGRGRG---GDDAARSAEEQDAPAEH---PAEAAGE-PAPAEAGA-P---- +-----DP------AETATEDADADSASDAPAAQAEADEDGRSGGRRRSRRRGGRRAESPQGSGAPASAPEASVEAEQDPE +EPAGA---AEAEEA-------------------LAAEEAPASPEPAAVVTFDGEPVAVPRRRRSRRATS------DGVSA +PRPSGM-DALEAAVDRRAEDAAAAA------------------------QRS-------------PATPAAT-------- +----PTAAP-----------EPAPAPVAGEGPAAAAPRRRSRRAVSADGATVQVQEG-AAAGGGRFTAQAAQAAPAGET- +-AAPVMLGVGVKAADIVR-GE +>GCF_023573625_PROKKA_00942 +MAANNEDTTRADERVEETAEQ----------------------AVTQTAADTAAGAVQPERTPASDDAAD---------- +-APEEPSAPTLQVDPTDPFAVPANLIEVLRTETTSRQRSED-------EDDPDTSGRSRRRRRPSREDD--RAEEGAADA +SADAEDREDASESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVSTASDTVQSVKGSTRLEAKR +QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT +GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIK +TVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRT +KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGIIIKDTPVERGRSGGEQRGEAEGRRR-RRRRG--NGEGEHA +HAAAATTT-GAEHADSEDERQRRERAEAARVALHSIAKASGKVAEDETPAQEPAPAEQAADAAEDSVAEAVEAASTGPAE +AGQPAAA-------DEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAA +APEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAE-----QGDRPRRSRRRRGGRGRSRRGGEAASTEADADAE------ +-----DHGA--ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPV---PAEDAPAPRRRRSRRASS------DGVVR +PAAGAD-ASAERTADRTDAAPVEAT------------------------EPSPEESTDATEVHEQPAAPAAVEEAVMVEP +AATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQ +GAAPVMLGVGVKAADLARRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000852.fa new file mode 100644 index 0000000000000000000000000000000000000000..b1df13dbab7d21fcafdda8a04a13249e3838d1d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000852.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01003 +MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID +RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLSRRPKDTATQQASAAVGQSKLMAHYTT +SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLSGVDVRVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT +AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS +SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQ---R +>GCF_003691675_PROKKA_00717 +MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID +RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT +SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLCKADLLVLLSDVDALYTGHPSHPDARRIPEVTSDDDLAGVDVRVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT +AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS +SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQ---R +>GCF_005280335_PROKKA_01887 +MSARRTVVTRYPTPATRGAEDPRANPVTTRDTMAAARRVVIKIGSSSLTTATGLDVAAID +RLVDVIAELRGRGTQVVLVSSGAIAAGFPHLGLDRRPKDTATQQAAAAVGQGRLLAHYTH +SFGRHETEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLVKADLLVLLSDVDALYTGHPSLPDSRRIPVVATDADLEGVDVHVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAPNAGSAFAGEDVGTWFEATGRRRSARAAWLGLT +AEVRGQLVIDDGAVAGAIDRGRSLLAAGIIGLSGRFTPGDVVEILDATGRVLARGLVQYS +SSQLPRMLGRSTSDLKEDLGAGYDGVVVHADDWVRLAPPR---R +>GCF_020097155_PROKKA_01815 +MARRPSTVHRHATPSSRGAEDPKANPVHTRADIGAARRVVIKVGSSSLTTGTGLNTDAID +ALVELVARLRGRGTQVVLVSSGAIAAGFPALGLSRRPKDTATQQAAAAVGQNRLVAYYSQ +SFARFDTTVAQVLLTAEELMRRGQYINAHRALARLLTLDVLPIVNENDAVATREIRFGDN +DRLAALTANLVKADLLVLLSDVDALYTGHPSRPGSRRIDTVTAETDLGGVDVRTPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAALASAALDGEDVGTWFSAAGRRRTARAAWLGLT +AQVRGRLTIDDGAVAGAIDRGRSLLAAGITAAEGDFTAGDVVEIADAQGTVLARGLAAYS +SSQLPRMLGRQTAQLKEEIGAGYDGVVVHADDWVRLAPTHSAFR +>GCF_023573625_PROKKA_00946 +MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID +RLVDVLAAERQKGTQVVLVSSGAVAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT +SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLAGVDVRVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGQDVGTWFSATGRRRSARAAWLGLT +AEVRGRLVIDDGAVAGAIDRGRSLLAAGITGCTGDFTPGDVVEIVDTHGRVRARGLVQYS +SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQ---R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000853.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000853.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2a30e9db2837174f0ed54e424b69f2419e255de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000853.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01004 +MQTTEST----------APQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRAR +KDAVLRHMAEALRANTAAILTANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETL +AGLPDPVGTVVRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILR +GGSAAESTNAVLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGR +ELIQRVVREARVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHR +DAEETGREVLRALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEM +AVRVVDSLGQAIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGEL +GLGAEVGISTQKMHARGPMGLEELTTTKWILRGDGQIRR +>GCF_003691675_PROKKA_00718 +MQTTEST----------APQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRAR +KDAVLRHMAEALRANTAAIITANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETL +AGLPDPVGTVVRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILR +GGSAAESTNAVLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGR +ELIQRVVREARVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHR +DAEETGREVLRALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEM +AVRVVDSLGQAIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGEL +GLGAEVGISTQKMHARGPMGLEELTTTKWILRGDGQIRR +>GCF_005280335_PROKKA_01886 +MENQEST----------APQDQSAGQEAEAPSQEVVDAIRQRAEWARLAVPELATAGRTR +KDAVLRHMAESLRSNAAAIITANQEDRARGAEAGTSAALLDRLKLDEPRVEALALGLEAL +AALPDPVGAVVRGGTLPNGVRMTQTRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILR +GGSAAQSTNAVLIQVLREALADQGFDPNVVQGIDDLGRPGVAALMATRGAVDVLVPRGGR +ELIQRVVREARVPVIETGEGNVHLYLDASAPKDMAVEIALNAKTHRTSVCNAAETLLIHR +EAEETGREVLRALMRGGVLLHVDEAAKAWLPGPTDRGDHARDAVDATEEDWGTEYLDMDM +AVRIVDSLDQAIEHIGRWSTGHTEAIVTNDLAAAEQFITEVDAAAVIVNASTRFTDGGEL +GLGAEVGISTQKMHARGPMGLEELTTTKWILRGDGQVRR +>GCF_020097155_PROKKA_01814 +M-TTEHTETEPAERVQQTPTPEQGASADGRPGADVVAEVRSRSARARAAAPELARAGRER +KDALLRSMADAVRAAAASILAANAEDLARGEENGTSAAMLDRLRLDEPRLESLAVALEDL +ASLPDPVGAVVRGGDLPNGIHMQQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNAVLLR +GGSAAEHTNAVLIQVLREALRDQGFESDLVQGIDDLGRPGVAALMSTRGAVDVLIPRGGR +ELIQRVVAEARVPVIETGEGNVHLFIDASAPADMAVDIALNAKTHRTSVCNAAETLLLHK +DAERAGREVLRALTRAGVLLHVDEASRARLPSPADRGQDAREPQAASDEDWGREYLDMEM +AVRTVDSIDEAMEHVRRWSTGHTEAIVTNDLANADRWVSEVDAAAVIVNASTRFTDGGQL +GLGAEVGISTQRMHARGPMGLEELTTTKWVLRGAGQVRR +>GCF_023573625_PROKKA_00947 +MQTTEST----------APQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAIAGRAR +KDAVLRHMAEALRANTAAILTANREDRGRGRETGTSAAMLDRLKLDEARVEALALALETL +AGLPDPVGTVVRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILR +GGSAAESTNAVLIQVLREALVDQGFDPNIIQGIDDLGRPGVAALMAARGAVDVLVPRGGR +ELIQRVVREARVPVIETGEGNVHLYVDASAPKQMAVDIALNAKTHRTSVCNAAETLLLHR +DAEETGREVLRALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEM +AVRVVDSLDQAIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGEL +GLGAEVGISTQKMHARGPMGLEELTTTKWILRGDGQIRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000859.fa new file mode 100644 index 0000000000000000000000000000000000000000..b59a51db343b1328b18203018be7c52cf632b9e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000859.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01017 +MYPTPMTF-DVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALL +KYGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPA--------------------- +----YEDDI------------------------------- +>GCF_003691675_PROKKA_00731 +MYPTPITF-DVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALL +KYGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPA--------------------- +----YEDDI------------------------------- +>GCF_005280335_PROKKA_01870 +MYPTPMTF-DVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALR +KYGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPA--------------------- +----YEDDI------------------------------- +>GCF_020097155_PROKKA_00705 +MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE +ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN +LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR +>GCF_023573625_PROKKA_00961 +MYPTPMTF-DVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALR +KYGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPA--------------------- +----YEDDI------------------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000860.fa new file mode 100644 index 0000000000000000000000000000000000000000..a064e6be72d9ebe8653b046eb3bfa687aa5b1f46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000860.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01018 +M-TATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGN +RLIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPG +ETRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGP +FAPEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEG +FLPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVT +GRAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNAD +DRIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPL +TIGEDLLKEGLSEVTKALQSA +>GCF_003691675_PROKKA_00732 +M-TATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGN +RLIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPG +ETRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGP +FAPEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEG +FLPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVT +GRAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNAD +DRIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPL +TIGEDLLKEGLSEVTNALQSA +>GCF_005280335_PROKKA_01869 +M-SSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGN +RLIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISG +QTRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGP +FAPEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEG +FLPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVT +GRAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHAD +DRIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPL +TIGEDLLKEGLSEVTKALQSA +>GCF_020097155_PROKKA_01761 +MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN +RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG +ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP +FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG +FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT +GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD +ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL +TIGEELLREGLAEVTTALQSA +>GCF_023573625_PROKKA_00962 +M-TATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGN +RLIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPG +ETRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGP +FAPEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEG +FLPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVT +GRAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNAD +DRIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPL +TIGEDLLKEGLSEVTKALQSA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000862.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e5ebfe8e4c21cdbc2eeaf6830031312e2549432 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000862.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01020 +MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSA---TASATPSPSPSPS +SARFTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEP +APSEEPTPAAA------AHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGG +DLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTY +DDGTQAAFEADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFN +NWVVQATRVA +>GCF_003691675_PROKKA_00734 +MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSA---TASATPSPSPSPS +SARFTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEP +APSEEPTPAAA------AHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGG +DLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTY +DDGTQAAFEADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFN +NWVVQATRVA +>GCF_005280335_PROKKA_01867 +------------------------------------------------------------ +------------------------------------------------------------ +-------------------MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAG +ELDPDPQTVGWYGAPQWGTDPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTY +DDGSQAVFEADADAVSVEKEALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFN +NWVVQATRVA +>GCF_020097155_PROKKA_01763 +MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP +SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA +ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG +ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY +DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN +NWVTQATRIG +>GCF_023573625_PROKKA_00964 +MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSA---TASV--------- +------------------SPSSAATTREAAVPVETQELAGTPTPSEEPTPT------EEP +APSEEPTPAAA------AHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGG +DLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTY +DDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFN +NWVVQATRVA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000863.fa new file mode 100644 index 0000000000000000000000000000000000000000..54fd190b6861dbe08ff8582df02c4aed44086491 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000863.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01021 +MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL +ESMLEGWG--VPS------DDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDRE +KNVLAAAEPEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELES +LAATLGEMGVIGSSGARTAEPSGFTGPIKIEG-TGADGGSVPSDFVPEPLQRVRSFRATQ +KPVLPSSSSPSSSSASGSASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPS +PSAS------------R +>GCF_003691675_PROKKA_00735 +MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDEVLGKDGVDQEIRATAERMKSEHEERARRL +ESMLEGWG--VPS------DDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDRE +KNVLAAAEPEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELES +LAATLGEMGVIGSSGARTAEPSGFTGPIKIEG-TGADGGSVPSDFVPEPLQRVRNFRATQ +KPVLPSSSSPSSSSASGPASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPS +SSAS------------R +>GCF_005280335_PROKKA_01866 +M----------------------------------------------------------- +------------------------------------------------------------ +--------------------------------------------PVTGDELRAGLLSERE +KNVLAAADAEDAGRIYLLQMHRVYQGALTISATEAESGTDEEAKALAASVVADHQEDMQR +MVEVLADMGAIGADASHTALPSGYTGPIKIEG-TGADGGPVPSDFVPEPVQRVQSFRATQ +RPVLPTSSSPG-------------DAEDRRGRDSATASPSPTPADTARPSPSPSSAASPS +PSATTGSPSGT----NR +>GCF_020097155_PROKKA_01762 +MNRATDATAPVCPVRWSAAAGG-LLGLSLVLAGCGTSAQPVPAG--SGSNTYLEGVLATP +SATKADPLAADQRFVASLLQNQYQVVQEADHVLSRPDMDGEVRDMAQQHKDVANQRIGDL +SSRLQAWGLEVPAAPEPLVDDTKPSG---RPTGDPSEIQASKGQQAAAD-IRAGLLTASD +QSALVTADDDAAGRIYLLQVHRLLQGGVSLAGTESDEGTDEETKKIASDLIDADRPRMQR +ILEKLGENGVVAAVPSPTAPNSGYQGPISLPSQAGGDGANV--DYTPSALYEMWS----- +--TLPPPATSS-------------SADGSSTGPSPSAQPTPTPADTASPRPTPGASAQPG +AASSTASTTGAASTRNG +>GCF_023573625_PROKKA_00965 +MSRADIAPARVHPRRWSVAVGGALLSITLATGGCSVVEEPGQTGDTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL +ESMLEGWG--VPS------DDVRGAGAEATPSAQPESTEDAEPAEIVGDELRAGLLSDRE +KNVLAAAEPEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELES +LAATLAEMGVIGSSGARTAEPSGFTGPIKIEG-TGADGGSVPSDFVPEPLQRVRNFRATQ +KPVLPSSSSPSSSSASGSASASGRDAEDQRGRDTASASPSPSPADTAQATPRPSSGASPS +PSAS------------R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000864.fa new file mode 100644 index 0000000000000000000000000000000000000000..0d0d021d0f5600a10b48c43ebb3d66381c1fd255 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000864.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01022 +M---RTARPTRLAVALGAGVLLTGVGAT---PALASPAHPA-GWTAEHGLPGGSFLVAGA +EGETGASFGTEFEVDESDVRLTVAPA-------------MEGEARGAETEVPFTYDDELE +RGDFDVAAARRSLGESGTGPVVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHEL +GFHMLPTAWDTTLLAAPGERHVFIS-SYTGD---EAAPLTLVAGPAEGRVVEV------- +---TEEETGGPRGYVYQAPEGFTGSDTV--TLRATRDGVTTTRTVTVRFGDPRVDLYDWE +NGRIPGFVTFPVAGLF--------DD--APGQPADPDTPTSPA-------EPETPADPAD +GEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRH-RVAA +>GCF_003691675_PROKKA_00736 +M---RTARPTRLAAALGAGVLLTGLGAT---PVLASPAHPA-GWTAEHDLPGGSFLVASA +EGETGASFGTEFEVDESDVRLTVAPV-------------LEGEARGAETEVPFTYDDELE +RGDFDVAAARRSLGESGTGPVVYTLY---------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------R +>GCF_003691675_PROKKA_00737 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---MLPTAWDTTLLAAPGERHVFIS-SYTGD---EAAPLTLVAGPAEGRVVEV------- +---AEEETGGPRGYVYQAPEGFTGSDTV--TLRATRDGVTTTRTVTVRFGDPRVDLYDWE +NGRIPGFVTFPVAGLF--------DDAPAPGQPADPDTPTSPA-------EPETPADPAD +GEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRH-RVAA +>GCF_005280335_PROKKA_00782 +MSARRTTRP--LSTALAAAVLAGGLAASTAAPALAAPAETTDGWQNGH-FVGGTFGSTEL +SPRTG-SFYTQHAV--KDVRVTVAPFYPAFTDLEEISYKVPGEM-GPETDVEFTYDAELE +AGYVDVLEQRRVLDEEGTAGAVFTLYVDGKATATLVFGEDRNLGDDVPGMFLDATGPQAY +DFSARPTVDHQTRLAAPGSRLVHLQGNSTGDAPVEDSTRTVVEQPEHGTLVELPRIGDPT +NWTSDGANGSFASTVYVADEGFTGTDQAVFTLTDGSTGEQKTLVVTFSIGDPRAA--DPH +LGVQGTGLPFDEARVWEALEAQGEDD--ASEAPA-PESPATPAPDSTDAPEASEPSEPAD +-EHTVPETVETGSGQAWWLAAVAAAGTGALVAGRRRFGLAR +>GCF_023573625_PROKKA_00966 +M---RTARPTRLAAALGAGVLLTGLGAT---PALASPAHPA-GWTAEHGLPGGSFLVAGA +EGETGASFGTEFEVDESDVRLTVAPV-------------LEGEARGAETEVPFTYDDELE +RGDFDVAAARRSLGESGTGPVVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHEL +GFHMLPTAWDTTLLAAPGERHVFIS-SYTGD---EAAPLTLVAGPAEGRVVEV------- +---TEEETGGPGGYVYQAPEGFTGSDTV--TLRATRDGVTTTRTVTVRFGDPRVDLYDWE +NGRIPGFVTFPVAGPF--------DD--APGQPADPDTPTSPA-------EPETPADPAD +GEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRH-RVAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000865.fa new file mode 100644 index 0000000000000000000000000000000000000000..87dc9c2a2f2057bf0d5bd9b88eae1d5d4a08bfb6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000865.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01023 +--------MSTSPTV-TRNDAESRYELHDG-GTLLAVLDFRDNGAAVSLNRAFTIPVHRG +RGHAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>GCF_003691675_PROKKA_00738 +--------MSTSPTV-TRNDAESRYELHDG-GTLLAVLDFRDNGAAVSLNRAFTIPVHRG +RGHAAALTAGAVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>GCF_005280335_PROKKA_01865 +MTARD---AAGGPAV-TRNDAESRYELHDG-GTLLAVLDYRDNGTAVALTRAFTIPVHRG +HGHAATLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR +>GCF_020097155_PROKKA_01758 +M---D---ASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRR +QGHAATLTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR +>GCF_023573625_PROKKA_00967 +MTTGGCPGMSTSPTV-TRNDAESRYELHDG-GTLLAVLDFRDNGAAVSLNRAFTIPVHRG +RGHAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000867.fa new file mode 100644 index 0000000000000000000000000000000000000000..762bd333ff557ba6ec34d1108830c7cfbfc2d883 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000867.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01025 +-MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREP +TLGATAPYVLMTPTYGGGSGPGA-VPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLA +GYIISRKCQVPLMYKFELMGTPDDVERVRGGLEGM----WT +>GCF_003691675_PROKKA_00740 +-MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREP +TLGATAPYVLMTPTYGGGSGPGA-VPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLA +GYIISRKCQVPLMYKFELMGTPDDVERVRGGLEGL----WT +>GCF_005280335_PROKKA_01860 +-MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREP +TLGATAPYVLLTPTYGGGDGPGA-VPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLA +GYIIARKCQVPLMYKFELMGTPEDVDSVRGGLEGL----WT +>GCF_020097155_PROKKA_01750 +MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP +TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA +GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA +>GCF_023573625_PROKKA_00969 +-MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREP +TLGATAPYVLMTPTYGGGSGPGA-VPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLA +GYIISRKCQVPLMYKFELMGTPDDVERVRGGLEGL----WT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000869.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000869.fa new file mode 100644 index 0000000000000000000000000000000000000000..05221ba7a34e3375995a9ab44a9ece7f13a3498a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000869.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01027 +MC-PAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDE +ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFST +LASTPEIDEAFRWSRENRNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMY +LSGHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYE +NEVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSD +ENHDFFSGSGSSYVIGKAENTEDEDWDF +>GCF_003691675_PROKKA_00742 +MC-PAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDE +ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFST +LASTPEIDEAFRWSRENRNLQAKAGLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMY +LSAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYE +NEVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSD +ENHDFFSGSGSSYVIGKAENTEDEDWDF +>GCF_005280335_PROKKA_01858 +MT-EVTDTVKTNHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDE +ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVLTNIAFMESVHAKSYSSIFST +LASTKEIDEAFRWSRENENLQRKASLIVERYDGEDPYKRKIASTLLESFLFYSGFYWPMY +LSAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEEKREELKAFTFELLFELYE +NEVEYTHDLYDAVGLSEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSD +ENHDFFSGSGSSYVIGKAENTEDADWDF +>GCF_020097155_PROKKA_01745 +MTEPHHGPSVHDHLVEAINWNRIQDEKDNEVWQRLVNNFWLPEKVPLSNDVQSWNQLTDD +ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVYTNIAFMESVHAKSYSSIFST +LASTKEIDEAFRWSRENPNLQRKAQLILERYDGEDPYKKKIASTLLESFLFYSGFYWPMY +LSSHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEERREELKAFTFELMFELYE +NEVEYTHSLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTDVNPAILSALSPNSD +ENHDFFSGSGSSYVIGKAEATEDEDWDF +>GCF_023573625_PROKKA_00971 +MC-PAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDE +ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFST +LASTPEIDEAFRWSRENPNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMY +LSAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYE +NEVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSD +ENHDFFSGSGSSYVIGKAENTEDEDWDF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000871.fa new file mode 100644 index 0000000000000000000000000000000000000000..c58bed75b812ef99fe16956b9fa772824050a259 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000871.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01032 +MSVAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI +EVVAEQLAVLGARTSG +>GCF_003691675_PROKKA_00747 +MSAAPRLRWAVQERTLGAVEDLDWAMDELAVFRAAAAEGRALDGLIRVYVPEPTVAFGQR +DARLPGFEAAAAAARAHGFEPVVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAW-AAAGL +EVVDEQLAVLTAGTAG +>GCF_005280335_PROKKA_01850 +MSAAPRLRWAVQERTLGATDDLDWAMDELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFEAAAAAARTHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL +KVVDEHLAVLAAGTSG +>GCF_020097155_PROKKA_01740 +MSAAPRLRWAVQERTLGAADDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFEAAAAAARAHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDATLTQQARFAEF +ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPAYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLGMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL +EVVDEQLAVLGAGTSG +>GCF_023573625_PROKKA_00976 +MSAAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI +EVVAEQLAVLGARTSG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000876.fa new file mode 100644 index 0000000000000000000000000000000000000000..5727afb320daa345b250e82f2073d75c6957a139 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000876.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01043 +MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSP--SSAKPAVETSAP +AS------TSETAGVSSSPT-ATESGS-GEYVPASADGPARSVPKPEMPADMKEETKEGA +EAAIRYFWDVHYYAEQTGDTELLDSLYSEYCEFCQFSSNDLQMIYKDGGWYTGTEVQIDS +ILTHRSETGYVSTLLVTTGTGTGYTKGGVVPEN-GDVEAASKQPWIAEVSFNPESSHWIV +DEMSYEGSIGSN +>GCF_003691675_PROKKA_00756 +MSLTAPGRALRRHRFAQAGTLSVALALTLTACGGQSEPAESSTTSP--SSAKPAVETSAP +AS------TSATAGVSSSPT-ATESGS-GEYVPASADGPARNVPKPEMPAAMKEETKEGA +EAAIRYFWEAIYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKS +LTLTPSEFGYTATLVRDASAVDVFDSQGVRDDS-ASGAETHDETWLADVVYEPSKGHWVI +DEMQNQQDAQ-- +>GCF_005280335_PROKKA_00543 +MSFTAPRRVLRRHRLTQVGALGAGLALLLTACGGGSEPAESSSPAPTGSSSSPAEATTAS +PSAESSPTTSPSGSVGSTAA-AGSSGSGGAYVPASAEGPARNVPKPEMPAVTKEETQEGA +EAAVEYFWEAAYYLQQTGDSEYQESVSSPTCKFCDLQRTSMEGHYRDGGWMKVEAVNIAS +MVTRPSANGYMSTLLLDMPKEEAFASQGGKAESIGTQPALEESPWIAETSFSEEAGHWVI +EAMIAGGS---- +>GCF_020097155_PROKKA_01734 +MTLPAPRRTLRRRRLARTGALSGALLLALTACAGGGADSGASSAST--TTTAPAASSTSA +AA------SSSTGGASASESDATTSGAAGEYVPASSKGPAQNVPKPVMPAAVKENTPEGA +EAAVKYWWEAVNYLQQTNDPEPLKSISMEECNLCSAHIKTIKRIYGDGGWATGENFAVNS +VSMEKKKDFTLATVAISTDDSATFNADGVKVDQ-APADAGTDAPWGVLLKFDSNKGQWVV +REAEYDFQEG-- +>GCF_023573625_PROKKA_00984 +MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSP--SSAKPAVETSAP +AS------TSETAGVSSSPT-ATESGS-GEYVPASADGPARNVPKPEMPAAMKEETKEGA +EAAIRYFWEAIYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKS +LTLTPSEFGYTATLVRDASAVEVFDSQGVRDDS-ASGVETHDETWLADVVYEPSKGHWVI +DEMQNHQDAQ-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000879.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000879.fa new file mode 100644 index 0000000000000000000000000000000000000000..de923ce8dcde2e6fc2b2ccedba3a5174a1c36e09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000879.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01046 +MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVDITEPEGLEVLRHSTAHVMAQ +AVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQISSLMQKIVKSGQTFRRRVVDEETARAEMAEEPYKLELLGKK +DAADTAGEGASVEVGAGEITIYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSRRRHTEAGYEFVYTPHITKQH +LYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYYLKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSG +VVHGLTRVRGMTQDDAHIYCTREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRPVMIHRALFGSIERFLGVLTE +HYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGIRARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVS +FRFRDGTQDNGVPVEEAIERIVKAVREREVTP +>GCF_003691675_PROKKA_00759 +MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVDITEPEGLEVLRHSTAHVMAQ +AVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQISSLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKK +DAADTAGEGASVEVGAGEITIYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSRRRHTEAGYEFVYTPHITKQH +LYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYYLKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSG +VVHGLTRVRGMTQDDAHIYCTREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRPVMIHRALFGSIERFLGVLTE +HYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGIRARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREAGAVS +FRFRDGTQDNGVPVEEAIERIVKAVREREVTP +>GCF_005280335_PROKKA_01842 +MSEPNNILLTVDGQMREVAHGITGLELFRDQSTTVVMRVDGVLWDLSREIPGGASVESVDITEQDGLDVLRHSTAHVMAQ +AVQQLRPDAKLGIGPYITDGFYFDFDVAEPFTPEDLRTLEKMMQKIINSGQAFRRRVVTEDEARAEMADEPYKLELLGKK +NDAATAGEGASVEVGAGEITIYDNVDRKSGDAVWCDLCRGPHLPQTKLISNAFALTRSAAAYWLGNQDNKQLQRIYGTAW +PTKADLKAYQERLAEAERRDHRRLGSELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSRRRHTEAGYEFVYTPHITKQH +LYETSGHLDWYADGMFPPMQIDEQRDPETGEVTRQGQNYYLKPMNCPMHNLVFRSRGRSYRELPLRLFEFGAVYRYEKSG +VVHGLTRVRGMTQDDAHIYCTREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTRDPEKSVGSDEIWEEATRTLDEVARA +SGLDLVPDPGGAAFYGPKISVQAKDAIGRTWQMSTIQLDFNLPERFDLEYQAPDGSRQRPVMIHRALFGSIERFLGVLTE +HYAGAFPAWLAPEQVVAIPVAEAFADYLGDVVKRLRAEGIRARLDDSSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVS +FRFRDGSQDNGVPVDEAIERIVRAVREREATP +>GCF_020097155_PROKKA_01730 +MSESNPILLTVDGEMREVTHAITGAELFKDQPTTVVMRVDGQLWDLSRELHGGEAVESVDITEQDGLNVLRHSTAHVMAQ +AVQELRPDAKLGIGPFITDGFYFDFDVAEPFTPEDLKQLEKMMQRIVKSGQTFRRRVVTEDEARAEMADEPYKLELLGKK +DDAEAAGEGATVEVGAGEITIYDNVDRKSGDAVWCDLCRGPHLPTTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +PTKEDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSRKRHAAAGYEFVYTPHITKQH +LYEVSGHLDWYADGMFPPMQIDEVRDPETGQITKQGQNYYLKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSG +VVHGLTRVRGMTQDDAHIYCTREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLELVPDPAGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGSRQRPVMIHRALFGSIERFLGVLTE +HYAGAFPAWLAPEQVVAIPVAEAFNDYLADVVATLKAEGIRVRLDESSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVS +FRYRDGSQDNGVPVDEAVARIVKAVREREVTP +>GCF_023573625_PROKKA_00987 +MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVEAVDITEPEGLEVLRHSTAHVMAQ +AVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQISSLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKK +DAADTAGEGASVEVGAGEITIYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSRRRHTEAGYEFVYTPHITKQH +LYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYYLKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSG +VVHGLTRVRGMTQDDAHIYCTREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRPVMIHRALFGSIERFLGVLTE +HYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGIRARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVS +FRFRDGTQDNGVPVEEAIERIVKAVREREVTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000881.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000881.fa new file mode 100644 index 0000000000000000000000000000000000000000..a97638edd1c85ab3ccca643a03b4ba5a39df2006 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000881.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01048 +MLDRHARDLTTRLFTPVAHTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWSAHVGIAERAERLVAALVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMAAVRRQARDDA +>GCF_003691675_PROKKA_00761 +MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMVAVRRQARDDA +>GCF_005280335_PROKKA_01840 +MLDRHARGATTRVFTPVARALLRAGVSPDAVTVVGTLGVSLGALVLFPLGELFWGTLFIT +AFVFSDLVDGIMAREAGTTGRWGAFLDSTLDRVQDAAVFLGLSLWGFGVGGEPAVGTLAA +VCLALGMLVSYVRAKAEALGLTANVGIAERAERLVAALVLAGLTGLGLPPAFLAATLGLL +AAASLVTVGQRVAAVRSQTRRAA +>GCF_020097155_PROKKA_01728 +MLDRRARGTTTALFTPLARRLLRAGVTPDAVTVAGTVGVSAAALLLYPAGHLFWGTIVIT +LFVFSDVLDGVMAREAGTTGPWGSFLDSTLDRVQDAAIFLALSWWGFGVGAHPAVGVLAG +VCLALGMLVSYARAKAESLGFTAAGGIAERAERLIVTLVFAGLTGLGLPSAVLTAVLGLL +ALASLITVAQRVAGVRRQSRTA- +>GCF_023573625_PROKKA_00989 +MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMAVVRRQARDDV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000886.fa new file mode 100644 index 0000000000000000000000000000000000000000..20926776496f65d9fe14f8a8f5db4c15ee17f524 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000886.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01057 +--------------MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAE +SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIE +HGEGAYADRFDEWWDLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG +RDGRVKALDPKVVMQLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQA +NPGVLPRHWHKFWALRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGG +GSHAAPAVAPDGLSSRPAS-AEGGDRVTA +>GCF_003691675_PROKKA_00776 +--------------MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAE +SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIE +HGEGAYADRFDEWWDLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG +RDGRVKALDPKVVMQLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQA +NPGVLPRHWHKFWALRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGG +GSHAAPAVAPDGSSSRPAS-AEGGDRVTA +>GCF_005280335_PROKKA_01829 +MTQPRLAHQTPLGRMYARSLTGLPEVPSITTVIGMERTDLDGWIGWMAAQSVTQDPRLAE +SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTLAETRAKLIE +HGEGAYADRFDEWWDLYDVRPLAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG +RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEEWRHGQAEMLLGVALGETEVAVHQA +NPGVLPRHWHKFWALRQVWKHAQAADDAGPALRVIGPPPPSVPL-HRG------------ +----------------------------- +>GCF_020097155_PROKKA_01719 +--------------MYARSLSGLPEVPSITTVIGMERTDLDGWVGWMAANAVAQDPRLGE +SLGSPARLRQVAKQSADAAARYRDAAAERGDRVHDYAEQVALRALGRPHTMAASREELQR +HGEGAYADRFDEWWDLYDVQPVAAEITVWNHSVGYAGTLDLVARIGGRLCLIDYKTKGTG +RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEPWAHGGAEMLLGVALGETEVAVHQA +NNAALPRHWHKFWALRQVWKHALAVDDAGPALRVIGPPPVSVPG-AAGGLSAARAAAFG- +---APPAVAHDPGTSAPAD------RLQP +>GCF_023573625_PROKKA_01004 +--------------MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAE +SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIE +HGEGAYADRFDEWWDLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG +RDGRVKALDPKVVMQLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQA +NPGVLPRHWHKFWALRQVWKHAQAVDDAGPALRVIGPPPPSVPASAATGLQAVRAAAFGG +GSHAAPDVAPDGSSSRPASAAEGGDRVTA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000887.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000887.fa new file mode 100644 index 0000000000000000000000000000000000000000..ecc995d83cfcee889c9782c5fb8f4e0f8539c769 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000887.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01058 +MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF +DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG +TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF +GAPGAPAAGTGAAR-------- +>GCF_003691675_PROKKA_00777 +MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF +DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG +TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF +GAPAVPAAGTGAAR-------- +>GCF_005280335_PROKKA_01828 +MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF +DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG +TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF +AAPAAPPTPARAPR----GGTR +>GCF_020097155_PROKKA_01718 +MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF +DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG +EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF +GAR--PSVSPSAARTTPRRGAQ +>GCF_023573625_PROKKA_01005 +MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF +DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG +TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF +GAPAVPAAGTGAAR-------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000891.fa new file mode 100644 index 0000000000000000000000000000000000000000..1c7ac626174abcb8ee73181bff5342f580e09686 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000891.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01062 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRQARRGHAEDAPAITPEWAGWRGRVFL +VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVA-R +>GCF_003691675_PROKKA_00781 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRRARRGHAEDAPAITPEWAGWRGRVFL +VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVA-R +>GCF_005280335_PROKKA_01824 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARKVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWNEARRGRSEHATAITPEWAGLGGRAFL +VLGMLIGTLALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLVWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLVGFFVWLRAKDRDKPAVETLLPDGPEEHAA-R +>GCF_020097155_PROKKA_01714 +MQWLVDVFNWTIPVAGGGLLMREVVGNVFGLASALGGMARKVWAWPVGILGNLLLLTVFL +ASLFNDAPHATLLGQAGRQVMFIAVSVYGWKRWRDAQRGRADHAPAITPEWAGWGNRAFL +AVALVLGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSSGYYASAVMYAFYGVFTLTGFFVWMRARDRDKPAVETLLPDGPAPEEAAR +>GCF_023573625_PROKKA_01009 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWRQARRGHAEDAPAITPEWAGWRGRVFL +VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVA-R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000892.fa new file mode 100644 index 0000000000000000000000000000000000000000..72bc6405e8d97a0ede383967537a5fecf52222f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000892.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01063 +MNAA-----ETPS-ADPMDLAVGAALRGVRGANPLVGAVLTDAAGRILAVGHHRGRGTAHAEVDALTRWRAARAADPALA +TLDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTGHDGGGAARLAAHGVHVTGPTGEAAALTLTARWRE +VRDAGRPWVTGHLAQSLDGHAAAADGTSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVP +VVQGHRPVPDGAALRTHPVLLHVPDHDPHAVLAALAAHPGPWPH-GRRAEHVLIEGGPRVLGAWLRAGLVDELMVYTAPL +LLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGVDVWTHLSPVPAPRLPTAPAPTRFQED---------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------ +>GCF_003691675_PROKKA_00782 +MSAA-----ETPS-ADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDALTRWRAARATDPALA +ALDPAGLTLHVTLEPCNHTGSTGPCSQAVLDAGVGALRYAVADPTGHDGGGAARLAAHGVRVTGPTGEVAALALTARWRE +ARDAGRPWVTGHLAQSLDGHAAAADGTSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVP +VVQGHRPVPDGAALRAHPVLLHVPDHDPHAVLAALAAHPGPWPH-GRRAEHVLIEGGPRVLGAWLRAGLVDELMVYTAPL +LLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGDDVWTHLSPVPAPRLPTAPAPTRFQED---------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------ +>GCF_005280335_PROKKA_01823 +M---------SGA-PDPMALAVGAALRGVRGANPLVGAVLTDDAGRVLAAGHHRGRGTAHAEVDALARWEAARAADPALA +ALDPAGLTLHVTLEPCDHTGSTGPCSGAILASGVGAVRYAVADPTGVDGGGAARLAAHGVRVSGPTGEPAALALTERWRR +ARDAGRPWITGHLAQSLDGHAAAADGTSRWITGAASRAHAHRVRARVDAIVVGTGTVLADDPRLTVRDAAGAETGPQPVP +VVQGRTPIPAGAALRARPETLHVPAHEPEAVLAALAARPGPWPHGGARPGHVLIEGGPRVLGAWIRAGLVDELMVYTAPL +LLGAGRPAVAGLDVGTLADGLRWHPDPAEDGPVRALGEDVWTHLAPVPAPA-PEGPDP---QEDCMFTGIVTHLGTVLAL +EPDPAADTARLVLDAGGALEGLPAGGSLAVDGVCLTALDGPGAEPGVFRADLMGQTLRMTSLGGRTPGDRVNLERCLRPT +DHLDGHVVQGHVDGVGEVLSVTPQGAWTTVRIGLPAALARYVPAQGAIALQGVSLTVSAVSEPGADAHWFEVGLIPATLE +ATTLGALRPGDRVNLETDVLARYAERLALLPAAPAASPSAAPAEEVRP +>GCF_020097155_PROKKA_01713 +MSAPAARHDDAGRPAEPLDLAAAAALAGVRGANPLVGAVITGPDGAVLAVGHHRGRGTAHAEVDALNRWAAARAADPSL- +HVDPAACTIHVTLEPCDHTGSTGPCAGAILDAGLGAVRYAVADATGTAGGGAARLTRAGLRVEGPTGHAASAALTARWRR +VRDAGRPWITVHLAQSLDGRAAAADGTSRWITGPASRAHAHAVRARVDAVVCGTGTVAADDPRLTARDAAGEQLPVQPVP +VVMGERDLPAGAALAARADLIHVRSHDPRAVLAALASRPGPWPHGGSRPGHVLIEGGPHVLGAWLAAGLVDEVFAYTAPV +LLGDGLPGVAGLDVPTLAAGHRWAPDPAEDGPVRALGDDVLTHLAPVTDPA------------D---------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------ +>GCF_023573625_PROKKA_01010 +MNAA-----ETPS-ADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDALTRWRAARATDPALA +ALDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTGHDGGGAARLAAHGVHVTGPTGEAAALTLTARWRE +VRDAGRPWVTGHLAQSLDGHAAAADGTSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAVGAELAHQPVP +VVQGHRPVPDGAVLRTHPVVLEVLDHDPHAVLAALAAHPGPWPH-GRRAEHVLIEGGPRVLGAWLRAGLVDELMVYTAPL +LLGPGRAAVAGLDVATLSEGLRWHPDPAEGGPVRALGVDVWTHLSPVPAPRLPTAPAPTRFQED---------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000893.fa new file mode 100644 index 0000000000000000000000000000000000000000..6863ad130143aefd707eec1f201cdd551213257c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000893.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01066 +MSGAGAPTFT------PDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLV +RVPGTVELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGF +GVLTVDTEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD +>GCF_003691675_PROKKA_00785 +MSGAGAPTFT------PDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLV +RVPGTVELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGF +GVLTVDTDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD +>GCF_005280335_PROKKA_01821 +--------------------------MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLV +RVPGTVELSVAAARLAEDFDAVVVLGVVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGF +GVLTVDTEQQARDRAGLPGSREDKGRESLEAAVLTELALRDV--QA +>GCF_020097155_PROKKA_01710 +MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV +RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF +GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAA--LG +>GCF_023573625_PROKKA_01013 +MSGAGAPTFT------PDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLV +RVPGTVELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGF +GVLTVDTDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000894.fa new file mode 100644 index 0000000000000000000000000000000000000000..8255b2db88146bf365d9585efebaadc6e90a6d69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000894.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01078 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL +>GCF_003691675_PROKKA_00797 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL +>GCF_005280335_PROKKA_01820 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGIALEDVYRHL +>GCF_020097155_PROKKA_01707 +MKTFEELFAELTRKVAERPEGSGTVAQIDAGVHAIGKKIVEEAAEVWMAAEYESHDAAAE +EISQLLYHVQTMMIAKGIGLKDVYRHL +>GCF_023573625_PROKKA_01027 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000895.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ab16f60c7d5de18890d889c709f679aab3277c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000895.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01079 +MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG +LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE +AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL +RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL +>GCF_003691675_PROKKA_00798 +MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG +LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE +AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL +RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL +>GCF_005280335_PROKKA_01819 +MLRIAVPNKGALAEAAREILQEAGYRQRRDSRELVLVDPENQVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFRDAQVDGGAEEIMALGFGRSVFRLAAPVGAFSSEAELSGKRIATSYDG +LLSAYLERTGLDAEVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGESILDSE +AVMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDVRRELLEQATAVTPGLESPTISPL +RDESMVAVRSMVRKADANRAMDDLYALGARGILISAIHAIRL +>GCF_020097155_PROKKA_01706 +MLRIAVPNKGALSESAREILIEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFRDARVGETAEEIMALGFGKSVFRLAAPVGSFTSAEELAGRRIATSYDG +LLTEYLAESGLDARVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGEPILDSE +AIMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEQATAVTPGLESPTVSPL +RDESMVAVRSMVRKADANRAMDDLYDLGARGILISAIHAIRL +>GCF_023573625_PROKKA_01028 +MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG +LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE +AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL +RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000897.fa new file mode 100644 index 0000000000000000000000000000000000000000..c45bd116a020beda98ad1a0ad46d7ad9cdc87c9b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000897.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01081 +MSISPPDDLVAS---VTFDDRGLVPAIAQQEGTGEVLMMAWMNEESLRATLETGWATYWS +RSRGELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMP-- +PAA-VDPE----EAAR +>GCF_003691675_PROKKA_00800 +MSISPPDDLVAS---VTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWS +RSRGELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMP-- +PAA-VDPE----EAAR +>GCF_005280335_PROKKA_01816 +MSISSHHDLVAS---LAFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRLTLETGWATYWS +RSRGELWRKGETSGHLQRVLAVHADCDADTLLLTVDQTGPACHTGTRSCFTDRLLAEPAA +PAG-DQAE----GAGR +>GCF_020097155_PROKKA_01704 +M---SPSDVVADLPPLIFDERGLIPAIAQQHDSGEVLMMAWMNEESLRRTLEDGWATYWS +RSRQEYWRKGETSGHLQRVLAVAADCDGDTLLLTVDQTGPACHTGTTSCFTDRRFAAP-- +TAADEDPQTEDAEAVR +>GCF_023573625_PROKKA_01030 +MSISPPDDLVAS---VTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWS +RSRGELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMP-- +PAA-VDPE----EAAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000899.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000899.fa new file mode 100644 index 0000000000000000000000000000000000000000..113d0144645dac92e75f77e45d4b8d7141e404f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000899.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01083 +MRRRTVVLAALAAGALVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT +>GCF_003691675_PROKKA_00802 +MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT +>GCF_005280335_PROKKA_01814 +MRRRTVVLAALAAGSLVLLAAGQTWVVGSGLTGGLSEEATTSGGAAAPGATAMALVVLAG +ALALTTARRVGVVVVGALLVLAGIVIVTGAAGAALDPAGTAASAVAEATGTTAAAGSYAV +TAWPWVAVTGGVLAALCGAVAALAGRGWVSVRRYEKAEATDAAEPAAPG-RAAAPGRTEA +ERRRTEQMDAWDELSRGNDPT +>GCF_020097155_PROKKA_01702 +MRRRWIVLAALLAGVLVLAATGQTWVTASGLEGSPVPQATAGGGRVAPVATALALVVMAG +ALALTTARRVGVVLVGVLMTLAGVVIASTAVTAALDPVAAAAGAVSELTGTTAPAAAYAV +SAWPWVSAAGGVMAAVLGVATLVVGPRWAASRRFESPATADEPAAAAP------------ +PSRHVDRMDAWDELSRGEDPT +>GCF_023573625_PROKKA_01032 +MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000908.fa new file mode 100644 index 0000000000000000000000000000000000000000..bea197f09a196da609b0cef754fc73d3d35b3472 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000908.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01092 +MSTLTPPEE----TGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHR +PDIVVMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTE +ADLVPAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQ +KTSMDRRLTMREVAQAVIDQVG- +>GCF_003691675_PROKKA_00811 +MSTLTPPEE----TGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHR +PDIVVMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTE +ADLVPAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQ +KTSMDRRLTMREVAQAVIDQVG- +>GCF_005280335_PROKKA_01804 +MPMTTPAEG----TGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQR +PDIVVMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTE +HDLVPAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQ +KTSMDRRLTMREVAQAVIDQVR- +>GCF_020097155_PROKKA_01693 +--MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHR +PDIVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTE +KDLLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQ +KTSMDRRLTMREVAQTVVDQIGA +>GCF_023573625_PROKKA_01041 +MSTLTPPEE----TGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHR +PDIVVMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTE +ADLVPAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQ +KTSMDRRLTMREVAQAVIDQVG- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000909.fa new file mode 100644 index 0000000000000000000000000000000000000000..3f9909f3a3e7edfc341f3888911193a10952eb1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000909.fa @@ -0,0 +1,70 @@ +>GCF_002008305_PROKKA_01094 +MLLTSLLLTLLSVVAAVPASRALGRDAGWVLAAPLLAAAGVLIAAWT---GDVRTEHHPWIPAVGVDLDLRLNGLALVFA +MIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLLLVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAI +RTLLVTVGGGLALLAAVALMAVRTGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSA +YLHAAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMSQLGLLVTAIGIGTPVAL +TAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRMPVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTP +GPAWLPVLVTAGIALTSVFTVAYSGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEASATFWGVPVLAAAAGVALGLLPG +VLDTPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPFSALDAVDEVRHRLIGVG +AVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQPSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVG +FGMTLWFLTLGAVDVALTQLMVEVLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIA +HFYLTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMRSPLAHVRENLVHIRVFG +RVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAADSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGF +LGAAGVKVLDYGLSTTLAFDMGVYLAVIGLIVAAFSLLGPER-------------PGEDPLRASSRDPGVAPAAPSSDPS +APTT--TTAREEVTR +>GCF_003691675_PROKKA_00813 +MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWT---GDVRTEHHPWIPAVGVDLDLRLNGLALVFA +MIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLLLVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAI +RTLLVTVGGGLALLAAVALMAVRTGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSA +YLHAAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMSQLGLLVTAIGIGTPVAL +TAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRMPVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTP +GPAWLPVLVTAGIALTSVFTVAYSGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPG +VLDTPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPFSALDAVDEVRHRLIGVG +AVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQPSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVG +FGMTLWFLTLGAVDVALTQLMVEVLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIA +HFYLTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMRSPLAHVRENLVHIRVFG +RVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAADSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGF +LGAAGVKVLDYGLSTTLAFDMGVYLAVIGLIVAAFSLLGPER-------------PGEDPLRASSRDPGVAPAAPSSDPS +APTT--TTAREEVTR +>GCF_005280335_PROKKA_01801 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +--------------------------------------------------------------------MDEARHGLVRLG +ALVDRASGSVAPRVHLLIPACVLGAFALAGVFTVDDLPAVVGTPSRWHDWALVVLVGAGVVATIRAKTRISAMVVVGVVG +FGVTLWFFTLGAVDVALTQLLVEVLTVCVMVLLLRRLPGRFRDEEAPRRVQAVVAATIAGVAATVGVLAFTGRSEMSEIA +HFYLTQTYAQAGGVNVVNVILVDFRALDTLGEMTVLGATGLTVAALLLNRRPAPPQRSAVDLRSPLAHVRENLVHIRVFG +RVFGVLIIALSVLLLLRGHYEPGGGFIAALVAGAGYALLYLAADHDTDRRLQWPYLTLIGGGIALGALTGVAGYLTGKGF +LGAAGVKILGYGLSTTLAFDLGVYLAVLGLIVAAFSLLGPERSETEAGAEPDPTSPIADP--AAEQTTGQTTEPTTAPGT +APTP--AAAREETSR +>GCF_020097155_PROKKA_01691 +MLLTSLLLTLLAVVLAAPLGRTLGRDAGWVLALPLLTSAGALVSARAGGGGETVVERRPWIPSLGAHLDLRLDGLAFVFA +LLVLVVGAGILAYSSRYLPRDRDEARAGSFYTLMTAFAASMLLLVLADNLVVLFVAWEFTSFASFLLIARSGDHARRPAI +RTLLVTVGGGLCLLAAVALTAARTGTASLSGALASDAWADPGFAAPVAALLAVAAFTKSAQFPFQSWLPDSMVAISPVSA +YLHAAAMVKAGIYLLLVFSPVLAGTPVWSALLIGSGLTTALLGAVSAIRRHDLKGLLAYSTMSQLGLLVTAIGVGTPTAL +AAAVVHTVAHALFKSTLFMLIGVVDHEAGTRDLRDLAARHVRMPVTGAAIAVAAASMAGLPPLLGFVSKEGLLDAALGAQ +GPAWLPGLVTAGIALTSVFTVAYSGRLVLGALGVWGTAPAGAADMWSAGRGEDVHEAPAAFWAVPVLGVVVTLVLGLVPG +VLDEAVAAAATAAAGAPVHAHLALWHGVTPALLVSAGVIAAGLALVAARRPVERVASHAGLPFSGLGVVDGILRGAVSLG +AAVSRVSGGIAPRAHLLMPALVLGAFAVAGVVASPDLPAVVGQPSRWHDWALVALVGVGVAATLRARTRIAAMVVVGTVG +FGVTLWFFTLGAVDVALTQLMVEVLTVCVMVLLLRRLPARFSAESTPHRAGAVAAAVIAGVASTLSVLAFTGRREISDIA +QYYLDRTYPDAGGHNVVNVILVDFRALDTLGEMTVLGVTGLTVAALLMNRRPAPPQPSAVDVRSPLAAVHENLVYARTFG +RALGPIILVLSVLLLLRGHYEPGGGFIAALVGGAGYALLHLSADTDDEPRLRWPYLALIGGGVTLGTVAGLAGYLTGKGF +LGSASVKVLGYSLGTTLAFDMGVYLAVLGLIVAAFRLLGPDN-------------ATAD------------DAAP----- +APTTGGESAREEAAR +>GCF_023573625_PROKKA_01043 +MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWT---GDVRTEHHPWIPAVGVDLDLRLNGLALVFA +MIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLLLVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAI +RTLLVTVGGGLALLAAVALMAVRTGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSA +YLHAAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMSQLGLLVTAIGIGTPVAL +TAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRMPVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTP +GPAWLPVLVTAGIALTSVFTVAYSGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPG +VLDTPVSYAAEAASGAEVHAHLALLHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPFSALDAVDEVRHRLIGVG +AVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQPSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVG +FGMTLWFLTLGAVDVALTQLMVEVLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIA +HFYLTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMRSPLAHVRENLVHIRVFG +RVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAADSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGF +LGAAGVKVLDYGLSTTLAFDMGVYLAVIGLIVAAFSLLGPER-------------PGEDPLRASSRDPGVAPAAPSSDPS +APTT--TTAREEVTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000911.fa new file mode 100644 index 0000000000000000000000000000000000000000..d74c9b6e5b8819b440736c7b47096b354fa2d120 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000911.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01096 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGSVLATSLGGWPGGIGIGFAAD +MLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILIGGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPL +RRVDGARLYVTLNLLTSTILLVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVRAVLSWQMVSGIGGILVGLGL +STRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLADLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVS +AGLDAGRGVTAALVLGASLVSLWVLLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPS------PSGRGSSTDHE +RTESWASQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAAQGLMDPSRYIEAVL +NP +>GCF_003691675_PROKKA_00815 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGSVLATSLGGWPGGIGIGFAAD +MLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILIGGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPL +RRVDGARLYVTLNLLTSTILLVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVRAVLSWQMVSGIGGILVGLGL +STRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLADLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVS +AGLDAGRGVTAALVLGASLVSLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPS------PSGRGSSTDHE +RTESWASQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAAQGLMDPSRYIEAVL +NP +>GCF_005280335_PROKKA_01799 +MSPEALGQLLPLFVAVPLITAGLLTLAGDRPRVHRLVVALVLCLTAGAGALIVARSLDGDVLATSVGGWPGGIGIGFAAD +MLTGLMLLLTSLLTLVGVNLAHGTRVVNSLYFGPLMLVLMAGVNGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPL +RRVDGARLYVTLNLLTSTILVVAVGFLYALTGTVNLAVMAGAAARDERVAIAGGLVLFALSIKASVVPLHGWLARAYPST +SPAVTAIFAALHTKVAVYALYRVFSVLFDNDARFLPLLLALAGLTLAVGALASVGVHGVRLVLSWQMVSGIGGILVGLGL +STQLGLSAGLFYLVHHMVAMGCLLAATAAVEVRYGTGRLADLRGLARREPLIAVVFFVGLLSIVGIPPFSGFVGKLMLVT +AGVEAGRLVTVAVVLVGSLVSLWALLRVWDAWFWGEPGTPHGLRERLATAALPVVGRGAERTG------PSGRGSSTDHE +RTESWTSTQTIDPPTGVLPVTFAADEDVTRSRIPVRLAMPGVVLAAATLVLGLAGQALWTLTDVAAQGLLDPARYIEAVL +AP +>GCF_020097155_PROKKA_01689 +MSDHAVGLLLPLFVAVPLLSAGLLVVAGSRPRLHRAVLAAVLAGGTVGGGLLMARAADGSVAAAGVGGWPDGIAIAFAAD +MLTGLMVALTAGLTLVGAWFAYGSRVANSAHFAPFMLVLMAGVHGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPL +RRVDGARMYVTLNLLTSTILVTGVGFVYALTGSVNMAVLAGAARGDVRVALAAGLVLFALSIKASMLPMHGWLARAYPST +SPAVTAIFAALHTKVAVYAMYRIYMVVYDGDPRLLGLILTLCLATLMVGAVASVGEHGARAVLSWQMVSGIGGIMVGLGL +ATQAGLSAGLFYLVHHMVVMACLLTATGAIEVRYGSGRLADLQGLAVREPLIAAAFFVGMLSLVGIPPFSGFAGKLALVL +AGVAAGRTVTVVLVLVASLISLWALLRIWDAWFWGRPRAPHGHRERLDTAALPLVHGDGVMPAAGAPVHPAGRGSSTDSE +RAEAWASTETLDTPTGVLPVVVDPDEDHTASRIPLRLAGPAALMAAATLALGLGAEGLWSVTDQAARGLADPTAYIEAVL +GR +>GCF_023573625_PROKKA_01045 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGSVLATSLGGWPGGIGIGFAAD +MLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILIGGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPL +RRVDGARLYVTLNLLTSTILLVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVRAVLSWQMVSGIGGILVGLGL +STRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLADLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVS +AGLDAGRGVTAALVLGASLVSLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPS------PSGRGSSTDHE +RTESWASQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAAQGLMDPSRYIEAVL +NP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000914.fa new file mode 100644 index 0000000000000000000000000000000000000000..92427433984a75910af329a2c8820cd5b5ee2f0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000914.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01099 +MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP +GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR +APDEV +>GCF_003691675_PROKKA_00818 +MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP +GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR +APDEV +>GCF_005280335_PROKKA_01796 +MDLVLTVIGSVLVVAGALVFVTAGLGLIRFPDPYTRISATGTAGGVGMILIVVGGLVLAP +SVANVVKVALIVVLQLGSAAVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR +TPDAS +>GCF_020097155_PROKKA_01686 +MDLVMTVAGSVLAVAGAVVFLGAAVGLIRFPDPYTRISATGTAGGVGMILIVTGGLLLMP +SVANLVKVVLIVVLQLGTAAIATMALGRSAYLTGVPMNLAHYDELAEDTPGREHGEPAPR +HPED- +>GCF_023573625_PROKKA_01048 +MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP +GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREGGRAAPR +LPDMD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000916.fa new file mode 100644 index 0000000000000000000000000000000000000000..69dbf744819f0a1cb8620cf6379f9e3daae7a71c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000916.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01101 +MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQRPTHVAVAFDLSGPTFRSEEY +GEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEADDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYP +KKGVSDIPPMDADAVKAKYGVAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR +EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGERVGEDAPPPEVEAAPEFTEA +TTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGTFGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEG +GLAKAVHDLKRTLKALAAPTEGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS +FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARMELTGIAVDVDALTGLREDFT +DAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLNMPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDAT +KLRQTVEGLLETVAPDGRIHTTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR 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+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFGLSKQLKISVDEARGLMKGYF +DRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDNRQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGL +ASRLLLQVHDELILEVPAAELEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000917.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000917.fa new file mode 100644 index 0000000000000000000000000000000000000000..4d1557de81aa7429be38e1f9030fa93b52db9da4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000917.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01103 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN +>GCF_003691675_PROKKA_00822 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN +>GCF_005280335_PROKKA_01791 +MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY +ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE +KLTGN +>GCF_020097155_PROKKA_01682 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY +ADAQTRWEAHKEQVRRSLEEEAQ--APAGNASTASSYSSEAPASDGGTLASDEALAALRE +KLTGN +>GCF_023573625_PROKKA_01052 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000918.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bebfa0c158af970ce86811ced51bccba57e49a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000918.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01104 +M---SEPLPRG-----------VTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHD +AADLLLLDTLAGWIASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDAN +LAAWR-AAGRLGGEAGELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGV +VLLAGGRDKHMSPRMNAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVP +GVGSLHLVAHAGAFGGAAADPGSRLLLASLADD----PRP-PGR---------------- +-----LVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVASTLATARANRVADRVRAVRD +DALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARVLEPGGRLWCVWNSHLRYRP +VLEDLVGPTRQTARDRTFTVTVSERR +>GCF_003691675_PROKKA_00823 +M---SEPLPRG-----------VTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHD +TADLLLLDTLAGWIASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDAN +LAAWR-AAGRLGGETGELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGV +VLLAGGRDKHMSPRMNAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVP +GVGRLHLVAHAGTFGGAAADPGSRLLLASLADD----PRP-PGR---------------- +-----VVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVASTLATARANRVADRVRAVRD +DALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARVLEPGGRLWCVWNSHLRYRS +VLEDLVGPTRQTARDRTFTVTVSERR +>GCF_005280335_PROKKA_01790 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRD +DALAGRPDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRP +VLEAEVGPTRQVARDRTFTVTVSTRR +>GCF_020097155_PROKKA_01681 +MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD +AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN +LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV +LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG +RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR +AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD +DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP +VLETAVGPTRQVARNRTFTVTVSTRR +>GCF_023573625_PROKKA_01053 +M---SEPLPRG-----------VTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHD +AADLLLLDTLAGWIASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDAN +LAAWR-AAGRLGGETGELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGV +VLLAGGRDKHMSPRMNAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVP +GVGRLHLVAHAGTFGGAAADPGSRLLLASLADD----PRP-PGR---------------- +-----VVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVASTLATARANRVADRVRAVRD +DALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARVLEPGGRLWCVWNSHLRYRS +VLEDLVGPTRQTARDRTFTVTVSERR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000921.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f586906a1e66f983d7ae779aaa5ba8cd6559774 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000921.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01108 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA +QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP +EEYIEQMVTLRRGAEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH +IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL +SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY +ADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSL +DRAPATGE-GAEAPAVDPASLPAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ +>GCF_003691675_PROKKA_00827 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA +QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP +EEYIEQMVTLRRGAEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH +IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL +SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY +ADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSL +DRDATTGE-GTEAPAVDPASLPAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ +>GCF_005280335_PROKKA_01785 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA +QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP +EEYIEQMVTLRRGEEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH +IDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL +SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY +ADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSL +DREEGQER-AGGGPAVDAASLPAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ +>GCF_020097155_PROKKA_01677 +MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAWVIEQLQRPTLVMVQNKTLAA +QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTP +EEYIAQMVTLRRGQEMDRDALLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH +IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL +SATPGQYELSQADGVVEQIIRPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY +ADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKIADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSL +DHEPPAGEVPSGSPAVDPAALPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ +>GCF_023573625_PROKKA_01057 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA +QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP +EEYIEQMVTLRRGAEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH +IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL +SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY +ADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSL +DRDATTGE-GTEAPAVDPASLPAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000922.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3f661ce5b871b6cdb06814b959dcd6973281d25 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000922.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01109 +MS---AAP-PVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQ +ALHRTWPDALRLTVRVTLALPPGLDLRFGIGLGQRR----ALDAG-GDGIEDGPAWYRAR +EAVERAHERAVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQA +EAARAERITQSAVSQAVARSGIDRLLELDAELAA-AAT----------------EVAP +>GCF_003691675_PROKKA_00828 +MS---AAP-PVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQ +ALHRTWPDALRLTVRVTLALPPGLDLRFGIGLGQRR----ALDAG-GDGIEDGTAWYRAR +EAVEHAHERAAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQA +EAARAERITQSAVSQTVARSGIGRLLELDAELAA-AAT----------------EVAP +>GCF_005280335_PROKKA_01783 +MT---RAP-QAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQ +ALHGVWPQAVRAVVRVSLALPPGLELRFGIGVGERR----SLDDGAGDRIEDGTAWYRAR +AAVERAHARADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQT +QAARAERITQSAVSQAVTRSGIDRLLELDAALAE-AAAGRPGHAGAAGEGAGDEGDAG +>GCF_020097155_PROKKA_01676 +MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ +ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDD-GRPILDGSAWHRAR +EALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQA +ETATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATA-------EEDRP +>GCF_023573625_PROKKA_01058 +MS---AAP-PVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQ +ALHRTWPDALRLTVRVTLALPPGLDLRFGIGLGQRR----ALDAG-GDGIEDGTAWYRAR +EAVEHAHERAAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQA +EAARAERITQSAVSQTVARSGIGRLLELDAELAA-AAT----------------EVAP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000924.fa new file mode 100644 index 0000000000000000000000000000000000000000..699a0929cf0fb4f7db00f4b9118c4d0a668840ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000924.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01113 +-----------MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGPHGRGTLTVF +AREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLDQRGTGRSTPATVATLTAPGAFATDEARAE +HLVHLRAPSIVRDAEMLRLALGAGPWTTLGQSFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRART +EEFFDRHPADRDAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRTGPAPRLSET +FLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPDFDPEATTVPLPTGEHVMPWSVEVDPRLRP +LAGTARLLAERTQWGPLYDVAALAQNTVPVAAAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERL +LAMT-----------------APDGAGTTTAPDPVD +>GCF_003691675_PROKKA_00832 +-----------MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGPHGRGTLTVF +AREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLDQRATGRSTPATVATLTAPGAFATDEARAE +HLVHLRAPSIVRDAEMLRLALGAGPWTTLGQSFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRART +EEFFDRHPADRDAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRTGPAPRLSET +FLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPDFDPEATTVPLPTGEHVMPWSVEVDPRLRP +LAGTARLLAERTQWGPLYDVAALAQNTVPVAAAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERL +LAMT-----------------APDGAGTTTASDPVN +>GCF_005280335_PROKKA_01780 +M----SAPAPRVPGDPRGFAPLEPARHRVGERTELYDGTVAVDHWFTVPVDHALTLAEAEAQDAAGTGVGPHGRGTLTVF +AREIRAAGDADGARPWALYLQGGPGGAGPRPARGGGWIGALASEHRVLLLDQRGTGRSTAASVAALTAPGAFASDEALAE +HLVHLRAPSIVRDAEMVRLALGAAPWTTLGQSFGGFCTLTYLSFHPEGLRRCLVTGGLAPLTGHADRVYQATYARMRDRA +HEFFARHTGDRAAWAEAVALIRAAEQAGEPVRLPDGGLLTVARAQALGMLLGGNTRVDRLHWILAEAVDRSGPAPRLSET +FLAAVAEQNDRHVNPLYTVLHESIYAQPAELAGGRAATDWSAARVLAEHPDFDPDAADAPLPTGEHVMPASLELDPHLRP +LRGAARLLAERTDWGPLYDVEALARNIVPVAAAVYTDDVYVDRDLSLETAGRVRGLRVWETDAFHHDGLADDGPAIVRRL +LEMTGEGAAPAAAEGAERSDSAPAASETTTAPGPVD +>GCF_020097155_PROKKA_01673 +MTRTGTGDAAFVPGDPRGFAPVGPAAHREGERTVLFDGTVAVDHWFTVPVDHALTLAEALAQDAAGTGLGPGGRGTLEVF +AREVRHPEDPEGERPWLLYLQGGPGSGGPRPARLGGWQCELAQHHRLLLLDQRGTARSTPVTAATL---AGLPDDAARAA +YLTHLRAPQIVQDAEMIRVALGAPPWTTLGQSFGGFCTLSYLSWRAEGLERCLVTGGLAPLTGHADRVYRATTARMHARW +QEFLERHPQDAGHWAEAVALIRAAQDDGDPYVLPDGTALTVGRAQQLGMLLGGNTRVDGLHWVLAEAVDRSGGEPRLSPG +FLAAVAAQTTRAVNPLYAVLHEAIYAQPAALTDGRGATAWSAQRVLAEHPDSSPAADPAPVPTGEHVLPWSFETEPELRA +LAGVAALLAAKDDWGALYDLDALAANEVPVAAAVYTDDVYVDRDLSLETAARVRGLQVWETDAFHHDGLADDGPGIVRRL +RGMLG----------------A-------------- +>GCF_023573625_PROKKA_01063 +-----------MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGPHGRGTLTVF +AREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLDQRGTGRSTPATVATLTAPGAFATDEARAE +HLVHLRAPSIVRDAEMLRLALGAGPWTTLGQSFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRART +EEFFDRHPADRDAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRTGPAPRLSET +FLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPDFDPEATTVPLPTGEHVMPWSVEVDPRLRP +LAGTARLLAERTQWGPLYDVAALAQNTVPVAAAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERL +LAMT-----------------APDGAGTTTAPDPVD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000925.fa new file mode 100644 index 0000000000000000000000000000000000000000..43c51edb79193eb5a787c6f85a9bd7f770794a14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000925.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_01114 +MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVILATPTGSGKSLVALAAHADA +LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY +ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG +LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA +AKFANVKDEAERAKRMKQSVKSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPADPDHALD +VVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYNDRMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPK +SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSADDWADALDAYFDDHEDIDDG +PAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDGDLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>GCF_003691675_PROKKA_00833 +MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVILATPTGSGKSLVALAAHADA +LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY +ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG +LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA +AKFANVKDEAERAKRMKQSVKSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPADPDHALD +VVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYNDRMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPK +SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSADDWADALDAYFDDHEDIDDG +PAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDGDLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>GCF_005280335_PROKKA_01779 +MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVILATPTGSGKSLVALAAHADA +LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY +ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG +LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA +AKFANVKDEAERAKRMKQSVKSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL +RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALELLDPAEPDHALD +VVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYNDRMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPK +SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSADDWADALDAYFGDHEDIDDG +PAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDGVHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>GCF_020097155_PROKKA_01672 +MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVILATPTGSGKSLVALGAHADA +LAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSSVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY +ADPSRGWAWQLPLLELPQARFLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQEG +RLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQSREFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAA +AKFAGIKDEAERAKRMKQSVKGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL +RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPAAPDHHLD +VVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSDRMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPK +SVVRDMFERAMGFGDYVRFYGLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS +GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSANDWADALDAYFDEHEDIDDG +PDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDGDHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL +>GCF_023573625_PROKKA_01064 +MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVILATPTGSGKSLVALAAHADA +LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY +ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG +LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA +AKFANVKDEAERAKRMKQSVKSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPADPDHALD +VVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYNDRMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPK +SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSADDWADALDAYFDDHEDIDDG +PAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDGDLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000926.fa new file mode 100644 index 0000000000000000000000000000000000000000..14c5602c589a33a5d7ebdfb02a6cb5e0e3d1e323 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000926.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01115 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGAPANLRFEAVDASQW +RPSGATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGAAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MAGQKPA- +>GCF_003691675_PROKKA_00834 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA- +>GCF_005280335_PROKKA_01778 +MSQIAPESPHPDTDAVAGDVTGRQGGGFTWDPAQYESFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLKRAREQAARTGAPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEECSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA- +>GCF_020097155_PROKKA_01671 +M-------------STVPAVTGRETAGFTWDPAQYEGFAEHRARPFHDLVARVEAEAPRV +VVDLGCGPGTLTRTLAERWPAAEVIGLDDSPAMLERAREGAADADLP-NLRFDRVDASQW +RPGPEVDVIVSNAMLQWIPTHRRLIRRWLGDLHPGAWFGAQLPRPYQQASHATIVALADE +PVFSEALHGVETTRTVAPPEEYTRLFLEAGWTPSVWETEYQQVLTGPDPVLRWTSGAALR +PSLQALAAWDAEEGAAEGAGLLELFVARYRQAMREAYPPVPGVSDADGGPLTVFPVRRMF +LVGRKPGE +>GCF_023573625_PROKKA_01065 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000927.fa new file mode 100644 index 0000000000000000000000000000000000000000..602187c3a8c140e7773da618b7f89fea9b45f5b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000927.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01116 +MPETARNRLLHDLPAVTVRTCSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA +ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR +HGDTVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVSDRIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERSW +>GCF_003691675_PROKKA_00835 +MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA +ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR +HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW +>GCF_005280335_PROKKA_01777 +MPETARNRLLHDLPAVTVRTSSVSEMDNNVYLLTSKTTGAQVLIDAADDAEAIRDLIASA +AGDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLH +HGDIVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVSERIFDAFDDDVVVHPGHGASTTLGAERPHLPKWAERGW +>GCF_020097155_PROKKA_01670 +MPATAEPRLLHDLPAVTVRAVSVSEMDNNAYVLTSKTTGAQVLIDAAAEPETLRDLLASA +AADTPCELRLELIVTTHRHWDHVRALPALATVTGARTAAGEDDADAIAAETGVTPDVRLA +HGSRTGAEGIELEVIALRGHTPGSVALAYRPEADEPAVLFTGDSLFPGGVGNTQGDAERF +ASLIRDVEDRVFAAFDDDVVVHPGHGASTTLGAERPHLQEWRERGW +>GCF_023573625_PROKKA_01066 +MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA +ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR +HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000928.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1f5ee26f33058a9cbd8f0fc2adf9f79a3c04b8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000928.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01119 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRTMVFTAAAVEWTVVGSELEA +LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA +GVFKRARAQDRPCLLGYIGKCSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEMVAHLLQQVYGDLEGPERI +PHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEI +TEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +ADDQEAG-RRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLYLLQRIRD +ESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPAD +TVES +>GCF_003691675_PROKKA_00838 +--MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAMVFTAAAVEWTVVGSELEA +LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA +GVFKRARAQDRPCLLGYIGKCSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEMVAHLLQQVYGDLEGPERI +PHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEV +TEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +GDDQEAG-RRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLYLLQRIRD +ESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPAD +TVES +>GCF_005280335_PROKKA_01774 +--MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTMVFTAAAVEWTVVGSELEA +LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA +GVFKRARAQDRPCLLGYIGKCSAPCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEMVTHLLQQVYGDLAGEDRI +PHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEI +AEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLE +GEEEGRD-RRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEALYLLQRIRD +ESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGSVAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTD +TVEP +>GCF_020097155_PROKKA_01667 +--MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTMVFTASAVEWTVVASELEA +LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVMRGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA +GVFKRAQAQDRPCLLGYIGKCSAPCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIA +ALRRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEAVAELLTQVYGDVPDTERI +PHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLMGTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEI +DEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQID +AEEAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLFLLQRIRD +ESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFGSVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGD +TVAP +>GCF_023573625_PROKKA_01069 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRTMVFTAAAVEWTVVGSELEA +LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA +GVFKRARAQDRPCLLGYIGKCSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEMVAHLLQQVYGDLEGPERI +PHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEI +TEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +GDDQEAG-RRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLYLLQRIRD +ESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPAD +TVES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000929.fa new file mode 100644 index 0000000000000000000000000000000000000000..857672d5752833b5a24c37a95a0680e175034981 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000929.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01120 +M-TEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIAR +SPEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPH +PMQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTI +MSFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVA +MLGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE +>GCF_003691675_PROKKA_00839 +M-TEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIAR +SPEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPH +PMQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTI +MSFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVA +MLGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE +>GCF_005280335_PROKKA_01773 +M-SEESLRPEKPPTSEVLVITGMSGAGRTTAAHALEDHGWYVVENMPPPLFITLADLVAR +SPEAFPRLAIVVDVRSRAYFPELHAALQQLENNGVEYRMVFLEADEHVLVRRFEAGRRPH +PLQGNASLLDGIRAERDMLAELKARADVVVDTTELNVHGLATEITELFSVSGPVTLRLTL +MSFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAEVSDYVLTRPGVEDFLRSYTA +MLAPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVQVQHRDMGRE +>GCF_020097155_PROKKA_01666 +MSADEHLQPDKPPSSEVLVITGMSGAGRTTAAHALQDHGWYVVENMPPQLLGTLSDLVAR +SPEAFPRLAIVVDVRSRSYFNELRTALQQLESTGVEFRTVFLEASDEVLVRRFEAGRRPH +PLQGNARLLDGIQAEREILSELKERADIVVDTSALNVHGLATEVTQLFSEDGPVTVRLNV +MSFGFKYGLPSDANFVADMRFVANPHWVPELRSKTGLDPEVSGFVLGQPGVQEFLSNYLA +ALGPVVEGYRRENKHYATLAVGCTGGKHRSVAVAEELARRVAQWPRVSVHVDHRDVGRE +>GCF_023573625_PROKKA_01070 +M-TEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIAR +SPEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPH +PMQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTI +MSFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVA +MLGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000935.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6f9a5bb722162877914d5dacb9b6180d47b3f91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000935.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01126 +MA-EQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSV +QTLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDAL +VARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEP +VWAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDV +DGALVGGASLDADEFAKIVRFDQA- +>GCF_003691675_PROKKA_00845 +MA-EQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSV +QTLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDAL +VARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEP +VWAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDV +DGALVGGASLDADEFAKIVRFDQA- +>GCF_005280335_PROKKA_01766 +MA-ETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAV +QVLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDAL +VARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEP +VWAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDV +DGALVGGASLDAEEFARIVRFDQA- +>GCF_020097155_PROKKA_01660 +MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV +QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL +VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP +VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV +DGALVGGASLDADEFARIVRSDAAH +>GCF_023573625_PROKKA_01076 +MA-EQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAV +QTLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDAL +VARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEP +VWAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDV +DGALVGGASLDADEFAKIVRFDQA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000936.fa new file mode 100644 index 0000000000000000000000000000000000000000..3df53734d2ce69bee7d6716c90f27c723465cf5f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000936.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01127 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTMES +>GCF_003691675_PROKKA_00846 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTMES +>GCF_005280335_PROKKA_01765 +MDMLTLILQILVVVLSVVIVLLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRLTV +GTVAAWALLIVTLGVLPRLAMES +>GCF_020097155_PROKKA_01659 +MDILTLLLQIAVVALSVVIIMLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRVTV +SATVLWGLAIVALALIARFSVES +>GCF_023573625_PROKKA_01077 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTLES + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000938.fa new file mode 100644 index 0000000000000000000000000000000000000000..d75fce792e6ab21cde7cecadf1681f449b06572a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000938.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01129 +M-AGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPAFSLVGFGRRSWSDEEFADY +VRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRLDEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQG +LADRSQPAEGPWRRVVIEKPFGHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDH +VQITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLEAVTVPDTPEGLAAASARGQ +YTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRWQGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDE +FGQNIIVIRVQPDEGVTIRFASKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIV +DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP +>GCF_003691675_PROKKA_00848 +M-AGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPAFSLVGFGRRSWSDEEFADY +VRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRLDEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQG +LADRSQPAEGPWRRVVIEKPFGHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDH +VQITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLEAVTVPDTPEGLAAASARGQ +YTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRWQGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDE +FGQNIIVIRVQPDEGVTIRFASKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIV +DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP +>GCF_005280335_PROKKA_01763 +M-PGESKAAARNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPSFSLVGFGRRDWSDEEFAEY +VRAAVEASARTTFDETVWDQFRGGLRFVSGAFDDEAAYVRLGEVLGELESSRGTRGNTAFYLSIPPDWFEDVSRHLADQG +LADRSQPADGPWRRVVIEKPFGHDLASAQELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRMFEPIWNAEHVDH +VQITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRTEKEKILEAVQVPDTPAGLEAASARGQ +YTSGWQGGERITGFLDEEGFNPESVTETYAALKVGIRTRRWQGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHEGDE +FGQNVIVIRVQPDEGVTIRFASKVPGTQSEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIV +DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRAWRRP +>GCF_020097155_PROKKA_01657 +MRPEPGGPARRNPLRDPRDRRLTRIAGPSALVLFGVTGDLARKKLLPAMYDLAHRGLLPPSFSLVGFGRRDWSEAEFADY +VRAAVEAGSRTAFNETVWDQFRGGLRFVSGAFGDADAYARLDEVLTELESSRGTGGNTAFYLSIPPDWFEDVSRHLADQG +LADRSQPADGPWRRVVIEKPFGHDLASAHELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRIFEPLWSAEHVDH +VQITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLALTAMEEPISFDAAHLRAEKEKVLAAVRVPCTPEGLEAASARGQ +YTSGWQGGEQVTGFLDEEGFNPASVTETFAALKVDIGTRRWQGVPFYLRAGKRLGRRVTEIAVVFKSPPHLLFPVHPGDE +FGQNVIVIRVQPDEGVTIRFASKVPGTQHEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQEEVELSWAIV +DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRTWRRP +>GCF_023573625_PROKKA_01079 +M-AGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPAFSLVGFGRRSWSDEEFADY +VRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRLDEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQG +LADRSQPAEGPWRRVVIEKPFGHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDH +VQITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLEAVTVPDTPEGLAAASARGQ +YTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRWQGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDE +FGQNIIVIRVQPDEGVTIRFASKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIV +DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000941.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ca216b3ae9e577071c4fcd89d7f888edfad68ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000941.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01132 +MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPVAWQLYQNVMHLDPTDDRWEG +RDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSRTPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGL +MDPDAAPGTSPFDHHVFVLASDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ +EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKLGTDEVAGLKESLGLDP +TKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANPENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGE +VLTALAPVMPELWGGSADLAGSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT +FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRPADANETAWAWRTVLEHRDRP +AGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDADGAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAP +CLEWFAEQDEAYRAEVLPDGPDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT +RGLL +>GCF_003691675_PROKKA_00851 +MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPVAWQLYQNVMHLDPTDDRWEG +RDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSRTPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGL +MDPDAAPGTSPFDHHVFVLASDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ +EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKLGTDEVAGLKESLGLDP +TKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANPENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGE +VLTALAPVMPELWGGSADLAGSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT +FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRPADANETAWAWRTVLEHRDRP +AGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDADGAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAP +CLEWFAEQDEAYRAEVLPDGPDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT +RGLL +>GCF_005280335_PROKKA_01760 +MTDAQHPSTAPALDRTAPARDFVYSEQDRRMVDTLKVLSADAVEQAGHGHPGTAISLAPVAWQMYQNVMHLDPQDDRWEG +RDRFILSAGHASLIQYLQLFAAGAGLELEDIRALRTEGSKTPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRLRGL +MDPDAAPGTSPFDHHVFVLASDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVSARYEAYGWHVQ +EVDWTNGALGHAVTEYTEDVEALYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGVHGSKLGAEELAGLKEGLGFDP +AESFDVDPEVLANSRSIAERSAAYRRTWEGAFQAWREAHPENARLYDRLAGRELPEGFAEAFPSWDADEKGLATRAASGE +VLTALAPVMPELWGGSADLARSNNTTMKGEPSFIPARRSTATWQGDEHGRTLHFGIREFAAGAIVNGITIGGLTRAYMGT +FLTFSDYMRPAVRLAALMGTPSVYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRPADANETAWAWRTVLENRDRP +AGMVLSRQNLPVLPRDTDGFASAEGVARGAYVLVDAVGGSGAPAPARVLLIATGSEVSVAVHARELLQAEGVPTRVVSAP +CLEWFAEQDEAYRAEVLPDGPDAPVRVSVEAGIAMPWFEHTVTAVSRGARVSLEHYGESADGARLMEKYGFTGEAVAQAA +RGLL +>GCF_020097155_PROKKA_01654 +MTDTASTA----LDRTLPARDFVYDEQDRRMVDTLKVLAADAVEKAGHGHPGTAISLSPVAWQLYQNVMHLDPSDDRWEG +RDRFILSAGHASLIQYLQLFAAGAGLELEDIAALRTEGSLTPGHPEYGHTHGVEVTTGPLGQGLAMAVGFAYEQRRLRGL +MDPDAAPGTSPFDHHVFVLASDGDIQEGVSSEASSLAGHQELGNLVVVYDANRISIEDDTDISFTEDVAKRYKAYGWHVQ +EVDWSNGAQGHEVTEYTEGVQDLYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKLGGDEVVGLKEALGFDP +QKSFDVDPEVLAHARSISERSAAYRETWEAAFAAWREAHPENARLYDRLASRELPAGFEDAFPSWDADEKGVATRAASGK +VLTALAPVMPELWGGSADLAGSNNTTMEGEPSFIPAHRSTAAWQGDPFGRTLHFGIREFAAGAIVNGITIGGLTRAYMGT +FLTFSDYMRGAVRLAALMGTPAVYVWTHDSVGLGEDGPTHQPVEHLAALRAIPGLDVVRPADANETAWAWRTILQHRDRP +AGLVLTRQNVPVLPRGTEGFAPADGVARGAYVLVDGADASGAAAPARVVLIATGSEVSVAVGARELLQAEGVPTRVVSAP +CLEWFAEQDEAYRAEVLPDGPGAPVRVSVEAGIAMPWHELTVTQSSRGARVSLEHYGESADGPHLLKKYGFSPENVADTA +RGLL +>GCF_023573625_PROKKA_01082 +MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPVAWQLYQNVMHLDPTDDRWEG +RDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSRTPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGL +MDPDAAPGTSPFDHHVFVLASDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ +EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKLGTDEVAGLKESLGLDP +TKTFDVDPELLARARSIAERSAEYRRGWEAAFQAWREANPENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGE +VLTALAPVMPELWGGSADLAGSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYMGT +FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRPADANETAWAWRTVLEHRDRP +AGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDADGAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAP +CLEWFAEQDEAYRAEVLPDGPDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT +RGLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000944.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000944.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b2ce1e44d17790608b78e161dca593bb7255cab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000944.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01135 +MSTPVVDHRA---------PAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVL +PLLALVGVHVTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT +TPLGTLGLVAGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTAL +GLLLAGTARPEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAW +SPVPLLVLTLWGAVAVAAALRWFRWRP +>GCF_003691675_PROKKA_00854 +MSTPVVDHRA---------PAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVL +PLLALVGVHVTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT +TPLGTLGLVAGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTAL +GLLLAGTARPEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAW +SPVPLLVLTLWGAVAVAAALRWFRWRP +>GCF_005280335_PROKKA_01757 +MSAPIAPGSAEPRTAGQVPEPGTAPHAGAAPLATRVLRQAAYETGTALRNGEQLLVTVVL +PLLALVGVHVTGLLDEPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT +TPLGTLGLVAGKALSVVALLLVQVAVIGGVGLALGWRPEAAGILPAVVALALGAAAFTAL +GLLLAGTARPEATLAAANLLWVLFGAVGGTVFPSRVPGVDLLPSGALGSALRAALVDGAG +APIPLLVLALWCAVAVAAALRWFRWRP +>GCF_020097155_PROKKA_01651 +MSAPA--------------APIPASHAGAAPLGARILAQARYETVTALRNGEQLLVTLVL +PLLALVGVHVTGLLDAPGRNGLDLAVPGVLALAVISAAFTATAISTGFERRYDVLAALAT +TPLGTGGLVAGKAAAVAAVLLLQTIVIGGVGLALGWSPDPAGIPPAVVALLLGAAAFTAL +GLLLAGTARPEATLAVANLVWVLLGALGGTVFPSRWAWMDLLPSGALGTALRSALQDGAW +APSALAVLAAWTVMAVAAALRWFRWRP +>GCF_023573625_PROKKA_01085 +MSTPVVDHRA---------PAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVL +PLLALVGVHVTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT +TPLGTLGLVAGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTAL +GLLLAGTARPEATLAVANLLWVLFGAVGGTVFPARVPGVGLLPSGALGTALRAALLDGAW +SPVPLLVLTLWGAVAVAAALRWFRWRP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000950.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000950.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b7cbea2f98db0275c051e5e0f36123fffb335eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000950.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01141 +MTETANQVPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>GCF_003691675_PROKKA_00860 +MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>GCF_005280335_PROKKA_01751 +MTETANQVPTEDVREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>GCF_020097155_PROKKA_01645 +MTDTAAQTPVEDIREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGKDQMRALGFNI +>GCF_023573625_PROKKA_01091 +MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000953.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba3ee8962c6380ee8ed5b088f456c7ce50f09f8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000953.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01144 +MS-IPAPMT--DPTARDAERLPALRFGFLATGPWILGFVVCVLFAFLCHALAQWQWDRRV +EVQHRVNRVLENYDDDPVPFAEASRLFTAFQTDDEWTPVTLTGEYLVDETLIVRNRPRAG +QPGYEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDR +DAPDGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVEPMPQKLVEPTLDEGPHLSYAI +QWYLFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDE +EAEDALFD---------------- +>GCF_003691675_PROKKA_00863 +MS-TPAPMS--APTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRV +EVQHRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAG +QPGYEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDR +DAPDGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAI +QWYLFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDE +EAEDALFD---------------- +>GCF_005280335_PROKKA_01747 +MT-APAPATGFRRD-PGSARPPRLRFDFLATPPWILGFVLCILFAFACHYLAQWQWERRV +QVQHQVNRVLENYDDAPVPFAQASRMFTDFDAQDEWTPVTLSGEYLAEETLVVRNRPRAG +RPGYEVLVPFRTDEGPVVVVDRGWLPVGNTPGRPDAVPAPPAGPAEVVVRVKPGEPALDR +DAPEGQVPSIDLAEIRGHVGGPVADTAYGIMVEEDPAVQDLPQKLVEPTLDEGPHLSYAI +QWYLFAAMGFGVWGYSAWMRARNDRADALEGVRDDGMLTARRAPRPKPVRRRRDGRPTDE +EAEDALFD---------------- +>GCF_020097155_PROKKA_01642 +MTPAPAPTD--TPDAPGAERLPPLRFGFLASGPWILGFVVCILFAFLCHGLAQWQWDRRV +QVMHDVNRVLANYDDDPVPFAEAPRLFTDFDSEDEWTPVTLTGRYETDETLVVRNRPRAG +APGYEVLVPFVTEEGVTVIVDRGWLPIGSQPGRPDAIPAPDPAAGEVVVRVKPGEPALDR +DAPEGQVPSIDLAAIERILGRPIADTAYGLMVSESPAAATVPNQLVAPTLDEGPHLSYAI +QWYIFAAMGFAVWGYSAWMKARNDRADALEDAEDDGLLAARRAPRPKARRRRRGGRPSDE +EVEDALQEDVLRDRPGQASEIRSR +>GCF_023573625_PROKKA_01094 +MS-TPAPMS--APTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRV +EVQHRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAG +QPGYEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDR +DAPDGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAI +QWYLFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDE +EAEDALFD---------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000954.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000954.fa new file mode 100644 index 0000000000000000000000000000000000000000..01e83827ca4237f4af5deafe88dfc737342bfd9c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000954.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01146 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDD-TAAP-EP +VVLTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA +>GCF_003691675_PROKKA_00865 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDD-TAAP-KP +VVLTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA +>GCF_005280335_PROKKA_01746 +MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL +FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPAD-APGPASP +VVLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA +>GCF_020097155_PROKKA_01640 +MAAIVREPDA-------------VQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAAL +FTHGWWQILFILGAVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGP +VVLVGEVVEDDDPAARRALP-----AGSPGETGRGRP +>GCF_023573625_PROKKA_01096 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDD-TAAP-KP +VVLTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000956.fa new file mode 100644 index 0000000000000000000000000000000000000000..347e04b850e7cdffa71a289131f2d3a8adaf10d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000956.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01149 +MSTLRRLVVTADPALLVTDAPP--AGVPDDAERLTDDGLLGWRF-----AADEWAAAPEP +GSGWDVLTVPATVAAAPAPLVVTDVDSTLIRQEVIELLAAHAGREAEVAEVTERAMRGEL +DFAASLHARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLA +PLAEAWGVHAYCANELEVQDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGD +GANDIDLLEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL +>GCF_003691675_PROKKA_00868 +MSTLRRLVVTADPALLVTDAPP--AGVPDDAERLTDDGLLGWRF-----AADEWAAAPEP +GSGWDVLTVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGEL +DFAASLHARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLA +PLAEAWGVHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGD +GANDIDLLEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL +>GCF_005280335_PROKKA_01743 +MSTLRRLVVTADPALLADRTPP--AGVPDDAERLLEDGLLGWRF-----AADEWAAAPEP +GPGWAVHTLPAAVAEAPVPLVVTDVDSTLIRQEVIELLAAHAGREAEVAAVTERAMRGEL +DFAASLHARVEALAGLPVGVVDDVVRAIRPTAGALALIEAVTAAGGRVCAVSGGFSQVLA +PLAQAWGVHAYCANELEVHDGHLTGRVAGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGD +GANDIDLLDAAGAGVALCAKPVLREHADVVVDVPSFTPLRWLLGL +>GCF_020097155_PROKKA_01637 +MTQARHLLYRAVPAGTDSPVAPAWAPLPADAEHLAADGLAGLRWEGSVPSAEEATALPE- +--DWALASLPQSVAAAPTPLVVTDVDSTLIQQEVIELLAAHTGREAEVAAVTERAMRGEL +DFAQSLHARVEALAGLPASVVDDVVARVRPTDGAVELIAAVNAAGGRVCAVSGGFTQVLA +PLAEAWGVHAYCANELEVRDGHLSGKVLGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGD +GANDIDLLEVAGCGVALCAKPILREHADVVIDVPSFTPLRWLLGL +>GCF_023573625_PROKKA_01099 +MSTLRRLVVTADPALLVTDAPP--AGVPDDAERLTDDGLLGWRF-----AADEWAAAPEP +GSGWDVLTVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGEL +DFAASLHARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLA +PLAEAWGVHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGD +GANDIDLLEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000963.fa new file mode 100644 index 0000000000000000000000000000000000000000..79ae1ee74d7630f835edac6886e76a47f5e9082f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000963.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01158 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR +>GCF_003691675_PROKKA_00877 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR +>GCF_005280335_PROKKA_01731 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID +TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE +DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR +>GCF_020097155_PROKKA_01629 +MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA +GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID +TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA +DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE +AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA +DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR +>GCF_023573625_PROKKA_01108 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000965.fa new file mode 100644 index 0000000000000000000000000000000000000000..8b03f4ff0cb316ed2299d421428616d3b16da74d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000965.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01161 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR +>GCF_003691675_PROKKA_00880 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR +>GCF_005280335_PROKKA_01729 +MTQ-----PETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVA +RFGLQGERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLA +DKIRLGRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAP +EPAGAGEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFR +GLDRDNNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAER +GLPVLAEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLH +EKGEGSLGLVSVCAAGGQGIVALLRGR +>GCF_020097155_PROKKA_01626 +MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA +RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA +DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP +EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR +GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR +NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH +EKGEGSLGLVSVCAAGGQGIVALLRGR +>GCF_023573625_PROKKA_01111 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000966.fa new file mode 100644 index 0000000000000000000000000000000000000000..301057919e6e03fbe97a2be473cd6aa59bec5563 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000966.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01162 +--MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTL +LASWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFED +PEAATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGR +AAYVSGQFVPVATADGAVPADA-ARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVD +VPAAGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDAVVHNAGITRDRMLA +NMDAARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAA +SKAGVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQ +DVAETVAWLASDAAGGTNGATLRVCGQSKLGA +>GCF_003691675_PROKKA_00881 +--MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTL +LASWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFED +PEAATDPALRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGR +AAYVSGQFVPVSTADGAVPADA-ARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVD +VPAAGETLAKVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLA +NMDAARWDSVLAVNTTAQLAMNEAFLAEDARDVAGHGLRIVGLASISGIAGNRGQTNYAA +SKAGVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQ +DVAETVAWLASDAAGGTNGATLRVCGQSKLGA +>GCF_005280335_PROKKA_01728 +--MTDRYGAFAASALGRRLTGALGLPQPVELRRHAPGEPVLHGSVLVLGAGPAAADARTL +LASWGLEVADAPREGARLAGVVACFDDAAAPGDLGETVLQIGGALRSLGASSRVVTVSVD +PEAAAEPAVRAARQGVQGLTRSLAQEMRRGGTANGIVLGEGVPLTAPGAAGALAFLLSGR +SAYVSGQFLPVTTRDGATPADA-ARPLADKVAVVTGAARGIGAAIVRTLARDGATVVGVD +VPVAGESLAAVVNEVGGTALALDITAPEAGARILEHCRARHGRMDVVVHNAGITRDRMLA +NMDAARWDSVIAVNTASQLAMNEAFLADDAREVTGEGLRIIGLASISGIAGNRGQTNYAA +SKAGVIGLTAASAPALAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNSLQQGGLPQ +DVAEAVAWFASDAAGGTNGATLRVCGQSKLGA +>GCF_020097155_PROKKA_01625 +MPANDPYGDLVRTRLGRRLTGALGLPQPAELRRHTAGDPAVRGTVLVLGATSAADAARAL +VTAEGARAVAHPAEGERLAAVIACFDGVAAPGDLSDTALALGGALRSLEPSAHVVTVVED +PEEAEVPAVRAARAGVMGLTRSLAHEMRRGGVANGLLLRGGARLGDAGPAGALRFLLSGR +AAFVSGQFLPAAAGAGSAPASADARPLEGRVAVVTGAARGIGAAILRTLARDGATVVGVD +LPAAGEDLVRIVNELGGTALPLDITAPDAGARIVEHARARHGRLDVVVHNAGITKDKLLA +NMDAARWDAVLAVNTASQLAINEVLLSAEAADVVSPDIRIVGLASISGIAGNRGQTNYAA +SKAGVIGLTAATAPDLAARGGGITAVAPGFIETEMTAKIPLVTRELGRRVNSLQQGGRPE +DVAEAVAFLSSPAASGINGTTLRVCGQSMLGA +>GCF_023573625_PROKKA_01112 +--MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTL +LASWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFED +PESATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGR +AAYVSGQFVPVATADGAVPADA-ARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVD +VPAAGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLA +NMDAARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAA +SKAGVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQ +DVAETVAWLASDAAGGTNGATLRVCGQSKLGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000969.fa new file mode 100644 index 0000000000000000000000000000000000000000..4359d50cdd08d253a4269ffec40046e57da69e29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000969.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01166 +MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE +RVPVDALEFGCRVLERMLEPR- +>GCF_003691675_PROKKA_00885 +MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE +RVPVDALEFGCRVLERMLEPR- +>GCF_005280335_PROKKA_01723 +MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL +FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT +SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV +ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE +RVPVDALEFGCRVLERMLEPR- +>GCF_020097155_PROKKA_01621 +MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL +IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV +DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA +ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG +RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT +AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV +ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE +RVPVESLRFGCRVLEHVLEPRA +>GCF_023573625_PROKKA_01116 +MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE +RVPVDALEFGCRVLERMLEPR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000977.fa new file mode 100644 index 0000000000000000000000000000000000000000..a920ff1fe828cf7e5cf933083adac386ce1008d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000977.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01174 +MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE +FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV +QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEH +PAWSVHLGDAQEEMPKVHEPGSVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQL +SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALR +LKKRSKVSEFRAEDVEAWQPADEARWTPEALGERPITDKKARKAAKEARLMAARSRAAEQ +GVDAYGGRTPTGEQD +>GCF_003691675_PROKKA_00893 +MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE +FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV +QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEH +PAWSVHLGDAQEEMPKVHEPGSVDRVVLDMLAPWECLDTVAEVLAPGGVWLNYVATATQL +SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALR +LKKRSKVSEFKAEDVEAWQPADEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQ +GVDAYGGRTPTGEQD +>GCF_005280335_PROKKA_01715 +MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE +FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV +QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERREEFADVARANVEAFFGAEH +PAWSIHLGDAQEQMTRVHEPGSVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQL +SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLATGEEALR +LKKRSKVSEFKAEDVEAWQPADEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAER +GVDAYGGSIQEQDQD +>GCF_020097155_PROKKA_01613 +MSDATAPETPAAPTTPDTAAPAGRPAGVTARRGPLRAGQRVQIKDAKGRLNTITLLPGGE +FHSYQGVLRHDDLIGGPEGIVVQNSSGHAYQVLRPLLNDFVLSMPRGATVVYPKDAGQIV +QQADIFPGAVVVEAGVGSGALSMSLLRAVGDAGRLHSYERRAEFAEIARGNVESFFGGVH +PAWSIHLGDAQEEMPKVHEPHSVDRVVLDMLAPWECLDAVATVLAPGGVWLNYVATATQL +SRVAEAIRASGKFTQIEATETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLAAGEDALV +MKKRLKVSEFTTEDVEAWTPSDGARWTPQALGERTVTDKKARKAAKEARLTARRARAALE +GRDP---RTVGQDKD +>GCF_023573625_PROKKA_01124 +MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE +FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV +QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEH +PAWSVHLGDAQEEMPKVHEPGSVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQL +SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALR +LKKRSKVSEFKAEDVEAWQPADEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQ +GVDAYGGRTPTGEQD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000982.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d3c099115f735c752b75c496c63a986d4c2ac75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000982.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01179 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>GCF_003691675_PROKKA_00898 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>GCF_005280335_PROKKA_01710 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>GCF_020097155_PROKKA_01608 +MAQEQIRPRPAGGPEDEGAAA-QAQAKAAPQDTGLDGLLDEIDSVLESNAEEFVKGFVQK +GGQ +>GCF_023573625_PROKKA_01129 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLVSNAEEFVKGFVQK +GGQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000986.fa new file mode 100644 index 0000000000000000000000000000000000000000..b12aac07b15f6774503e1906447ff40123be6198 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000986.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01184 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEG-----KGT-- +-TDERS-GAGSTAADEPVEGRVVERDETD--PRDPR +>GCF_003691675_PROKKA_00903 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEG-----KGT-- +-TDERS-GAGSTAADEPVEGRVVERDETD--PRDPR +>GCF_005280335_PROKKA_01704 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTED-----KGAKD +GKDARS-GSGSTAADEPVEGRVVERDETDVRPRDER +>GCF_020097155_PROKKA_01603 +MR-FTPTHLIVLIIVVLLLFAAPKLPALARNLGQSMRIFSSEVKQMKEENTTKKAEGAAT +-ADAPSQGAGSTAA-EPVEGRVVDRDVRD--DR--- +>GCF_023573625_PROKKA_01134 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEG-----KGT-- +-TDERS-GAGSTAADEPVEGRVVERDETD--PRDPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000989.fa new file mode 100644 index 0000000000000000000000000000000000000000..85e4adbb69ff30d1fa355e4326b4097a1f073de6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000989.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01187 +---MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVV +PVFVEPLARPADARDALSRGTAVVTVLAGPEDTG---AAPADEDVQTVVYRHADRVDAEA +AGVWLPVGTDTDPATLTGLLTASTQAGEQAYLVP------DGGADAGPAAQDVALTALRS +VAEELGTAALGRVRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAV +TVCLGAGPAGDPWAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRL +SVSAPAVFGVWDADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRI +AAEDVARDAHDAATPA +>GCF_003691675_PROKKA_00906 +---MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVV +PVFVEPLARPADARDALSRGTAVVTVLAGPEDTG---AVPADEDVQTVVYRHADRVDAEA +AGVWLPVGTDTDPATLTGLLTASTQAGEQAYLVP------DGGADAGPAAQDVALTALRS +VAEELGTAALGRVRHRLVVTHSVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAV +SVCLGAGPAGDPWAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAAGLSVAPRL +SVSAPAVFGVWDADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRI +AAEDVARDAHDAATPA +>GCF_005280335_PROKKA_01701 +MGRVTAHLLTTGIIHSVTDPYAQALLVRDGVIAWLGADDSAERVADPADARTDLDGAVVV +PAFVEPLARPEDARDALSRGTAVVTVLAGP--AG---DVAPAEGVQAVVYRHAEGPAEGA +VGVWLPVAADADAADLAAALAEATRAGEQAYLVPAADAAGHGDAEAPAAAQAAAIAALRR +VAEELGAPALGRVRHRLVVTSPVTAEDRAFLASVAVSATVVPAADGTLRAPVASLLADAV +PVALGAGPGRDPWAAVRAALSHPEEAERISARSAFAAATRTPLRALPDAADADLVAAPRL +AVSAPGVFGVWEAEAVAVQSPDGRVAAWSTDTRAGTPLLPALDDQTPLPRWRATWVGGRI +AAEAADGDARGTGDHA +>GCF_020097155_PROKKA_01600 +---MSSTLFLNGIVHSASDPYATAALVSDGVVAWLGDDSSADRVADPDVPRVDLAGAVLA +PAFVEPGGPSVDPAQALRHGVAIVTVLAEPGQTAQALQAAADPALQTVVYRAADTVDAEA +AGVWLP----AEGEALAALVVASTRAGEQVHLVP------PAGGD-PSEGQAAALAALRS +AAEELGAPALGRVRHRVVLTAPITAEDRALLAAISASVTVGPEADGLLRAPLGTLLAEGV +PVCLSTAGEAGPWAAVRAALSHPDEAERISARSAFTAATRTPLRVLPDAPGATVQAAPRL +TVSAPATFAVWEADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRP +AAVEVA--------DA +>GCF_023573625_PROKKA_01137 +---MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVV +PVFVEPLARPADARDALSRGTAVVTVLAGPEDTG---AAPADEDVQTVVYRHADRVDAEA +AGVWLPVGTDTDPATLTGLLTASTQAGEQAYLVP------DGGADAGPAAQDVALTALRS +VAEELGTAALGRVRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAV +TVCLGAGPAGDPWAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRL +SVSAPAVFGVWDADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRI +AAEDVARDAHDAATPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000993.fa new file mode 100644 index 0000000000000000000000000000000000000000..6485ecc685ada79119630019c9d4f5b9283b7d58 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000993.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01191 +MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV +EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADG-A +>GCF_003691675_PROKKA_00910 +MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV +EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADG-A +>GCF_005280335_PROKKA_01697 +MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV +EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWE-DGRS +>GCF_020097155_PROKKA_01596 +MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV +VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV +EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD +>GCF_023573625_PROKKA_01141 +MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV +EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADG-A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000998.fa new file mode 100644 index 0000000000000000000000000000000000000000..dbd1cde06dde7e9b3855b699c0dc2625d36b0c77 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000998.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01196 +MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRAYSSEDLGEGWALGFDS +>GCF_003691675_PROKKA_00916 +MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS +>GCF_005280335_PROKKA_01691 +MVTAIVMIKTDKSSIPETAETLAALEGIGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVEGIQDTETMLAFRTYSSEDLGEGWALGFED +>GCF_020097155_PROKKA_01589 +MVTAIVMITTDKSTIPETAQAIASLEGVSSVYSVTGAWDLVAMVKLKRYEDLADVIADQL +SKVDGIEDTETMLAFRTYSTEDLEEGWALGFDG +>GCF_023573625_PROKKA_01150 +MVTAIVLIKTDKSSIPETAEALAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000999.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000999.fa new file mode 100644 index 0000000000000000000000000000000000000000..5bdc86a7f19dd0b725ccb3032f38cf9379302d53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000999.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01197 +MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVTAQALGCSSQAMVPLLAQVLADRGVRGFVFRGADGRDKITT +SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV +LLNAAAGLTAWDRGADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS +>GCF_003691675_PROKKA_00917 +MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT +SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV +LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS +>GCF_005280335_PROKKA_01690 +MSIPNTTAAAPETTWPDVFRALTFGEDLSDEAAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAARPVQVTGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPREKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVSAQALGCSSEVMVPLLARVLADRGVRGFVFRGSDGRDKITT +SGPSTVIEVRHEVTAHELDPRDFGIELAPVEALAGRDGAYNATLVHALLAGEKGPIRDAV +LLNAATGLTAWDTEAQGPLADRLAANMARAAESLDSGAARDVLDRWVAFSRS +>GCF_020097155_PROKKA_01587 +MR------ETVTHTWPEVFRRLTLGQDLDDAAAEWAMGEMMSGDATEGQVGAFLLALAAK +GETVPELRGLTDAMVAKARRVHVSGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPPAKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQASAQALGCSSEEMVPLLAQVLADRGVRGFVFRGSDGRDKITT +SGPSTIMEVRGGVTAHEIDPRDFGIELAPVEALAGRDGAYNATLVRGLLAGEHGPIRDAV +LLNAAAGLTAWDVEAEGPLMDRLRTNMARAAESIDSGAAADVLERWVQFSRS +>GCF_023573625_PROKKA_01151 +MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT +SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV +LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001001.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f729f2cc5fa4cc7d099a79c2de02df7adc1c81c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001001.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01199 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF +NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA +QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>GCF_003691675_PROKKA_00919 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF +NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA +QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>GCF_005280335_PROKKA_01688 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF +NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA +QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA +PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>GCF_020097155_PROKKA_01585 +MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF +NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA +QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA +PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG +PVAEGLFIWTAGLALIVGFMVWLTSRSS +>GCF_023573625_PROKKA_01153 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF +NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA +QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001003.fa new file mode 100644 index 0000000000000000000000000000000000000000..b24c49294225abdc81e89d65559b6060ea3914cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001003.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01201 +MSTTVNEFQPATSTGRIANFVDTRTGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLLSGAFLTFFFDPSMSEVVYNG +AYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALMFVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAG +FTGYSLPDEVLSGNGLRIIDGILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQAGTQPDWYIGVFDGALRLMP +GMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGMCAWPWIERWITKDDTEHHLLDRPRNAPARTGIGVAAVVWY +CVMWAAASSDLIATHFHLSLNDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRP +LTDYELYRLVAFEDRRPVPAIPGRNGKVGALEKARAGLNRMFYQERVAPVSREELVEARTHGQHGH---EE---HPVELG +HGSDAPRLER +>GCF_003691675_PROKKA_00921 +MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLLSGAFLTLFFDPSMSEVVYDG +AYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALMFVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAG +FTGYSLPDEVLSGNGLRIIDGILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQAGTQPDWYIGVFDGALRLMP +GMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGMCTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWY +CVMWAAASSDLIATHFRLSLNDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ +LTDYELYRLVSFEDRRPVPAIPGRNGKVGMLEKARAGLNRMFYQDRVAPVSREELVEARTHGQHGH---EE---HPVELE +HGSHAPHLDR +>GCF_005280335_PROKKA_01686 +MSTTVNEFQPATSTGRIANFVDTRMGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLLSGAFLTFFFDPSMSEVVYNG +AYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALLFVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAG +FTGYSLPDEVLSGNGLRIIDGILKSLPIVGTYLSAFFFGGEFPGHSIIGRLYALHIMVVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQAGTQPDWYIGVFDGALRLMP +GMIGDFSFLWNIPMPWGSSVSLPMGVLVPLIPIGVLIVGMCAWPWIERWITKDDTEHHLLDRPRNAPTRTGIGVAAVIWY +CVMWAAASSDLIATHFRLSLNDVLYALRTLFFLGPVIGFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPDGGFHERHRQ +LTDHELYRLVSFEDRRPVPALPNRSGKVGMIEKARAGLNRMFYQDRVAPVTREELVEARAHGHHGV---EDGGHHELGAD +PSSHNPKIDG +>GCF_020097155_PROKKA_01583 +MSTATHEYQPATGTGRLANFLDTRVGLSPIVKFFGRKTFPDHWTFMFGEVALYSFVILLLSGAFLTFFFDPSMSHVTYDG +AYAPLRGIEMSAAMASALDISFDIRGGLFMRQLHHWSALLFVASMSVHMLRIFFTGAFRRPRELNWVVGCFLLMAGWAAG +FTGYSLPDDVLSGNGLRIIDGILKAMPLVGSYLSAFLFGGEFPGYSVIGRLYALHIMIVPAIILLLIAVHLFMVVVHKHT +QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINSIWIYGPYDPSPVSAGTQPDWYIGPFDGALRLMP +GMIGDFSFLWNIPMPWGSRVSLPMGVLTPLIPVGVILVGMISWPWIERWITKDDREHHLLDRPRNAPARTGIGVGMMIMW +CTMWAAASSDLIATHFHLSLNDVLYFLRALFILGPILGFIVTRRICISLQRRDRETVLHGHESGVVEMSPEGGFSERHRQ +LTDYEMYRLVSFEDRRPVPATPGRNGKVSGAERMRAGLNRMFYQERVAPVSREELVEARTHGHGEHVGAVQGGSHSAELG +H--------- +>GCF_023573625_PROKKA_01155 +MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLLSGAFLTLFFDPSMSEVVYDG +AYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALMFVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAG +FTGYSLPDEVLSGNGLRIIDGILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQAGTQPDWYIGVFDGALRLMP +GMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGMCTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWY +CVMWAAASSDLIATHFHLSLNDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ +LTDYELYRLVSFEDRRPVPAMPGRNGKVGALEKARAGLNRMFYQDRVAPVSREELVEARTHGQHGH---EDGGHHELGAD +PSSHNPKIDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001004.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5cdd5fd361cae6937dd06491f661edae853e0ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001004.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01203 +MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPAIYALGGMSWMIAWYLNAAERKYGV +GPADDEDGQIVEYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFVIGIIAGAYFTF +GWVYEFSRGKFAH +>GCF_003691675_PROKKA_00922 +MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLNVTERKYGV +GPADDADGQIADYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWIFIIGVIAGAYFTF +GWVYEFSRGKYAH +>GCF_005280335_PROKKA_01684 +MKVAANIFWIIGLFFIAAATLYGFWVEWTEWAGIPAIYAVGGMSWMIAWYLQSTEKKFGL +GPADDEDGEITDYAGTYGTFAPWSWWPLGLGVACAILITGLAVGWWVFIIGAVAAAYFTF +GWVYEFSRGKYAH +>GCF_020097155_PROKKA_01582 +MKIASNIFWIIGAFLVAVATLYGFWVKWTEWAGIPAIYALGAMCWMIAWYVQSTDKRHGL +GPADDEDGEIVEYAGTYGTFAPSSWWPLGVAVACAMLVTGLAVGWWIFALGVIAGVYFTF +GWVYEFSRGKYAH +>GCF_023573625_PROKKA_01160 +MKVAANIFWVIGLFFVGAGTLYGFWNEWTEWAGIPALYALAGMSWMIAWYLNAAERKYGV +GPADDEDGQIVDYAGTYGTFAPWSWWPLGLGLACAIIVTGLAVGWWVFIIGVIAGAYFTF +GWVYEFSRGKFAH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001006.fa new file mode 100644 index 0000000000000000000000000000000000000000..17c9e739d27f02a2582d283734419d3e5ddd4b63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001006.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01205 +-------------------MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNS +WIAAMVVGLLVWGAMIWCMVAYRRRKNDQGFPKQTAYNVPLETMFTAIPILTVFTLWGFT +DRVQTEVDRPVDDSPLTVTVYGKQWSWDFNYSYEQEDGEVIEAHYSGIQAQLDGTEGVRD +TLPVLYLPNDVPVHFELKSRDVVHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCA +ELCGEFHSEMLFNVEVVDEAEFVQRLEEMESGQVGEEYSRNPNNNPDGAGTMERDLQTPR +GGGSH +>GCF_003691675_PROKKA_00924 +-------------------MGTTSLLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNS +WIAAMVVGLLAWGAMIWCMVAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFT +NRVQTEVDRPVDDSPLTVTVYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRD +TLPVLYLPNDVPVHFELKSRDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCA +ELCGESHSEMLFNVEVVDEAEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPR +GGGSH +>GCF_005280335_PROKKA_01682 +-------------------MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNS +WIAAMVVGLLAWGAMIWCMVAYRRRKNDQGFPKQTAYNVPLETMFTIIPILMVFTLWGFT +NRVQTEVDRPVDDSPLTVTVYGKQWSWDFNYSYEQENGEVVEANYSGIQAQLDGTEGVRD +TLPVLYLPKDVPVHFELKSRDVAHSFWIPQFLQKRDLIPGKTNHLYLTPQELGSYDGKCA +ELCGEFHSEMLFNVEVVDEAEFVDRLAEMEPGLVGDEYSRNPNNNPDGAREMERDLQTPR +GGGSH +>GCF_020097155_PROKKA_01580 +MRAQNDAGRRTRRRLTAGALGATALVALTGCSAEAQRGWLPGTDNTTNHNAQLTDLWVNS +WIAALAVGLIAWGAMIWCMIAYRRRKNDQGFPRQTAYHMPIETMFTVIPILMVFTLWGFT +DRVQAEVDTPIDDSPLTVTVYGKQWSWDFNYSYEKD-GQTREAHFQGVQAQLDGSDGKRE +TLPTLYLPKDVPVHFELKSRDVAHSFWIPQFLQKRDMLPGKTNNLYLTPQEIGRFDGKCA +ELCGEFHSEMLFNVEVVDEATFVQKMNEMEPGLVGDELNRNPNQNPDGARNMEVDLQTPR +GGGNH +>GCF_023573625_PROKKA_01162 +-------------------MGTTALLVLTGCSAEVQRGWYPGTRETTNHNAQLTDLWVNS +WIAAMAVGLLAWGAMIWCMVAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFT +DRVQTEVDRPVDDSPLTVTVYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRD +TLPVLYLPNDVPVHFELKSRDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCA +ELCGEFHSEMLFNVEVVDEAEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPR +GGGSH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001007.fa new file mode 100644 index 0000000000000000000000000000000000000000..d72a6e43b1c45950ccd71563f88d1c2fe6661140 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001007.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01206 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH +>GCF_003691675_PROKKA_00925 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH +>GCF_005280335_PROKKA_01681 +MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV +GSCACGDSFH +>GCF_020097155_PROKKA_01579 +MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV +GSCACGDSFH +>GCF_023573625_PROKKA_01163 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001008.fa new file mode 100644 index 0000000000000000000000000000000000000000..a12eddd23d41edb460d26a959a3441a77daa7f70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001008.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01207 +MTDITSRAPQDAA----LVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSA +EAVAGLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDED +LWDTPPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAG +SPTFRTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGM +FGGPVLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAG +RGPVADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHL +EAQSAAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTA +DLAEVFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA +>GCF_003691675_PROKKA_00926 +MTDITSRAPQDAA----LVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSA +EAVAGLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDED +LWDTPPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAG +SPTFRTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGM +FGGPVLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAG +RGPVADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHL +EAQSAAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTA +DLAQVFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA +>GCF_005280335_PROKKA_01680 +MTETTPPVRDDAA----LVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSS +EAVAALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEA +LWDTEPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAG +SPTFRTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGM +FGGPVLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAG +RGPVADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHL +EAQSAAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTA +DLAEVFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG +>GCF_020097155_PROKKA_01578 +MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA +AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG +LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG +SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM +FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG +RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL +EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA +DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA +>GCF_023573625_PROKKA_01164 +MTDITSRAPQDAA----LVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSA +EAVAGLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDED +LWDTPPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAG +SPTFRTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGM +FGGPVLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAG +RGPVADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHL +EAQSAAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTA +DLAEVFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001014.fa new file mode 100644 index 0000000000000000000000000000000000000000..75008cb76118c0041b104bf0e6ff919cb80c02db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001014.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01214 +MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL +SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVMVEEM +SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF +>GCF_003691675_PROKKA_00933 +MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL +SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM +SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF +>GCF_005280335_PROKKA_01674 +MTDLVDPARAADGHRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGQRLNDLVAETLGEVDAVGFCLPADEAIGPGDRFIAQQL +AHLHRTPVVAVVTKTDKVGPEQLMAQLLAVTALGEEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLEVLRGLLPEGPPLYPDGELTDEPEAVMIAELIREAALEGVRDELPHSVAVVVEEM +ALREGRPDDRPLMDVWANLFVERDSQKGIIIGKGGSRLREIGARARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF +>GCF_020097155_PROKKA_01571 +MTSLLDPA-VPEGHRSGFACLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +RPDFQLVLVDTPGLHRPRTLLGERLNALVQETLSEVDVVGFCLPADEKIGPGDRFIAQQL +AALRRTPVVAIVTKTDKTDPQRVAEQLLAVTALGDEVLGPENGGRGFAAVVPVSAVAGRQ +VEDVESVLAQLLPDGPPLYPDGELTDEPEAIMVAELIREAALEDVRDELPHSVAVVVEEM +NPREGRPEERPLLDVYANVFVERDSQKGIIIGKGGSRLRAIGTQARTGIERMLGTPVHLD +LRVKVAKDWQRDPKHLNRLGM +>GCF_023573625_PROKKA_01171 +MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL +SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLGVFAGLLPAGPPLYLDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM +SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001017.fa new file mode 100644 index 0000000000000000000000000000000000000000..51e8af00006d35f05bef9b78fcb02d48d67bdcc7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001017.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01217 +MSRPRDPEVIRPIVTVPPT---TPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVF +PTVDVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGR +GAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQAL +QAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGT +IEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGT +QSGLAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARG--------PAERSQK +RGGARRGR +>GCF_003691675_PROKKA_00936 +MSRPRDPEVIRPIVTVPPT---TPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVF +PTVDVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGR +GAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQAL +QAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGT +IEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGT +QSGLAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARG--------PAERSQK +RGGARRGR +>GCF_005280335_PROKKA_01671 +-----------------------------------------MVRTLGPQDALLRILGGVF +PAVDLTVRDQRLEMAGPVPDVASVRRVVEDLRSIARRDQAVTPEVMEQVVTHVRGAAAGR +GAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQAL +QAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGT +IEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGT +RSGLSQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARG---------AEPAPR +GGRGHRGR +>GCF_020097155_PROKKA_01568 +--------MIRPIVSDPSSHVVLPPVSVPGAESVSFESAELMVRTLGAHDALLRILAGVY +PDVEVTVRDQSLGMSGPPRHVAQARRIVEDLRSLARRDAPVTPDVVEQVVSLVRDGETGR +ASGTLHLDSILSGRGRKIRAKTLHQQDYVEAIDRATIVFGLGPAGTGKTYLAMAKAVQAL +QAKEVTRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMESGT +IEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGV +RSGLAEAVEVLEGVDGLEMVRFDSSDVVRHSLVSAIVDAYDGARGSGSAADPRPAGRGAQ +RGRSGRGR +>GCF_023573625_PROKKA_01174 +MSRPRDPEVIRPIVTVPPT---TPTPPATAHEGVAFESADLMVRTLGPQDALLRILGGVF +PTVDVTVRDQRLDLAGPVAEVATVRRVVEDLRSIARRDQAVTPEVMGQVVHHVRDAATGR +GAGQLHLDSILSGRGRRIRAKTLHQQDYVEAIDRSTVVFGIGPAGTGKTYLAMAKAVQAL +QAKEVNRIILTRPAVEAGERLGFLPGGLSEKIDPYLRPLYDALHDMIEPESIPRLMEAGT +IEVAPLAYMRGRTLNDAFVILDEAQNTTGEQMKMFLTRLGFGARMVVTGDTSQVDLPRGT +QSGLAQAVEVLEGIEGLEMVRFDSSDVVRHSLVSAIVDAYDAARG--------PAERSQK +RGGARRGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001019.fa new file mode 100644 index 0000000000000000000000000000000000000000..1fb5d3bfcbbdeaff4de8d94251198aebe3a94159 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001019.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01219 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQA-GFPGGFGGAGGFGGFADIFETFMNAAGQGGRG-GPASRARRGQDAL +VTARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLL +GTVMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEA +GPGGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLD +PGVQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVH +GA-PQAKGMFARLRENLRNL +>GCF_003691675_PROKKA_00938 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQA-GFPGGFGGAGGFGGFADIFETFMNAAGQGGRG-GPASRARRGQDAL +VTARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLL +GTVMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEA +GPGGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLD +PGVQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVH +GA-PQAKGMFARLRENLRNL +>GCF_005280335_PROKKA_01669 +MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQS-GFPGGFGGGGGFGGFADIFETFMNAAGQGGRG-GPASRARRGQDAL +VTAPIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLL +GTVMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEA +GPGGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLE +PGVQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVH +GT-PPARGMFARLRENLRNL +>GCF_020097155_PROKKA_01566 +MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR +RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL +VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML +GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA +GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE +PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH +GAPPQSKGMFARLRENLKNL +>GCF_023573625_PROKKA_01177 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQA-GFPGGFGGAGGFGGFADIFETFMNAAGQGGRG-GPASRARRGQDAL +VTARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLL +GTVMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEA +GPGGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLD +PGVQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVH +GA-PQAKGMFARLRENLRNL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001025.fa new file mode 100644 index 0000000000000000000000000000000000000000..d14da85d626156c4ee44e1011cc261243ba34be7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001025.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01226 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>GCF_003691675_PROKKA_00945 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>GCF_005280335_PROKKA_01662 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>GCF_020097155_PROKKA_01559 +MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>GCF_023573625_PROKKA_01184 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001029.fa new file mode 100644 index 0000000000000000000000000000000000000000..73dfa6e36aa8354c33d3cc029cd40774e316c9d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001029.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01230 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR +ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD----- +>GCF_003691675_PROKKA_00949 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR +ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD----- +>GCF_005280335_PROKKA_01658 +MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG +IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR +ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR +SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA +AHLGLGALGVVVCPLESPTGGSGD----- +>GCF_020097155_PROKKA_01555 +MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG +IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR +ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV +AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR +TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA +AHLGLGTLAVVLSPLEPVPSTSSSPAQAN +>GCF_023573625_PROKKA_01188 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR +ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001030.fa new file mode 100644 index 0000000000000000000000000000000000000000..72c8a9d48582163ebd154722938ed43eee0252df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001030.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_01231 +MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPSGDLHMGHAEAFAMGDVVARH +WMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYR +RGLAYRKDSPVNWCPQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYREDLKKVSDIDRQATDRPKSGV +FLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQRDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNS +GELDGLDKTAAIARAIEIVQERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA +PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPEALRRWLPVDQYVGGVEHAILHL +LYARFFTKALHDLGLVPFTEPFRALLNQGQVLNDGKAMSKSLGNGVDLGDQLDQFGVDAVRLTMVFASPPEDDVDWADVA +PGAAGKFLARAWRLARDVRATGTPAGTDPADGAVALRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA +ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVIRAGWPAVDEALLVEDTVTAVVQVKGKVRDTLEVPADITAEDL +EARARASQKVRNFIGDAQIVKVIVREPKLVNLVIR +>GCF_003691675_PROKKA_00950 +MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPSGDLHMGHAEAFAMGDVVARH +WMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYR +RGLAYRKDSPVNWCPQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYREDLKKVSDIDRQATDRPKSGV +FLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQRDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNS +GELDGLDKTAAIARAIEIVQERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA +PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDALRRWLPVDQYVGGVEHAILHL +LYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSKSLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVA +PGAAGKFLARAWRLARDVRATGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA +ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQVKGKVRDTLEVPADITAEDL +EARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR +>GCF_005280335_PROKKA_01657 +------------------------------------------------------MFPYPSGDLHMGHAEAFAMGDVVARH +WMQRGYDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYR +KGLAYRKDSPVNWCPQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQIEDGPQITVFTTRPDTLHGATFMVVAADAPLAAELADESVRAELEAYREELKKVSDIDRQATDRPKTGV +FLGRHAINPLNGERLPVWASDYVLADYGTGAIMAVPAHDQRDLDFARAMGLPVRAVLDTGEENPAVSGVATTGDGTLVNS +GELDGLDKTAAIARAIEIVEGRGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCEACGEVLVPEDQLPVTLPTDLNGEQLA +PKGQSPLAAATSWVEVACPDCGGPARRDTDTMDTFVDSSWYTLRYASPNDDTQVFDPEAVRRWLPVDQYVGGVEHAILHL +LYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGRAMSKSLGNGVDLGAQLDEFGVDAVRLTMVFASPPEDDVDWADVA +PGAAGKFLARAWRLARDVREAGTPADADPATGSVALRRVTHRSVHEAGQLLDDGKFNVVIAKTMELVNAARKEIDGGAGA +ADPAVREAAEAVAVLLSLVAPYTAEDMWVMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQVKGKVRDTLEVPADITAEDL +EARARASQKVRTFIGDAEIVKVIVREPKLVNLVIR +>GCF_020097155_PROKKA_01554 +MSQTPESAAPATPQVPEDAEYAFSEVEARWAGYWEQAGTFTPRGDGSATRTVVDMFPYPSGDLHMGHAEAFAMGDVLARY +WLQRGYDVLHPIGWDSFGLPAENAAIKRNAHPAEWTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYR +KGLAYRKDSPVNWCPQDQTVLANEQVVDGKCERCGAEVTKRELNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPAVTVFTTRPDTLHGATFMVVAADAPLALELVDDEHRAALEAYREELKKASDIERQATDRPKTGV +FLGRHAVNPLTGERLPMWASDYVLADYGTGAIMAVPAHDQRDLDFARAMDLPVRTVVDTGEEDPAVSGVATTGEGTLVNS +GELDGLSKADGIARAIEIVQERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPEHGEVLVPEDQLPVLLPTDLKGGQLA +PKGQSPLAAAEEWVNVPCPECGAPARRDSDTMDTFVDSSWYFLRYASPWDEQQVFDPELVKTWLPVDQYVGGVEHAILHL +LYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSKSLGNGVDLGQQLDEFGVDAVRTTMVFASPPEDDVDWADVA +PAAAGKFLARAWRLARDVRAAGTPAG-DPAQGSAALRRVTHRTVHEAAALVEDHKFNVVVAKTMELVNATRKEIDGGAGA +ADPAVREAAEAVAILLSLVAPYVAEDMWAMLGHEPSVVRAGWPAVDESLLVEDTVTAVVQVKGKVRDQLQVPADVSAADL +EAAARASAKVRAFIGDAEIVKVIVREPKLVNLVIR +>GCF_023573625_PROKKA_01189 +MSQTPDSAVPATPSIPADAEYSFRDVEARWAGYWEQAGTFAPREDGSETRTVVDMFPYPSGDLHMGHAEAFAMGDVVARH +WMQRGFDVLHPIGWDSFGLPAENAAIKRDAHPAEWTYANIETQKRSFQRYGIAVDWSRELHTSDPEYYRWTQWLFQQLYR +RGLAYRKDSPVNWCPQDQTVLANEQVVDGRCERCGTEVTKRTLNQWYFRITEYADALLDDMDQLTGHWPERVLAMQRNWI +GRSEGAHVDFQVEDGPVVTVFTTRPDTLHGATFMVVAADAPLAAELAGDDVRAELEAYREDLKKVSDIDRQATDRPKSGV +FLGRHAVNPLTGERLPIWASDYVLADYGTGAIMAVPAHDQRDLDFARAMGLPVRTVLDTGEEDPAVSGVATTGEGILVNS +GELDGLDKTAAIARAIEIVQERGTGRGTTTYRLRDWLLSRQRFWGTPIPVVHCPDCGEVLVPEDQLPVTLPTDLKGEQLA +PKGQSPLAAATSWVEVDCPQCGGPARRDTDTMDTFVDSSWYMLRYASPNDDARVFDPDALRRWLPVDQYVGGVEHAILHL +LYARFFTKALHDLGLVPFTEPFRALLNQGQVLNGGKAMSKSLGNGVDLGDQLDEFGVDAVRLTMVFASPPEDDVDWADVA +PGAAGKFLARAWRLARDVRATGAPAGTDPAGGAVTLRRVTHRTVHEAQQLLDDGKFNVVVAKTMELVNAARKEIDAGAGA +ADPAVREAAEAVAVLLSLVAPYTAEDMWVLLGHEPSVVRAGWPAVDEALLVEDTVTAVVQVKGKVRDTLEVPADITAEDL +EARARASQKVRNFIGDAEIVKVIVREPKLVNLVIR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001031.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ddd6fd61e061bc1e19a9762109dbfe9a2da5325 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001031.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01232 +MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI +LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW +AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ +ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST +LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG +RYRPVFAGVTLLAFAVSFVGFGDLINVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL +RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPDAVTEALEDEVAQVLEEDD---- +-ALTSEGARPGPDAGPERPAGGSHSA-- +>GCF_003691675_PROKKA_00951 +MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI +LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW +AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ +ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTVLLLMAST +LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIYNTAIGMFYALGRRLTADHPG +RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL +RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDD---- +-AVTPDEVHPGPDAGPERPAGGSHSA-- +>GCF_005280335_PROKKA_01656 +------------------------------------------------------------ +-------------MVFRSVSHPVMARILDVTVTVTLFAIGFVMLAGAGSTLAQQLGWPTW +AGAGLMTALVLVTGMLDVEKVSAIISLITPLIILAVVAGFVHVLLTHEGSFTANEALAVQ +AATPVAPWWLSSVNYFGLVVVMAVSMCLVIGGSITNPREAFAGGLTGGVLYTVLLLLASV +LLYLGYAEIGRADVPMLQLFASIAPWLGWTMVVVIYLMIYNTAIGMLYALGRRLTAERPG +RYRPVFIGVTLLAFAVSFVGFGDLMNVVYPALGYLGIVLALVLIAWWVLHRRQISAESGL +RLRLRALLRLREHPEKTFTAQHAVLLQEAADESVAATAVVTEAVEEEVVQAIEADE---- +-----------PYGDPRRS--------- +>GCF_020097155_PROKKA_01553 +MQKSAALRSVQLALAFVGLLVGAGFATGAEVIQYFVGFGEVGIGGALLAGVLVAVGGAVA +LQLGSLFLAADHKVVFRSVSHPVMARILDAVVTVTLFAIGFVMLAGAGSTLAQQLGWPVW +AGAALMTAMVIVTGMLDVEKVSAIIGMITPLIIIAVVAGFAYVVATHEGPFTVNDSLAVQ +AVTPVSPWWLSSINYFGLVVVMAVSMCVVIGGSTSSPREAFVGGLVGGVVYTVLLVLASV +LLYLGYAELGTADVPMLQLFASIHPALGWAMVVVIYLMIYNTAIGMFYALGRRLTAERPG +LYRPAFVGVTLAAFAVSFLGFGDLMNYVYPALGYLGIVLAVVLLVWWAAHRDDIAAESGL +RLRLLALLRLREHPEKTFTRQHAVILQETAEESVAPTETVTEMMEADAVAVIEAEDPDLL +PAADETAGRGGADHG---GADGSAAARG +>GCF_023573625_PROKKA_01190 +MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI +LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW +AGSTLMTLLVVVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ +ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST +LLYLGYADIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG +RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL +RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDD---- +-ALTSGGARPGPDAGPERPAGGSHSA-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001034.fa new file mode 100644 index 0000000000000000000000000000000000000000..547e5e46ca8ce0b858d52485f26bdeb2c2fc4234 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001034.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01235 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL +>GCF_003691675_PROKKA_00954 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL +>GCF_005280335_PROKKA_01653 +MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH +VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER +IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL +>GCF_020097155_PROKKA_01550 +MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK +VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ +SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL +TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH +VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET +IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV +>GCF_023573625_PROKKA_01193 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001039.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0ed681d7c1f332a1ad1ebb5f5baf1e1870dfc0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001039.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01240 +MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL +EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD +GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEVGRGVFVLALTSNPEGREVQHV +GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL +APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR----- +--------- +>GCF_003691675_PROKKA_00959 +MTTTATGGAGPRAPFGRRLAQAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL +EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD +GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV +GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL +APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR----- +--------- +>GCF_005280335_PROKKA_01648 +----------------------MAQAGPLCLGVDPHPSLLRQWGLPDTPAGLEAFSLTGL +EAAVGPDGPRVAAIKPQVALYERHGSAGLAALERLLAEARDAGVLTIADAKRGDIGSTMD +GYAAAWTSDASPLAADAVTLSPYLGFGTLVPTIEAAHAAGRGVFVLALTSNPEGREVQHV +GRDAGEGAVARRIAAAAADLNAALRAEDEWGPVGLVLGATVAEDAERLGLDLPGLAGPLL +APGFGAQGATAAGMREGFGRAWPQVLATSSRGILAGGPTVAALVERIERDRADLG----- +--------- +>GCF_020097155_PROKKA_01545 +--MSVPAASMTREPFGRRLAAAMAAAGPLCLGIDPHPSLLQAWGLPDTAAGLESFGLTAL +EAAAGDGAARVAAVKPQVALFERHGSAGLAVLERLLAEARDAGVLTIADAKRGDIGSTMD +GYAAAWLDDASPLAADAVTLSPYLGYGTLTASIERAAAAGRGVFVLALTSNPEGASVQHV +GASEGQGAVAARIVTSAAADDARLAGLDGWGPVGLVVGATVAGHARELGIDLAALRGPLL +APGFGAQGATGAGMREAFGAAWPQVLATSSRGILAAGPTVTSLTRAIDAARADLGVEGPD +PRHAAGRDA +>GCF_023573625_PROKKA_01198 +MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL +EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD +GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV +GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL +APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR----- +--------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001041.fa new file mode 100644 index 0000000000000000000000000000000000000000..3084c968dd6102a60a6ed853a55bf3c76f413018 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001041.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01242 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTP-ATEGA +>GCF_003691675_PROKKA_00961 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTP-ATEGA +>GCF_005280335_PROKKA_01646 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA +HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG +DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG +RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA +>GCF_020097155_PROKKA_01543 +MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT +APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR +AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD +HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG +DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG +RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP +EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA +>GCF_023573625_PROKKA_01200 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTP-ATEGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001047.fa new file mode 100644 index 0000000000000000000000000000000000000000..e13833740257b70020a81995017fd6d9ddd49ed7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001047.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01249 +MTDREPDITEQETPGAAPAAAPAAP--EDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLP +DLLGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL +GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTA +EGKNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQ +NPHSPRLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVS +VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL +RFVLLDGLAQPTTVDIPDASLLFAAYQEIAE +>GCF_003691675_PROKKA_00968 +MTDREPDITEQETPGAAPAAAPAAP--EDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLP +DMLGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL +GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTA +EGKNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQ +NPHSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVS +VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL +RFVLLDGLAQPTTVDIPDASLLFAAYQEIAE +>GCF_005280335_PROKKA_01639 +MTDRHPDPAEPEIPGEPPAAEPAAAGQEDVTVIPVSGGQEAAAHGGYDVVVGRGLLARLP +EMLGPGVQRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL +GQNDFTRSDAVVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTS +EGKNLVGAFHPPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEQDPAQSQ +NPHSARLRELIERSIRVKADIVSRDLRESGEREALNYGHTMGHAIELAERYQWRHGAAVS +VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL +RFVLLDGLAQPSTVDIPDPSLLFAAYQEIAE +>GCF_020097155_PROKKA_01536 +MTEHQPD---QSDPIAEHSAA-APE--QDVTVIPVAGGPENRAGGGYDVVVGRGLLGRLP +AVLGPQVRRVLVIHPRALRATGDVVKNDLEAAGLVSLTAEIPDAEEGKHLQVAGFCWQVL +GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTA +EGKNLVGAFHPPAGVLADLDTLLTLPSNELVSGLAEVVKCGFIADPRILELIEEAPEQAQ +NPHSAVLRELIERAVRVKAEVVSGDLREAGPREALNYGHTLGHAIEHAERYQWRHGAAVS +VGLVFAAELARSLGRLDDATADRHWSVLQSLGLPVSYRGDRWQTLLEGIKRDKKNRGDQL +RFVLLDGLARPTTVDIPDASLLFAAYQEIAE +>GCF_023573625_PROKKA_01207 +MTDREPDITEQETPGAAPAAAPAAP--EDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLP +DMLGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL +GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTA +EGKNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQ +NPHSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVS +VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL +RFVLLDGLAQPTTVDIPDASLLFAAYQEIAE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001048.fa new file mode 100644 index 0000000000000000000000000000000000000000..2bdbb39fbca257b3aa309863f2d1f17f34184602 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001048.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01250 +MTDTPGTAPAPGPDPSTRPVPGPVTVCP-WEGMTGALEARLTAAATVAAAADEDPAARPA +RRVVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEAR +VIGHVLGRPTPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVL +AGDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP +>GCF_003691675_PROKKA_00969 +MTDTPGTAPAPGPDPSTRPVPGPVTVCP-WEGMIGALEARLTAAATVAAAADEDPAARPA +RRIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEAR +VIGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVL +AGDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP +>GCF_005280335_PROKKA_01638 +-------------------MPGPVSLCA-WEAMTGALEARL---ATAAAAAD----GAPA +PRIVLVGPMGAGKTTVGRALAATTGLPFVDADELFVQVHGPIPEFFAARGEAAFREEEAR +VIAHVLGRPSPCVLSCGGGAVLHPATRRALRGPGSDVVHLAVDEAVALRRVGGGAGRPVL +AGDPAGTWRRILAEREPFYREVADLVVDTTGLTAAEAAWRIVEGVHRPRRSESHP +>GCF_020097155_PROKKA_01535 +MSA----------------QPAPTDGVPSWEAMVRGLDGRL---AETS--------RDPG +PVVVLVGPMGAGKTTVGRALAEATGRVFVDSDALFEDAFGSIPAYFTSRGEPEFRRQEER +VIAHVLAHPAPCVLACGGGAVLSAATRARLADPRAVVVSLQVAEPEALRRLGGGAGRPVL +AGDPAGRWKAVLAERAPLYAEVADLTLDGTGHRPGDIASRIVEAIPTLPRRHTRP +>GCF_023573625_PROKKA_01208 +MTDTPGTAPAPGPDPSTRPVPGPVTVCP-WEGMIGALEARLTAAATVAAAADEDPAARPA +RRIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEAR +VIGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVL +AGDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001050.fa new file mode 100644 index 0000000000000000000000000000000000000000..b94351c22c852dc12de3195adaa3d56b61bbf53e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001050.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01252 +M----------------RPVLRAAVLGRPIAHSLSPVLHAAAYRVLGLDVDYGRRDLGED +EVLAFAAEHLGAPGAADGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANT +LVRDHPAAPGVVHAENTDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLG +ANAVLFGVRDAARAAEVTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAA +HVPADAALPPLLDAAYDPWPSVLAAAWSREGGPVASGLSMLLHQGVEQVRLFTARPRAAA +GMPEPDWAAVTRAAADALGPAAG +>GCF_003691675_PROKKA_00971 +M----------------RPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGED +EVLAFAAEHLGAPGTADGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANT +LVRDHPSAPGVVHAENTDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLG +ADAVLFGVRDPARAAEVTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAA +HVPAGAALPPLLDAAYDPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAA +GMPEPDWAAVTRAAADALGPAAG +>GCF_005280335_PROKKA_01636 +MGAPSDVRAEASAGAPAAPRLRAAVLGRPIAHSLSPVLHGAAYGVLGLDVDYRRRDLGED +EVGAFVAGRLGAPRTADGGDAAARGEDWLGCSVTMPLKRAVVGCAGRVSERVRLLGTANT +LVRDHPEHPGLVSAENTDVDGILGALASAGLAERGSGGAVGILGNGGTATAAVLAAATLG +ADEVVFGVRDAARAAEVTALADALGLAWRTVGQPELAAAAPGLRAVVATLPPRAADPLAA +HVPVGAALPPLLDAAYDPWPSALASAWTEAGGAVASGLSMLLHQGVEQVRLFTARPRAAA +GMPEPDWAAVTRAAARALGPAAG +>GCF_020097155_PROKKA_01533 +M---------------AGATFRAAVLGRPIAHSLSPVLHAAAYRALGLDVDYGRADLGEE +EVGPWLAARLGAPGSA-ARPAGPSGGDWLGVSVTMPLKPAVVPLADELSARVRELGVANT +LVRDHPDHPGSLLAHNTDVDGIVRALAERGLDAGAGGGAVGILGNGGTATAAVAAASLLR +AETVVLGVRDAGRARDVVALADRLGLGVRVEAQDALVRQAADLRAVVATLPPRAADPLAD +KVPAG-VLPPLLDAAYDPWPSAIARAWSAAGGGVASGLSMLLHQGVEQVRLFTERPRRAA +GGVEPDWAEVTAAASRALGLPGR +>GCF_023573625_PROKKA_01210 +M----------------RPTLRAAVLGRPIAHSLSPVLHAAGYRVLGLDVDYGRRDLGED +EVLAFAAEHLGAPGTADGGAAAARGQDWLGCSVTMPLKRAVVAAAGHVSDRVRLLGTANT +LVRDHPSAPGVVHAENTDVDGILGALAAAGLDRAARGGTVGVLGNGGTATAAVLAAATLG +ADAVLFGVRDPARAAEVTALADALGLRWATLTQADLLRRAPGLRAVVATLPPRAADALAA +HVPAGAALPPLLDAAYDPWPSVLASAWSREGGPVASGLSMLLHQGIEQVRLFTARPRAAA +GMPEPDWAAVTRAAADALGPAAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001052.fa new file mode 100644 index 0000000000000000000000000000000000000000..cd1080fdb07b3f9ece0946589f12a99d4d2c45bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001052.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01255 +MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVVSVQKCIRTADIEEVGKTVRH +GTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLDPERLWVTVYREDDEAERIWREDVGVRPERIQRMGKEDNYW +HTGQPGPGGPCSEIFYDRGPAYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLISDGVRPGNEGRGYVLRRLIRR +VVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERIARIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPD +AFELHDTYGFPIELTLEIAEEAGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVPSAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPVKGLSVHRVKVLDGEVAAGAQ +ALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGSFNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVL +TQEMSLEEARALGAMSLFGEKYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAAQARDVTTSGGTSVRVLAHHAGDV +AGDQLRSLALDLRARIESAGGNAAGTPVFVALTAEAKGRPLVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQ +GGGQDVTRVGDALDAVVAAVRAA +>GCF_003691675_PROKKA_00974 +MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVVSVQKCIRTADIEEVGKTVRH +GTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLDPERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYW +NTGQPGPGGPCSEIFYDRGPAYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLISDGVRPGNEGRGYVLRRLIRR +VVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERISRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPD +AFELHDTYGFPIELTLEIAEEAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPVKGLSVHRVKVLDGEVAAGAQ +ALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGSFNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVL +TQEMSLEEARALGAMSLFGEKYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAGQAQDVTTSAGTSVRVLAHHVGDV +AGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRPLVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQ +GGGQDVTRVGDALEAVVAAVRAA +>GCF_005280335_PROKKA_01633 +MKSQEIARRWIAFFESKGHQHVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAVSVQKCIRTADIEEVGKTVRH +GTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLDPERLWVTVYEEDDEAARIWEESVGVRPERIQRMGKDDNYW +NTGQPGPGGPCSEIFYDRGPEYGADGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELENKNIDTGLGLERLAML +LQGVENMYETDQVRPVLDRAAELSGREYTSTEDPTDPHYEDDVRLRMVADHVRSALMLIGDGVRPGNEGRGYVLRRLIRR +VIRALRLMGVTEPVLPELLPVSRDAMKGSYPVVADEFERISRIAYAEEKAFLRTIAAGTARLDAAVGQARTAGGGIAGAD +AFELHDTYGFPIELTLEIAEESGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTALYQRLRAEGQTHFTGYTEHTTES +VVRGLLLDGEEVASASAGTELEVILDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPVRGLSVHRVKVLDGEVPAGAE +ALGAIDLQRRLDGEKAHSGTHLVHAALHQVLGPEATQSGSFNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVL +TQEMSLEEARALGAMSLFGEKYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIAASMDRLKAAEKQIAELQAKALQAQAGELAAQAQDVTTASGVSVRVLARHVGEV +AGDQLRGLVLDLRSRIESAGGNAAGTPVLVALTGEAKGRPLVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQ +GGGQDVTRVGDALDAVVAAARAA +>GCF_020097155_PROKKA_01530 +MKSHEIARRWTAYFEKQGHLVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRATSVQKCIRTADIEEVGKTVRH +GTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLDPERLWVTVYEEDDEAARIWREDVGVRPERIQRMGKADNYW +NTGQPGPGGPCSEIFYDRGPEYGVEGGPEADDTRYIEIWNLVFMQYRLSQVRSKYDFDVAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAELAGKSYTSTEDPADPHYDDDVRLRMVADHVRSALMLISDGVRPGNEGRGYVLRRLIRR +VVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERISRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPD +AFELHDTYGFPIELTLEIAEEAGVAVDEAGFHALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGVITGDGFSLEVLDVQAPVKGLSVHRVKVLDGEVPVGAE +AVGRIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGSFNKEGYLRFDFRWAEAVSAMARSEIEDVVNIAIRDDHQVL +TQEMSLDEARAMGAMSLFGEKYGDRVRVVEINGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSDLSEMFKAPADQLKDRITATMDRLKAAEKQVADLQAKALQAQAGTLAAQAQDVTTTSGASVKVLAHHAGEV +AGDQLRSLVLGLRSRIESAGGNAAGTPVLVALTGEAKGRPLVVVATNEAARGAGLKAGAMVKLATAALGGGGGGKDDVAQ +GGGQDVTAVAAALDAVLDAVRDA +>GCF_023573625_PROKKA_01213 +MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVVSVQKCIRTADIEEVGKTVRH +GTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLDPERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYW +NTGQPGPGGPCSEIFYDRGPAYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLISDGVRPGNEGRGYVLRRLIRR +VVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERISRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPD +AFELHDTYGFPIELTLEIAEEAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPVKGLSVHRVKVLDGEVAAGAQ +ALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGSFNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVL +TQEMSLEEARALGAMSLFGEKYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLVGQAQDVTTSAGTSVRVLAHHVGDV +AGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRPLVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQ +GGGQDVTRVGDALEAVVAAVRAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001054.fa new file mode 100644 index 0000000000000000000000000000000000000000..603a80094814446b3a4b908070557aace6ed94b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001054.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01257 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>GCF_003691675_PROKKA_00976 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>GCF_005280335_PROKKA_01630 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>GCF_020097155_PROKKA_01528 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIEKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>GCF_023573625_PROKKA_01215 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001057.fa new file mode 100644 index 0000000000000000000000000000000000000000..68487e52ee93765f03ff8b96305a772e4382fc6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001057.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01260 +MS--PAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRA- +-SSDAAAEGVRQGFARRAREEGGLDVPV---VLVDVGTLRRALELHDALPWAGGE----- +-PKRTQLTVLEDDPAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTP +ARLDRALGVR--------GTARNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGR +DVTVRSHPCDGVTPSSASLP +>GCF_003691675_PROKKA_00979 +MS--PAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRA- +-SSDAAAEGVRQGFARRAREEGGLDVPV---VLVDVGTLRRALELHDALPWAGGE----- +-PKRTQLTVLEDDPAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTP +ARLDRALGVR--------GTARNLTTVRVLAGLPSED----------------------- +-------------------- +>GCF_005280335_PROKKA_00445 +MSEHPASP----THVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTP- +-DTGDHVDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLL--APGETLDSV +DPKTVHLVLLDTVPHPEAGEALAAVDAGD------DRAVVVGRGVWVRYAGPSHSSHLGL +PRIERAASGDAPPAQRRVGTARNLATVRVLAGR--------------------------- +-------------------- +>GCF_020097155_PROKKA_01525 +MS--RAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLP +DADDDAGPAFLRAFRDAALADDGPDVPL---ILTTPAELRGALAMHDRLPWSGGE----- +-AKLTQLTVLAESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTP +ARLEKALGVT--------GTARNLATVRVLAGMA-------------------------- +-------------------- +>GCF_023573625_PROKKA_01218 +MS--PAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRA- +-SSDAAAEGVRQGFARRAREEGGLDVPV---VLVDVGTLRRALELHDALPWAGGE----- +-PKRTQLTVLEDDPAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTP +ARLDRALGVR--------GTARNLTTVRVLAGLPSED----------------------- +-------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001061.fa new file mode 100644 index 0000000000000000000000000000000000000000..26bccccb69714560eb61d2550e7abf609e3a133c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001061.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01264 +--MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALC +NALSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAVAATLGLYLVPD +DAAAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAA +ALGV-DSPVQ-----GVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTV +ALYLLLATALISGLGTSGLARSPAPVRELLETALGSGWGWVAVAGAALAAAGAMLTLLTG +ISRTALAMAREADLPRPLARVHAGTGTPWTAQLTVAAAVVLLLLTTDILTVVGFSSFGVL +VYYAVANLSALTLRGDDHGHRPARP---RPLRVPRAVNVLGLALCLLLAFSLPPMSVAAM +AGVFLIGVGGRAFVRAGR-----RGG--- +>GCF_003691675_PROKKA_00983 +--MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALC +NALSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPD +DDAAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAA +ALGV-DSPVQ-----GVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTV +ALYLLLATALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTG +ISRTALAMARESDLPRPLARVHAGTGTPWTAQLTLAAAVILLLLTTDILTVVGFSSFGVL +VYYAVANLSALTLRGDDDGRRPARPRPLRPLRVPRAVNVLGLALCLLLALSLPPMSVAAM +AGVFLIGVGGRAFVRAGR-----RGR--- +>GCF_005280335_PROKKA_01623 +-----MLQRRLTLTHAVVIGLGSMIGAGVFTAIGLAAALTGGHPGLLYAALALALLTALC +NALSTAQLATVHPESGGAYVYGRRQLHPLAGFVAGWGFVTGKTASVAAMAATIGLYLFPD +DAAAARLTGVAAVVVLTAVAMAGVTRTAQATMAILVPVAAVLALAIGAGLALGAPSEADA +FAGVADSPVT-----GVLMGAGILFFAFAGYARVATMGEEVIDPRRSIPRAILIALGLTA +GLYVLLTAALFAGLGPTGLALSPAPVRELLETTLGATWGWAALAGAALAAAGAALNLLTG +ISRTALAMARESDLPRPLARVNARTGTPWVGQLTIAVAVILLLLTTDILTVVGFSSFGVL +VYYAVANLAAATLRGGEDGRDPALP---RPLRVPRAVNVLGLVLCAVLAATLPPMAVVAM +LAVFLVGVGGRAFVLAGRGRPGRRGAVAP +>GCF_020097155_PROKKA_01520 +MTATSPAPRGLPLRGALAIGVGSMVGAGAFTSLGLAALLTGGHVGALAAALGLAVAVATC +NALSTAQLAAVHPASGGTYVYGRRQIGPTAGFVAGWGFVTGKTASVAAMATTAGLYLFPD +SPLAARLAGAAAVVILTAVALRGITRTAQATVAILVPVLAVLGLTIVAGLA----GGRAA +A----DTPVSAADPAGVLAAAGVLFFAFAGYARVATMGEEVEDPRRTIPRAVLGALAFTV +VLYALLAAALVAALGGTGLAASEAPVRATLEASLGAGWGWAAVVGAVLACAGAMLNLLAG +ISRTGMAMAREGDLPRPLARVDERTAVPWAGQVTVAVAVILLVLTTDVLTVVGFSSFGVL +VYYAVANLSALTLRPEQ-----------RTLRVPRAVNVLGLGLCLVIAFTLPPASVAAM +VGVFLIGLGGRWFVRSRR--PDRIG---- +>GCF_023573625_PROKKA_01222 +--MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALC +NALSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPD +DAAAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAA +ALGV-DSPVQ-----GVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTV +ALYLLLATALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTG +ISRTALAMARESDLPRPLARVHAGTGTPWTAQLTVAAAVILLLLTTDILTVVGFSSFGVL +VYYAVANLSALTLRGDDDGRRPARP---RPLRVPRAVNVLGLALCLLLALSLPPMSVAAM +AGVFLIGVGGRAFVRAGR-----RGR--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001062.fa new file mode 100644 index 0000000000000000000000000000000000000000..05b51b7836bf70c3e3e3eecccaba1ba0432522dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001062.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01265 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGRREPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAVDPADWTPPTEDLLPQITRTQD--- +>GCF_003691675_PROKKA_00984 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD--- +>GCF_005280335_PROKKA_01622 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGRREAKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGELSPRHDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLTDAAGVLRSIDKLEKIGADEVARLLQEEVGASPEQARQALALAAIRTE +DVSFVEQVRALGVSDPLLEEGLAELADVVETLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQEMAQASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFLGRDDAG +ARVHEVKDIRSGDQHPADPADWTPPSEDLLPQVTRTESTEG +>GCF_020097155_PROKKA_01517 +MSRKQSLSGFHEWLPAERIVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDQEVAEGVREAKDPSDPKRLALHFDLTVPFARYVTENAGHLAFPFRRHQIQ +KVWRGERPQEGRAREFTQADIDVVGDGELSPRYDADVALVMAEALGALPIGDFRIRVNNR +KLAEGFYRGIGLEDAAGVLRSIDKLEKVGAEEVARLLQEEVGATAEQAAQALKLAEIRTP +DTAFVEQVRALGVEDPLLEEGLAELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALATKGNRAFPGVGLSIGVTRLVMRMLSQEMAVASRAVPTVV +YVALTHDDDWSRAQDVAAGLRGRGIAAEVAVSAEKFGKQIKYADRRGIPFVWFLGAEGAS +---DEVKDIRSGEQVPADAATWAPPAEDLVPQVTESPRAED +>GCF_023573625_PROKKA_01223 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001066.fa new file mode 100644 index 0000000000000000000000000000000000000000..950bde7a895b55b2087092d02b3c6205fedbc774 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001066.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01269 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL +>GCF_003691675_PROKKA_00988 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL +>GCF_005280335_PROKKA_01618 +MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG +VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL +AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP +LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL +>GCF_020097155_PROKKA_01513 +MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF +TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG +VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL +AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP +LYALLRRGDADVVAHDARVGADHDEREQEEDLADA------RGAVL +>GCF_023573625_PROKKA_01227 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001069.fa new file mode 100644 index 0000000000000000000000000000000000000000..ddd1e26fc34bc5b6bb81bd8ae5e5de2754239950 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001069.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01273 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR-- +>GCF_003691675_PROKKA_00992 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR-- +>GCF_005280335_PROKKA_01614 +MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF +GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA +RKIIVELSGRLTPTGEQVPAPEEPAAPE-TPEAAWHADVVQAMTGLGWSEKEALKAVEAT +VAARPELDEARDVAALLRATLRDVGTAGTVRGGR-- +>GCF_020097155_PROKKA_01509 +MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF +GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA +RKIIVDLAGRLAPTGEVEPEA-AVVEPE-AAADAWHADVVQAMTGLGWSEKEAAKAVAAT +VATHPDVDASGDVAALLRATLRDVGAAAAVRGGRRA +>GCF_023573625_PROKKA_01231 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001072.fa new file mode 100644 index 0000000000000000000000000000000000000000..7beefddc2883871a40f50036c19050c2e120613c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001072.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01276 +MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAATAPTFENTVRALELSGQLLRR +SAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLAARVASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAR +EELRGINTELASLSAAYTRRLVADTAARAVLVTDRERLAGLSEDDLAAAAG-AAAEAGHGDGDAA----AGPWLLTLSLF +TSQPWLASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRAAPSTAAVEELLAAMA +PRAMANARADAATAAAHAGRADAEVAPWDWPALSAGYAREEFAVDADALRPYFELDRVLTEGVFAAATALYGLTFAERPE +LARHLYRPGIRVFEVTGEDGAGVGLFVADLFARPTKSGGAWMHTVRDRADALGERPVVFTTMNVPAPAAGRPALLTLDET +TTLFHEFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVETGEPLPAGTLERLEAADLWGEG +HRTVEYLGATLVDWAWHSLTEETVDAATADPAAFERRVLTEAGIDPDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLD +ADAVEWFREHGGMTRENGRRFADELLSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA +>GCF_003691675_PROKKA_00995 +MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAATAPTFENTVRALELSGQLLRR +SAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAR +EELRGINTELASLSAAYTRRLVADTAARAVLVTDRERLAGLSEDDLAAAAG-AAAEAGHGDGDAA----AGPWLLTLSLF +TSQPWLASLQDEGMRREVFEASTGRGGSGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRAAPSTAAVEELLAAMA +PRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVDADALRPYFELDRVLTEGVFAAATALYGLTFAERPE +LARHLYRPGIRVFEVTGEDGAGVGLFVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEA +TTLFHEFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPAGTLERLEAADLWGEG +HRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGIDPDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLD +ADAVEWFREHGGMTRENGRRFADELLSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA +>GCF_005280335_PROKKA_01611 +MTPTPASSVLPADHPLATPSELPYGLPDFSAVTDAQLAEAVRAGMAAQRAEVEQILGAATAPTFENTVRAFELSGQLLRR +SAAMFFTLVSADGTDARQGLAEELSPELAAHEDALLLDPRLAERVAAIDGAGLTGEDARLLEVLRRRLDLAGAGLGEAER +AELGRINTELAGLTAAYTRRLVADTAERAVLVTDRERLAGLSEDDLASAAA-AAREAGHGGADGEGGDEAGPWLLTLSLF +TSQPWLASLEDEALRREVFEASVGRGAAGDHETLSTAMEVVRLRLRKARLLGSASWAEHALKDRAAPSTTAVEELLATMA +PRAMANARTDAATAAAHAGRVGGAVAPWDWPALSAAYARERFAVDAGALRPHFELDRVLHAGVFAAATALYGITFEERPE +LAGRLYRPGIRVFEVRDEDGAGVGLFVADLFARSTKSGGAWMHTVRDAADALDERPVVFNTMNVPAPAPGRPALLTLDEA +TTLFHEFGHALHGLLAKGEYVSLSGTHVPRDVVEFPSQVNEVWLREPALLAEYARHVETGEPLPAGTLERLEAADLWGEG +YRTVEYLGATLVDWAWHSLTEDTVEAATADPAAFERRVLTEAGIDPELVPPRYGTGYFKHIFGNDYAAGYYSYIWAEVLD +ADAVEWFREHGGMTRENGRRFAEELLSRGETRDLLESYRAFRGRDAELEPLLRRRGLVDAAA +>GCF_020097155_PROKKA_01506 +M--TQITHRLPAGHPLLSPSPLPHGLPDFAAVSDADLATGMRQGMAEQRAEVEEILSSPEAPTFENTVRALELSGALLRR +VAPMFSTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLSARVAAVDDAGLAGEDARLLERTRTRLEIAGAGLDEAGR +AELARLNGELATLSAAYTRRLVADTAARAVLVTDRERLAGLRADDLAAAAERAAAEAGHRRADAAEG--AGPWLLTLSLF +TSQPWLADLEDAGLRREVFEASVGRGSSGEHETLTTAMRIVRLRLEKARLLGAASWAEHALRDRAAPSVAAVEGLLGSLT +GPAMANARRDAEAVA----EGDAPVVPWDWPFLSAAHAREAFDVDAGALRPWFELDRVLTRGVFAAATALYGLRFAERED +LAGHLYRPAIRVWEVTDEDGRGVGLFVGDFFARPTKSGGAWMHNVVDASAALGTRPVVFCTMNVPAPAEGRPALLTLDEA +TTLFHEFGHVLHGLLAEGEYPSLTGTAVPRDTVEFPSQVNEVWLREPSLLADYARHVETGAELPTGTLERLEAADLWGEG +YRTVEYLGATLLDWAWHTLTEDTVDAATADPAGFERRVLTEAGIDVDLVPPRYGTGYFKHVFGNDYAAGYYSYIWAEVLD +ADAVEWFREHGGLTRENGRRFAEELLSRGDTRDVLESYRAFRGRDAELEPLLRRRGLLPEGA +>GCF_023573625_PROKKA_01234 +MTHTSAPSVLPADHPLATPSDLPYGLPDFSAVSDAQLAEAVRAGMAAQRAEVDQILGAATAPTFENTVRALELSGQLLRR +SAAMFFTLVGSDGTDARQALAEELSPELAAHEDAILLDPRLAARAASIDDGGLTGEDARLLETLRLRLSLAGADLDEAAR +EELRGINTELASLSAAYTRRLVADTAARAVLVTDRERLAGLSEDDLAAAAG-AAAEAGHGDGDAA----AGPWLLTLSLF +TSQPWLASLQDEGMRREVFEASTGRGGAGEHETLTTAMAMVRLRLRKARLLGAQSWAEQALKDRAAPSTAAVEELLAAMA +PRAMANARADAATAAAHAGRTDAEVAPWDWPALSAAYAREEFAVDADALRPYFELDRVLTEGVFAAATALYGLTFAERPE +LARHLYRPGIRVFEVTGEDGAGVGLFVADLFARPTKSGGAWMHTVRDMADALGERPVVFTTMNVPAPAAGRPALLTLDEA +TTLFHEFGHALHGLLARGEYASLTGTNVPRDVVEFPSQVNEVWLREPSLLAAYARHVESGEPLPAGTLERLEAADLWGEG +HRTVEYLGAALVDWAWHSLTEETVDAATADPAAFERRVLTEAGIDPDLVPPRYGTGYFKHIFGGGYAAGYYSYVWAEVLD +ADAVEWFREHGGMTRENGRRFADELLSRGDTRDLLESYRAFRGRDAELEPLLRRRGLADAAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001073.fa new file mode 100644 index 0000000000000000000000000000000000000000..a32ab128d6d31d583c07296bb755026da1115fa2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001073.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01277 +MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRG--------------- +--------------R +>GCF_003691675_PROKKA_00996 +MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRG--------------- +--------------R +>GCF_005280335_PROKKA_01610 +---------------------------------------------------MRTGVKAAS +PLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAVVDTPTGPEV +ILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGDLAAATRGRL +TGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAIMVHGRGARR +NEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIRYALDNGASD +VVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRIPEAVGVLGQ +WLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGPSQDLAERNP +GLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAE--------------- +--------------R +>GCF_020097155_PROKKA_01505 +MAC-PR--------------------------RHSPRLRARPDLRDALLGSLRGSAAVAR +PAARLAPAAASVAASAAFVLAGASAGLAGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDV +ILPADEHTTVPGTYSLTFHGGEGCARIGAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRF +TAFIWPGPAEAGLEAADVEVPVPGGAAPAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVR +NEGLRAVPTAARLGMTSLLVSYRNDGDAPDAEDARYGLGTTEWEDVEAAVRYALDHGARD +VVLFGWSMGGAVVLQTADRSDLTSRVRGIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQ +WLLSNRAGRLVTGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +ALVRFVRFHQARHTREQNVDPVKWDRSVRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRR +RSSGSSSASRPRNAR +>GCF_023573625_PROKKA_01235 +MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRG--------------- +--------------R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001075.fa new file mode 100644 index 0000000000000000000000000000000000000000..866f22e5c3c28d3f48817c9974344278f0b98c29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001075.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01279 +MSVIGPRRLS--AAPGAVEAPVP---PGVFRRALADLRDARPRTEVRLREIPAPEGQAPF +AVALAADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLA +GAVAWTWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLG +SHLEAWSDMICAFAGLPPEHAADVHTAGP--- +>GCF_003691675_PROKKA_00998 +MSVIGPRRLS--AAPGAVEAPVP---PGVFRRALADLRDARPRTEVRLREIPAPEGQAPF +AVALAADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLA +GAVAWTWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLG +SHLEAWSDMICAFAGLPPEHAADVHTAGP--- +>GCF_005280335_PROKKA_01607 +MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH +AVALAAEVCGSPGAD-DVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLA +GAVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLG +AHLEAWSDMIGAFAGLPPR------------- +>GCF_020097155_PROKKA_01502 +MTESGPRAPA--PAAGGA--------SGAFADALADLRAAHPRPEVRLRPIPDPPGLAPF +AVTLAADVLDPHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLA +GAVAWDWLAEALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLG +AHLEAWSDMICAFAGLPPLADDDVPAAVPLRP +>GCF_023573625_PROKKA_01237 +MSVIGPRRLS--AAPGAVEAPVP---PGVFRRALADLRDARPRTEVRLREIPAPEGQAPF +AVALAADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLA +GAVAWTWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLG +SHLEAWSDMICAFAGLPPEHAADVHTAGP--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001076.fa new file mode 100644 index 0000000000000000000000000000000000000000..760c637e26fb455b9fed2df5e50b67c968f663e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001076.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01280 +M--------------TDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTG +PVAVDAERASGIRYGQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQ +DLPCLAEQGLRPDRLFDTELAARVAGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPE +AMLTYAALDVELLVPLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQ +TLRRPVQRAVLKRLWEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHG +RAASREAP-------RWIAAIRAGVEDAERG--DAPAAQIRTGDGPPPPRAWKDRDPVAD +RRLRTAKARVARRAEQLGMPTENLLTPDTLRRICWTPPAPITPETVDAFLTE----RGAR +PWQVENVGAIVTVAL-------------LDPDPAGA------------------- +>GCF_003691675_PROKKA_00999 +M--------------TDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTG +PVAIDAERASGIRYGQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQ +DLPCLAEQGLRPDRLFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPE +AMLTYAALDVELLVPLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQ +TLRRPVQRAVLKRLWEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHG +RAASREAP-------RWIAAIRAGVEDAERD--DAPAAQIRTGDGPPPPRAWKDRDPVAD +RRLRTAKARVARRAEQLGMPTENLLTPDTLRRICWTPPAPITPETVDAFLTE----RGAR +PWQVENVGAIVTVAL-------------LDPDPAGA------------------- +>GCF_005280335_PROKKA_01606 +M--------------TDVPEPAEPDATPRLIAEPADGVPRVTDTPAGLEACAAALAAGTG +PVAVDAERASGIRYGQRAMLVQLKREGAGIWLVDPEALDGLEPLQEALSGVEWILHAASQ +DLPCLAEQGLRPDRLFDTELAARVAGLPRVGLAAVLESMLGVTLAKEHSAADWSVRPLPE +AMLAYAALDVELLVPLRAAMLELLEAEGKREWAEQEFEHVRTAPAPGPRADPWRRTSGSQ +TLRRPVQRAVLKRLWEAREDLARHRDVAPGRLIPDRSLIAAAESQPRTVPALRQTSGFHG +RAASREAPPLDHRDPRRRRGRRARRRPARPGARRGRPAPAPGVEGPRPAR----RPPPED +RQGARGPARRA-AGPAHGEPAH---------------PGHPAPALLGAAAAADARGRGRV +PPRARGP------ALAGGPGGRGGHRGPAGPGPRRGLSRGGRRADAAVGRGPTHR +>GCF_020097155_PROKKA_01501 +MTSPTSPAVATSPDPSDRP--GGEQAAPTLVAEPAGGVPVVTDTPAGLAACAAALAAGTG +PVAVDAERASGIRYGQRAFLVQLKRAGAGIWLVDPEAFEDLAPLDEALRGVEWVLHAASQ +DLPCLADCGMRPDLLFDTELAARLAGLPRVGLAAVLESQLGLTLAKEHSMADWSTRPLPV +DWLNYAALDVELLVELRDALAVLLEEQGKLAWAEQEFEHVRTTPPAAPRQDPWRRTSGMA +ALKRPVQLAVLRRLWQAREDLAQHRDLAPGRLLPDSALVAAASTLPRTVPELRATRGFHG +RSAAREAP-------RWITAIRAGIEDAAAG--QAPPRHGPGSDAPPPPRAWRDRDPLAD +RRLTTAKPRIARAAEALGMPPENLLTPDTLRRVCWTPPETITPETVAAALAE----RGAR +PWQVEQTSAIITVAL-------------LDPDPARD------------------R +>GCF_023573625_PROKKA_01238 +M--------------TDAPETAAPDAPPRLIATPAGGVPRLTDTRAGLEACAAALAAGTG +PVAVDAERASGIRYGQRAMLVQLKREGAGIWLVDPEALDGLAPLQEALAGVEWILHAASQ +DLPCLAEQGLRPDRLFDTELAARVSGLPRVGLAAVLEELLGVTLAKEHSAADWSVRPLPE +AMLTYAALDVELLVPLREALIARLEADGKLAWAEQEFEHVRTAPPPTPKKDPWRGTSGSQ +TLRRPVQRAVLKRLWEAREDLARHRDVAPGRLIPDRSIVAAAAAQPRTVPALRQTSGFHG +RAASREAP-------RWIAAIRAGVEDAERG--DAPAAQIRTGDGPPPPRAWKDRDPVAD +RRLRTAKARVARRAEQLGMPTENLLTPDTLRRICWTPPAPITPETVDAFLTE----RGAR +PWQVENVGAIVTVAL-------------LDPDPAGA------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001077.fa new file mode 100644 index 0000000000000000000000000000000000000000..9dc2267265c53976f1dceb8aaeb64cb8c0ef9982 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001077.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01281 +M--TSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATLLGLGRVLDEQAARAAAGE +IQALAVTGVEGTFAAGADLSLIASIT-D-DVGRDLALLGHAVYDRLAALEIPTVALVNGLALGGGLELALAAGHRVVAAD +AKGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTG +DESVAAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQAEADALGTLLHSPEFRR +TVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLALVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMV +SRGRLSAEDGQALAGLITADTDKAVYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPE +RLVGFHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMGEVQNSFDEGTDAHEAD +HALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSANLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIP +EATAALLEQGSTPQTSEELLRRVEDALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRR +FHPAAQA +>GCF_003691675_PROKKA_01000 +M--TSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATLLGLGRVLDEQAARAAAGA +IQALAVTGVEGTFAAGADLSLIAGLT-D-DVGRDLALLGHAVYDRLAALEIPTVALVNGLALGGGLELALAAGHRVVAAD +AKGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAG +DESVAAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQAEADALGTLLHSPEFRR +TVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLALVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMV +SRGRLSAEDGEALAGLITADTDKAVYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPE +RLVGFHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMGEVQNSFDEGTDAHEAD +HALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSANLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIP +EATAALLEQGSTPQTSEELLRRVEDALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRR +FHPAAQA +>GCF_005280335_PROKKA_01605 +MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPASLLELGRAVDAQAERARAGE +VQALALTGVEGTFAAGADLSLIAGIE-DRTVGRDLARLGHAVHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAAD +ARGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAG +DDAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREESAEAEAEALHGLIGSDEFRR +TVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAGQLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMV +SRGRITAEQGEALAGLITASTDKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPE +RLVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLRMMGEVQASFDEGTDAHTAD +HALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFPVSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIP +AGTAALIERGSSPQTAEELRRRVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTR +FHG---- +>GCF_020097155_PROKKA_01500 +MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSASLLELARAVDEQAARASAGE +IQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGHAVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPE +VKALGLPEVRLGLIPGWSGVWRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG +R-------TVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEADALADLIGSAEFRR +TVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLFATALRVPVVMTDLDQERVDRGLAYVRSQLERSV +TKGRMKAEDAEAVAGLITGATDVSAHAEAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPE +RLVGFHFFNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQNSFDQGTDAHTAD +HALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQRLIEAKKTAIWAKDV---KSPEEAGGATGETIP +ADTAALIEQGDTPQTADELRVRVEDALAEEIGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGAR +FHQA--- +>GCF_023573625_PROKKA_01239 +M--TSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATLLGLGRVLDEQAARAAAGE +IQALAVTGVEGTFAAGADLSLIAGLT-D-DVGRDLALLGHAVYDRLAALEIPTVALVNGLALGGGLELALAAGHRVVAAD +AKGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAG +DESVAAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQAEADALGTLLHSPEFRR +TVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLALVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMV +SRGRLSAEDGEALAGLITADTDKAVYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPE +RLVGFHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMGEVQNSFDEGTDAHEAD +HALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSANLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIP +EATAALLEQGSTPQTSEELLRRVEDALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRR +FHPAAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001078.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcc18ba145bab57980f5a44b05116e0a7e4a7bf2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001078.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01282 +MTDPAP-RPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRTGFAPTTAQRAA +RDGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLL +ARVAA---EGPLAV-DRLEEASPLQGGLRVPRAELR-----------PADAGGSD----- +VRVAVVADGVELGAHLVREGA------VVASDWGGGTASTPVADQAAATAGLDAHVVTFA +GLPIA +>GCF_003691675_PROKKA_01001 +MTHPAP-RPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAA +RGGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLL +ARVAA---EGPLAV-DRLEEASPLQGGLRVPRAELR-----------PADAGGSD----- +VRVAVVADGVELGAHLVREGA------VVASDWGGGTASTPVADQAAATAGLDAHVVTFA +GLPIA +>GCF_005280335_PROKKA_01603 +MTDPAPVRPS----LDLTPFERWEAVTLDGEHVGFLHRVLDGTLLTTRMGFAPTPAQRRA +RPELPERYLAQSQVSFTADGTSWDWTSHEDSAGAQRVRIDRERAGLDADVLPSYAEYLLL +AVAAA---DGPVVVAARLEESSPLQGGLRMPRAELR-----------PADAGDGD----- +VSVTVVADGAALGAHLVRDGA------VVASDWGGGTASTPVAGRAEATEGLDEHVVTFS +GMPLV +>GCF_020097155_PROKKA_01499 +M----------SARYDLTPFETWEAVALDGVHAGFLHRRLADGILTTRMAFQPTGAQRRE +RADLPQRYLAQARVRFSADGSTWEVCDFEDSLTTQNVRIARERAGLGAEVVPSWAEHLLI +TAQRTPEHDGAPYL--RLEESSPLQGPVRMPPAVLRIGAREAVPAAGPAGSEAGQARPEG +LRVEVVSEGHVLAVHWLGEPATEGRRPLVASDWGGGTVSVPVATAAEALEGLPADLHTFA +QLPTD +>GCF_023573625_PROKKA_01240 +MTHPAP-RPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAA +RGGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLL +ARVAA---EGPLAV-DRLEEASPLQGGLRVPRAELR-----------PADAGGSD----- +VRVAVVADGVELGAHLVREGA------VVASDWGGGTASTPVADQAAATAGLDAHVVTFA +GLPIA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001079.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c47ef4ccb0e173013230623a51834b38139af45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001079.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01283 +MTTQDSPLTPN-------SSRSACCGGH-----ARP-DTSRRTVLGRGAAVAAAGAGALA +LTGCTDQLREKDTAQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAF +TNVCTHQGCLLQVVDRQEGPAYACPCHGSHFDVTSGKPFGGPARQALMDYDAAVVDDRIV +VKL +>GCF_003691675_PROKKA_01002 +MTTQDSPLTPN-------SSRSGCCDDH-----ARP-DTSRRTVLGRGAAVAAAGAGTLA +LAGCTDRLREKDTAQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAF +TNVCTHQGCLLQVVDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIV +VKL +>GCF_005280335_PROKKA_01602 +MTAQDSTPTPDPSAVAPPSAPAGCCGGRAAADAARP-EASRRTVLGRGAAVAAAGAGALA +LSGCTEQLREKENAQDHFAGADAVEALPAADLPVGAAREVEVEGRTLMMHRVDETTVTAF +TNVCTHQGCLLQVVDRAEGPSFACPCHGSHFDVQTGKPFGGPARQPLMDYEAVVDGDRIV +VKL +>GCF_020097155_PROKKA_01498 +MTSQDP--APH-------TSASPCCSGCS----AEPAGSSRRSVLGAGSLVALAGAGSVV +LSGCTQQLKDEAAAGDHHVGSETTDAMALAELPVGGTTSVQVQGRTLLLHRADESTVTAF +SNVCTHQGCLVQVVDRPEGTAYACPCHGSNFDVATGEPFGGPAKAPLTDYQAAIEGDRIV +VKL +>GCF_023573625_PROKKA_01241 +MTTQDSPLTPN-------SSRSGCCDDH-----ARP-DTSRRTVLGRGAAVAAAGAGTLA +LAGCTDRLREKDTAQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAF +TNVCTHQGCLLQVVDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIV +VKL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001081.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001081.fa new file mode 100644 index 0000000000000000000000000000000000000000..f280d10a7aea51952198ebfa66df50e220d32457 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001081.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01286 +MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG +EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQ---------- +---EG +>GCF_003691675_PROKKA_01005 +MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG +EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQ---------- +---EG +>GCF_005280335_PROKKA_01599 +MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL +LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG +EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQ---------- +---ED +>GCF_020097155_PROKKA_01495 +MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL +MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG +EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD +ADGEG +>GCF_023573625_PROKKA_01244 +MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG +EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQ---------- +---EG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001083.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a24ae1e1496fccc802a87e0bdf83d85fc13dcba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001083.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01295 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIKALAAWDPNAQPDTEIQFTPA +RVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAELVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQ +TAFDDFKVVPPGMGIVHQVNIENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIGNMSPEFGSTAAIFPIDEVTL +DYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLELDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQD +EAGEGRPSKLVDVAMPDGRQFQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYA +LAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIIDASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKST +YVRKPPYFEGMTMQPDPVSDISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGSSRDWAAKGTALLGVKAVITE +SFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDISGITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEA +EYYRNGGILQYVLRQIASKA +>GCF_003691675_PROKKA_01018 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIKALAAWDPNAQPDTEIQFTPA +RVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAELVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQ +TAFDDFKVVPPGMGIVHQVNIENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIGNMSPEFGSTAAIFPIDEVTL +DYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLELDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQD +EAGEGRPSKLVDVAMPDGRQFQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYA +LAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIIDASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKST +YVRKPPYFEGMTMQPDPVSDISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGSSRDWAAKGTALLGVKAVITE +SFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDISGITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEA +EYYRNGGILQYVLRQIASKA +>GCF_005280335_PROKKA_01597 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIKALASWNPDAQPDTEIQFTPA +RVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAELVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQ +TAFDDFKVVPPGMGIVHQVNIENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIGNMSPEFGSTAAMFPIDEVTL +DYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLELDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQD +EAGEGRPSKLVDVSMEDGRQFQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYA +LAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIIDESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQST +YVRKPPYFEGMTMQPDAVSDISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGSSRDWAAKGTALLGVKAVITE +SFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDISGITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEA +EYYRNGGILQYVLRQIASKA +>GCF_020097155_PROKKA_01493 +MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIKALASWDPTAEPDTEIQFTPA +RVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAELVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQ +TAFDDFKVVPPGMGIVHQVNIENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIGNMSPEFGSTAAMFPIDDVTL +DYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLELDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQD +EAGEGRPSKLVDVHMEDGREFQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY +YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYA +LAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIIDESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEAST +YVRKPPYFEGMPAQPEPVQDIAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGSSRDWAAKGTALLGVKAVITE +SFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAISGIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEA +DYYRNGGILQYVLRQIAAKA +>GCF_023573625_PROKKA_01253 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIKALAAWDPNAQPDTEIQFTPA +RVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAELVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQ +TAFDDFKVVPPGMGIVHQVNIENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIGNMSPEFGSTAAIFPIDEVTL +DYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLELDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQD +EAGEGRPSKLVDVAMADGRQFQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYA +LAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIIDASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKST +YVRKPPYFEGMTMQPDPVSDISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGSSRDWAAKGTALLGVKAVITE +SFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDISGITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEA +EYYRNGGILQYVLRQIASKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001084.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b3e2d80a563d133f54e7520b3b2acfb85502917 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001084.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01296 +MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ +AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA +RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE +RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ +SAPAAAVVEI +>GCF_003691675_PROKKA_01019 +MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ +AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA +RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE +RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ +SAPAAAVVEI +>GCF_005280335_PROKKA_01596 +MAVIDTSTGVTGIGGTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEEG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIAGLTVEPEVCFAGPEDEPTGQRWRTRNAFTVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEAKLGRLRTRIRQ +AANACGVDVSTGLALPGPKRHSPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +RHAPATLVDAVLEDARIEPGQTVADLYGGAGLFSAYLADAVGPEGRVFSVEAAGQASKDA +RRNLHGQPQATVLNGPTDKALGSWIKYPERTVADGGLEGASLDTVVLDPPRAGAGRRAIE +RLLALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPATQ +LAAVPAIVEI +>GCF_020097155_PROKKA_01492 +---MDTSTEVVAPGGVIEVEAGAMAHGGHCVARHEGRVVFVRHAIPGEIVRVALTEAEPG +ARFWRGDVVEVVRPSEFRRIHQWKLADSLRAHASGRLPVGGAEYGHIVVHHQRRLKAQVF +RDTVARIAGVTIEPEALHAGHEDEPTGQHWRTRTAFAVTPQGRIAMHAHRSAVLLPVRNM +PLGVHALDALALWDWDFTGAARVDVATPADGTQPLVLATPTPQTLADEARLGKLRTRIRQ +AANACPVDVSTGFAVPGPKKFSPTGIQRITGRTWVHETVSSERGGERTFRVTGDGFWQVH +QHAPATLVDAVLEDVDPQPGEVIADLYAGAGLFSAFLSDAVGEEGRVYSVEASRQASKDA +RRNLLSLPQAGVLNGPTDKVLGSWIKEPERTTRDGGLDGDRLDAVVLDPPRAGAGRRAIE +RILALAPGRICYVSCDPASFARDLAWLREGGYEVERARVFDLYPDTHHLESVTLLRPAGE +VEQTT----L +>GCF_023573625_PROKKA_01254 +MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ +AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA +RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE +RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ +SAPAAAVVEI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001085.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea2a4dfc96d7d5466616ef1cd46313f9f14b9939 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001085.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01297 +MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGTSALALGPAVGWAVVAVMLLI +VVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLL +AALRGVRLSRWVLPVLVSVFVALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT +GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAAGAEVTPDRAPAPVLAQLADT +VYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAEDGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTA +LLVQLYVIGVLLAFTLAQAGMLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL +GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPSSLEAVVVDAERAATLEVIDA +WERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLTMVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSV +PWQVHEGQ---------------GS-------- +>GCF_003691675_PROKKA_01020 +MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGTSALALGPAVGWAVVAVMLLI +VVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLL +AALRGVRLSRWVLPVLVSVFVALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT +GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAAGAEVTPDRAPAPVLAQLADT +VYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAEDGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTA +LLVQLYVIGVLLAFTLAQAGMLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL +GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPSSLEAVVVDAERAATLEVIDA +WERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLTMVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSV +PWQVHEGQ---------------GS-------- +>GCF_005280335_PROKKA_01595 +MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGTAALALGPLVGWGVVVVMLLI +VASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLL +TSLRSARLSRWALPVLVSAFVALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT +GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAAGRPVAEADTPAPVIAQLADT +VFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAEDGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTA +LLVQLYVIGVLLAFTLAQAGMLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL +GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPSSLEAVVVDAERAVTEDVIDA +WSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLTMVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSV +PWQIHEGQ---------------GD-GQRSTTV +>GCF_020097155_PROKKA_01491 +MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGTGALALGPLVGWAVVAVMVLI +VLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDFVFTAAVSVAAFAHHASALVPALR-GHVGIVSAVALVLVLV +SALRGERGSGALVTVLVAAFVGLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGL-GPVGDAATALLALRAFSAGSVLLS +GVEVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGAPLAPDTAPAPVVAQLAET +VFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDGWLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTA +LLVQLYVIGVLLAFALALVGMLRLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGV +SAVVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATLEAVVVDADRRQTERVVED +FARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMVFIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSV +PWQIREGDPHRPVEGGIVACAAPGDVPEGVESS +>GCF_023573625_PROKKA_01255 +MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGTSALALGPAVGWAVVAVMLLI +VVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLL +AALRGVRLSRWVLPVLVSVFVALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT +GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAAGAEVTPDRAPAPVLAQLADT +VYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAEDGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTA +LLVQLYVIGVLLAFTLAQAGMLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL +GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPSSLEAVVVDAERAATLEVIDA +WERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLTMVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSV +PWQVHEGQ---------------GS-------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001086.fa new file mode 100644 index 0000000000000000000000000000000000000000..2aa05ed853372371d850ef7601a468045212a049 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001086.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01298 +MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL +AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI +QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR +LGDGQLPRPGDRLQEGDVLHAVYPVDRRDRVEAALQGEARVP--DGTDEDEEGRA +>GCF_003691675_PROKKA_01021 +MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL +AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI +QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR +LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVP--DGTDEDEEGRA +>GCF_005280335_PROKKA_01594 +MAHYVIVGGGRVGTRLACALDAAGHSVALVDRDPRTVDGLVPGFSGELVAGVGFDRAALL +AAGVDRAQGLAAVTAEDNTNIIAARVARETFHVEHVVARIYDADQAKVYQRLGIPTVASI +QWTADQVLHRLLPAGTADVERRDASGRLLVTGLVPHPSWWGRRLTDVESGAGLRIAYLTR +RGEGLLPRPGDRLQEGDLLHAVYPVDRRDQVEAALQGEAVRSDRDAEDEDEEGRA +>GCF_020097155_PROKKA_01490 +MAHYVIVGAGRVGTRLAGALDTAGHSVAVIERSPELTAGLGPDFGGTVVAGIGFDRDALR +RAGIEQAQGLAAVTTEDTTNVIAARVARETFGVQHVVARIYDAQRARVFQRLGIPTVASV +EWTADQVLHRLLPAGTAEPSRRDASGRLAMGDYMPHRSWWGSPLHAVEAAVGARIAYLTR +YGEGVLPSPDGVLQEGDVLHVAYPAARRDRVEAALQGEA-GDVRAGEDEDQEEDA +>GCF_023573625_PROKKA_01256 +MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL +AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI +QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR +LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVP--DGTDEDEEGRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001088.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2c90e66f55c359bdf794a90fef2ecdd0c39cd68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001088.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01300 +M-TEPR---GPVTA--APDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMV +GYVATQQVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYY +LWGFVTNAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVF +ALRLAVQVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVS--SPGQDDGVPADSAASE +RP----- +>GCF_003691675_PROKKA_01023 +M-TEPR---GPVTA--APDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMV +GYVATQQVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYY +LWGFVTNAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVF +ALRLAVQVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVS--SPGQDDGVPADSAASE +RP----- +>GCF_005280335_PROKKA_01592 +M-TEPR---GPESP--APDVAGALPSRARVDEQGRLDALASVGGWRGIVEASLPTLVFMA +GYVVSQQVWPSGVAAVAVALVLGAVRLVQRQSPVQVLAGLAVVVLSVVVALTTGQARDYY +LWGFVTNAAYGLAFALSVVVGWPAAGLVLGLVRGEGTHWRRSPRRRRAYATATWILVAVF +TLRLAVQVPLYLADAVTALGVARLVMGLPLYALGLWLAWSVSAPAPGEDDGL--RPAAED +EPAPGRA +>GCF_020097155_PROKKA_01488 +MSAHPRPDHGPDAAPSAAEGLQALGARTRVDEDGRIDALATVGGVRGIVEASLPTLVFLV +VFLLAGQVWTAGAAALGVAAVMTAARLAQRQSAAQALAGLLVVGVSVVLALTRGEARDFY +LWGFVTNIAYGLALPLSAALGWPLAGLLFGMVRGEGLHWRADPARRRAYGIATLIVAAVS +WLRLAVQAPLYLADAATALGVARVVMGLPLYALGLWLAWSVSTPRPGA-------PPLRR +DPAAG-- +>GCF_023573625_PROKKA_01258 +M-TEPR---GPVTA--APDGAGPLPSRARLDERGRLDALGSVGGWRGIVEASLPTLVYMV +GYVATQQVWPSGVAAVAVALVLGVARLVQRQSPVQVLAGLAVVVLSVVVSLTTGQARDYY +LWGFVTNAAYGLAFAVSVLVGWPAAGLVLGLVRAEGTRWRAHRRRRRAYAAATWILVAVF +ALRLAVQVPLYLGDAVTALGVARLVMGLPLYALGLWLAWSVS--SPGQDDGVPADSAASE +RP----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001090.fa new file mode 100644 index 0000000000000000000000000000000000000000..b31293e546db2a6d8f840e5279840cd5d4d3f9fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001090.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01302 +MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAA---DVGPHDVATRPDPAGMIDLGSL +RLRAVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLST +TAHATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPE +AAEPLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRP--APDEGRDVLADTATG +PGDGAAPEATALPERGPEITETR +>GCF_003691675_PROKKA_01025 +MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAA---DVGPHDVATRPDPAGMIDLGSL +RLRAVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLST +TAHATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPE +AAEPLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRP--APDEGRDVLADTATG +PGDGAAPEATALPERGPEITETR +>GCF_005280335_PROKKA_01590 +MIFGRNRKVRHEQVSLPEELLEERDHEVAALPEAA---ETGPHDVATRPDPAGAIDLGSL +RMRAVQGMKLRLDVEDSTKRIVAATITLGRSALQVQAFSAPRRAGLWDEVREELRDSLDT +TPNATVQEQAGRFGTEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPE +AAAQLEQVFSDIVVVRGDEPMPPRELLPLRPPANARPVQRRRPGAARDAGRDVLADTERG +P-----QEAPALPERGPEITEIR +>GCF_020097155_PROKKA_01486 +MIFGRNRNVRHEQVAVPEQLKDERDRLVEARPAPAAEGDRGPFDVEAAPSGRPSVDLGAL +RVPAVQGMQLRLDVEDATQRIVAVTVTLERSALQIQAFSAPRAAGVWDDLRAEIKEALVG +TPGAQVQEQSGGFGPEVLTRIPATLPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAYLPD +AARALEDVFAGVVVVRGDAPLPPRELLPLRPPADAQPV-RRRP--RPHAGGEPDVH-ARR +PDDAPETGAETLPERGPEITEIR +>GCF_023573625_PROKKA_01260 +MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAA---DVGPHDVATRPDPAGMIDLGSL +RLRAVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLST +TAHATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPE +AAEPLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRP--APDEGRDVLADTATG +PGDGAAPEATALPERGPEITETR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001092.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7b89b7a74c094fdca821189107010b4c5b49e1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001092.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01304 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR +>GCF_003691675_PROKKA_01027 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR +>GCF_005280335_PROKKA_01588 +MREPQQHPVSDAPVDRPQDPAQGSDRVLFEERLTPSAGVWVVALMLASLTILVFAPIDLW +FGVAAAVVFFGLEALLLLTTTPRIVVRERTLQVGRASIERRHVGEVTGHRGEDARRQRGP +LLHGLAYVVVRGWISPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMVQEDPADEDR +>GCF_020097155_PROKKA_01484 +MQDASATP----DHHAPRTVAASADPVQYEERLSPSVGVWLVALLLAGLCIFVLAPVALW +AGFLAAAVFFVVEAVVLLASTPRIVVRERTLQVGRAQIERRHLGAVTGHRGEAARAQRGP +LLHGLAYVCVRGWISPVVRIQIEDERDATPYWLASTRHPEDLVAALGGRMAGEG------ +>GCF_023573625_PROKKA_01262 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001094.fa new file mode 100644 index 0000000000000000000000000000000000000000..0ee0d4ce0187ecb0a62705b7f4058a37b681c61b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001094.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01307 +M--------TGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDG +LGRSLLKRFGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PDRDVVINQLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGG +RFVAGRTLIARAQAAERALKDARVPTLVYFYVNELDRAGHRDGVGSDRWLHALEEIDAAV +RRLVDRVPAGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADAALLEGVAHTAGEPRLV +QLHFRSDAGPDVRARVRRAWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVA +VHGDLALYDGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>GCF_003691675_PROKKA_01030 +M--------TGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDG +LGRSLLKRFGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PDRDVVINQLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGG +RFVAGRTLIARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAV +RRLVDRVPAGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLV +QLHFRSDAGPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVA +VHGDLALYDGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>GCF_005280335_PROKKA_01585 +M--------SGPAVPVGVVPPERALRSVLTSAAAALGVPGCENALGVPASRRVVVALVDG +LGRSVLKRFGGHAPTLRAAMADGGRVLQAAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PERDAVVNQLGGWDEATDPVAWQPRPTVFERAGAAGVDAVTVSLPAFEHSGLTRAGLRGG +RFVAGRGLLARAQAAERVLKDAREPTLVYFYVNELDKAGHRDGVGSDRWLHALEEIDGAL +RRLVDRVPAGTVVLATGDHGMVDVPPTRRVDYAAADESGALADPALLEGIAHTAGEPRLV +QLHFRPDADADVRARVRRAWEDRFGAHAWVLTRDEAVAAGWFGTVVEERVRGRIGELLVA +VHGDLALYDGRRVAPHAFEMVGQHGSPTRAEREVPLLTWRR +>GCF_020097155_PROKKA_01481 +MTGPDAAAPAGPGLPPGPVPPERALRSVLTSAAAALGVPGCANALGVPVTRRVVVALVDG +LGRGVLKRFSGHAPTLRAAMADGGRVLTAATPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PDRGVVVNMLGGWDEATDPLAWQPHPTVFERAVEAGVDAVTVSLPEFEHSALTRAGLRGG +RFVGGRGLLARAGHAERVLADACVPTLVYFYVNELDKAGHRDGVGSRSWLHALEEVDAAL +RRLVSRVPAGTVVLATGDHGMVDVAESRRVDYAALGDDGAPVRPGLLAGVAHTAGEPRLV +QLHFAPTATPAEREGTRRAWEDAYGDQAWILTRDEAVAAGWFGERVADRVLPRIGDLLVA +CHGELALYDGRRVSPRAFAMVGQHGSPTRAEREVPLLTWRR +>GCF_023573625_PROKKA_01265 +M--------TGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDG +LGRSLLKRFGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PDRDVVINQLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGG +RFVAGRTLIARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAV +RRLVDRVPAGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLV +QLHFRSDAGPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVA +VHGDLALYDGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001096.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b66d1b62de16d6a8ffbe888655342fc399416fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001096.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01309 +MGETEADRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHRDRVA +FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAAAARENGIRRFTAEVLPENRKMLSVFQESGFE +VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGTVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAGAEGLEAQRRLVSLARAHGMR +VIGPASTGLVRTDPAIRLNASPSPGLAQRGPVSLFSQSGAVGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEAD +PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPADTLVSAVRDAVCHEQADAVVVLA +RLGLHQADDEPERLAHALADATREARIPVLGCLTDVVSPRYRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMAVLGA +LADYVHWRHQEVGEPLEPTGLHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSVRFETAEEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAGQACMLTALEDPLLGPVVSFG +IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGTGGVPPVDLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAP +ERVTVLQAEVHVANAARRTDSARRALRGR +>GCF_003691675_PROKKA_01032 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHRDRVA +FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFE +VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAGAEGLEAQRRLVSLARAHGMR +VIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGAVGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEAD +PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETLVSAVRDAVRHEQADAVVVLA +RLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPRYRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGA +LADYVHWRRQEVGEPLEPTGLHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAGQACMLTALEDPLLGPVVSFG +IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGTGGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAP +EGVTVLQAEVHVANAARRTDSARRALRGR +>GCF_005280335_PROKKA_01583 +MGDTEPVRDYPSHWEADVVLRDGATARLRPITPEDADELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHKDRVA +FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAVAAREHGIRRFTAEVLPENRKMLSVFQESGFE +VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAEARSVAELVAPESVAVVGASRDPQAVGSMVLRHILEGGFAGPVHAVN +RAAGEVQGLTAHASLAEIGEEVELVVVAVPVDQVEALVPEAAAAGAAGLLVLTSGYADAGAEGLEAQRRLVSLARAHGMR +VIGPASAGLVRTDPAVRLNASPSPGLAQRGPVGLFSQSGAVGAMVSAGAKRRGVGVSTSISAGNRADVSGNDAMQFFEAD +PHTAAVGVYLESFGNPRKFTRITRRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGAVDSMLDQTGVLEVHTHEAMLD +LLMAVASQPLPTGRRVVLVADSLAVDRLARDAAAEAGLDVVATVGLAGSEQGVAPPAETLVASVREAVAHEQADAVVVVG +RLGLHQEDDDPETVARALAEATAGARMPVLVCLTDVVSPRYAGATLGASGPVADDAEPGSLQPGVPFYPSPQQAMSVLGA +LADYVRWRGEEAGEPLEPADVRLHAAEDLVEAAAARAEGTELVRLSAAETEELLGHYGIAVLPSARFETADEAVAAAERL +GFPVAVKAVDPHLRHRLDLGGVRLNVVDAASLRRNVEQMRRVLAPFGVTELEVQAMAPAGQACMVTALEDPLLGPVVSFG +IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAAKLEGRGGVPAVDLAALEDLVGRVSVLKDDLPQVARLRFSPVLASP +EGVTVLQAEVDVANAAGRTDSARRALRGS +>GCF_020097155_PROKKA_01479 +MAEPDTETAYPSQWEADVVLRDGATARLRPIREDDVDGLRALHAGQSESSIYLRYFTFKSELSAKELERFTHVDHRDRVA +LVIERGGRILGVGRYDRYGDSDAAEVAFNISDAAQGQGLGSILMEHLAVAAREQGIRRFTAEVLPENRKMLSVFQDSGFE +VARHFEDGVVAVEFPIDPTARWRAVVESREHRAEARSVAELVEPESVAVVGASRDPHAVGSIVLRHILEAGFTGRVHAVN +RAAEDVQGLTAHASLKDIGEPVDLVVVAVPVAEVDAVVAEAAEAGAQGLLVLTSGYADAGEDGLRAQRRLVARARARGMR +VIGPASAGLVRTAPDVRLNASPSPGLASRGPVGVFSQSGAVGAMITAGMKRRGVGMSTSLSAGNRADVSGNDAMQFFEDD +PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRALPPGHETRTTQAPEGAVDSMLEQTGVLEAATHEDMLD +LLMAVATQPLPTGRRVTLVADSLALDRLGRDAAAVAGLEVVATHGLGGSEQGIAPTADDVVASVEAALAAGDTDAVVVVT +RLGLHQDEDAAHEVAQALARVAEGATVPVLGCLTDVVSARYGGARVGGAAAPAADAEPGALQPGLPLYPSPRKAMTVLGR +LCDYVAWRREDAGEPIELTDVDVRAAEALVDRALERALGTELIRLTGAETEELLRIYGIGVLRSRRFTTPDEAVAAAEEL +GFPVAVKAVDPYLRHRLDLGGVRLNLEDAESLRQNVRQMRAVLAPFGVTELEVQSMAPSGQPCMVTALEDPLLGPVVSFG +MAGDATDLLGDWVHRVPPLTDQDVRRMVRSPRAAVKLDGVGGVPAVDLDALEDLLARVSCLKDDLPAVARLRFAPVLAAP +TGTTVLSAEVDVANAAGRTDSARRALRAS +>GCF_023573625_PROKKA_01267 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHRDRVA +FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFE +VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAGAEGLEAQRRLVSLARAHGMR +VIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGAVGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEAD +PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETLVSAVRDAVRHEQADAVVVLA +RLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPRYRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGA +LADYVHWRRQEVGEPLEPTGLHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAGQACMLTALEDPLLGPVVSFG +IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGTGGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAP +EGVTVLQAEVHVANAARRTDSARRALRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001100.fa new file mode 100644 index 0000000000000000000000000000000000000000..d25fe113f5a58ee8153d2f4e150bb0a595120819 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001100.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01313 +MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLINFIMGVATGIVQEFQFGMAW +SEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRVPRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVD +GRPVLNDIGAVLANPIVLTHFPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI +TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAGDRTTCTDVTTVIELPGLLSY +LAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGAPIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGT +VPDSRGWTATAVASIGAPFAANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL +LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY +>GCF_003691675_PROKKA_01036 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLINFIMGVATGLVQEFQFGMAW +SEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRIPRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVD +GRPVLNDLGAVLTNPIVLTHYPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL +TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSGGATTCEDVQGVIEVPGLLSY +LAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGSEISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGT +VPASRGWMRLAVASIGAPFAANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL +LGVEVFLLTRFVRGGVPAAMPELTAAEHS--DEQKRDRDDVLAFAY +>GCF_005280335_PROKKA_01579 +MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLINFIMGVATGIVQEFQFGMAW +SEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRVPRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVD +GRPVLNDIGAVLANPIVLTHFPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI +TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAGDRTTCTDVTTVIELPGLLSY +LAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGAPIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGT +VPDSRGWTATAVASIGAPFAANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL +LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY +>GCF_020097155_PROKKA_01475 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLINFIMGVATGLVQEFQFGMAW +SEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRLPRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVD +GRPVLNDIVAVLTNPIVLTHFPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI +TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTPGATTCDDVTGVIEIPGLLSF +LAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQEISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGT +VPDSKPWMITAVASIGASFAANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL +LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY +>GCF_023573625_PROKKA_01271 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLINFIMGVATGLVQEFQFGMAW +SEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRIPRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVD +GRPVLNDLGAVLTNPIVLTHYPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL +TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSGGATTCEDVQGVIEVPGLLSY +LAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGSEISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGT +VPASRGWMRLAVASIGAPFAANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL +LGVEVFLLTRFVRGGVPAAMPELTAAEHS--DEQKRDRDDVLAFAY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001103.fa new file mode 100644 index 0000000000000000000000000000000000000000..2bf98f1ffb6800a1eff8b40ca7a122d49c3d02b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001103.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01318 +MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG +VAGARDVQGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR +HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH +HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLSWTPTVSIDEGLHRVAAYYRDR +>GCF_003691675_PROKKA_01039 +MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADAGNDVTTLQRRPSG +VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR +HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAALSAADVH +HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR +>GCF_005280335_PROKKA_01574 +MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG +VAGARDVQGSVTDPAAVERAVAGVDTVVHVAAKVSVSGPEHEFEAVNVEGTRILLHAAQR +HGARRFVHISSPSVAHAGDSIVGEGAGPASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDMQLTDRIVQRARAGRMPVLGTGAPLIDTLYTGNAVEAVVAAVSAADHH +HGEALVVTNGEPRPVGELVRQIALAGGAEEPERHVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLDWTPSVSIGEGLHRLAAYYRAR +>GCF_020097155_PROKKA_01470 +---MGFEVHLGDDGLLQLAERVEHRRVLVTGASGLLGSGVARVLAEAGNPVTTLQRRPSG +VPGAVDVLGSVTDPAAVERALEGVDTVVHVAAKVSVSGPEEEFAAVNVEGTRILVHAARR +RGVHRFVHVSSPSVAHAGASIVGEGAGPADPEHARGPYARTKAAGELIALGADADDFRVL +ALRPHLMWGPGDLQLTDRIVQRAREGRMPVLGSGAALVDTLYTGNAVEAVVAAVSAVDHT +HGEALVVTNGEPRPVGELIRRIALAGGAPEPERTVPAGVARRAGALIERAWERDLFGVRS +SGRGSADGEPPLTEFLAEQLSTSHWFDQRRTREVLDWTPSVSMDEGLLRLAAYYRDR +>GCF_023573625_PROKKA_01274 +MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADADNDVTTLQRRPSG +VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPKHEYEAVNVEGTRILLHAAQR +HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH +HGEALVVTNGEPRPVGELIRQIALAGGATEPERRVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001104.fa new file mode 100644 index 0000000000000000000000000000000000000000..27e44fe69ff002a78106b40e0fc3e7cb3c5272fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001104.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01319 +MSGPRSRLDRPLSSTERPAPVPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGK +VHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL +IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT +CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLA +EPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP +AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARL +EREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRARID +A +>GCF_003691675_PROKKA_01040 +--------------------MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGK +VHQMSFRRGEPGRFQDGSRPSPAAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL +IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT +CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLA +EPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP +AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARL +EREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERID +A +>GCF_005280335_PROKKA_01572 +--------------------MPANSEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGYGQSI +EITLHPDGSVEVEDSGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGK +VHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFIKDAAFSADDLHARARQTAYL +IPGLRITVKDLRRRPGTPGAEGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGSFKERVPVLGEDGRTAMQDVQRT +CEVDLALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRTQVESNARRLKAGSDKVEKDDVLAGMTAVLTVRLA +EPQFEGQTKEILGTSAVRRIVAQVVEKELTARLTATARAQKQQVHVLLEKVVAEMKSRISARTHKENQRRKNALETSTMP +AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVFAAVPPLHRIEAVTKGVKEREVIYTYSEQELYATLARL +EKEGRSYKEPIQRYKGLGEMDADQLAETTMDPRHRTLRRVNIAEVEAAERVFDLLMGSSVAPRKDFIVSHADELDRERID +A +>GCF_020097155_PROKKA_01468 +--------------------MPANTEYSARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +DVTLHPDGSVEVADNGRGIPVDVEPRTGLTGVEVVFTKLHAGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVVRGGK +VHQLSFRRGEPGRFQDGSRPTPDAPFEPAADAAPLDVVGKAKRGQTGTRVRYWADEQIFTPDATFSMEDLQARARQTAYL +IPGLRIAVTDLRRLTGTAGEAGPVQEVYQYDGGIAEFVDHLTPAKPVTDVWRIQGSGTFTERVPVLGEDGRTQMQDVQRT +CEVDVALRWDVGYETVFRSFVNIIATPKGGTHQSGFESALLKVFRAQVEAGARRLKAGSDRPDKDDVLAGMTAVLTVRLA +EPQFEGQTKEILGTPAVRRIVARVVEKELTALLTSTARGQKQQVGALLEKVVAEMKSRISARTHKENQRRKNALETSTMP +AKLADCRSNDVAASELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILSNAECAALIQVVGGGAGRGFDL +DAARYGKVILMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGKKEREVIYTYSEAELHEVLARL +EAEGRTYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRVTISEVEAAERVFELLMGSSVAPRKAFIVSNADELDRERID +A +>GCF_023573625_PROKKA_01275 +--------------------MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGK +VHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL +IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT +CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLA +EPQFEGQTKEILGTSAVRRIVSQVVEKQLTARFTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP +AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARL +EREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERID +A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001105.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ceb8903c6cc9c481fae0b99f4495292835cb9d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001105.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01320 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD +ETDRLTAGA-- +>GCF_003691675_PROKKA_01041 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD +ETDRLTAGA-- +>GCF_005280335_PROKKA_01571 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD +ETDRLTAGA-- +>GCF_020097155_PROKKA_01467 +MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD +QTEELDGSTAA +>GCF_023573625_PROKKA_01276 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD +ETDRLTAGA-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001107.fa new file mode 100644 index 0000000000000000000000000000000000000000..049cb13b6c1bcfee5347db8b0980392e4283ad6d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001107.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01322 +--------MEAP-----------TSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTL +RDGRLRAVVRVDLPPEEVDVGA--WACAVAEVCRRDAAADATLCLALPDGARATLARPGW +AAALDDALASAGRPLTAAWTCARGRARPWWGSGVAEEGPL---DPRAAPLSLHLMTRGSV +WDRAAVPDPVPRRGPAAARADDARWRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAP- +-------------------AVLGSPLTRPAWRDGLLLHAAAPSGAATGDPGDEERILTAA +SGRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARGHGSDADAHLTAAAALS +PDDPFVSVLRRIVAAGCVAGWATDPATAWRP-------DGGRP +>GCF_003691675_PROKKA_01043 +--------MEAP-----------TSLDAPVLPARGPEDLLAYVGHALGRLPEDSLVLLTL +HDGRLRAVVRVDLPPEEVDVDA--WACAVAEVCRRDAAADATLCLALPDGARATLTRPGW +AAALDDALASAGRPLAAAWTCAHGRARPWWGSSIAEEGTL---DPRAAPLSLHLMTRGSV +WDRAAVSDPVPRRGPAAARPDDARWRPPEQDAPPARRAWLAQWEPVLTGTARGRGAPAP- +-------------------AVLGSPLTRPAWRDGLLLHAAAPSGAATGDPGDEERILTAA +SRRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARGHGSDADAHLTAAAALS +PGDPFVSVLRRIVAAGCVAGWATDPATAWRP-------DGGRP +>GCF_005280335_PROKKA_01569 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------MWLSQWESVLAG---ERGAAGPV +TAEGTAPVSGTEEHPSADAAVLGAPLTLPSWRDALVLHAAVRPGDPPPEPAERERFLIAG +SEQAPPWERLDRLRAGLRRLVPAAPPPAAAQALALAGWVGWARGQGSDAAAHLAAAAELA +PDDPFVTLMRRVVDTGCVAGWAAHPDTAWRP----------GA +>GCF_020097155_PROKKA_01465 +MRPRTLEGMDHPPAVPSAVPAGVTPPHLPVLRARGVDDLLGYAFHVLGTEPRESILLVTL +ARARLRAVVRVDRPGRETPPAARHWAEAVAAVARRDAAADAVVCVSL-TGRAGGLEPPGW +WPPLVRALRDRGIPAREGWGVVAGHAARWPVEPGAGPGPLEEVDPRHSDLSLHLIGAGSV +WGLRAGHRSVPTPAALDPAAPDRPHWTAARARPEAPGPWLAAWERVLDGGGLPERPAGR- +-------------------ARLGAGLEHPARRDALLIAAAGAAADELP-AAERAALLTGT +RDPGPDWRRLDRLWDALRALAADAPAPCAAPALALAAWICWARGEGTAAGAHLDVARRLA +PRDPLVGVLRRILDAGAVCAWAADPRRAWTPWDPQDPASGMRG +>GCF_023573625_PROKKA_01278 +--------MEAP-----------TSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTL +RDGRLRAVVRVDLPPEEVDVGA--WACAVAEVCRRDAAADATLCLALPDGARATLARPGW +AAALDDALASAGRPLTAAWTCARGRARPWWGSGVAEEGPL---DPRAAPLSLHLMTRGSV +WDRAAVPDPVPRRGPAAARADDARWRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAP- +-------------------AVLGSPLTRPAWRDGLLLHAAAPSGAATGEPGDEERILTAA +TGRAPAWDRLDALRAGLCALVPAATPAVAAQALALAGWVGWARGHGSDADAHLTAAAALN +PGDPFVSVLRRIVAAGCVAGWATDPATAWRP-------DGGGP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001111.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001111.fa new file mode 100644 index 0000000000000000000000000000000000000000..de56ce768a556d0062f2770d44b0054665245f76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001111.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01326 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS +GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDGAPS---AGGEASEVTLPALGESVTEGTVT +RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGS----SGQDE +ASAEEIEDKATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQGYVTPLVRRLA +HQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAAAPSSAPAAASAPAASSSVDPSVRGEVEKAPR +IRQVIAQRMRESLDLSAQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI +TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP +QVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLRTLRQRLEGGEFANELGL +>GCF_003691675_PROKKA_01047 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS +GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDGAPS---AGGEASEVTLPALGESVTEGTVT +RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGS----SGQDE +ASAEEIEDKATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQGYVTPLVRRLA +HQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAAAPSSAPAAASAPAASSSVDPSVRGEVEKAPR +IRQVIAQRMRESLDLSAQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI +TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP +QVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLTTLRQRLEGGEFANELGL +>GCF_005280335_PROKKA_01565 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEILADEDETVEVGAPLATIGDGD +GGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPEERSST-QDSEEKSSGGASGGDASEVTLPALGESVTEGTVT +RWLKAVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDE +ASAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAA--ADAPEATSPGQGYVTPLVRRLA +HQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQEQGSK----EQAAAASSAPAVASSVDPSVRGEVEKAPR +IRQVIAQRMRESLDLSTQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI +TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP +QVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLTTLRQRLEGGEFANELGL +>GCF_020097155_PROKKA_01461 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS +GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDEAPS---AGGEDSEVTLPALGESVTEGTVT +RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAA--PAASQDPA----PAADT +ASPEEIEDKATEAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAET------SASEPGPGYVTPLVRRLA +KQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAA------AEEQQTPAAASAPAPA-----AVRGETEKAPR +IRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVKLTYLPFITQAVTEALKQHPKLNASFSEDNKEI +TYHASEDIAIAVDTDRGLLVPVVKDAGTLNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQP +QVAILGTGAIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAELGL +>GCF_023573625_PROKKA_01282 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS +GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDEAPS---AGGEASEVTLPALGESVTEGTVT +RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGS----SGQDE +ASADEIEDKATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQGYVTPLVRRLA +HQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAAAPSSAPAAASAPAASSSVDPSVRGEVEKAPR +IRQVIAQRMRESLDLSTQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI +TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP +QVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLTTLRQRLEGGQFADELGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001113.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b0948f6f6248821b5477d5e65a711bf53987b8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001113.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01328 +MR-------------------DW---------------DEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLG +AGAQAEVWLVEDGRGVRAALKVPRAGAAPDALAAEAQA-GRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDMVQRVG +PLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVVGGASGAGATPGFAAPEALAAVEGAG +AEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAGHRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATA +RPEPVPLGEAAPAEVAHLLPTVLP-----GSGPTRRRRGRRAAPRR-----RALARRRGAAPRR---------GVLVAAG +LATALAVGGGT-------AGLWWPASLGDA-----TEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDA +AGEDAV----DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVEQAG---PAR +RAGDDALR-----VDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRDGGAAGRTWRVETVDPR +>GCF_003691675_PROKKA_01049 +MR-------------------DW---------------DEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLG +AGAQAEVWLVEDGRGVRAALKVPRAGAAPDALAAEAQA-GRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDMVQRVG +PLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVVGGASGAGATPGFAAPEALAAVEGAG +AEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAGHRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATA +RPEPVPLGEAAPAEVAHLLPTVLP-----GSGPTRRRR-RRAAPRR-----RALALRRGAAPRR---------GVLVAAG +LATALAVGGGT-------AGLWWPASLGDA-----TEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDA +AGEDAV----DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVEQAG---PAR +RAGDDALR-----VDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRDGGAAGRTWRVETVDPR +>GCF_005280335_PROKKA_01563 +MR-------------------DW---------------DEADDGAVGRVGGGPETEPERTSELGTAAPRAPGWAPVRLLG +AGAQAEVWLVEDGRGVRAALKVPRAGAAPDALAAEAQA-GRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDMVQRVG +PLSPGHAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVVGGASGAGATPGFAAPEALAAVQGAG +AEPEASPAVGAPSDVHAWAALGWYALTGRAPGAAGHRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATA +RPEPVPLGEAAPAEVAHLLPTVLP-----GSGPTRRRR-RRAGPGR-----RALVGRRGAAPRR---------GVLLAAG +LATALAVGGGT-------AGLWWPAAPGSAAEGAPAEGAPEPAGTEPTGTPVDAARPADGTPESGTPARATDTGAPGEDA +AGADAV----DVGEALAAVGQARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVEQAG---PAR +RAGDDALR-----VDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEDPEARDGGAAGRTWRVETVDPR +>GCF_020097155_PROKKA_01459 +MEAEDAERSGGVPPVGRPATDDWFADGGRDVSAWADPPRGGEGPAAVEPGVGDVGSPAELG-PADRPPQAPGLRVVSRIG +MGGQAEAWLVRREDGTECVLKVPRADGDPDAVAKEAAVYGHLRHPHLLRVLGTVDTDRGTGVLSERLPAGSLASMVHDAG +PLRPGQAVTVLVPVAQALAHLHEHGVVHGDVSPGNVLFGVDGRPALADLGVARVVGGPRGRGGTPGFTAPEDEAGV-GEG +---------GAAADVYAWGALGWFALTGRAPGPREHRAPLPVLVPDVPVELALLLSAALDPDPAGRPGAAEAAVAAYDAA +PPEPVPLHESAPAEVAHLLPTVVPPARPGGSGDARRSR-PRAGGRRDAGRGRGGRKRRNRSPRSRGWHPVMLVGAAVLAG +TVVSAAVGGLTDRPEDQGEGAGSRAVAAPP-----TSPTAAPANPRASVTPTGAADPKDAI----TPTR--DGGVPSAAG +TGPAAVLPAEDAAAALAAVAEGRTAALTDPDPARVDAYAVPDGPAWRRDRAIQDQLREGGSAFSGLVVTLEAVGRPRPAE +AGGSGGAEAGWVVVPAVLRMSAHTVLDDAGSVVGEVPASEEDVSVTLVPG-GEG-----------RWRAAAVDPR +>GCF_023573625_PROKKA_01284 +MR-------------------DW---------------DEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWAPVRLLG +AGAQAEVWLVEDGRGVRAALKVPRAGAAPDALAAEAQA-GRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDMVQRVG +PLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVVGGASGAGATPGFAAPEALAAVQGAG +AEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAGHRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATA +RPEPVPLGEAAPAEVAHLLPTVLP-----GSGPTRRRR-RRAGPGR-----RALARRRGAAPRR---------GVLVAAG +LATALAVGGGT-------AGLWWPASLGDA-----TEGAPEPAGAVPAGTSVDAARPADGTRESGAPARVPDTGAPGEDA +AGEDAV----DVGETLAAVGHARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVEQAG---PAR +RAGDDALR-----VDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRDGGAAGRTWRVETVDPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001114.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001114.fa new file mode 100644 index 0000000000000000000000000000000000000000..92c0a9ecad89401787002368b2503ec0be7b7c5f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001114.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01329 +MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>GCF_003691675_PROKKA_01050 +MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>GCF_005280335_PROKKA_01562 +MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>GCF_020097155_PROKKA_01458 +MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE +DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF +GVTAVRVDGRAGIWITA---REGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYET +IIACGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA +>GCF_023573625_PROKKA_01285 +MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001115.fa new file mode 100644 index 0000000000000000000000000000000000000000..6611274accde5ff2b5991c4a11bccef5fec1f5c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001115.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01330 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS +>GCF_003691675_PROKKA_01051 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVHWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS +>GCF_005280335_PROKKA_01561 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMDEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHAFNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLKVLSMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITVTQYVRPSKLHHPIDRWVKPQEFVEWSRRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLEHLAGEKTARQEASAVVAQMS +>GCF_020097155_PROKKA_01457 +MTTAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNTVKGSGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDIASGRPLPLDMDEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHELNPSTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKEQELVTKSNLILGMGETDEEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVAWSQRAEEIGFAGVMAGPLVRSSYRAGKLYA +QAMERLGREVPEHLAHLRGERTARQEAAAVVARMS +>GCF_023573625_PROKKA_01286 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001117.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a648a82413544dbdb07193f38d3e33a3d92592d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001117.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01332 +-------------------MARRAPDPA----QEPEPTRRDEPLITRRDLAGWVDGPGGG +LAGGRWPGDLLGLPEHGPTSMATAARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATM +HILGITLLATTVGKAVCRTQVVRLG-GRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHD +KVAGTVEIRM +>GCF_003691675_PROKKA_01053 +-------------------MARRAPDPA----QEPEPTRRDEPLITRRDLAGWVDGPGGG +LAGGRWPGDLLGLPEHGPTSMATAARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATM +HILGITLLATTVGKAVCRTQVVRLG-GRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHD +KVAGTVEIRM +>GCF_005280335_PROKKA_01559 +-------------------MARRAPDPA----QEPEPTRRDEPLITRRDLAGWVDGPGGG +LAGGRWPGDLLGLPEHGPTSMATAARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATM +HILGITLLATTVGKAVCRTQVVRLG-GRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHD +KVAGTVEIRM +>GCF_020097155_PROKKA_01455 +MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG +RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM +HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD +RVAGTVELHM +>GCF_023573625_PROKKA_01288 +MVA-----------HYAGGVARRAPDPQ----DRTETTGRAEPLITRRDLAGWVDGPGGG +RAGGRWPGDLLGLPERGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAM +HVIGLTLLATTVGKAVCRIQVVRVG-GRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHD +KLADTVEIRM + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001118.fa new file mode 100644 index 0000000000000000000000000000000000000000..886cb1eb7418674f59f0ef021a4f468e5bbcacc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001118.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01333 +MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>GCF_003691675_PROKKA_01054 +MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>GCF_005280335_PROKKA_01558 +MFTSPADVLAYIKEEGIEFVDIRFTDLPGMQHHFNVPASTVDEDFFTTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVAAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>GCF_020097155_PROKKA_01454 +MFTSVEDVLAYIKDEGVEFVDIRFTDLPGMQHHFNVPASTVDEDFFVTGQLFDGSSIRGF +AGLAESDMQLIPDVTTAFVDPFRVRKTLAMNFSIVNPRTGEDYRRDPRGVAQRAEAYLAS +TGIADTAFFAPEAEFYVFDDVRYESSARSSFYRVDSTEAHWNTSRDEEGGNLGHKTPRQG +GYFPVTPVDKQADLRDEICAVLAEVGLEVERSHHEVGSAGQAEINYRFNTLTHSADDLQK +FKYVVKNVAEMFGKSVTFMPKPVFGEAGSGMHCHQSLWLGGEPLFYDEKGYANLSDTARW +YIGGLLQHASAVLAFTNPTVNSYRRLVPGFEAPVSMVYSQGNRSAGVRIPVTGSNPKAKR +LEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPPEEAADIQKAPTSLE +EALNALEEDHEFLLAGDVFTEELIRTWIDYKREMELTPLAARPNPYEFELYYSC +>GCF_023573625_PROKKA_01289 +MFTSPQEVLTYIREEGVEFVDVRFTDLPGLQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICAVLAEVGLTVERSHHEVGAPGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001119.fa new file mode 100644 index 0000000000000000000000000000000000000000..e22ee1710e8a608ef4c730cd8f8ae550024b40fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001119.fa @@ -0,0 +1,75 @@ +>GCF_002008305_PROKKA_01335 +MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRALLLWVRLAEREPRVHHALRD +PETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATAPALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPV +AAVTGKDAAVALRRAYRRQLAAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG +MGKCGAGELNYVSDVDVVFAH---------AVREAADGADPDAE-VPDGPRAAALAAELAAGIGRVIQGAAPEPGLWEVD +ANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERYIAEIWPRVWESSSRDGFVESVRAMRARVL +DTLAPAEREREIKLGPGGLRDVEFTAQLLQLVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRI +QLVHLRRTHLMPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSAEDVRLSAEA +VRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD +AARRLCLVLSGSRFVGDLLEHSPEAVAWVGDDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVAL +ADISGLLDLEAVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR +AREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL +ATDFRRWADGVRYAGDLTTADAREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGT +LPALRAIARHGLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGG-ELEERYLRVTRL +ARQVFETRFYGL +>GCF_003691675_PROKKA_01056 +MSALPDAATADA-PDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRALLLWVRLAEREPRVHHALRD +PGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATAPALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPL +AAVTGKDAAVALRRAYRRQLAAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG +MGKCGAGELNYVSDVDVVFAH---------AVREAADGADPDAQ-VPDGPRAAALAAELAAGIGRVIQGAAPEPGLWEVD +ANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERYIAEIWPRVWESSARDGFVESVRAMRARVL +DTLAPAEREREIKLGPGGLRDVEFTAQLLQLVHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRI +QLVHLRRTHLMPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSAEDVRLSAEA +VRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD +AARRLCLVLSGSRFVGDLLEHSPEAVAWVGDDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVAL +ADISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR +AREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL +ATDFRRWADGVRYAQDLSAADAREIRRIKARVEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGT +LPALRAIARHDLLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGG-ELEERYLRVTRL +ARQVFETRFYGL +>GCF_005280335_PROKKA_01556 +MSALPDAATADA-PDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRALLLWVRLAEREPRVHRALRD +PETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATAPALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPR +AGLTGADAAVALRRAYRRQLAAIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIG +MGKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAAGIGRVIQAAAPEPGLWEVD +ANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPIAGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVL +ETIAPAEREREIKLGSGGLRDVEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRI +QLVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRPLLSTTAALSDDEVRLSAEA +VRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAMLGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD +AARRLCLVLAASRFVGDLLEHSPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVAL +ADISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR +AREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL +ATDFRRWADGVRYAGDLTTADAREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGT +LPALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSGVGTAGG-ELEERYLRVTRL +ARQVFEARFYGL +>GCF_020097155_PROKKA_01452 +MAPTPDSHVPGP---RRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLLYIRLAERDPQVHRVLAE +ADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPALAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPV +AGLTGADASVALRRAYRRQLTAIALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIG +MGKCGARELNYVSDVDVVFVHDVLEPG------------APDA---PSAQEAARLAAELAAGISRVLSGPAPEPGLWEVD +ANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPRVWESSAREGFVENVRAMRTRVL +DTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADESVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRI +QLVHLRRTHLMPVKEGPRRVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSADA +VQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAFRRLSESLGSSPWFLRMLRDSTD +AARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPRGLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTAL +ADITGVVGLEEVGHALADVDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADETA +AAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYARWAEVWERQALLRARVVAGPAGL +AEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLPRGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGT +LPALRALARLDLLPPSEAALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVTRQ +ARQVFEQRFYGL +>GCF_023573625_PROKKA_01291 +MSALPDAATADA-PDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRALLLWVRLAEREPRVHHALRD +PGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATAPALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPL +AAVTGKDAAVALRRAYRRQLAAIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIG +MGKCGAGELNYVSDVDVVFAH---------AVREAADGADPDAQ-VPDGPRAAALAAELAAGIGRVIQGAAPEPGLWEVD +ANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERYIAEIWPRVWESSARDGFVESVRAMRARVL +DTLAPAEREREIKLGPGGLRDVEFTAQLLQLVHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRI +QLVHLRRTHLMPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSAEDVRLSAEA +VRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD +AARRLCLVLSGSRFVGDLLEHSPEAVAWVGDDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVAL +ADISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR +AREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL +ATDFRRWADGVRYAGDLTTADAREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGT +LPALRAIARHGLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGG-ELEERYLRVTRL +ARQVFETRFYGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001120.fa new file mode 100644 index 0000000000000000000000000000000000000000..983340ae6738af04217153b1749e7486219e7140 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001120.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01336 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG +SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG +GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI +EEGYEVPEAAAEDISALTTHERRVLGHVPLPGTLHDALRTAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>GCF_003691675_PROKKA_01057 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +QGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG +SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG +GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>GCF_005280335_PROKKA_01555 +MDRQQDYVLRTIEDRDVRFVRLWFTDVVGTLKSVALSPAEVENAFAEGLGFDGSSIDGYT +RISESDMLLQPDPATFQILPWRGDGGQSSRMFCDVLTPDGRPAPADPRHVLRRVLEKASD +MGFSCFMHPEIEFYLLTSDQPGPDGRPVPVDRAGYFDNVPGSDAADFRRDAVTLLESMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG +SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG +GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHDPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>GCF_020097155_PROKKA_01451 +MDRQQDFVLRTIEDRDVRFVRLWFTDVIGTLKSVALAPAEVEAAFTEGLGFDGSSIDGYT +RISESDMLLQPDPATFQILPWRGEAGQTSRMFCDVLTPDGRPAPADPRNVLRRVLDKASD +MGFSCYTHPEIEFYLLASDRPGPDGRPVPVDSAGYFDHVPGGAAQDFRRDAVTLLEDMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVQTFRTIMKEVAARQGHYATFMPKPFGDQPG +SGMHTHFSLFEGDSNAFYDPADEFRLSVTGRRFIAGLLKHSVEISLVTHQFVNSYKRLWG +ADEAPAYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGLDASANPYLAYALLLAAGLKGV +EENYDLPEPASEDVGALTPQERRVLGHVSLPGTLHDAVRAAEESEFVADVLGEHVYEALL +RNKRQEWDDYRVEITPYELRRYMTGL +>GCF_023573625_PROKKA_01292 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQEQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG +SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG +GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001121.fa new file mode 100644 index 0000000000000000000000000000000000000000..6312bb5119d2ead2bbfecf4198dd6d5d8b721b13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001121.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01338 +MSA------PQSPRQPDDTAPYGPP----------APSRYRTVHLQRAKDEGRRFAMLTT +YDAMTAALFDEAGVEVLLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVAD +LPFGSYEASPRQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQ +SEHVLGGYRVQGRGAGAVERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGI +GAGPGTTGQVLVWQDMLGLREGRVPRFVRQYARLHEVVGDAVRAYRADVLDGAFPAPEHG +FQG +>GCF_003691675_PROKKA_01058 +MSA------PQSPRQPDDTAPYGPP----------APSRYRTVHLQRAKDEGRRFAMLTT +YDAMTAALFDEAGVEVLLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVAD +LPFGSYEASPRQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQ +SEHVLGGYRVQGRGAGAAERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGI +GAGPGTTGQVLVWQDMLGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHG +FEG +>GCF_005280335_PROKKA_01554 +--------------------------------------------------------MLTA +YDAMTAALFDEAGIEVLLVGDSVGNTVLGHSSTLPVTLDQMILFSQAVVRGAQRALVVAD +LPFGSYEASPQQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVIAHIGFTPQ +SEHVIGGYRVQGRGEGAVEAMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGI +GAGPGTTGQVLVWQDMLGLREGRTPRFVRQYARLHEVIGAGVRAYRRDVLDGAFPAPEHG +FEA +>GCF_020097155_PROKKA_01450 +MDSRTVTPPASSPAASEAAAPYGGAATAAAAAPVEAPARYRTVHLQRAKDEGRRFAMLTT +YDAMTAALFDEAGVEVLLVGDSLGNTVLGHGSTLPVTLEDMIVFSAAVARGARRAFVLAD +LPFGSYEASPEQAVRAGVRLMKEAGVHGVKVEGDERFAPHIAAMVAAGVPVMGHIGFTPQ +SEHVLGGYRVQGRGEGAAERLIASARALEDAGAFAVLMEMVPSDVAAAVDAALRVPTVGI +GAGPKTTGQVLVWQDMLGLGAGRTPRFVKRYADLRAVMGDAVRAYRADVLSGAFPDPAHA +FES +>GCF_023573625_PROKKA_01293 +MSA------PQSPRQPDDTAPYGPP----------APSRYRTVHLQRAKDEGRRFAMLTT +YDAMTAALFDEAGVEVLLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVAD +LPFGSYEASPRQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQ +SEHVLGGYRVQGRGAGAAERMTVSARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGI +GAGPGTTGQVLVWQDMLGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHG +FEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001123.fa new file mode 100644 index 0000000000000000000000000000000000000000..3417fa495257e2022b3ca85652fa03af57f8569f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001123.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01340 +MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT +PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP +SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT +IVVTDDGAEILTLP +>GCF_003691675_PROKKA_01060 +MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT +PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP +SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT +IVVTDDGAEILTLP +>GCF_005280335_PROKKA_01552 +MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT +ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP +SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT +LVVTDDGAEILTLP +>GCF_020097155_PROKKA_01448 +MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT +ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP +SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT +LVVTEDGAEILTLP +>GCF_023573625_PROKKA_01295 +MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT +PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP +SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT +IVVTDDGAEILTLP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001124.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0c3e590712b60b9e12dbc44f6dbb2d6c1325f5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001124.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01342 +MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR +>GCF_003691675_PROKKA_01062 +MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR +>GCF_005280335_PROKKA_01550 +MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFADAIAELRAGT-DERGRPAVQPRLFSR +>GCF_020097155_PROKKA_01446 +MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA +YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR +>GCF_023573625_PROKKA_01297 +MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001126.fa new file mode 100644 index 0000000000000000000000000000000000000000..f8f0d6cc3f504a1997efa99abcb7cc800111748e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001126.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01344 +MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDE------D +>GCF_003691675_PROKKA_01064 +MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDE------D +>GCF_005280335_PROKKA_01548 +MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA +KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG +PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK +VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV +TSEHPDDLAHALARLRRDG------S +>GCF_020097155_PROKKA_01444 +MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA +KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG +PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK +VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL +ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI +VSPYPDDLAHALRVLRGEDRGAAPDA +>GCF_023573625_PROKKA_01299 +MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDA------D + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001131.fa new file mode 100644 index 0000000000000000000000000000000000000000..8b43eab14cf84fb7ca00093b3aa76fc89f8f3d75 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001131.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01349 +MTAPATAGPTPTDP----RAREIADALAAVHARIADAARDAGREAEPALVVVTKTHPAED +VVRLAALGVTDVGENRDQEARPKAEAVAAALGAD---APRWHFVGQLQTNKAKYVVRYAS +VVESVDRPELAEALSRALVLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGAR +PEDVPALADVIAGLPGLRLGGLMCVAPRGLDPEHAFRRLAALGARLRQTHPEATALSMGM +SADLEAAVRAGATQVRIGSDVLGARDAVG +>GCF_003691675_PROKKA_01069 +MTAPATAGPTPTDP----RTREIADALAAVRARLADAARDAGREAEPALVVVTKTHPAED +VVRLAALGVTDVGENRDQEARPKAEAVAAALGAD---APRWHFVGQLQTNKAKYVVRYAS +VVESVDRPELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGAR +PEDVPALTDAIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAHLRQTHPEATALSMGM +SADLEAAVRAGATQVRIGSDVLGARDAVG +>GCF_005280335_PROKKA_01543 +MSTPEQH-PTPHDAAAETRTREIAAGLAAVRERIARAAREAGRADEPALVVVTKTHPAED +VVRLAGLGVAAVGENRDQEARPKAAAVAEALGDA---APRWHFIGQLQTNKAKHAARYAS +VVESVDRTELAEALSRALVLRREREPGVEVPDLECLVQVDVDDRADEDRPEGIGPRGGAA +PEDVPALAAAIAALPGLRLGGLMCVAPRGLDPEASFRRLAALGEELRSAHPDASTLSMGM +SADLESAVRAGATQVRIGSDVLGARPAVG +>GCF_020097155_PROKKA_01439 +MAE-----PLQDDP----RVAEIAAGLDGVRRRIADAAAAAGRADLPELIVVSKTHPAED +VVALAGLGVRQVGENRDQEARPKAAAVAEALGGAGVPAPAWHFIGQLQTNKAKHVARYAS +AVHSVDRLDLVDALSRAVVLRREREGADAVSALDCLVQVDVDDRADEDRPEGIGPRGGAA +PEDVPELARAIAAADGLRLRGLMCVAPRAADPAAAFARLAALSARVRAEHPDADALSMGM +SGDLEAAVAAGATHVRVGSDILGARGAVG +>GCF_023573625_PROKKA_01304 +MTAPATAGPTPTDP----RAREIADALAAVRARIADAARDTGRAAEPALVVVTKTHPAED +VVRLAALGVTDVGENRDQEARPKAEAVAAALGAD---APRWHFVGQLQTNKAKYVVRYAS +VVESVDRPELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGAR +PEDVPALADVIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAGLRQTHPEATALSMGM +SADLEAAVRAGATQVRIGSDVLGARDAVG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001132.fa new file mode 100644 index 0000000000000000000000000000000000000000..4552aa88f28402a7769c4d8e86712d274966cec8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001132.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01350 +MTAAEGPAGTARVPAGPFVHRETVRT-ATGAV-HVAWTSVAAGNLALHVVPPDEAEGLAR +VSAARRALERVMGVPEGATLYLDQVHSADVVWADGPGRGGASAPVADAAVSRDGSRPLAV +MVADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPEADRTGPGLRAWIGP +GVCGRCYEVPAAMRDEAAARLPATAATTSWGTPALDLPAGAAEVLRARGVATATIDVCTR +EDERLFSHRRAPGEGRFAGLVWR--ADPDATVPRGDA-- +>GCF_003691675_PROKKA_01070 +MTAAGGPAGTARVPAGPFVHRETVRT-ATGAV-HVAWTSVAAGNLALHVVPPDEAEGPAR +VSAARRALERMMGVPEGATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAV +MVADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGP +GVCGRCYEVPAAMRAEAAARLPATAATTSWGTPALDLPAGAAQVLRARGVATATIDVCTR +EDERLFSHRRAPGEGRFAGLVWR--ADPDATTPRGEA-- +>GCF_005280335_PROKKA_01542 +MTAAEGPVGTVPVPAGPFVHREAVAT-AGGTV-HVAWSGVAAGNLGLHVVADEDAAGRRA +VGEARRGLERAMGVPVGSTLYLDQVHSADAVWADGPGWGEEAGPTADAAVSRDGGRALAV +MVADCLPVVLVDEATGATAVAHAGRRGLVDGVLEGTVDRLLSLRPADRRDAPGLRAWIGP +GVCGRCYEVPEQMRAEAAERVPATAATTAWGTPGLDLPAGAVAILRGRGADVAVVQACTL +EDERLFSHRRAPGQGRFAGLVWR--ADEDASTPTRAA-- +>GCF_020097155_PROKKA_01438 +MSLAGGPVGTQPVPSGPFVHREDLRADARGRVAHVAWTSAEAGSLAFHILGAEQEQARAD +VVAARHRVEDAMGVPRGSVFYLEQVHSVDVVTA-GPGWEEGFAPTADASVSPDGHTPLAV +MVADCLPVVFVDGLTGATAVAHAGRRGLLDGVLENTVDALLALRPEGSAGAFGLKAWIGP +GISGESYEVPQAMQDEAVARIPELEATTSWGTPALALASGAQAVLRARGVAVERIALDTF +TDERVFSHRRAPGRGRFAGLVWTTPADVDQDHDAGDARG +>GCF_023573625_PROKKA_01305 +MTAAEGPAGTARVPAGPFVHRETVRT-ATGAV-HVAWTSVAAGNLALHVVPPDEAEGLAR +VSAARRALERAMGVPEDATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAV +MVADCLPVVFVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGP +GVCGRCYEVPAAMRTEAAARLPATAATTSWGTPALDLSAGAAQVLRARGVTTATIDVCTR +EDERLFSHRRAPGEGRFAGLVWR--TDLDATTPRGEA-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001136.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a6dd2f66c58357cce45e6719443829c71327a7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001136.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01354 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>GCF_003691675_PROKKA_01074 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>GCF_005280335_PROKKA_01538 +MPQTPDPARELRVVLAGGGTAGHISPMLAIARALESDDAGPVRCTMVGTASGMETRLVPE +AGYELDLIERVPMPRRPSMDVVHFPARMRAAVAAAGRILAERRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAQRRAARAALGLDPERTTVVVTGGSSGALAVNRTVRDSLDDLLGAGLQVFHLTGRDKAL +TEADGTPLRREGYVQREYLDGMEQAYAAADLLVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALTVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAEEGARR +>GCF_020097155_PROKKA_01434 +MTTPNDASRPLRVVLAGGGTAGHISPMLAIARALGRQDPSTV-CTMVGTDSGMETRLVPQ +AGYELDFVERVPMPRRPSMDVVRFPGRFQASVRQAGEILRRRGADVLVGVGGYVSTPMYL +AASRAGVPVVVHEANARPGLANRVGALRAARVGTALPDTRLPKAQWVGMPMRPEISGLDR +AAARDAARAELGLDPERTTVVVTGGSSGALNVNRTVRESLDDLLGAGLQVFHLTGRGKEL +TDEAGQRVTRPGYVQREYLDGMEKAYAAADLIVARSGAGTVCEIAAVGLPAVFVPLPVGN +GEQALNARPVVDAGGALLVRDETFRADWVRRELIPLATDPQRLAAMGEAAARLGVRDADV +RTADLVREAAREGARR +>GCF_023573625_PROKKA_01309 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEDDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAAGRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001137.fa new file mode 100644 index 0000000000000000000000000000000000000000..fe70b3dd008269ab47544e3b39021c080e6a4255 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001137.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01355 +MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP +HRMVRVQAWMGDCSDAT-DPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIF +TILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMV +SGVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLP +VIPTPALQEPR +>GCF_003691675_PROKKA_01075 +MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP +HRMVRVQAWMGDCSDAT-DPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIF +TILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMV +SGVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLP +VIPTPALQEPR +>GCF_005280335_PROKKA_01537 +MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV +LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS +LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV +LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP +HRMVRVQAWLGDCSDAS-DPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIF +TILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMV +SGVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLP +VIPAPASQES- +>GCF_020097155_PROKKA_01433 +MPSTATRPEASSRASARTAVRPR-LAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMV +LSASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLA +LVAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPV +LPFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAA +NRMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIF +TILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMV +TGLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHER------DLLPAAEASAADP-- +-ASSASPQESR +>GCF_023573625_PROKKA_01310 +MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP +HRMVRVQAWMGDCSDAT-DPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIF +TILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMV +SGVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLP +VIPTPALQEPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001140.fa new file mode 100644 index 0000000000000000000000000000000000000000..c95b03a017b6b2ea9b37b14199f51a47dc14ebd2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001140.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01359 +MT-TPSDPPAPLTPAQQDAAFRPSHTPAAAWPALAQALAEAGIAAHVHGAAPADGVTGVSLDSRVVRPGDLYVAVPGARA +HGAAFAATALEAGAVGVLTDAAGRALLAEQGLADVPVLEVDAVRTAAGTVAARVYGGGGDTGPRLLGVTGTNGKTTTSFL +AAALLEALGRRSGIVGTILIRAGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTN +LTQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALGPAAPTPGALAEHDPGLRAD +WEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANAALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGR +MEVVGREPDAVVDFAHNPDGMVQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSE +DPAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHETTMDYDGELVPLDDRVALR +EALAARVAAASASGSGP----AREGKVIES +>GCF_003691675_PROKKA_01079 +MT-TPSDPPAPLTPAQQDAAFRPSHTPATPWPALAQSLAGAGIAAHVHGAAPADGVTGVSLDSRVVRPGDLYVAVPGAHA +HGAAFAARALEAGAVGVLTDAAGRALLAEQDLADAPVLEADAVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFL +AAALLEALGHRSGIVGTILIRAGEREVPSTLTTPEATQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTN +LTQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALGPAAPTPGALAEHDPGVRAD +WEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANAALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGR +MEVVGREPDAVVDFAHNPDGMVQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVVIVTDDTPHSE +DPAPIRAHILAGARAEADRIAREEGRTVVIEEVADRAAAIRRAVELAGPQDGILLAGRGHETTMDYDGELVPLDDRVALR +EALAAGAAVASASVSGP----VREGKVIES +>GCF_005280335_PROKKA_01534 +MS-SQPAQPQPLTPAQQDDAFRPSRTPATPWDELTRALQAAGVAARTHGRGPAAGVTGACLDSRVVRPGDLYVALPGARS +HGADFARAAVDAGAAGVLTDAEGRARLAEQGLDGSAVIEVDSVRTAAGVVAARVYGGGQDAGPRLIGITGTNGKTTTSFL +AAALLEALDRRSGVIGTILIRAGGREVPSTLTTPESTQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTN +LTRDHLDMHGSMEEYFEAKAGLFDPERTARAVITVDGGEGPRWGLSMARAVRTPVTTLALGPAAPHPGALAEEDPDFRAD +WEIAELVPDGLGHRFTLRHGATGRALRASVGLPGRFNAANAALAVLLVLYAVGEEHLDALAAVLDVPAGEGPLAAAVPGR +MEVVGRAPDAVVDFAHNPDGMVQALRSLADAREAAGRSGRTLIVFGSAGDRDREKRPIMGEIAARAADVVIVTDDTPHTE +DPAPIRAQILEGARAEAARLLQAEGRTVLVEEVADRAVAIRRAAELAAPQDGILVAGRGHETTMDYDGELVPLDDRQALR +EALAARAAAASPRASDPGSGAPRGGKVDES +>GCF_020097155_PROKKA_01429 +MTDDAPQTTAPLTPAEQDAAFRPAAVTPVAWAEVAAALRAAGQDVRERSAAAAPAVTGAALDSRVVRPGDLYVALPGARA +HGAAFAAAAREAGAAGVLTDGDGVALLAEQGLDDLPVLEVESVRAAAGVAAARIYGGGPDAGPRLLGVTGTNGKTTTSFL +AASIVEALGERSGIIGTILTRAGDRQVPSTLTTPESAQLHALMALMRQEGVDTAVMEVSSHAVEYRRIAGLHYAVAGFTN +LTQDHLDQHGTMEGYFRAKLGLFEADRTDRAVVVLDGGEGPRWGVKTARRAGAPVTTLALGAASPTPGALAEEHPDVVPD +WQVTDLVADGLGHRFALVHAATGRRLPASVGLPGLFNVANAALAALMVLESIGEDRLDELAAVLDVPAGTGPLAAAVPGR +MEVVGREPDAVVDFAHNPDGMVQALRALGDARAAAGRAGRTLIVFGAAGDRDATKRPLMGRIAAEHADVVIVTDDTPHTE +DPAPIRAQLLEGAREEAARAA-AAGREVRVEEFADRAAAIRRAAELAAPEDGILVAGRGHETEMDYDGTLVPLDDRVALR +DALAAR------RPGDAQEPGVAGGKVAGK +>GCF_023573625_PROKKA_01314 +MT-TPSDPPAPLTPAQQDAAFRPSHTPATPWPALAHALAEAGIAAHVHGAAPADGVTGVSLDSRVVRPGDLYVAVPGARA +HGAAFAATALEAGAVGVLTDAAGRALLAEQGLVDVPVLEVDAVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFL +AAALLEALGRRSGIVGTILIRAGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTN +LTQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALGPAAPTPGALAEHDPGLRAD +WEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANAALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGR +MEVVGREPDAVVDFAHNPDGMVQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSE +DPAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHETTMDYDGELVPLDDRVALR +EALAARVAAASASGSGP----AREGKVIES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001141.fa new file mode 100644 index 0000000000000000000000000000000000000000..0a3c8e499b7cd1c3f42cc5ffe053a4e1767a73e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001141.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01360 +-------------------------MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILD +RDGDVLAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGSRPYAVVRRSVTPEVR +DAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPA +VDGADLRLTVDKDAQWFAQETLGALAAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPG +STGKALPIAAAVDAGKVTATDGFTVPGSQDFDGQ-TIRDFSPHPTFDMTVAGIYARSYNTGTVQIAEKITDEQRYEYMRS +FGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHTAQMYQALANGGVLIPARLIDATVDGDGAEKRWES +SAEPHRVVSEETAAQMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSMH +RPPSKQGSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW +>GCF_003691675_PROKKA_01080 +-------------------------MRTRILLLLVLVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILD +RDGDVLAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGSRPYAVVRRSVTPEVR +DAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPA +VDGADLRLTVDKDAQWFAQETLGALAAEYDAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPG +STGKALPIAAAVDAGKVTATDGFTVPSSQDFDGQ-TIKDFSPHPTFDMTVAGIYARSYNTGTVQIAEKITDEQRYEYMRS +FGVGQPIDLGLPQQAGSVLVPPEKWDGRQRLTTAFGQGYTQTTLHTAQMYQALANGGVLIPARLIDATVDGEGAEKRWES +SAEPHRVVSEETAAQMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNFGFTAVAPLDDPRFVVSVSMH +RPPSKQGSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW +>GCF_005280335_PROKKA_01533 +M-TDRPAFSSPRGGSTVGPAPGLPDARIRGLLLLVLVLLGGLALRLVYVQGVDPTGQAAAAMDKRLTHQETLPERGSILD +RDGDVLASSVRRYDMVVDQRLVKDFNEWDREARKTVLVDVDSRLASLAEVLELPEEQVREATIGSRPYNVVKRSVTPEMR +DAAMALKVPGLLAEPVDRRVYPNGSVAGSIVGFMGGDGTPLEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPA +VDGADLRLTLDKDAQWFAQETMGALAAEHDAEWANAVVLDAKTGDVLVMADSTTVDPADPEGTEPYFRSSTVMSTPYEPG +STGKALPIAAALDAGAVTATDGYTVPSSQEFDGQ-TIRDFAPHETYDMTVAGIFARSYNTGTVQVAEEISDELRYEYMRS +FGVGKPIDLGLPRTAGGVLVPPGEWDGRQRLTTAFGQGYTQTTLHTAQMYQAMANGGVMEPARLIDATVDGDGAEKRWEP +AAEPHRVVSEATAADMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGRYDGYNFGFTAVAPLDDPRFVVSVSMH +RPPSQLGSRAVTSAAAQIMEHMLRQADVPADGAAPQDYDVFVDDPQDRPW +>GCF_020097155_PROKKA_01428 +MPVSRSRVSG--AGSRTAPPIGTARVRSRTVLLLLLALVTVLGLRLVWVQGIDASGAAATAMSERLKTQEIRPERGAITD +RDGAVLASTVRRYDIVVDQRLVKDFKEWDAEKRQSVLVSIDSRLSSLAEALGMSEDEVRAAAIGDRPWAVLKRSVTPEVR +DRVLALKVPGVLADAVDRRTYPSGAVAGSLVGFMSSDGTPLEGLEKSQDAVLSGTPGTRTFEVGATGIRIPNAPEDVTPA +VDGATLRLTLDKDAQWYAQEAMARLADTYSAQWANAVVMDAKTGEVLALADSATVDPGDPQAADARARTPGVVYTPYEPG +STGKTATMAAALDMGLVTPETGLEVPDRLELKGQPPIRDASPHETYTMTVAGVYARSYNTGTVMVAEKMSDEQRYEYMRS +FGIGRPIDLGLPQPARSVLAAPGDWDGRQRLVTAFGQGYTVTTLHTAQMFQAIANGGVLEPARLIAATVGADGTEHRWDP +GVASRRVVSEQTAEEMLRMMETVVTQGTSTVAQLPGYRVGGKSSTAQVAGETGTYDGYNYGFTAVAPLDDPRYVVSVSMN +RPSAGGSSKVVAAAAADVMQHMLRQGGVPPGGAEPDDYRVFVDDPQERPW +>GCF_023573625_PROKKA_01315 +-------------------------MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILD +RDGDVLAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGSRPYAVVRRSVTPEVR +DAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPA +VDGADLRLTVDKDAQWFAQETLGALAAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPG +STGKALPIAAAVDAGKVTATDGFTVPGSQDFDGQ-TIRDFSPHPTFDMTVAGIYARSYNTGTVQIAEKITDEQRYEYMRS +FGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHTAQMYQALANGGVLIPARLIDATVDGDGAEKRWES +SAEPHRVVSEETAAQMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSLH +RPPSKQGSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001143.fa new file mode 100644 index 0000000000000000000000000000000000000000..6659fb352e4e629cb484a943c5df16bf54420405 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001143.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01362 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA +>GCF_003691675_PROKKA_01082 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSAKVRAVEKIRTSRTTA +>GCF_005280335_PROKKA_01531 +MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE +LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE +KPTEEEILENRRASSAKVRAVEKIRTSRTPA +>GCF_020097155_PROKKA_01426 +MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT +LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS +YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR +AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP +AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE +KPTEEEIEENRRASSAKVRAVEKIRTSRTTA +>GCF_023573625_PROKKA_01317 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001145.fa new file mode 100644 index 0000000000000000000000000000000000000000..35de8be8115434d8b90ecf7ca78b62382106bd0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001145.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01364 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPR-AVASGASGPEARRSGAP---RRQG---GGDFM +GRLERRWDERRAGGD +>GCF_003691675_PROKKA_01084 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPR-AVASGASGPEARRSGAP---RRQG---GGDFM +GRLERRWDERRAGGD +>GCF_005280335_PROKKA_01529 +MPLSEHEQRMLDQLEHQLRTEDPRLATQMADTRRDPVPVKRVVLGAVLAVVGLLVIVMGV +ANQLVPVGVLGALVVGAGIFLVTTRPRGGRAAGADRPGPGRGGRPGGGRPEGGRPGGDFM +GRLERRWDARREQGD +>GCF_020097155_PROKKA_01424 +MPLSDHEQRVLDELERQLHADDPSLASQLS-TPRGPAPVRRIVLGAAMMLAGLAVVLVGV +STHLVVVGVLGAVLLGGGILVLTSR-R-VSASRAPGAPVAGDGGPHAGRRRG---G--LM +DRLDREWDSRGRADT +>GCF_023573625_PROKKA_01319 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPR-AVASGASGPEARRSGAP---RRQG---GGDFM +GRLERRWDERRAGGD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001146.fa new file mode 100644 index 0000000000000000000000000000000000000000..a89f416d1e6ddd793e2c89fb8540f0b8d0148f68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001146.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01365 +M-------SETAPAAPRDEATILHVDMDAFFLSVELRERPDLEGRPAAVAAPSGRSVVLS +ASYAARAYGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVD +EAFLDVAGARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLI +VPPERTLDFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWA +SLARGIDPRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQATAGA +VTVRLKAPDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGD +EADQPPAQEALFGGPAWGTEGEAS-EAGDWAGAEAALDAVARRFPTAAVRPASLLGRREA +RADARRDAPRPGPGGPDRE +>GCF_003691675_PROKKA_01085 +M-------SESAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLS +ASYAARAYGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVD +EAFLDVAGARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLI +VPPQRTLDFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWA +SLARGIDPRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQVTAGA +VTVRLKAPDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGD +EADQPPAQEALFGGPAWGTEGEAS-EAGDWAGAEAALDAVARRFPTAAVRPASLLGRREA +RADARRDAPRPGPGGPDRE +>GCF_005280335_PROKKA_01528 +M-------SDTAAAQARPEASILHVDMDAFFLSVELRERPDLTGRPAAVAAPSGRSVVLS +ASYEARAYGVRSAMPLAHARALCPPLVVVPPRQDVYRSVSADVMALLGQVTPVLEQLSVD +EAFLDVAGARRRLGPPARIGGLIRRRVREELGLPCTVGAAGVKFVAKMASTAAKPDGLLV +VPPERTLEFLHPLPVGRLWGVGPKAAEALRRRGMATIRDLAAADPEQLERAFGAAGRSWA +QLSRGIDPRPVAPRPAARSIGADHTFDVDPLDVAGVDLEVLRLCHRVAARLRAEEVAAGA +VTVRLKDPDGRVRSRTARLARPTTTAHGLLGPARRLVAELHAQRPHPVRLVGVRAERLTD +ADEPAPEQEALFGGSGFGDDDAAEGGAGDWAGAEAAADAVARRFPTAAVRPASLLRRAAG +RPDTRRDVPGP-------- +>GCF_020097155_PROKKA_01423 +MSAPDPGPAPSSPPPPRREPSILHVDMDAFFLSVERRERPELRGVPAAVAHPEGRSVVLS +ASYEARAYGVRSAMPLAQARALCPPLRVTPPRQELYRSTSARVMDLFGRVTPVVEQLSVD +EAFLDVAGARRLLGPPERIAALIRERVRAELGLPCTVGGAGVKFVAKMASTAAKPDGMLL +VPPQCTLAFLHPRPVGALWGVGPQAARRLRERGVETIGDLAARDPRWLREAFGAAGAAWA +ELAAGRDPRPVAPREPARSVGADHTFDVDARDPAALDREVLSLCHRVAARLRSGGHTAAA +VTVRVKDPALATRARTVRLPAPTASGRVLHAHAGPAVAGLLTERPHPVRLVGVRAERLSD +AEAHGAVQEALFAPE--GHEGPTD-DAG-WRRAEEAADAVARRFPGAGVRPASLLGPPEG +S------------------ +>GCF_023573625_PROKKA_01320 +M-------SETAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLS +ASYAARAYGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVD +EAFLDVAGARRRLGPPEHIGHLIRERVRSELGLPCTVGGSAVKFVAKTASTAAKPDGLLI +VPPERTLDFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWA +SLARGIDPRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEGVTAGA +VTVRLKAPDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPIRLVGVRAERLGG +EADQPPAQEALFGGPAWGTEGEAS-EAGDWAGAEAALDAVARRFPTAAVRPASLLGRREA +RADARRDAPRPGPGGPDRE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001147.fa new file mode 100644 index 0000000000000000000000000000000000000000..742a25bf2fadb4c4fbfe53d36f74a5bdb3350618 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001147.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01366 +MPADVAV--PRPRPADQDRFRAAVADALDRLLAEHRDLARDVHPLTAPLVDAIADLTAGG +KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR +FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG +VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA +FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL +DADLGDPDLGADRVAHWQGVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSAE +LTQLIDAYTSRRH +>GCF_003691675_PROKKA_01086 +MPADVAVPRPRPRPADQDRFRAAVADALDRLLAEHRELARDIHPLTAPLVDAIADLTAGG +KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR +FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG +VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA +FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL +DADLGDPDLGADRVAHWQAVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSTE +LTRLIDAYTPRRH +>GCF_005280335_PROKKA_01527 +MPVDAAV--TRPRPADQDRFRAAVAEELTRTLDEHRERARAVHPLTVPLVDAVGDLAAGG +KRLRAVLGWLGWRAAGGDPENPRIARTGAALELFQAAALIHDDILDRSDTRRGMPSVHRR +FEAEHRASGWRHDAGHFGVSAAILAGDVALGMSETAFAAALEGAGRPARARDEFERMRFG +VMVGQYLDVAAEMAPPATDPAEAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDALVAA +FAEVSLPFGLAFQYQDDLLGVFGDPAATGKPAGDDLREGKRTVLIARAVALLSPADAAAL +DADLGDPGLSAERIAHWQRALEECGARQAVTDRVAALSARAAEAVGALEAHGVPADVRAE +LTALIEAATTRRH +>GCF_020097155_PROKKA_01422 +M--------PTPETASVSDFRAAVAERLTAVLDGHARGAARIHPDADPVVEAVSVLTSGG +KRLRAVLCWLGWRAAGGSPTDPRAAVAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR +FEARHREHGWRHEAEHFGVSAAILAGDVALALSDSMFSRAIEGTPRAERARREMERMRFE +VMVGQYLDVAAEMAPPAADPAAAERAARAVVEHKSARYSAVHPLALGALLAGADDDLVAA +FEAVSLPFGMAFQLQDDLLGVFGDPAHTGKPAGDDLREGKRTVLVARAEALLPRGEAAAL +DAELGDPALSAERVAHWQRRLEEVGARTAVADEVDRLSAEARRGLERLAALGVGTDVRGE +LAELIDAYTVRTA +>GCF_023573625_PROKKA_01321 +MPADVAV--PRPRPADQDRFRAAVADALDRLLAEHRERARDVHPLTAPLVDAIADLTAGG +KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR +FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG +VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA +FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEVAAL +DADLGDPDLGADRVAHWQAVLEACGARQAVEERVAVLSHEAAGAVAGLLAHGVPEDVSAE +LTRLIDAYTSRRH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001149.fa new file mode 100644 index 0000000000000000000000000000000000000000..46791d21bca742c1e8aec7e4af0dd766ba067f4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001149.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01368 +----------MPRSAVPH-TPVRSRCLRSVLTGGAVPLLLLTGLPAQAHAQEAA-----V +HTVRPGDSLTRISAARGVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQP +NDGWWVIARRTGVSAAQLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATA +PASTTPTAAGGTVRYTVVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDG +TLEVEPVSAVQAVGDTFLGRTYAPHVTASANENLRLLRAVPQPTPEQMQQIVRETAERMG +VDPRLALGHAYTESRFRMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAG +VAFIKYVQDRTPTLDEGIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF +>GCF_003691675_PROKKA_01088 +----------MPRSAVSH-TPVRSRRLRSVLTGGAVPLLLLTGLPAQAHAQEAA-----V +HTVRPGDTLTRISAARGVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAVGTYTVQP +NDGWWIIARRTGVSAAQLQRLNGMSASSMLHPGMVLTTQRTAAAPKTPASTAPATTPASA +PASTAPAAAGGTVRYTVVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDG +TLEVEPVSAVQAVGDTFLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIIRETAERMG +VDPRLALGHAYTESRFRMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAG +IAFIKYVQDRTPTLDQGIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF +>GCF_005280335_PROKKA_01525 +----------MPRSSVSH-TP--SRRLRHALAGGAVPLLLLTGLPAQAQAQEAP-----V +HTVRPGDTLTAISAAHGVPLVDLFRLNGLDHESIIYPGDAIRLTGEAAPAAAAGTYTVQP +DDGWWIIARRTGVSAAELQRLNGMSASTMLHPGMVLTTAGKAAA------PAPTPAP--- +PRCSLAPATRDVVRYAVVSGDSMWGISQRFEMSIPRLRELNGLTRSSMLHPGQVLVISDG +TLEVEPVSDVQPIGDTFLGRTYPAHVTASANENLRLLQSVPQPSPEQMREIVRETAVRMD +VDPRLALGHAYTESRFRMASVSPANAIGAMQVIPITGEFASELVGRELNLLDPYDNAVAG +VAYIKYVQDRTPTLDTGIGAYYQGLGGVLQGGLSAEGRTYVATVRAAMAMF +>GCF_020097155_PROKKA_01420 +MPPARKVTPLMPQPAAPRASATTARRSLGLVAGGVVPLLMTGALPVAAQAAEAAHAAPRT +HTVRAGENPYRIAEAEGVRLSDLLRLNGLRADSVIYTGQVLALTGAPAPAAAPGTVEVER +GEGWWQVSRRAGVDAAVLQRINGLGARSMLHPGQILLTE----APARP--TTPATPVAAA +P---APVRQAAPTTYTVRNGDSMWSISQRVEVSIPRLRELNGLTWRSVLHTGDVLVIADG +TEQAPVIDG--PVGSTFLSTTYAPHVTASANDNLRALQAVPQPSPAEVQALVRQTALELG +VDPALALGHAYTESRFQHASVSPGNAIGAMQVIPITGEFASQLVGRELNVLDVRDNVTAG +VVLIKYLQEHTDTVDQGISAYFTGLGGSDDPVKQQEARNYVARVKAAAAMF +>GCF_023573625_PROKKA_01323 +----------MPRSAVPH-TPVRSHRLRSVLTGGAVPLLLLTGLPAQAHAQEAA-----V +HTVRPGDSLTRISAARGVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQP +NDGWWVIARRTGVSAAQLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATA +PASTAPTAAGGTVRYTVVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDG +TLEVEPVSAVQAVGDTFLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIVRETAERMG +VDPRLALGHAYTESRFRMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAG +VAFIKYVQDRTPTLDEGIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001152.fa new file mode 100644 index 0000000000000000000000000000000000000000..c73cbe5a072e26c49f830202b7917e8abcb2534f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001152.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01372 +M--------------PRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAE +GLAAGGSPVSVPLLPGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGA +LALDAAAHRPVAGVLVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPR +TPVAGVAALGRIQRAARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGL +PRSRHVATLDYDLPLLIDHGRSAVAAMTTH +>GCF_003691675_PROKKA_01092 +M--------------PRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAE +GLAAGGSPVSVPLLPGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGA +LALDAAAHRPVAGVLVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPR +TPVAGVAAVGRIQRAARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGL +PRSRHVATLDHDLPLLIDHGRSAVAAMTTH +>GCF_005280335_PROKKA_01520 +MDRPVPPVEPAPPAVPAP-AVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAE +GIAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGA +LALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPR +TPVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPL +PRSRHVATLDYDLPLLIERSRAAVEAATRA +>GCF_020097155_PROKKA_01416 +MTRLRP---AAPDRRPAP-GVDPAQRPFRLPATSLPGV--AVVMLHGFTSGPDSVRAWAE +GVAAGGAAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGA +LALDAAAHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYER +APVAGVAQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRL +LHSRHVATLDRDLPLLVARSRDAVAAAAR- +>GCF_023573625_PROKKA_01327 +M--------------PRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAE +GLAAGGSPVSVPLLPGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGA +LALDAAAHRPVAGVLVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPR +TPVAGVAALGRIQRAARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGL +PRSRHVATLDYDLPLLIDHGRSAVAAMTTH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001158.fa new file mode 100644 index 0000000000000000000000000000000000000000..37f07831722473b22daedf6801b8d7476375b1f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001158.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01378 +MIDPRPLPDAVPTARPAG-RLGIGEVVAALEAEFPGVTASKVRFLEDRGLVLPERTPAGY +RRFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAVPASSDAARLG +REVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGH +GLEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVA +VGLEQWDD---- +>GCF_003691675_PROKKA_01098 +MTDPRPRPDAVPTARPAG-RLGIGEVVASLEVEFPGVTASKVRFLEDRGLVLPERTSAGY +RRFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAAPASSDAERLG +REVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGH +GLEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVA +VGLEQWDD---- +>GCF_005280335_PROKKA_01514 +MTEPQH-ADAGPRTRPAG-RLGIGEVVAALKSDFPGVSASKVRFLEDRGLVLPERTPAGY +RRYRPEDVDRLRFVLTVQRDHFLPLKVIAAQLAALDRGEVPADLPGGVVAPGASDASRLG +REVAAGRRGWTRSELAEESGAGEELLAELDQYSLLPADEDGAYSSHAMEVARAAVVLAGH +GLEPRHLRPFRAAADRELGLVERAVAPLQARRDANMRPRVARSAQEIAQASLRLHSALVA +EGLEQWDDGAVG +>GCF_020097155_PROKKA_01409 +MSAPHE-PSAAP--PPAGAALGIGDLVAALEPSFPGVSASKVRFLEDRGLVRPERTAAGY +RRYRPADVDRIRLVLTLQRDRFLPLKVIREHLDALDRGERPEDL--GEAPAAAQEAVRLG +HGIADPDRRWTRAELAREAEVPAPLVDELDQYALLPRAEDGLHPPAALGVVRAAGRLAAH +GIEPRHLRPFRAAADRELGLVQSAVAPLATRRDAGTRERAARTAEEIATACLALHAALVR +AGLESLDG---- +>GCF_023573625_PROKKA_01333 +MTDPRPRPDAVPTARPAG-RLGIGEVVASLEVEFPGVTASKVRFLEERGLVLPERTSAGY +RRFRPEDVDRLRFVLALQRDHFLPLKVIAEHLAALDRGERPTGLPGTAAAPASSDAERLG +REVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGH +GLEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVA +VGLEQWDD---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001159.fa new file mode 100644 index 0000000000000000000000000000000000000000..466fac0732f85bbe3f9e262b00be921e1ffcce02 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001159.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01379 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DKDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAAPARG +>GCF_003691675_PROKKA_01099 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAGPARG +>GCF_005280335_PROKKA_01513 +MNQPGREPDLSTSSINLTELAPLVAADLSAEESDAIRALPAGSALLLADGGPEKAARFLL +DQDVVTVGRHPDADIFLDDVTVSRRHAEFRAEAGGHRLVDMNSLNGTFVNHDRVDDVLLR +SGTHVQIGKYRLTYFTSTQRG +>GCF_020097155_PROKKA_01408 +MTQ--QEPSLHTSSISLTDLAPVAETGLSPEETAAVRALPAGAALLVAHEGPDAGARFLL +DTPVVTVGRHPESDILLDDVTVSRRHAEFRAVDGGHELVDLSSLNGTYVNNDRVDQVRLR +TGMQLQIGRYRLSYHAA-EPA +>GCF_023573625_PROKKA_01334 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAGPARG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001160.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001160.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0227a1de2ac45134041ae98b77ddec3d4af5b18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001160.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01380 +MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG +EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA +EGYASHTS +>GCF_003691675_PROKKA_01100 +MSSIPEGLKYSAEHEWIAKAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG +EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA +EGYASHTS +>GCF_005280335_PROKKA_01512 +MSSIPEGLKYSAEHEWIAEAGQAGTVRIGITDFAQDALGDVVYVDLPEVGSEVTAGTAVG +EVESTKSVSDIYAPVTGTVAAVNEDLDGEPGLVNSAPYEGGWLFEVTLADEAQLEGLLDA +EGYASHTS +>GCF_020097155_PROKKA_01407 +MSSIPEGLKYSTDHEWAQDAAEPGVVRVGITDFAQDALGDVVYVDLPSVGDEVTAGAAIG +EVESTKSVSDIMAPVSGTVTAVNEELDGEPALVNSAPYEGGWLVEIKLSDPAEVDGLLDA +AGYAAHVG +>GCF_023573625_PROKKA_01335 +MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG +EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA +EGYASHTS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001164.fa new file mode 100644 index 0000000000000000000000000000000000000000..d151944d4c0f74c244ec6e809595c20c2684347c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001164.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01406 +MSAPAESAAKL-GDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAA +DIRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVA +AGVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGAL +AAGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLR +DTTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAE +GNAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRV +GMVEISVLPGRRDELVAALTAAGWKVV +>GCF_003691675_PROKKA_01136 +MSAPAESAAKL-GDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAA +DIRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVA +AGVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGAL +AAGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLR +DTTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAE +GNAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRV +GMVEISVPPGRRDELVAALTAAGWKVV +>GCF_005280335_PROKKA_01490 +MSAAAETAAAVPGALPAGIPQPVLVRGTGLLGASIGIGLSAAGADVLLHDLSPAALAVAA +DIGAGRPMRIDDDGADAGPAPALVVVAAPPDVTADVVVDSLRRWPEALVLDIASVKEAIA +AGVRAAVDDGRLGPSDPDRHLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTLPAAV +QAGRALALALRATPYRMDARAHDESVAMISHLPQIAASLVAARLQDTPDQALALAGNGLR +DTTRIAASDPQLWVQILSGNAERIVPALHGLRDDLDRLIRTLEAPGAPGSRLDMARLIAE +GNAGRARVPGKHGAPPQAFAVVTVIVDDTPGQIAAVLDEVGRTDVNVEDLRLEHASGHRA +GMVDISVLPGRRDELVAALSAAGWKVV +>GCF_020097155_PROKKA_01401 +M-IPAEG-----GAGPAGLSGPVLVRGTGLLGASIGLGLRAAGADVLLDDPSPTALAVAR +DIGAGAVVDLD----DPALAPGLVVVGAPPDVTPAVVVDSLRRWPHAVVTDIASIKGAIL +AEVREAATRGDIAPGDVARYLPGHPMAGSERSGPVAARGTLFTASPWVLCPAAETDPAAL +AAGEALARTLQATVHRMSAADHDASVALISHLPQIAASLVASRLQDAPDPSLALAGNGLR +DTTRIAASDPHLWVQILAGNAPQIVPTLHGLREDLDRLIGTLEAPSAPGARLDVARLIAE +GNAGRARIPGKHGAPPQAFALVTVIVDDTPGQLAALFEEIGRAGVNVEDIRLDHASGYRV +GMVDVSVLPGRKDELVSALTDAGWKVV +>GCF_023573625_PROKKA_01356 +MSAPAESAAKL-GDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAA +DIRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVA +AGVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGAL +AAGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLR +DTTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAE +GNAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRV +GMVEISVLPGRRDELVAALTAAGWKVV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001170.fa new file mode 100644 index 0000000000000000000000000000000000000000..43f63d1e8812223e015f7bf1539512220e1aefcd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001170.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01416 +MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT +DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA +NALIRPLSAYDGPEQRELPAG +>GCF_003691675_PROKKA_01147 +MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT +DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA +NALIRPLSAYDGPEQRELPAG +>GCF_005280335_PROKKA_01483 +MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT +DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA +NALIRPLSSYDGPEQRELPAG +>GCF_020097155_PROKKA_01390 +MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT +DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA +NALIRPLSAYNGPEQRELPGK +>GCF_023573625_PROKKA_01366 +MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT +DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA +NALIRPLSAYDGPEQRELPAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001171.fa new file mode 100644 index 0000000000000000000000000000000000000000..411c47f2201daf135fc92db427043791f9b610d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001171.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01418 +MSADPA--------PRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY +RRWLEAQGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEG +LTPADPALDVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS +EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR +PTIMAGAARSTPALFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA +GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR--- +>GCF_003691675_PROKKA_01149 +MSTDPAARGSGEAEA---RGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY +RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEG +LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS +EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR +PTIMTGVTRSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA +GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR--- +>GCF_005280335_PROKKA_01481 +MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY +RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG +LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS +EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR +PTIMTGAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA +GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR--- +>GCF_020097155_PROKKA_01389 +MS---------------------ASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRY +LAWLEASRVDRPADVDPGHVAGFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEG +LTPTDPAADVAPPRPPERLPKALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVS +EAVGLDVDDVVGVAGDRGAGRGDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGR +PALAAAATRPVPALFLNLRGGRLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQ +GGADVRVVQELLGHASVTTTQVYTRVTAEALREVYASAHPRARWTT +>GCF_023573625_PROKKA_01368 +MS--PHAP---------------QTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARY +RRWLEAAGVRAPGDVDPGHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEG +LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS +EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR +PTIMTGVTRSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA +GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001173.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7ef1ba8f5a3cdcc3975da745d12ffc5f69c06eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001173.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01420 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSSRAVVDAGVRVTADHAALRLA +QEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRSVPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGG +AELAAALRAYRADHAAWTAARREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGDLARYTADLDADAASDLDAAQ +SRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGRLEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEE +LHALFMPDASFHVGLTPVAGDGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLTADERVEELARMLAGHGD +SAAAREHARELLESSARERG +>GCF_003691675_PROKKA_01151 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSSRAVVDAGVRLPEAHAALALA +EDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRTVPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGG +AELAAALRAYRADHAAWTAARREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGDLARYTADLDADAASDLDAAQ +SRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGRLEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEE +LHALFMPDASFHVGLTPVAGDGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLTADERVEELARMLAGHGD +SAAAREHARELLESSARERG +>GCF_005280335_PROKKA_01479 +MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAARAVVDAGVRLPEAHAALALA +EDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRTVPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGG +AELAASLRAYRADHAAVSAARRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE +AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAADLARYTADLDTDAASDLDAAQ +SRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGRLEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQE +LHALFMPDASFHVDLAPVGGDGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLSAEERVEELARMLAGHGD +SAAAREHARELLEASARERG +>GCF_020097155_PROKKA_01387 +MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSRRAAVDAGVRLPADHPALSLA +VEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRAVPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGG +PQLVAAAAAYRADHTAYVAARRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG +GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAADLARFSADLDGDAVSDLDAAQ +TRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGRIDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAE +LHALFMPDASFHVSLVPLDDGDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV +DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVVTLGQQERVDELARMLAGHGD +SAAARAHARELLEASAAERA +>GCF_023573625_PROKKA_01370 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSSRAVVDAGVRLPEAHAALALA +EDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRTVPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGG +AELAAALRAYRADHAAWTAARREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGDLARYTADLDADAASDLDAAQ +SRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGRLEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEE +LHALFMPDASFHVGLTPVAGDGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLTADERVEELARMLAGHGD +SAAAREHARELLESSARERG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001174.fa new file mode 100644 index 0000000000000000000000000000000000000000..49e91156eb34a109073678ba56a8c74b9c02e37c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001174.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01421 +MPYTPGRRILVLTHTGREDAISAALQATRMFAEEGLVTVMLEQDVAAIRAAAGDPPEFAP +ETLGVDCELEDITLGLVLGGDGSVLRAADFVRGYNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVHVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +SFGCDGVVLATPTGSTAYAFSAGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARVEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVT-AQERAGVLHEVETVEPRHAGPRPDVVEPATMPLSVPSPADIQRHRDRGARHPG +EDA +>GCF_003691675_PROKKA_01152 +MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP +EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVT-AQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPG +EDA +>GCF_005280335_PROKKA_01478 +MPHNPGRRVLVLAHTGREDAISAALQATRILEEEGLVSVMLEQDVAAIRENADAPAGFAP +QTLGVDCGLEDIVLGLVLGGDGSVLRAADFVRGYDVPLLAVNLGHVGFLAESERTDLQRT +VQAIASEAYVVIERMALDVVVRVEDREVARTWALNEASVEKSNRERMLEVVISVDNAPIS +SFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVT-AQEREAVLREVETVEPRHAGPRPDVVEPATMPLSVLSAADIQRYRDRGARYPG +EDA +>GCF_020097155_PROKKA_01386 +MSETPSRRVLVLAHTGRADAIAAALQATAMLAEEGLDTVMLAEDVAAILESGTDAVGFRP +LTLGRDCTLDDVQLGLVLGGDGSVLRAADFVRGHGIPLVAVNLGHVGFLAESERTDLHRT +VKAIADGAYVVIERMALDVTVRVEGREVARTWALNEASVEKSNRERMLEVVVSVDDSPLT +SFGCDGVVLASPTGSTAYAFSAGGPVVWPGVEALLCVPISAHALFSRPLVVGPHSTVAVD +VLTRTRETGVLWCDGRRTVELPPRARIEVTRSAEPVRLARLRPTPFAERLVRKFRLPTEG +WRGPVTEADRRTGPLAEVETVEPRHAAPRPDVVPPPSEPLTVLSPEALARYRGRDGREGD +RTS +>GCF_023573625_PROKKA_01371 +MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP +EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVT-AQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPG +EDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001175.fa new file mode 100644 index 0000000000000000000000000000000000000000..427c9729a777c35c5a118b028063ef890ac97d31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001175.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01422 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP +PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF +LRLRRPDATAADNPAGG-TSPAPPAGERAAGWVRGAHIDWS +>GCF_003691675_PROKKA_01153 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP +PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF +LRLHRPDATAADDPAGR-TSPATPADERAAGWVRGAHIDWS +>GCF_005280335_PROKKA_01477 +MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR +WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD +LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM +VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF +LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA +>GCF_020097155_PROKKA_01385 +MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR +WVSRAAHKLVSALEAFP-VPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQ +ELRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLM +VKPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFF +LHLRAPAAPRDGGAVAG-DADEDERRRRAAALVAAADVDWS +>GCF_023573625_PROKKA_01372 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP +PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF +LRLHRPDATAADDPAGR-TSPATPADERAAGWVRGAHIDWS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001176.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad2244552d56766371ceef18a322ab5067e5680d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001176.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01423 +----MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPE +SVAEHLRTLGVPAEAGQVFGSAPAGVDLLEETLGRR----TGRVLVVGSAYLRAVVEERG +YEVVASAAQCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNG +ALVEAVGRATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVL +VLTGIDTRETAAAAPGPDRPTWVRAHLPALLA--GGAEASADPRRG +>GCF_003691675_PROKKA_01154 +----MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPE +SVAEHLRTLGVPAQAGQVFGSAPAGVDLLEETLGRR----TGRVLVVGSAYLRAVVEERG +YEVVASAAQRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNG +ALVEAVGRATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVL +VLTGIDTRETAAAAPGPDRPTWVRAHLPALLA--GGAEAFADPRRG +>GCF_005280335_PROKKA_01476 +----MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPE +SVAEHLRSLGVPARPEQVFGSAPAGVDLLEETLGAR----TGRVLVVGSDYLRQVVRDRG +FEVVAASQDRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNG +ALVGAVGQATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVL +VLTGIDTRENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG +>GCF_020097155_PROKKA_01384 +MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE +AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG +HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG +ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL +VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEP------AEAARG +>GCF_023573625_PROKKA_01373 +----MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPE +SVAEHLRTLGVPAQAGQVFGSAPAGVDLLEETLGRR----TGRVLVVGSAYLRAVVEERG +YEVVASAAQRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNG +ALVEAVGRATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVL +VLTGIDTRETAAAAPGPDRPTWVRAHLPALLA--GGAEAFADPRRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001177.fa new file mode 100644 index 0000000000000000000000000000000000000000..14cc0a7db7e4c72d5ee081182aef50fa3ddc9df5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001177.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01424 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLA +FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDASRLD +RAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALGRRDEARLWARAVRVAEKALGVGG +FADPEIIDVDTEPVEDP------RNRRPSPRERRHERYAAEAGAEPTADGSPAEEPEAAAEPTLVPRQEAVA--QPPAAV +DTPDEVDPNQLSLFDALEAPEADER +>GCF_003691675_PROKKA_01155 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALA +FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDASRLD +RAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALGRRDEARLWARAVRVAEKALGVGG +FADPEIIDVDTEPVEDP------RDRRPSPRERRHERYAAEAGAEPTADGSPAEEPEAATEPTEAPRPEAAA--EPPAAV +DAPDEVDPNQLSLFDALEAPEADER +>GCF_005280335_PROKKA_01475 +MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSEGFRGGRSGDGPRRERSSDGP +RRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSGAGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRG +QDRTERTERRERPAHNPRDLRAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA +FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERALGRPAKALQLAAEIDTARLD +RAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYPFSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGG +FAEPEIVDVDTEPVDDR------RERGPSPRERRYAENAAPA-AEEVPDTPEADDEVAADADTEAPASTESELDAPPAAV +AQADEVDPNQMSLFDELDGGEGEGR +>GCF_020097155_PROKKA_01383 +MA------------------------------------------------------------------------------ +--ERSAREPRDDRRGDGHDGTRSGT-PRGRRDGDGGRRQGEGRP---FRPHRDG---EGVGRSRNVGGRDGAAPR----- +PGRPERAQ-RERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGGLDERPATWVAKHLVMAGRYIDEDPELA +FQHALAASRKGGRLARVREAVALTAYAAGEYHEALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLD +RAARVELAMVVSGVREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAERALGIGG +FAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESA--PVGEGSAEEHGQAA------PAERES--------- +------------------------- +>GCF_023573625_PROKKA_01374 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALA +FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDASRLD +RAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALGRRDEARLWARAVRVAEKALGVGG +FADPEIIDVDTEPVEDP------RDRRPSPRERRHERYAAEAGAEPTADGSPAEEPEAATEPTEAPRPEAAA--EPPAAV +DAPDEVDPNQLSLFDALEAPEADER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001178.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd57d5869de131ca932d06b120310f7ac6a88d1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001178.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01428 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDALAGRHLLVRRGKKNMAGADLGEA----- +>GCF_003691675_PROKKA_01159 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDALAGRHLLVRRGKKSMAGADLGEG----- +>GCF_005280335_PROKKA_01471 +MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP +TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES +LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE +EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT +PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL +SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT +REDALAGRHLLVRRGKKNMAGADFGSQDADRG +>GCF_020097155_PROKKA_01378 +MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP +TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES +LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE +EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT +PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL +AELPQADAAQW-GAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFG +ADEALAGRYLLVRRGKKNMAAADLRSGE---- +>GCF_023573625_PROKKA_01378 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDAFAGRHLLVRRGKKNMAGADLGEA----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001179.fa new file mode 100644 index 0000000000000000000000000000000000000000..9099b47b02b43e1dd9e2c0fa9613844e4ab1d9c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001179.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01429 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFASLYEDRLAQLYAVDDRLVFGR +LDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAGAFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLG +EDGVRADAQGALLAAVTARRTGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDAVAHAVAQRQRLLVEPRRLMI +DGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRELAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCW +MPLTPEKLIGDLLTREDLLRAAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQELSPMQWRLLARRCPMKSFTI +VGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSPARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGD +VAALALDAVEAERDRVPEALTAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE +>GCF_003691675_PROKKA_01161 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFASLYEDRLAQLYAVDDRLVFGR +LDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAGAFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLG +EDGVRADAQGALLAAVTARRTGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDAVAHAVAQRQRLLVEPRRLMI +DGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRELAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCW +MPLTPEKLIGDLLTREDLLRAAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQELSPMQWRLLARRCPMKSFTI +VGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSPARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGD +VAALALEAVEVERDRVPEALTAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE +>GCF_005280335_PROKKA_01470 +MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFASLYEDRLAQLLAVDDRLVFGR +LDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAGAFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLG +QEGVRADAQGALLAAVTARRTGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQVIAHAVAQRQRLLAQPRRLMI +EGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRELAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCW +MPLTPQKLVGDLLTREHLLRAAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA +RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQELSPMQWRLLARRCPMKSFTI +VGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSPARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGAD +LVALTLDAVAGERDRVPEGLVAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL +VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA +>GCF_020097155_PROKKA_01377 +MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFASLYEDRLAQLYAVDERLVFGR +LDLDADDAGDV-EQRYIGRIGLTDEGQERLLVDWRAQEAGAFYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIA +EGAAGAQSQGALLAAVTARRTGRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSG +VLVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVVAAAVAQRQRLIPETRRLEI +EGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVRELAEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCW +MPLTPQKLVGDLLTKEHLLRAAAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENA +QASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQELSPMQWRLLARRCPLKSFTV +VGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPARITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGAD +PTRLAQRVVEAERGRVGDGLVAVIVPADDAAEHLTHLQDRWG-SLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERI +VADADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA +>GCF_023573625_PROKKA_01379 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFASLYEDRLAQLYAVDDRLVFGR +LDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAGAFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLG +EDGVRADAQGALLAAVTARRTGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDAVAHAVAQRQRLLVEPRRLMI +DGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRELAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCW +MPLTPEKLIGDLLTREDLLRAAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQELSPMQWRLLARRCPMKSFTI +VGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSPARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGD +VAALALDAVEVERDRVPEALTAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001180.fa new file mode 100644 index 0000000000000000000000000000000000000000..9efa5f3389a248215464002a85cc0355be45b1b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001180.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01430 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG +SVVDAR +>GCF_003691675_PROKKA_01162 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG +SVVDAR +>GCF_005280335_PROKKA_01469 +MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA +GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID +GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG +SVVDAR +>GCF_020097155_PROKKA_01376 +MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR +SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH +HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID +GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD +VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA +TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD +EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG +SVVDAR +>GCF_023573625_PROKKA_01380 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG +SVVDAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001182.fa new file mode 100644 index 0000000000000000000000000000000000000000..39499499695621b988d7af2740e74f3ad5d9612f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001182.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01432 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESSGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVD---AAPVAVERTATVQRQSAADETAADQAAAEQAAADQA-----AAEQA +AADQAAAERWAAKQAAADQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE +KAAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT +ALYEANKGAVSDAAVIYVGQELVLPQA +>GCF_003691675_PROKKA_01164 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA +AADQAAAERWAAEQAAAEQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE +KPAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT +ALYEANKGAVSDAAVIYVGQELVLPQA +>GCF_005280335_PROKKA_01467 +MDTMTLFTS--TRTRRTTASVAAGMTLMGAAAVGFSAPAQAATEETWDAIAFCESTNRWD +INTGNGFYGGLQFTLSSWQGVGGQGYPHQASKAEQIKRAEMLQDLQGWGAWPKCAA--GL +TQADADA-----TDAAPVAVERTSSVQRQAAAEQAAAEEAAAEQA--------------- +----------AAEEAAAEQAAAEQWAAEQAAAEQAAAERAEAKRAAAAEKAAAKKAAAAE +RAAAHQ------------------AAAEQAVVAEAETIVVKAGDSLWKLAAEHEVEGGWT +ALYEANKDTVSDAAMIYVGQELVLPQA +>GCF_020097155_PROKKA_01374 +---MTFFTTS---SRRATATALTGMTLVGAAA-AFAAPAQAASVETWDKIAACESNGNWA +INTGNGYYGGLQFSLTSWRGVGGTGYPHEASKAEQIKRAEILQDMQGWRAWPVCSVKAGL +SGAD----------TAPDAYS-TTPVQRQS------------------------------ +--------------TQASASAAQDWAAEQSAAEQRAAEKAAAQRAAAAAHTPKSVLKAAE +KANTENAT--------------ELAAAE-------DTVFVKPGDSLWKIAKTHKVAGGWK +ALHEANKDIIEDASVIYVGQELVLPTA +>GCF_023573625_PROKKA_01382 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSALAQAATVDTWDRLAECESNGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA +AADQAAAERWAAEQAAADQAAAERWAAEQAAAEQAAADKAAAQRAAAAEKA--------- +--AAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT +ALYEANKGAVSDAAVIYVGQELVLPQA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001188.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d5138bbf07355bb82e50aaa5f09c3a2506f3675 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001188.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01438 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR +GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>GCF_003691675_PROKKA_01170 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR +GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>GCF_005280335_PROKKA_01460 +MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE +TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR +GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD +ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>GCF_020097155_PROKKA_01368 +MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD +TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH +AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT +SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR +GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD +PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP +>GCF_023573625_PROKKA_01388 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR +GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001189.fa new file mode 100644 index 0000000000000000000000000000000000000000..629316c475f27a434e1c187afb3074144f3a6e83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001189.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01439 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS +>GCF_003691675_PROKKA_01171 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GTYAMDLPFTPGTEGSGEVVALGEGVDAALLGARVATATATGAYAEHFTAPADRLLAVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS +>GCF_005280335_PROKKA_01459 +MPHASSPAVPRTHHAVVVAETGGPEVLRWTQADVPAPGPGRVLVRTAAVGLNYIETYQRA +GVYPMDLPFVPGTEASGTVVGLGEGVDPTLLGARVATATAQGAYAEHFTAPADRLLTVPE +GVDLADAAALPLQGMTAHYLCRSTFPVEEGQTVVVTAGAGGVGLLLTQLAAARGARVITT +ASTEAKRELSRAAGAAAAVDYPELAATVDRLTDGHGAHAVFDGVGKDTFETSLRVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGGLYVTRPSLVHYTRTEEETRGRSDELFAAWAAGELD +VRIGERIPLAEAAAAHAALESRATTGKVLLTLG +>GCF_020097155_PROKKA_01367 +M--STHAEIPARHHAIIAEEVGGPEVLRWTETAVPTPGAGEVLVRTAAAGLNFIETYQRS +GVYAVPHPFTPGSEGSGVVVALGPGVDEALRGARVATAAGRGTYAEHFTAPADQLLHVPA +GVDLADAAALPLQGMTAHYLCRSTFPVEPGHVVALTAGAGGVGLLLTQLAAARGATVITA +ASTEDKRALSAAAGASAAVPYAELRQTVLDATGGEGAHAVFDGVGADTFEDSLASLRVRG +TLVLFGGASGQVPPFDLQRLNSGGGLYVTRPSLAHYTRTAEETAWRGRELFDAWSAGALD +VRIGARVPLAEAGRAHTLLASRATTGKVLLPLS +>GCF_023573625_PROKKA_01389 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHAVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001190.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5c61b0996f6bf058edd3b2fb7f106068d7e2cc7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001190.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01441 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLHQRVPAYLLSVQIGRYRLVDA-------APPAEGLPPLRLVVSPRTEQRALRA +LAPQPAMMATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIA +HEMSHQWFGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVE +QALAEPGPEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTH +VHAWAPHAGVSRAQVDELFDAWTLRPELPPFPG +>GCF_003691675_PROKKA_01173 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLDQPVPAYLLSVQIGRYRLVDA-------APPAEGLPPLRLVVSPRTEQRALRA +LAPQPAMMATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIA +HEMSHQWFGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVE +QALAEPGPEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTH +VHAWAPHAGVSRAQVDELFDAWTLRPELPPFPG +>GCF_005280335_PROKKA_01457 +MSTDPYVPGVGTDAAVIEHVVLDLDVRLAANRVSGTAVLSVRLTRQSRRIELDLHRLRVS +KVGAAVDGRALPASFSQPRRWPSRLVVDLGESRPEGTLVELTVAYAGTPTPRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPVSRSTADITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLTQPVPAYLLTVQIGRYRLVDA-------AAPADGLPPLRLVASTRTEQRARAA +LATQPAMMAAFIAAYGPYPFEEYTAVVADDVLEIPLEAAGMSLFGTNHLDGSWESERLIA +HEMAHQWFGNAVTLGRWADLWLHEGFACWSEWLWAEASGRSSIASMARRAWQRLAEDPVE +HVLTEPGAAEMFEDWVYKRGALTVEALRVLLGREVFGSMLRAWVDEHRFGTVDTAGLRAH +VHAWAPRAQVTPEQVDELFEAWTRRPELPPFPG +>GCF_020097155_PROKKA_01365 +MSTDPYIPGVGSDTATIEHLRVELDVRLASNRVAGVAELHVRLCRQSDTVELDLHRLAVD +GAAGTHDGRPLKVRATTPRNRPHRVVVHLGASLPEGSLVVLRLSYSGHPRPRRSPWGTIG +WEELTDGVLVAGQPHGASTWVPCIDSPAVRQTADITVTCDAGYLPVANGRGTRLRSRGSR +ETWRWVMDRPVPAYLLTLQIGRYRQVTAPGSGTPESAAAGGVPPLRLVVSPRLQARAEAA +MAGQGRMMEAFTAAYGPYPFDDYAAVVADDVLEIPLEAAGLSLFGVNHLDGSWESERLIA +HEMAHQWFGNAVTLGRWSDLWLHEGFACYSEWLWAEASGRAALRHEAKQAWHGLKRQGED +LVLAAPGAADMFDDRVYKRGALTVLAVRTLLGDAVFGEMLRDWVARHRFATVDTPGFRAH +VLAWAPRADVAPEDVDALFDAWTLRPELPAFPG +>GCF_023573625_PROKKA_01391 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLDQPVPAYLLSVQIGRYRLVDA-------APPAEGLPPLRLVVSPRTEQRALRA +LAPQPAMMATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIA +HEMSHQWFGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVE +QALAEPGPEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTH +VHAWAPHAGVSRAQVDELFDAWTLRPELPPFPG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001192.fa new file mode 100644 index 0000000000000000000000000000000000000000..f56212ffe7f55427b876ec847796b77c1242f2c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001192.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_01443 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEPQKNGKTINWCSVRVVPEGAA +QPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVALPGAVLPGDFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDL +GLDPEPGTDARDVLDLHGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDADTLSGEIVVRRARAGETLTTL +DGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTTIVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIAD +EAAERAVQLLVELAGGTAEPGVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGLTEVLAYPFVSEEQNRRFGAD +SDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNLGRGFRDLALYEMGLVFLPG-AQLGSATIPPRAVHPSAEVL +ADLEAGIPAQPWHVAGLYAGHDSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGD +RVVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVDEAVVAGDVRATLAEGAGEL +LEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVSEARAAATALAAQRHGAVQR +>GCF_003691675_PROKKA_01175 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEPQKNGKTINWCSVRVVPEGAA +QPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPGDFRISPRKTYGHVSAGMIASSTELGVGDDGTDGIIVLGDL +GLDPEPGTDARDVLDLHGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDADTLSGEIVVRRARAGETLTTL +DGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTTIVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIAD +EAAERAVQLLVELAGGTAEPGVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGLTEVLAYPFVSEEQNRRFGAD +SDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNLGRGFRDLALYEMGLVFLPG-AQLGSATIPPRAVHPSAEVL +ADLEAGIPAQPWHVAGLYAGHDSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGD +RVVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVDEAVVAGDVRATLAEGAGEL +LEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVSEARAAATALAAQRHGAVQR +>GCF_005280335_PROKKA_01455 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPSDELRGPIVVGQVLSKEPEPQKNGKTINWCTVRVVPEGAE +QTLTGEGIDPSGVQGVVCGAHNFEVGDKVVVTLPGAVLPGDFRISPRKTYGHVSAGMIASVRELGIGDD-HDGILVLSTL +GLDPEPGTDALEVLDLQGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAALTPPAADDAGHPVRIADDAPIYGA +PGATRFVARTVSGVDASRPTPPWMAARLRLAGIRSISLPVDISNYVMWELGQPLHFYDAQKLAGEIVVRRARAGETLRTL +DDKERTLDPEDLLITDDSGPIGLAGVMGGLATEVTDATTTIVIESANFDPISIARTRRRHRLPSEASKRNERGVDWEIAD +EAAERAVQLLVELAGGTAEPGVTDVGTRPELAVVEMAADFPTALVGVEYTADEVAETLRALGAQVEAAEAADGAAPRLRV +TAPSWRTDLRIPEDLVEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGHTEVLAYPFVSAEQNRRFGVD +SEEQGEALEMVALANPISSQYRYMRLSLLPGLVEIARRNLGRGFRDLALYEAGLVFLPG-TQLGSASIPPRAAHPAPEVL +ADLEAGIPAQPWRVAGLYAGHDSAPGPDHAPRPVDWQDAVSGALAVADVLGVELAVRQGRHHAFHPGRVAELVVLGERGD +QVVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPPAVVAVPLSTYPMSTQDVALVVEEAVVAGDVRASLAEGAGEL +LESVELFDVYRGPGVPEGSKSLAFSLRFRAPDRTLTAEEASEARAAATALAAQRHGAVQR +>GCF_020097155_PROKKA_01363 +MRIPLDWLREFAQVPADATAEDVLADLVTVGLEEEDVHRPSDELTGPLVVGQVLTREPEPQKNGKTINWCSVRVVPEGAE +QTLTGEGIDPSGVQGIVCGAHNFEVGDKVVVCLPGAVLPGDFRISPRSTYGHVSAGMMASARELGLGDD-HDGIIVLGDM +GLDPEVGTDVVDLFHLREEAAEVNVTPDRSYAFSIRGIAREYAHATGTAFTDPAAAVTAPEANDAGPAVTLADGAGIYGV +PGCDRFVARVVEGIDPAAATPPWMAARLRLAGIRPHSLAVDVSNYVMWELGQPLHFYDADRLTGGITVRRAAAGETLRTL +DDKERTLDPEDLVIADESGAIGLAGVMGGAATEVSEGTTRVLIESAHFDAVSIARTRRRHRLPSEASKRNERGVDWEIAD +EAAERAVQLLVELAGGTPAQGVTDVGTRPEPVVVELDPEYPARRIGVDYPRERVVELLTGLGASVE------DAGDLLQV +TAPTWRHDLRIPEDLVEEVARLDGYANIPSTLPVAPPGRGLTRAQVHRRRVADTLAAAGLTEVLDYPFVSEGQNRLFGSA +TPEEGAAQRMVRLANPISSEFGWMRTTLLPNLLETVRRNVSRGFKDVALFEVGAVFLPGDGALGSPSNEPIGVKPSAETL +AELDAGIPAQPRHVAGAFAGHEAAPGAGFAPRAFDWQDPIAAALAVGRAVGVELTVVQGTHQAFHPGRTATLSLPD---G +TAVGVAGELLPAWLEDADMPARTGAFELDLDAVLAAAADRVVARPLSTYPASQQDVALVVADDVVAGDVRATLAEGAGEL +LEEVALFDVYAGKGVPEGHKSLAFSLRFRAPDRTLTADEASEAREAATALAAERHGAVQR +>GCF_023573625_PROKKA_01393 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEPQKNGKTINWCSVRVVPEGAA +QPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPGDFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDL +GLDPEPGTDARDVLDLHGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDADTLSGEIVVRRARAGETLTTL +DGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTTIVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEVAD +EAAERAVQMLVELAGGTAEPGVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVTEAADGAAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGLTEVLAYPFVSEEQNRRFGAD +SDAQGQVPAMVALANPIASQYRHLRLSLLPGLVETARRNLGRGFRDLALYEMGLVFLPG-AQLGSATIPPRAVHPSPEVL +ADLEAGIPAQPWHVAGLYAGHDSAPGPDHAPRPVDWQDAVAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGD +RVVGVAGELHPQWLEAEDLPARMSVWELDLDALCAAAPETVVAAPLSTFPVSTQDVALVVDEAVVAGDVRATLAEGAGEL +LEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEASEARAAATALAAQRHGAVQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001196.fa new file mode 100644 index 0000000000000000000000000000000000000000..cfc1039cee3ec0759df384a827d2b4547a375847 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001196.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01448 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRP---SAPA------ +-------------AQPALF +>GCF_003691675_PROKKA_01180 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRP---SAPA------ +-------------AQPALF +>GCF_005280335_PROKKA_01451 +MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV +PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ +AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL +TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA +YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPA--AP-- +-------------AQPALF +>GCF_020097155_PROKKA_01355 +MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV +PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL +SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ +AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL +TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA +YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPL---SAPAGTTGAE +QADTAADAVRPVIAQPTLF +>GCF_023573625_PROKKA_01398 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRP---SAPA------ +-------------AQPALF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001205.fa new file mode 100644 index 0000000000000000000000000000000000000000..32972231497c30f83e7c018cd41873d7d8ae4a48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001205.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01459 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVALAQVRPFTAPTLFHRDIVGSR +ARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVVRAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQ +HGRWPAPEEPSGLWAGGTPRVGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIREIHHRVKNNLQTVGSLLRMQA +RRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVDGLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLA +LVLNELAANAVEHGTAPGGGCVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGE-SPRAGEGSGLGLRIVHSLVEGDL +RGTLRWERSDDGGTRVVLRLPLT +>GCF_003691675_PROKKA_01191 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVALAQVRPFTAPTLFHRDIVGSR +ARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVVRAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQ +HGRWPAPEEPSGLWAGGTPRVGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIREIHHRVKNNLQTVGSLLRMQA +RRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVDGLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLA +LVLNELAANAVEHGTAPGGGCVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGE-SPRAGEGSGLGLRIVHSLVEGDL +RGTLRWERSDDGGTRVVLRLPLT +>GCF_005280335_PROKKA_01441 +MVSSLAQDPLTSHPDLADEDRSWLQLLVGDWQLVADLALADLVLWCPAPRPDPAEGFVAVAQVRPFTAPTLFHRDIVGSR +ARADLRAVVASTWSGGERPEGAGPVETPDGTLQVRLWPVVRRGRVVAVLSAHGDPNGRPSRSVIEENYIRTADSLLDMMQ +HGRWPAPEESAGLWAGGTPRVGDGLVVLGPDSVARFTSPNAVSALRRLGIGATLEGHRLTDVLAGTDAARQPSEEGTWAV +LTGLRAGRREVQSRGASLTVRSVPLLGPDGWHGALLLLRDVTELRRQEQRLVSKDATIREIHHRVKNNLQTVGSLLRMQA +RRTSSPEADRALRQAMRRVDTIALVHQTLSEEIDGQVPVDDLLKRQFRLAVEVSGDGRPLEAAASGEFGELPSHVTTPLA +LVLNELAANAVEHGTAPAGGRVELHAERELTPAGSVLVVSVTDGGSGVQDGWSPGE-FQPAADGAGLGLRIVQTMVEGDL +RGTLRWERLPDGGTRVVLRIPTA +>GCF_020097155_PROKKA_01344 +MVSTIASDPLNTHPDLGAEDRAWLQQLVGDWQLIADLALADLVLWCPLPVEVDGTGHLAMAQVRPFTAPTLFHRDIVGSR +ARADLRALVDRVWAAGAPADGTGPLVEPGATLKVRLWPVVRAGRVVGVVSAHEDPRTRPARSAVEDNYRTSADTLLDMVQ +HGRWPNPEDPPAYWIGGTPRVGDGLVVLGDDSRATFTSPNAVSALRRLGLPTTLAGHSLTELLGGTEAARRPVEEGSWAM +LNGQRAGRTEVQANGATLTVRSVPLRNRDGWCGALIMLRDVTELRRQEQRLISKDATIREIHHRVKNNLQTVGSLLRMQA +RRSDSPETGRALRQAMQRVDTIALVHQTLSEQIDAQLSVDALMARQFRLAVEVAGDGRPLGTRVEGTFGELASHVVTSVA +LVLNELATNAVEHGTGEEGGVVSLQAHREDTPAGDVLVFSVTDGAS-VEDG--PGEGFVPQPAPNGLGLRIVHSLVEGDL +RGSIQWRRMPDGGTRVTVRLPVE +>GCF_023573625_PROKKA_01409 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVALAQVRPFTAPTLFHRDIVGSR +ARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVVRAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQ +HGRWPAPEEPSGLWAGGTPRVGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIREIHHRVKNNLQTVGSLLRMQA +RRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVDGLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLA +LVLNELAANAVEHGTAPGGGCVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGE-SPRAGEGSGLGLRIVHSLVEGDL +RGTLRWERSDDGGTRVVLRLPLT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001206.fa new file mode 100644 index 0000000000000000000000000000000000000000..8fad0bf81747abc442e44e8de173a6cad7f76128 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001206.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01460 +--MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDLAELLAIARSGLVDAVLVAGDTESLTAAFLEETARLPRPVGVAA +LSEVRTERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEGRRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPG +LTDPWRGADEPDDAGPGAAPAAATPDGG---------------PATADEGA----------------------------- +----------DPAPSPEEGEPAGPA---------------RESLVTVVWGPTGAPGRTTVAVNLAAEHAVAGRNTLLIDL +DTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADLTVLTGLTRVDRWPELRPAAVSALIAAARE +RWDRVVVDVGFGLEQDEELSFDVPAPQRNGATLAALAAADEVIAVGGPDAVALPRLVRGVEELAEVAPAARLRVVVNRLR +PAAAGVAPRGQVEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPARRGRHRARP +SQTIAAVSSDAARDATDTGRPARRRTLIPWSVRSRRTP +>GCF_003691675_PROKKA_01192 +--MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLTAAFLEETARLPRPVGVAA +LSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEGRRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPG +LTDPWRDADEPDDAGPGAAPAAATPDDG---------------PATAGEGA----------------------------- +----------DPAPSPEEGEPTAPA---------------RESLVTVVWGPTGAPGRTTVAVNLAAEHAMAGRNTLLVDL +DTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADLTVLTGLTRVDRWPELRPAAVSALIAAARE +HWDRVVVDVGFGLEQDEELSFDVPAPQRNGATLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLR +PAAAGVAPRGQVEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPARRGRHRARP +SQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP +>GCF_005280335_PROKKA_01440 +MTVRIALATTVLPGLDHIGPLERHQTRITVVRRAEDLAELLAIARSGLVDAVLVAGATEAVTGAFLEELARLPRPVGAAA +ISEVRAERRRLRALGVPCVRADAGPEPLAAAVVEAALAAADGRRARADAVAEDEGGEDPVDGLDGIELTYGVL--DDDPR +LGPPLLGGDPERSAVSAARPEAGAGDEAVDDGRRGGRAGDDLVPADAAQGGVTRDGVAQDRAQDGFARDDAQDFAAWDAD +AAGRSVPDVDRPDPRDPDGDAAEHAEDRPDVEASGTP---GDARVIVVWGPTGAPGRTTVAVNLAAEHAVAGRSTLLVDL +DTYGPSVGAHLGLTEESAGVARAVRRADHGPLGPADLEAAGVRVRVAGAELTVLTGLTRVDRWPELRPSALTSLLAAARG +RWERVVVDVGFGLEQDEELSFDVPAPQRNGATLAALAAADEVLAVGGPDAVSLPRLVRGTEELVEAAPEARLRVVVNRLR +PAAAGVSPRSQVEAVWSRYASAGIPLAAFLPWDPAAADRALLGGQVLAEAAPNSALRRALAELADVDPRGARRTGRRRRP +TGQGPAGAARRHPQDEGAARPSRRRTLMPWSARSRRTP +>GCF_020097155_PROKKA_01343 +--MRVALATTLMPGRDHVGPLEQAQAEVTVVRRAEDLAELLAAARSGLVDAVLVAGDLSALARGFVDEVREAPRPVAVVA +MGEVRAERERVRTLGVPCLSADADPLALAAAVQSAVRARLTGARPE--LGSETPPADPPA------------------PA +PGTP-DGGDPEAVRVAAVRDREGT-------------------PRLPEPNPVRVDALAASEVDALFTEETSPVAAADEAG +PA--------SPDAAGPDAVTASPADTAPEDGPEGGPERGRTGRTVAVWGPTGAPGRTTVAVNLAAESAVAGLRTLLVDL +DTYGPSVGVHLGLTEETAGLARAVHRAERGSVTREDLVDAAVRVRVAGGDLDVLTGLTRPDRWPEVRPGALREVLQAARD +GWDRVVLDLGFCVEEDEELSFDVPAPQRNGATLAGLAAADRVLVVGGADAVAMPRLLRAVEALPAGVEQDRVRVVVNRVR +PQASGVAPQAQVAGVWERYGPP-IPLVAQLPWDPGAADRALLGGQVLAEAAPGSALRAAVLELARLDP------------ +--AVAARTQSAGRGRRPAVRGLRRR-LAPWSAPSPRTP +>GCF_023573625_PROKKA_01410 +--MRIALATTVQPGLDHIGPLERHQTDITVLRRAEDIAELLAIARSGLVDAVLVAGDTESLTAAFLEETARLPRPVGVAA +LSEVRAERRRLRSMGVPCVRADADPEQIAAVVVESASAAAEGRRPETSHGEDADHARDHAEDLDDLPITLETLGADEVPG +LTDPWRDADEPDDAGPGAAPAAATPDDG---------------PATAGEGA----------------------------- +----------DPAPSPEEGEPTAPA---------------RESLVTVVWGPTGAPGRTTVAVNLAAEHAMAGRNTLLVDL +DTYGPAVGVHLGLTEESAGVARAVRRADHGRLGAADLAAAGVRVRVAGADLTVLTGLTRVDRWPELRPAAVSALIAAARE +HWDRVVVDVGFGLEQDEELSFDVPAPQRNGATLAALAAADEVIAVGGPDAVALPRLVRGVEELAEAAPAARLRVVVNRLR +PAAAGVAPRGQVEAVWNRYASPATPLEAFLPWDPAAADPALLAGQVLAEAAPNSPLRRALATLAGVPARPARRGRHRARP +SQTIAAVSSDAARDATDPGRPARRRTLIPWSVRSRRTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001210.fa new file mode 100644 index 0000000000000000000000000000000000000000..f916807512c0bb572f14e12123182843e8e2d721 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001210.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01464 +ME--RSTSPA------------GPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGT +SAPGAELTRVLGLGAGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLG +RVAGAVVGAQLLAAPAAWAD----AAHPVPDASWTVAAVPAHATGVEAPA--PDAAWTP- +RPPAPAPPGAGTGRADPDHPTVTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRR +VIGDDPHLLLPGTVLTSPVFTPHAGVDG-----PRP------------------------ +------------------------------------------------------------ +-- +>GCF_003691675_PROKKA_01196 +ME--RSTSPA------------GPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGT +SAPAAELTRVLGLGAGLAGLGLLAWWAVGLTGLALVALGRRAGRPAWARLGRSLTPALLG +RVAGAVVGAQLLAAPAAWAD----AAHPVPDASWTVAASPTHATGVEAPA--PDAAWTP- +RPPAPAPPGAGTGRADPDHPTVTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRR +VIGDDPHLLLPGTVLTSPVFAPHAGVDG-----PRP------------------------ +------------------------------------------------------------ +-- +>GCF_005280335_PROKKA_01436 +MQ--RITEPARRGRAALSEADGHRADGHRVDTVDAVGLVVLALAAPALLIGAAALLEPGE +GAASSELVRLLGLGAGIAGLGLVAWWAVGLLGLVLATVGRRTGRLGFARLGARLTPALLG +RVAGAVLGAHMLAAPAAWAEQP--AVGPVPDAGQTVSHAAPASTTASAPAAVPEAAWTP- +RTPVPAPPGATAARNLSDRPTVTVRRGDCLWDIAAAELGPDATPREIDARWRRWHEANRR +VIGDDPHLLLPGTVLTAPVFSPHAAPQEGLAMTPRPRTTPTTTRPQEPAMTALAARPPSP +PSTAAPAVSPGTPTVAPTVPPPRCCTVPPTARPCCPAARRSPAGPPSSRAGRSCVGSAPW +PR +>GCF_020097155_PROKKA_01339 +MSFVASQPPA------------AGVHAPRASALDVAALAVLAAAVPALGWAAATLLGPAA +PTPDAALGRALGLGAAGLGLALAAWWALGLLGLAALALGRRTGHRGWSRLGERMTPALLR +RAGAAVLGAQLLAAPAAWADAPPAPSAAVVDASWT---------SAAASPTLPDAAWTPG +APPTPQPGSPAAPRDTGDRPTVTVRAGDCLWDIAADELGPDATPREVDRRWREWHRHNRD +LIGEDPNLILPGTVLTAPDFTPHVQRGG----TP-------------------------- +------------------------------------------------------------ +-- +>GCF_023573625_PROKKA_01414 +ME--RSTSPA------------GPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGT +SAPGAELTRVLGLGAGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLG +RVAGAVVGAQLLAAPAAWAD----AAHPVPDASWTVAAVPAHATGVEAPA--PDAAWTP- +RPPAPAPPGAGTGRADPDHPTVTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRR +VIGDDPHLLLPGTVLTSPVFTPHAGVDG-----PRP------------------------ +------------------------------------------------------------ +-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001212.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0923c8325017a9bf97df43180b6820f773e3bb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001212.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01466 +MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLDLLLPEAFAAVREAAGRTLGQ +RHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNALSGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQ +TPAVRREQYAADITYGTNNEFGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKELFKRDKDYVVLDGEVQIVDE +HTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQNYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRER +QRVDRNDVVYKNEKVKFDAVVDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVEDAHRAVIEAGGLYVVGTERHD +SRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVAQRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRK +NVLKYDDVMNRQREAIYTDRRSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL +DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYEMDYLKEGIGLRAMAQREPLV +EYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLPGVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSA +VTRSGTDSGATVAAGTNRRSRRQAERRGRRG-- +>GCF_003691675_PROKKA_01198 +MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLDLLLPEAFAAVREAAGRTLGQ +RHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNALSGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQ +TPAVRREQYAADITYGTNNEFGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKELFKRDKDYVVLDGEVQIVDE +HTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQNYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREP +QRVDRNDVVYKNEKVKFDAVVDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVEDAHRAVIEAGGLYVVGTERHD +SRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVAQRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRK +NVLKYDDVLNRQREAIYTDRRSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL +DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYEMDYLKEGIGLRAMAQREPLV +EYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLPGVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSA +VTRSGTDSGATVAAGTNRRSRRQAERRGRRG-- +>GCF_005280335_PROKKA_01434 +MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLDLLLPEAFAAVREAAGRTLGQ +RHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNALTGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQ +LPAVRREQYAADITYGTNNEFGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKELFKRDKDYVVLDGEVQIVDE +HTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQNYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRER +QRVDRNDVVYKNEKVKFDAVVEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVEDANREVLEAGGLYVVGTERHD +SRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVAQRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRK +NVLKYDDVMNRQREAIYADRRSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL +EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYEMDYLKEGIGLRAMAQREPLV +EYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLPGIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGA +VTRAGTETGATVEAGTNRRSRREAERRERRS-- +>GCF_020097155_PROKKA_01337 +MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLDLLLPEAFAAVREAAGRTLGQ +RHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNALTGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQ +DPATRRAQYAADITYGTNNEFGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA +RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKELFKRDKDYVVLDGEVQIVDE +HTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQNYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREK +QRVDRNDLVYKNEKVKFDAVVKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQDAREKVREAGGLYVLGTERHD +SRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAAQRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRK +NVLKYDDVMNRQREAIYADRRAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL +EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYEMDYLKEGIGLRAMAQREPLV +EYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLPGVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGV +EEKDLAADGAQTPAGANRASRRAEARRRRRGED +>GCF_023573625_PROKKA_01416 +MPSIIDRVLKISDHRVLKRMQATVDAVNLLEDDFRALSDAELRAETDALRARHADGESLDLLLPEAFAAVREAAGRTLGQ +RHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNALSGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQ +TPAVRREQYAADITYGTNNEFGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKELFKRDKDYVVLDGEVQIVDE +HTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQNYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRER +QRVDRNDVVYKNEKVKFDAVVDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVEDAHRAVIEAGGLYVVGTERHD +SRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVAQRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRK +NVLQYDDVMNRQREAIYTDRRSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL +DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYEMDYLKEGIGLRAMAQREPLV +EYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLPGVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSA +VTRSGTDSGATVAAGTNRRSRRQAERRGRRG-- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001217.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc80c3321c514fb4d5188a68fb160b436f98e601 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001217.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01472 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR +SAALLQQLAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA +VRVRGPLSLLACLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD +EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP +GAELPGPAALSTLTGESLP--RPDAAADAPAPAPVSLVVGVGALDDGADGTPGTREAWEA +AAGWADIGRGLTLAPEPGVRPVEVVRTWERLGVDPGRVGDVGLTAAGLHDPVVLHTLRRD +AEELTARLAELRG +>GCF_003691675_PROKKA_01204 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR +SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWHEDAHRWADTAGAEGAVVERLA +VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD +EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP +GAELPGPAALATLTGESLP--RPDAAADAPVPAPVSLVVGVGALDDGADGTPGTREAWEA +AAGWADIGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGSHDPAVLRTLRRD +AEELTARLAELRG +>GCF_005280335_PROKKA_01428 +MPEA-HDDGA-RPVALGGSPWAGTDAAEAQRVTLGELGAEHWPVLPELPSRGPGADATGR +SAALLSELAVDLQPHGWRVSPPGAAGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLA +VRVRGPLSLLGGLWLPGGERVLADHGARRDVAASYLEGLLEAVPRLRAATGAAGLGLLVD +EPWAAAVLAGALPTASGYRTVRSLPRDEARGLWRELLAGLTALPGVASVWLAPGRRTAS- +AADVPATAELAALAGECLP--AA-GGEDDDAGAPVRLVVPVGDLDDGPDGTAGTRAAWES +AAGWADAGRGLTLSPAAHLRPADVVTTWERLGADPAHLRGTGLTAPGRHDATVLRRLRTD +AAELAARLDDALG +>GCF_020097155_PROKKA_01330 +MPEASDDVGAVRVAALGGAPWRGTDAAEAQLATLGELGAEHWPVLPELPDRGPGADATGR +SAALLHELAVDLQPHGWRVSPPGVVGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLG +VRLRGPLSLLGSLWLPGGERVLVDHGARRDVAASYVEGLRDAVPRLAAATGARTLGVVLD +EPWAAAVLAGALPTASGYRTVRSVPRDEVRALWRDALAALADLPGVGRVWLAPGRRSAGV +DVPLPDVSALAALAGESLPAAAPSADDDAPAPTRVDLVVPVGALDPGPDGTGGTRAGWET +AAGWTDAGRGLTLSTATGVRPADVARTWERLGADPGHLAGVGLTVPGPHDAAVLGRLRAD +AEELAARVGELLG +>GCF_023573625_PROKKA_01422 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPERGPGADATGR +SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA +VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAARLGVVVD +EPWAGAVLAGTLPTASGYRTVRSLPREEARGLWRAALARLTALPDVARVWLAPGRRAASP +GAELPGPAALATLTGESLP--RPDAAADAPARAPVSLVVGVGPLDDGADGSPGTREAWEA +AAGWADVGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGPHDPAVLRTLRRD +AEELAARLAELRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001220.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e281faede1a2bd3b5a6f7098cf78e303f619f45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001220.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01475 +M---TTP----DRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLRLEEAR +ERIAAALGAHPTEVILTSGGTEADNLAIQGLYRARRAAAPERTRIVLTGIEHHAVLDVVD +WLAAHEGAEPVLVPVDDDGRVDLAAWGAALATAPERTALATLMWANNEIGTVQPVAEAAR +LAADHGVPLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVV +HGGGQERRLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLT +GPRDLDPATGQALSPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEP +SHVVAALPGRTEADARATQRFTLGRTTTPAEAAALIDALRTLLGPGV------------- +-------- +>GCF_003691675_PROKKA_01207 +M---TTP----DRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEAR +ERIAAALGAHPPEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVD +WLAAHEGAEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAAR +LAADHGIPLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVV +HGGGQERRLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLT +GPRDLDPATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEP +SHVVAALPGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV------------- +-------- +>GCF_005280335_PROKKA_01425 +MPSAATPRPLGERVHLDHAATTAVRPSALAALAEAAALPGNPASLHASGRRAKLALEQAR +EAVAAALGAHPSEVVLTSGGTEADNLAVQGLFRARRAADPQRLRIVLTGAEHHAVLDAVD +WLAAHEGAEPVIVPVDADGVVDLAAWEAALAAAPERTALAALMWANNEIGTVQPVAEAAR +IAAAHGVPLHTDAVQAVGAVPVDFAASGAATLAVSGHKAGAPVGVGALLVRRDVALTPVV +HGGGQERRLRSGTVSVALAAALAAALTEAVAEQPAEAVRLGVLRDRVIEAVEALETVVLT +GPRDADPATGEPLPPGTRRLPGNVHVTVPGRTADALLFTFDTAGLDTSSGSACTAGVAEP +SHVVAALPGRTEADARATQRFTLGRTSTSADVDALIAALRAL-APAPRRGAPT--PKGA- +PTTKEESR +>GCF_020097155_PROKKA_01327 +M---TTP----DRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEAR +ERIAAALGAHPTEVILTSGGTEADNLAVQGLYRARRAAAPERTRIVLTGIEHHAVLDVVG +WLAAHEGAEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAAR +LAADHGVPLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVV +HGGGQERRLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLT +GPRDLDPATGEPLPPGTRRLPGNVHITVPGRTADALLFFFDMAGLDTSSGSACTAGVAEP +SHVVAALPGRTEADARATQRFTLGRTTTPAEAAALIDGLRTLLGPASRLDRPSVVERGVR +P------- +>GCF_023573625_PROKKA_01425 +M---TTP----DRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEAR +ERIAAALGAHPSEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVD +WLAAHEGAEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAAR +LAADHGIPLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVV +HGGGQERRLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLT +GPRDLDPATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEP +SHVVAALPGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV------------- +-------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001221.fa new file mode 100644 index 0000000000000000000000000000000000000000..432e574d5aede9c8477ae157f51ab84aafbda54f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001221.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01478 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGH-RAHR--------- +----GGRA +>GCF_003691675_PROKKA_01210 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGH-RAHR--------- +----GGRA +>GCF_005280335_PROKKA_01424 +MRQ------------------NVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTP +DSFYDDGAAFALEAAVDQARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALR +-GEAAEHSEAVAGLILSADTFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLV +LTHSLAHVHGPRAVVPRPRYGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNT +LHTLEITRRLDEIAGLGLPVLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARIL +RMHDAAASVSAARLLECVFGWREPARLVHNMGEANPAPDRTSLAEH-RAGRVRA------ +----GGTR +>GCF_020097155_PROKKA_01324 +------------------------MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFFDDGAGFAFDAALAQVHTAADAGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVR +AGRGEGASEAARRLILSADTFQPAVAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLV +VTHSLAHVSGPRTVVPRPRYDDVVAEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTT +VHTLEVTRRLDEIADLGFPVLAAVSNKDFIGESLDRHRHDRLAGTLASAAFCALAGARIL +RMHDADASVSTAHMLECILGWREPLLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPT +HDPEEARP +>GCF_023573625_PROKKA_01428 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGH-RAHR--------- +----GGRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001222.fa new file mode 100644 index 0000000000000000000000000000000000000000..81c24cb3e1de5d974638db53c0c9982838b3cd91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001222.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01479 +MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD +QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD +PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA +RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH +DDGMLFLRLHHERHA-----SPGPDPTP---------- +>GCF_003691675_PROKKA_01211 +MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD +QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD +PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA +RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH +DDGMLFLRLHHERHA-----SPGPDPTP---------- +>GCF_005280335_PROKKA_01423 +MRRLAAVGPELSDEDLLALRRAPSTQD-APGPWVRAVFVSSLDGATALDGRSGTLGSPAD +RRQFALARTDADVILVGAGTVRAEGYAGPLVDAAARARRAARGLPEHPAVAVVTGSLDLD +PDGEFFRAAPVRPWVIASERAVAAQPERAAALAEVADVLTAGVRDVEPRELLALLAGRGA +RVVHCEGGPTLLGALAAAGAVDELLLTLSSLLAGGAGPRLIPAVEGIGLPARMLPHHVLT +QDGDLYLRLLHERHAALLADAPGLDGRAGTGR------ +>GCF_020097155_PROKKA_01323 +MRLLTATGPEIDDDALLALRRAPAPDL-VPGPWVRAVFVSSLDGAATLDGRAGGLGSPAD +QRQFTLARTDADVVLVGAGTVRAEGYEGPLVGPAARARREEAGLPAHPGIAVVSGALGLD +PDGDFLRQAPVRPLILTTQTALERCPDRAEALAARADVVASGAEVVEAPALVDALTARGH +RVLHCEGGPRLFGTLAAADLVDELLLTISPLLAGGDGPRVLSGGDGPGLPTRLRPHHVLT +EDGELYLRLVHERHAAVLAEAPGLEADPADADPAPGAP +>GCF_023573625_PROKKA_01429 +MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD +QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD +PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA +RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH +DDGMLFLRLHHERHA-----SPGPDPTP---------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001225.fa new file mode 100644 index 0000000000000000000000000000000000000000..44107186b3ed71e85d5836ea85af6463910f8740 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001225.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01482 +MQTPDASE-PHADRPDDAGQPA---LDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMF +GPGDDAAAATVRTYLTAWEEASEAGLDLSEQDDATHRERQVFTWLEVLAHRVMTSLRRAG +GSAAERGRR-------PGPAGPAALPEDLMDRVDPDAFEAVRLAWLGGCTDREVADRLDL +PADRARTLLRDGVRQVVAARRDITQDAARPSAPAPATGPALGADVREDVDAGRALELADL +SAVHALDTAGHTAAFSAVQRRG-GELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVL +RRLPAQDVGMDLIGDESTPAGPPRDRLRWLKVTALLLLAALVLGIGGWTVWSQFTRPGIV +HRIDQSKDLFTTSEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGT +APASLGTYDANGFGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPI-VGVDLDPTAQTGP +RYGGRPSTN +>GCF_003691675_PROKKA_01214 +MQTPDASE-PHVDRPDDAGQPA---LDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMF +GPGDDAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAG +GSAAERGRR-------PGPAGPAPLPEDLVGRVAPDAYEAVRLAWLGGCTDREVADRLGL +PADEARTLLRDGVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADL +SAVHALDTAGHTAAFSAVQRRG-GELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVL +RRLPAQDVGMDLIGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIV +HRIDQSKDLFTTSEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGT +APASLGTYDANGFGEPITFRGLDRFAAMGISVEPSSGSEVPTSEPV-VGVDLDPTAQTGP +RYGGRPSTN +>GCF_005280335_PROKKA_01420 +MQTPDASE-PRADRSAAAGAPA---LDTLLRRSAEGDRAAFSAFYDATVPWVHGLASAMF +RSADDAAEATTLTYLTAWEEASEAGLDLSEHDAASHRERQVFTWLEVLAHRVMTTLLRSD +G-LPEAGHGLLPDRAGPGSAGPAERPEDLDSRVDPAAFEAVRLAWLGGLSDRQVAARMGR +PVAESRTLLRDGVRQVVEAHRALTRDAADRS-PETSARPALATSVREDVEAGHALELADL +SAVHALETAGHTAAVSAVQRRG-GDLPRWRSRVDGARQAVAWAFRSVTAEPPSAVLDDVL +RRLPAQDVGMDLIGEEAAPARPPKDRLRWLKITVMVLLAALVLGVGAWTVWSQFTRPGIV +HRVDQSEDLFTTSENPARDGGTAQAFLSRDQNSGYVTVSGMPQLPDGQAYQVWLYPDDGT +APASLGTFDANGFGEPVTFRGLDRFAAVGITVEPSSGSEVPTTDTL-VGVDLDPTAHTGP +RYGGRPSTN +>GCF_020097155_PROKKA_01320 +MQTPQHPETPGADASTAPQQPSRRGVDELLHASARGDRAAFSAFYDATVPWVHGMATAMF +RSRRDAAEATAQTYLAAWSEAPEAELDLSDRDAAAARERRVFAWLEVLAHRVMTGLLRTD +A-LPEQGRRLLPERAGLGTGGPTALPATLEGSVSPETHRAVRLAWLGGRTDAQVAEALDV +PVDRARTLLRDGVQELVAAHRA---DQGLPA-PVAGARPALAATTREDVDAGRGAELADL +SALHALDAAGHTAAAAAAQQRGAGELALWRTRVDAGRRAVAWAFRDVVAEPPSDLLDGVL +RRLPAQDMGLELVEETAAPRGAA-ERRRGLKTVLLGLLALVVLALGVYAGWSQFSRDGIT +HRVHGAKDLYTTSEYPAAGGGTMQGFLSDSENSGYVTVSGMPQLEDGQTYQVWLYPKDGS +APSSLGTYDADGFDDPISFRGLDRFAAVSMTVEPSGGSPEPTADDVLLGLDLDPSNQSGP +QYGGMPSNN +>GCF_023573625_PROKKA_01432 +MQTPDASE-PHADRPDDAGQPA---LDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMF +GPGDDAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAG +GSAAERGRR-------PGPAGPAPLPEDLVDRVAPDAYEAVRLAWLGGCTDREVADRLGL +PADQARTLLRDGVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADL +SAVHALDTAGHTAAFSAVQRRG-GELALWRSRVDGARQAVAWAFRSVTAEPPSALLDEVL +RRLPAQDVGMDLIGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIV +HRIDQSKDLFTTSEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGT +APASLGTFDANGFGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPV-VGVDLDPTAQTGP +RYGGRPSTN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001226.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4731234a1b183e539d502a06a149b4db8a78f85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001226.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01483 +-----------------------MAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGD +AGGFDSEGAEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVR +PDVVLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRNL +LLYAAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRHAAGPAA +GPGHAEAFHLVTVNGPGTIAGF +>GCF_003691675_PROKKA_01215 +---MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGD +AGGFDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVR +PDVVLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKVRNL +LLYAAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAA +APGHAEAFHLVTVNGPGTIAGF +>GCF_005280335_PROKKA_01419 +----MTTPITPAALAAEHGWRTVLAVGAHPDDLDFGAAATLAGLSAAGLRVELCVVTDGD +AGGFDSEGPEAMTARRHAEQRAAAAVVGAHEVHFLGERDGHLEPDHGVRRKLVALMRRVR +PDVVLSTHPERDWELMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRHL +LLYSAPAARRNTVVDVTGLEDVKLRALDAHISQHPDVAAMRRHVLAQMTEHHRRAAGPAA +APGLAEAFHLVTVNGPGTISGF +>GCF_020097155_PROKKA_01319 +MSAVPESLPTPADLAVRHGWRTVLAFGAHPDDLDFDASATLAGLAAAGVRVELCVVTDGD +AGGFDSDGPEAMTARRHAEQRAAAAVIGAADVHFLGERDGHLEPTHEVRRRIVELMRRVR +PDVVLCPHPERDWESMQASHPDHLACGEAVVRAAYPAVENPYAYPELADAGLDAFRIRHL +MLYTAPAARRNLTVDVTGLEDVKLRALDAHVSQHPDAPAMREAVRAKLTRRHREAAGPDA +PAGSGEAYHLVTVNGDGVIAGF +>GCF_023573625_PROKKA_01433 +---MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFRAAGLHIELCIVTDGD +AGGFDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVR +PDVVLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAAENPYAYPELAAEGLEAFKVRNL +LLYAAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAA +APGHAEAFHLVTVNGPSTIAGF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001230.fa new file mode 100644 index 0000000000000000000000000000000000000000..a5dd3be050673852e4408a073219bf76357a267e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001230.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01487 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR +>GCF_003691675_PROKKA_01219 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR +>GCF_005280335_PROKKA_01415 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL +PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL +VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG +GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP +GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR +>GCF_020097155_PROKKA_01314 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDS +ASLNSVSGTATDILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTES +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLI +IAGLSWAVVGIWDAIAEAAIIAAVFLVRSDPARKS-------AVPA +>GCF_023573625_PROKKA_01437 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001234.fa new file mode 100644 index 0000000000000000000000000000000000000000..edfd014a11fd01d186879389902c9a680373aff1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001234.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01516 +M-----RTVAETVTTVPHDAAASALEPG----AWAPPTDVHVAGLDAVGAAIAHALAGAG +ALRLALWDPRPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQ +ATVAVGSVLDADLAAHALAADHPLLPVTVGPRAVTVGPWCAPVVRGCPLCRWPADPAGVP +GAPTAPGPSAHRGQ-----VDGLAALRAAVLTVDAL--RTGPAPGVLRADRVTGRTRRVK +VRPRPGCACDPDALG-------WAF------------------ +>GCF_003691675_PROKKA_01225 +M-----RTVAETVTTVPHDAAASALEPG----AWAPPTDVHVAGLDAVGAAIAHALAGAG +ALRLALWDPRPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQ +ATVAVGSVLDADLAAHALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVP +GAPTAPGPSAHRGQ-----VDGLAALRAAVLTVDAL--RTGPAPGVLRADRVTGRTRRVK +VRPRPGCACDPDALG-------WAF------------------ +>GCF_005280335_PROKKA_01409 +MPAAPSSALSDALSSAEPGAVRPEVEPGPPGAGWEPPVDVHVAGLDAVGVAVAHALAGAG +AHRMALWDPRPVDAADLGTGLLPGDLGRPRARALERRLLDVAPGLRVYAHHGPLPVLVGQ +ASVAVGDVLDADLAAQALAADHPLLPVHVGPRAVTVGPWCAPDVVGCPLCSLPADPVGPP +GRRSARGRATSSGESGAAAVDALTAQRAAVLVADAL--RAGPSAGVVRADRASGRTRRAR +VRPRAGCACDPDALA-------WGT------------------ +>GCF_020097155_PROKKA_01308 +M------ATTD---------AHGPRESG----LLADPAGIQVAGLGPAGGALAAALAAGG +VAALALWDPTPVGASDLGLGLLPADLGRPRDRAWEARLSRTWPALPVYAGAGTRPGALGA +ATVAVDLPGLPDLAARAIAAQHPLLPVRTDLHGVSAGPWTGGGAPGCVLCTEDVPGTALT +APPAAPPRRDPGAA-----REPGHALRAVVLALDVLTGRRDATSAVLRVDAATGRLTRIP +VRTRPGCGC-ADLLAGDGTGDDWAAALAAVEESLDGALADARP +>GCF_023573625_PROKKA_01443 +M-----RTVAETVTTVPHDAAASALEPG----AWAPPTDVHVAGLDAVGAAIAHALAGAG +ALRLALWDPRPVDAADLGTGLLPGDLGRPRAGALERRLGDVAPGLRVFAHHGPVPVLVGQ +ATVAVGSVLDADLAAQALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVP +GVPTAPGPSAHRGQ-----VDGLAALRAAVLTVDAL--RTGPAPGVLRADRVTGRTRRVK +VRPRPGCACDPDALG-------WAF------------------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001236.fa new file mode 100644 index 0000000000000000000000000000000000000000..625915f79f47d95444ca5ae2ff1fee7881a01782 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001236.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01518 +M------ASCPPSSSDPTVAP----PLALPLAREELDRGAVARLDPGHLAASWAREGTEV +LWLQGGRAPVADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPP---- +-------AALPEDAAT--ALADAVWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCA +FCGGVTDVEAAGWVRRCRDCSREQFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLA +GFVEPGESLEHAVVREIAEESGVTVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDG +EEILSVRWFEREELARLAREGDVTLPGAVSIARALIEDWYGGTLPDAQTLIT +>GCF_003691675_PROKKA_01227 +M------ASCPPSSSDPTAAP----PLALPLAREELDRGAVARLDPGHLAASWAREGTEV +LWLQGGRAPVADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPP---- +-------AALPEDAAT--ALADAVWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCA +FCGGVTDVEAAGWVRRCRDCSREQFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLA +GFVEPGESLEHAVVREIAEESGVTVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDG +EEILSVRWFEREELARLAREGDVTLPGAVSIARALIEDWYGGTLPDAQTLIT +>GCF_005280335_PROKKA_01407 +MPVPDPAAPAPEPRHDPAPAPAPAAPLALPLAREEVDRGAVARLDPGHLAAAWEREGTEV +LWLQGGRAPVADGRLRFTTPSGPVPPQAAYLGRGTAADLGPGGRERAVVAVALEPP---- +-------AVLPPDAAA--ALGDAAWVGLRDAAAALSDADAGLFVAAVANANWHAAHRFCS +FCGGATAVEAAGWVRRCEACGREHFPRTDPAVIVAVTDPDGRILLGRNAAWPAGRYSCLA +GFVEPGESLEHAVVREVAEESGVTVADPRYRGSQPWPFPRSLMLGFTAQAPAGAEPVADG +TEILSVRWFEREELAALAREGEITLPGAVSIARALIEDWYGGTLPDAQTLIT +>GCF_020097155_PROKKA_01306 +MPV--------PSAPDAVPAA----LPHLTLAREALDRSGAEREDPGLLGRLAADPATGV +LHLVGGRAPVRDGALVLVPPAGPFPPEAVFLGRRLTDAAAPSAAGRPLVLVARESAPGSS +GDGGPTRPAEPTDAPTRDPLAGAAWLGLRDVAAGLSDADTGLFVEAVAIANWHAGHGFCS +RCGGRTDTESAGWVRRCRDCSARHFPRTDPAVIMAVMDDQDRILLGSNAAWPAGRHSCLA +GFVEPGESLEHAVAREVLEEAGIVVVDAAYRGSQPWPFPRSLMVGYRAHALPGQEPVADG +HEIRSVRWFTRDELAAEVRAGAVTLPGAVSIARALIEDWYGGTLPDPTTLIS +>GCF_023573625_PROKKA_01445 +M------ASCPPSSSDLTAAP----PLALPLAREELDRGAVARLDPGHLAAVWAREGTEV +LWLQGGRAPVADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPP---- +-------AALPEDAAT--ALADAVWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCA +FCGGVTDVEAAGWVRRCRDCSREQFPRTDPAVIVAVTDPAGRILLGRNAAWPEGLYSCLA +GFVEPGESLEHAVVREIAEESGITVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDG +EEILSVRWFEREELAHLAREGDVTLPGAVSIARALIEDWYGGTLPDAQTLIT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001241.fa new file mode 100644 index 0000000000000000000000000000000000000000..bea2440062e82dbd77d4510e7d1a2aff73ace405 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001241.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01523 +---MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEA +AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARHHGL +TPLEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA +ARYEQLRVAPVDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER +>GCF_003691675_PROKKA_01232 +---MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEA +AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL +TPLEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA +AQYEQLRVAPADLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVDAER +>GCF_005280335_PROKKA_01402 +MSPVNWHQSIRAGFDLETTGRDPRSALIVTATLVMVDAQGRATASAEWLLDPGVPIPAEA +AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL +APVEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA +ERHEQLRVDPAELHERQVRWKAEQAESFEEYLRRKDPQATVSRDWPVESGR +>GCF_020097155_PROKKA_01301 +---MSWNEQIRAGFDLETTGRDPRQARIVTATIVMVDAAGKAVSSAEWLLDPGVPIPEEA +AAVHGVTTERARAEGLEARRGVSEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGV +APLEPRPVVDPYVVDKQVDRFRKGKRTLGAVSEHYDVVLEDAHTSAADALAAVQVMDELV +RRHPKADLPLDELHAAQARWKAEQAESFEEYLRRKDPQATVSRAWPVEPDV +>GCF_023573625_PROKKA_01450 +---MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEHGRAASSAEWLVDPGVPIPAEA +AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL +TPLEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA +ARYEQLRVAPTDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001243.fa new file mode 100644 index 0000000000000000000000000000000000000000..95b95943a2e97469145404e5afda3e5637e32e6a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001243.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01525 +MSFPLHRPRRLRRSAAMRRLAAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGAVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>GCF_003691675_PROKKA_01234 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>GCF_005280335_PROKKA_01400 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAPEPIAIASMPGVVQHTSDT +LKAAAAEAAELGLGGIMLFGVPETRDAVGSISLDPEGVLNQAIRDVKSEVGDALVVMSDL +CLDEFTDHGHCGVLTEDGAVDNDATLEIYAQMGVAQAEAGADVLGPSGMMDGQVRVIREA +LDAAGHVDTGILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRTEALHEVALDLE +EGADMVMVKPAMSYLDIVRDVAELADVPVSAYQISGEYAMIEAAAANGWIDRKASIVESV +LSIRRAGADTVLTYWATELGRWMKEGSL +>GCF_020097155_PROKKA_01299 +MSFPLNRPRRLRQSAAMRRLVAETRLHPNELILPAFIKEGAAEPVPIASMPGVVQHTTDT +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALREVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>GCF_023573625_PROKKA_01452 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRGVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001249.fa new file mode 100644 index 0000000000000000000000000000000000000000..8553077afdbf34fb6790d9cdcbafe637ab81abd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001249.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01531 +----------MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDA +LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAI +EAELAARGLDLPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDM +GMAMEQTGLTGKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHS +IPTSDAAAAGPRGLAADLRAQAGAEPGD-EGADVYSAQHLDVAREILAGVPEAADVPWSL +VYQSRSGPPSVPWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDL +DTEAKETAEGLGVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRP +DCCVKVMRDGSTRPTTSAVDAAVRGLAEHEAGAAAPAEEA----- +>GCF_003691675_PROKKA_01241 +----------MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDA +LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAI +EAELAARGLDLPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDM +GMALEQTGLTGKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHS +IPTSDAAAAGPRGLAADLRAQAGAEPGD-EGADVYSAQHLDVAREILAGVPEAADVPWSL +VYQSRSGPPSVPWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDL +DTEAKETAEGLGVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRP +DCCVKVMRDGSTRPTTSAVDAAVRGLAEHEAGAAAPAEEA----- +>GCF_005280335_PROKKA_01394 +MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA +LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI +EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM +GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS +IPTSDAAAAGPRGLAADLRAQAGAEPGE-EGADVYSAQHLDVAREILAGVPEAADVPWSL +VYQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDL +DTEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRP +DCCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEE---S +>GCF_020097155_PROKKA_01285 +MTA-----------------VPTHRVPEDARRP-VHEPERAAAGVDYDACGAMAPKAYDA +LILASFGGPEGQEDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAI +EAELVRRGLELPVYFGNRNWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDM +GLAMERTGLEGKVDLDKTRQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHS +IPTADAAAAGPRGLAAALREQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSL +VYQSRSGAPHVPWLEPDINDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDL +DTEAKDTAAELGVAFRRTPTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRP +DCCVKVMRDGSVRPTTSAVDAPVRGLAEHR-GEQDGADDAGAQDS +>GCF_023573625_PROKKA_01458 +----------MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDA +LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAI +EAELAARGLDLPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDM +GMAMEQTGLTGKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHS +IPTSDAAAAGPRGLAADLRAQAGAEPGD-EGADVYSAQHLDVAREILAGVPEAADVPWSL +VYQSRSGPPSVPWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDL +DTEAKETAEGLGVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRP +DCCVKVMRDGSTRPTTSAVDAAVRGLAEHEAGAAAPAEEA----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001255.fa new file mode 100644 index 0000000000000000000000000000000000000000..d44a8eeb15e6877c300ff344da79f47f97942dcd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001255.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01537 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVSDGTPLVLADAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS +>GCF_003691675_PROKKA_01247 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLADAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS +>GCF_005280335_PROKKA_01388 +MEIRIGVQHVGREVVIESEQPAEEVRSLVDAAVADGSTLVLADAKGRQVVVPGDRIGFVE +INAKKSGPLGFAAS +>GCF_020097155_PROKKA_01279 +MEIRIGVQHVGREVVLESDHTAQEVRALVDAALADGTTLALTDTKGRQVIVPADRIGFVE +IGAKKSAPLGFAAV +>GCF_023573625_PROKKA_01464 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLTDAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001256.fa new file mode 100644 index 0000000000000000000000000000000000000000..b256d48bab346dcb172adc028047025467f07e76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001256.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01538 +MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHADRTALPFVTVDPAGSTDLDQA +LLLTPADD-DGILVRYAIADVPAFVTPGGAVDGEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDA +AGAVVETGLERARIRSRAQLTYGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAA +RGGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTMPAPDTDAVAAFRERTRALG +APWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTAFDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDR +FVLALCHAHAIGAPAPAWVRSALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDP +AVSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR +>GCF_003691675_PROKKA_01248 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHADRTALPFVTVDPAGATDLDQA +LLLTPSDD-DGILVRYAIADVPAFVAPGGAVDAEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDA +AGAVVETGLERARVRSRAQLTYGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAA +RGGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTMPAPDADAVAAFRERTRALG +VPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTAFDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDR +FVLALCHAHASGAPAPAWVRSALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDP +AVSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR +>GCF_005280335_PROKKA_01387 +MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYADRTDVPFVTVDPAGSTDLDQA +LYLEAADG-DAITVRYAIADVPAFVAPGGAVDVEARRRGQTVYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDA +AGAVVDTSLERARIRSRAQLTYAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAA +RGGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTMPAPDAEAVAAFRSRTRALG +APWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTAFDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDR +FVLALCHAHATGAPAPEWARAALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDP +AVTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR +>GCF_020097155_PROKKA_01278 +MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRADLTAVPFVTVDPAGSTDLDQA +LHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDA +EGAVASTDLVRARIRSRAQLAYPQVQALLD---------------DDAAPEAAD-WPAEVRASLALLPEVGARRTAQEAA +RGGASLSMPDQEISVV-DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTRALG +LPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPEDPEQAALAAPYAHTTAPLRRLVDR +FVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRASAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDP +AVSLRVPGRAEPGTVVRVRVDAVDVAAGKVTASGVDWPHSAR +>GCF_023573625_PROKKA_01465 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHADRTALPFVTVDPAGATDLDQA +LLLTPSDD-DGILVRYAIADVPAFVAPGGAVDAEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDA +AGAVVETGLERARIRSRAQLTYGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAA +RGGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTMPAPDTDAVAAFRERTRALG +APWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTAFDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDR +FVLALCHAHAIGAPAPAWVRSALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDP +AVSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001257.fa new file mode 100644 index 0000000000000000000000000000000000000000..1d44bd0d0dac884af3bcc38356fb371cb3b47add --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001257.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01540 +MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAQAARETGL +TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGRARDARLTRAQEMVRRLGADFSI +TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV +ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD +RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG +>GCF_003691675_PROKKA_01250 +MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL +TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI +TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV +ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD +RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG +>GCF_005280335_PROKKA_01385 +---MSRYDLHTHSVESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWEAAAEAALAEGI +AFVPGMEMSCMAADGTSVHVLSYLHDPADPSLLREIGTARSARLTRAQEMVHRLARDYPI +TWELVQEHAAEGATIGRPHLADTLVTLGVVEDRSAAFAHILTGRSKYYVPHYAPDPAIAV +ELIRSAGGVPVFAHPRAVTRGRVVGVEVIEEMIDAGLAGLEADHRDNPEEERSWLREVAA +RHDLFVTGSSDYHGTGKPNLLGEFSTGEDVLAEIERQGTGAAVVRG +>GCF_020097155_PROKKA_01276 +-MSTARYDLHTHSTESDGTEPAADVVHAAALAGLDGLALTDHDTTAGWAAAADAARETGL +LLVPGMEMSCMAADGTSVHLLSYLHDPADPSLLAELGASRDARLTRAQSMTDRLAEDFPI +TWDLVREHASENATIGRPHIADALVTIGAVPDRSAAFSSILRGGSKYYVPHYAVDPVEAV +RLVRAAGGVPVFAHPRARLRGRIVGDDVLEAMIEAGLAGLEADHRDNPEQERTWLRETAT +RHGLFVTGSSDYHGAGKPNLIGEFTTGPEVLAEIEHQGTGAAVVRG +>GCF_023573625_PROKKA_01467 +MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL +TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI +TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV +ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD +RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001261.fa new file mode 100644 index 0000000000000000000000000000000000000000..4252317dc318dda1e1fd5f1fc3dbd83ed4c4f8fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001261.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01544 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDA-ETR +PAT +>GCF_003691675_PROKKA_01254 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVASELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEPV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDA-ETR +PAT +>GCF_005280335_PROKKA_01381 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAVPPFATGLVIEVPGKKRVFVPM +TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAADLFDRRVRLTDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLDWDEARWTGQAEPQAATSFLAAHEDLKPA +DLADMLHEMPEKRRVEVARELQDERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEEAEDVRRLLEYEEGTAGSVMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAVGNIMDKDLEPV +SDLAPIAHVTRELATYNLTSIPVVNEHHRVVGAVSVDDVLDHILPDDWRAMDHDDH-DPR +PAA +>GCF_020097155_PROKKA_01272 +MNSPRIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGRGARSAATGLVIEVPGKKRVFVPM +TRVTSMDSGQIITTGLINLRRFSRRGAEQTVAGDLFDRRVHLTDGSGRAVVEDLGIEQQR +NGDWLVTDYYVRRDDGRTAFGRP-RGEHLLVSWDEVAWGAAAEPQGASSFVAAHDDLKPA +DLADMLHEMTDKRRVEVANELQDERLADVLQELPDDDQVQILSHLDIERAADVLEEMDPD +DAADLLNELPDSQQELLLELMEPEDAEDVRRLLEYEEDTVGSIMTPVPVVLPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRYLGVVHFQRLLRYPPPEAIGNIMDKDLEPV +SDMDSVAHVTRELATYNLTSIPVVNAQHRVVGAVSVDDVLDHILPEDWRAMDPEDHPETE +GQD +>GCF_023573625_PROKKA_01471 +MSSPKIFVARLLGLDVFDPLGDRLGRLRDVVVLDRGPAAAPFATGLVIEVPGKKRVFVPM +TRVTSMDSGRIITTGLINLRRFSRRGAEQMVAADLFDRKVRLSDGSGEAFLEDIGLEQQR +NGDWLVSDLYVRRIVGRGPFGRAQRGEHLLLNWDEARWTAQADPQGATSFLAAHEDLKPA +DLADMLHDMSEKRRVEVARELQNERLADVLQELPDDDQVQILSQLDIDRAADVLEEMDPD +DAADLLHELPDSQQELLLERMEPEDAEDVRRLLEYEEGTAGSLMTPVPVILPPEATVAEA +MATIRQQEISPALASLVIVARPPLETPTGRFLGVVHFQRLLRYPPPEAIGNIMDKDLEAV +SDLAPIAHVTRELATYNLTCIPVVNEQDRVVGAVSVDDLLDHILPDDWRAMDLDDA-ETR +PAT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001263.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf3d65e66767bea847c93998006ec7bb3bce2c29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001263.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01546 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ +IAQRVAVRPRGLAGRRLPVTPR +>GCF_003691675_PROKKA_01256 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVAVVPGCESVDVRVGVMEPERRLALQDALRATRPTNPFGEGTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLDTQVPLLGTVPLDPALRAGGDAGEPVVVSAPESPAGRALTQ +IAQRVAVRPRGLAGRRLPVTPR +>GCF_005280335_PROKKA_01379 +MSDLGLHVPEVRTDLERRVLDRLATVQDPEIRRPVTELGMVESVVETAPGTVEVTVLLTI +EACPMRGTIQGDVAAAVADVPGCDAVDVRTGVMSPERRLALQDALRAARPANPFGEGSLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTASPTKLDRM +ILPPVVRDVKVISIGMFLDEDRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQAVAGVIENMGPMTLPDGTVL +DVFGAGGGQEVAERLERVLGSAVPLLGSVPLDPALRRGGDAGDPVVLSAPDSPAGRALAG +VAERLAVRPRGLVGRRLPLSPR +>GCF_020097155_PROKKA_01270 +MSAPALPRPEVRTPLEAAVLAALDGVVDPEIRRPITELGMVRSVAETGGGHVAVEVLLTI +AGCPLKGTIQADVAAAVADVPGCAGVDVRLGVMTPTERAALQEALRGARPANPFAEDSLT +RVLAVASGKGGVGKSTVTANLAVALAGRGLSVGLIDADVHGYSIPGLLGVQASPTRVGEL +ILPPVSRGVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELVVVTTPQHAAAQVAARAGQLAAQTGQRVAGVVENMGPMALPDGTVL +DVFGAGGGQEVADRLSGALGTSVPLLGTVPLDPALRRGGDAGEPVVVSAPESPAAAALQE +VAARLAVRPGSLRGRGLPVSPR +>GCF_023573625_PROKKA_01473 +MSALGLPVPEVRTDLERRVLERLATVQDPEIRRPITDLGMVESVVETAPGVVEVAVLLTI +AACPLRGTIQTDVAAAVADVPGCGSVDVRVGVMEPERRLALQDALRAARPTNPFGKDTLT +RVLAVASGKGGVGKSSVTANLAVALAARGLAVGLIDADVHGYSIPGLLGVTGTPTKLDRM +ILPPVVRDVKVISIGMFLDADRPVAWRGPMLHRALEQFVTDVHWGDLDVLLVDLPPGTGD +IAISTAQLLPASELLVVTTPQHAAAQVAARAGQLAEQTGQTVAGVVENMGPMTLPDGTVL +DVFGTGGGAEVAERLSGVLGTQVPLLGTVPLDPALRAGGDAGDPVVVSAPESPAGRALAE +IAQRLAVRPRGLAGRPLPFTPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001266.fa new file mode 100644 index 0000000000000000000000000000000000000000..d00ce96f5c522c20174cb0131fa07caa935d550d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001266.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_01550 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA +>GCF_003691675_PROKKA_01260 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA +>GCF_005280335_PROKKA_01375 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQG +>GCF_020097155_PROKKA_01266 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEAKELQQCLEGVTQA +>GCF_023573625_PROKKA_01477 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001267.fa new file mode 100644 index 0000000000000000000000000000000000000000..40f07d06cbd711d5c6e6675d0bf13bb2c8bc6952 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001267.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01551 +MRAPLGGEGRRVSGPQWIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQCEDEVTALRARVAELE---AADPS +RSDPAGRA +>GCF_003691675_PROKKA_01261 +MRAPLGGEGRRVSGPQGIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEVTALRARVAELE---AADPS +RSDPAGRA +>GCF_005280335_PROKKA_01374 +-----------MSTPLWIAVIAALVVVVAALAAAAAGRLTLRAGEPAGQAPVHPVALPER +PRADDVAFVRLAVAVPGYQRDQVDAVLLRLRDALADHEDEVAALRARLAELEADAARDAE +RTGPR--- +>GCF_020097155_PROKKA_01265 +-----------MTQPIWIAVLVVAVVAVAALAAAALGRALPRPADPAGQAPPHPVLLPEH +PRAADVDRLRLATAVPGYQRDQVDEVLARLRAALAADEERIAALEARLGEGDG-VGR--- +-------- +>GCF_023573625_PROKKA_01478 +MRAPLGGEGRRVSGPQGIVLVAVLVVVLGALAASLAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEAAALRARLAELE---AADPS +RSDPAARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001268.fa new file mode 100644 index 0000000000000000000000000000000000000000..01df913228ead9a001070b6c10af8bf513bd8604 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001268.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01552 +MAPHEHPSGGDVAAKPQRVRRGGQVLRGDAAHTPTFDQLLLDGRR--PGDAARPAADVAS +TTSEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYT +VITGGGPGTMAAANRGAHEAGGESVGLGIDLPFETGLNPWVHVGVDFRYFFVRKVMFLKY +AQGFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWSPLVDWIRGTLVERGMIS +PEDPDLFHLVDTAEEAVACVLRSAGRADA +>GCF_003691675_PROKKA_01262 +MAPDEHPLDGDV-AEPEHVRRGGQVLRGEAERTPTFDQLLLDGRQ--PGDATQPAADIAS +TTSEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYT +VITGGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKY +AQGFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMIS +PEDPDLVQLVDTAEEAVACVLRSAGRADA +>GCF_005280335_PROKKA_01373 +MDPDQHPR-TDAVPAPERVRRGGQVLRGEAARRPTSDQLLLDARR--PGDALPPAADLAS +TTSEAWRVLRIQAEFVEGFGTLAGIGPAVSVFGSARTPEASPEYALAREVGARLAEAGFT +VITGGGPGSMAAANRGAHEAGGESVGLGIELPFEAGLNEWVHVGVDFRYFFARKVMFLKY +AQGFVVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVDSTFWGPVVDWIRGTLVERGMIS +PGDPEIFHVVETAEEAVDCVQRVCGPGAP +>GCF_020097155_PROKKA_01264 +MTDKPDPARADRVDR-HRVHRGGQILRGDAAASPTFDQLLLDARRAPAGKTRTPS---TS +STSDAWRVLRIQSEFVEGFGTLADLGPAISVFGSARTGEGTDEYALGVEIGRRLAEEGWA +VITGGGPGAMESANRGADEAGGVSVGLGIELPFETGLNPWVGIGVDFRYFFARKVMFLRY +AQGFVVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVGTEFWGPLVDWIRGTLTARGMIS +PGDADLITVVDTAEEAVAHVSATCGGARA +>GCF_023573625_PROKKA_01479 +MAPHEHPSGGDVAAKPQRVRRGGQVLRGEAARTPTFDQLLLDGRR--PGDATQPAADIAS +TTSEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYT +VITGGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKY +AQGFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMIS +PEDPDLVQLVDTAEEAVACVLRSAGRADA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001269.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d589a1741d7a4fc96018693e33fb1c67a9a23db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001269.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01553 +MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA +IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL +FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH +>GCF_003691675_PROKKA_01263 +MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA +IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL +FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAAQARKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH +>GCF_005280335_PROKKA_01372 +MTQITPEEPHGAHARDEAAPRRPRAAPGDDLIVLENVNKHFGDFHALKDIDLRIPRGQVA +IVVGPSGSGKSTLCRTINRLETIDDDGGRILLDGQPLPAEGKQLAQLRAEVGMVFQSFNL +FAHKSILENVTLGPIKVKGKRKADAERHAMELLERVGVAQQAKKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPESFFTAPQHERARDFLGKILAH +>GCF_020097155_PROKKA_01263 +MSEITSGTVHGS----TAASGPAPAAASDALIRLEHVNKHFGEFHALKDIDLAIPRGQVA +IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPSEGRELARLRAEVGMVFQSFNL +FAHKSILENVTLGPIRVKGRKKAEAERHALELLERVGVAHQAKKMPAQLSGGQQQRVAIA +RALAMEPQALLFDEPTSALDPEMVQEVLDVMVGLAREGMTMVVVTHEMGFARKAGDRVVF +MADGEILEDTDPESFFTRPQHPRAQEFLGKILVH +>GCF_023573625_PROKKA_01480 +MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA +IVLGPSGSGKSTLCRTINRLETIDDDGGRILVDGRPLPTEGRQLAQLRAEIGMVFQSFNL +FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001270.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a4759e642d8e00f02ab21871a8cec904c35a0bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001270.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01554 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA +>GCF_003691675_PROKKA_01264 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGERLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEKDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVDFAGPYFVAGQDLLVRADDTAITGPESLEGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA +>GCF_005280335_PROKKA_01371 +MFRKKLLTLSAVTAAAALSLTACSPSAQQ-GGGEGSGSASAGGSQSAGSGEGLRIGIKFD +QPGLGFREGSGAPTGFDTDVARYVADKLGVAEGDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVDFAGPYFVAGQDLLVRADDTEITGPDALDGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGNTFTTERYG +VGIAKGDDRCEDINDAIKEMKDSGAWKESLDANTEGTGYEYDEALNSGADAEFESCS +>GCF_020097155_PROKKA_01262 +MARSRILSVAAVAAAAALSLSACSPSSS--GGSGSASSASGSTAAQSGSSDTLRIGIKYD +QPGLGFREGQNAPTGFDTDVARYVAGKLGVAEDKIEWVQTPSANRENALENGEVDMIFAT +YSITDARKQRVDFAGPYFVAGQDLLVRQDDTSITGPDSLNGKNLCSVTGSTSAQKIKDNY +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGQPFTTERYG +VGLQKGSDKCKDINEAIKAMKDSGEWEKSLKANTEGTGYEYSEDKNSGADAEFEPCA +>GCF_023573625_PROKKA_01481 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWKKALESNTEGTGYTYDETLNSGEDAEFEPCA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001271.fa new file mode 100644 index 0000000000000000000000000000000000000000..446b2f4e108e640e8504a08e06b22c306d8529ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001271.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01555 +MESISSLLADYGADIPLAFWMNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR +>GCF_003691675_PROKKA_01265 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR +>GCF_005280335_PROKKA_01370 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRAIGTAYVN +VVRNTPLTIVMLLGVLAVWGQLKITFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARAIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASDKWAVAR +>GCF_020097155_PROKKA_01261 +MESLSTLVEQYGAAVPQAFWMNIRLAALATLGAFVLGVLLALCRISPVPSLRAVGAGYVH +IVRNTPLTIIMLIGVLAVWGQLKVTFAPDFKVNFFVYAVLALSLYHAAFMCEAIRSGVNT +VPLGQAEAARAIGLGFLPAARLVILPQALRGAITPIGNTVIALTKNTTVAAAASVAEASG +LMKTMIEFRPDAMVAIFLTIAIGFCLIVIPIGLLTTWASDKWAVSR +>GCF_023573625_PROKKA_01482 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001272.fa new file mode 100644 index 0000000000000000000000000000000000000000..e782cf743d93c2a4910f7840c0e90acd8e865051 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001272.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01556 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG-- +>GCF_003691675_PROKKA_01266 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLHYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG-- +>GCF_005280335_PROKKA_01369 +MSSQASVLFDAPGPLARRRILIANLVALAAVLALAVAVLMRMADADQLEARRWTAALDAN +AWTNYYLPGLQFTVQAAAIAVLTSVVFGLVLGFLRLAPFAPVRGAAGLVVEFFRAVPVLI +MMVFFYQVFAQVARTGVIAPADGPYYAVIVALTLYNGSVIAELVRSGVRSLPKGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG +NILQSLVVAALIFIVINFLLTWVATRLSRRLSSRTAGDAGAPTTPVVGAPTDKPA-- +>GCF_020097155_PROKKA_01260 +MSAQASVLFDAPGPATRRRILIVNLVALALVLAVAVVVGMALQDRGQLEPRRWLAALDAN +AWTNYYLPGLQFTLQSAGIAVVTSVVFGLVFGFLRLAPVAPVRWLAAVVVEFLRAVPVLV +MMVFFYQAFALAARGGAINAADSPYYAVIVGLTLYNGSVIAELVRSGVTGLPKGQREAAA +AIGMTPNQSLRLVEVPQALVAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG +NILQTLVVAAVIFILINMLLTWLATLLSRRLSSRTSGR----TKPHAGSTAVTIGKD +>GCF_023573625_PROKKA_01483 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001273.fa new file mode 100644 index 0000000000000000000000000000000000000000..109c28c82fd88a482df74fb9f090d532e7b974b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001273.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01557 +M--SLTPNTLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFG +DAVVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQ +LALAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDG +VVEGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYRE +GLHAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDD +ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDE +HVSREAVHACLAALTAWLAG +>GCF_003691675_PROKKA_01267 +M--SLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEHALRALGGLEVRRFG +DAVVARTALGRPTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQ +LALAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDG +VVEGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYRE +GLHAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDD +ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDE +HVSREAVHACLAALTAWLAG +>GCF_005280335_PROKKA_01368 +MTETSAP-ALPDLADPGLDVAELTAVLLDVPSVSGDEGPLADAVETALRALGGLEVRRFG +DAVVARTDLGRDTRVILAGHLDTVPLPTVPGSRGTVPSAWEGDVLYGRGAVDMKSGVAVQ +LALAGRYGRADGPAPAHDVTWVFYDHEEVASDLSGLARVARQAPELLEGDFAVLLEPTDG +VVEGGCNGTCRYRVSFSGVAAHSGRAWRGENAIHKLGAVLTALAAHEPATVTVEGLDYRE +GLNAIRVAGGVAGNVIPDAAHVDVNYRFAPDKTLEQAHARVREVLEGAGVDWDAQVRIDD +ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDE +HVHRAAVHACLDALDAWLAG +>GCF_020097155_PROKKA_01259 +MTDAVAP-VLPDLAAADLDVAALTATLLDAPSVSDDEGPLADAVEAALARLPRLGVRRFG +DAIVARTELGLPGRVILAGHLDTVPLPTAPGARGTVPSAWEGDVLYGRGAVDMKSGVAVQ +LALAGLFGRADGPDPVHDVTWVFYDHEEVDSARSGLARIARQAPELLEGDFAVLLEPTDG +VVEGGCNGTCRYRVRFEGVAAHSGRAWRGDNAIHKLGALLSALAAYEPATVTVEGLDYRE +GLNAIRVSGGVAGNVIPDAAATEVNYRFAPDKTLEQAHAHVREVFAAAGVDWDAQVEVTD +ASPAARPGLDRPAAAAFVAAVGGEPMPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDE +HVERAAVERCRDALEAWLRG +>GCF_023573625_PROKKA_01484 +M--SLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFG +DAVVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQ +LALAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDG +VVEGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYRE +GLHAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRTVLEGAGVDWDAQVRIDD +ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDE +HVHREAVHACLAALAAWLAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001275.fa new file mode 100644 index 0000000000000000000000000000000000000000..a77b2703613814b70b036678c0c3aadad7f992f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001275.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01560 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDQEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPAAKIGRPRQIYVGE +QLRQYPQR +>GCF_003691675_PROKKA_01270 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTY +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +QLRQYPQR +>GCF_005280335_PROKKA_01366 +MTQNESVRLTVGEQSLDLGVERATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDEGILRYRGYAIEDLAANSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYEIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRTIQSDGIKPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILSKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +PLRQYPQR +>GCF_020097155_PROKKA_01257 +MSEIESARLTVGEKTLDLGVEKAAEGNDGIVVAPLLKETGKVTYDPGFMNTANAKSAITY +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKEALEAWETNILRHNMVHEDL +KMFFNGFPRDAHPMPVLSSSVSALSTFYADSLDPKDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNNLNYVENFLRLCFGVPAEEYEIDPDMVKALDLLLMLHADHEQNASTST +VRLVGSTDANLFASVSAGINALYGPLHGGANEAVLNMLRRIQAEGIKPEDFMEKVKHKED +GVRLMGFGHRVYKNYDPRAKIVKKTAEDILAKLGGNDELLEIAMRLEEKALADDYFVERR +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELTEDPATKIGRPRQIYVGE +QLRQYPQR +>GCF_023573625_PROKKA_01487 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +QLRQYPQR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001276.fa new file mode 100644 index 0000000000000000000000000000000000000000..b3d30c21ed6471ed9374ad4b97ad1395ad4d6c1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001276.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01561 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG +TDDLRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT +YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARDV +GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPQLVATLINTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG +HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGELADLGIIAGPGVFYGAGGDGYVRVA +ITATDEAVARAAARLTARGPRTG +>GCF_003691675_PROKKA_01271 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG +TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT +YAVGALLAGAEAVAADGLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV +GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG +HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGAGGDGYVRVA +ITATDEAVARAAARLTARGPRTG +>GCF_005280335_PROKKA_01365 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPELIRRALTEAADAHGYPTTHG +TADLRRAVVDWYARRRGVAGLDPEAVVPTVGSKEFIAWLPTLMGLGAGDVVVHPEAAYPT +YAMGALIAGAEAVAADDLASLAPEVRERVRLVWTNSPANPTGAVLDAAALKRVVDDARAL +GAVVCGDECYAELGWDEWDGELVPCILSEEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPGLVATLVNTRKHAGMIVPAPVQHAMAVALADEGHVAQQKDRYRRRRDALRAALEASG +HAVDHSEAGLYLWTRRADTDPAAATEQDSWDLLGELADLGIIAGPGVFYGAGGHGYVRVA +ITASDEAVEQAARRLAARGPLRR +>GCF_020097155_PROKKA_01256 +MLTLPDYPWDTLAPYRERAAAHPEGTVDLSIGTPVDPTPALIRDALTAAADAHGYPTTHG +TAELRQAVVDWFARRRGVPGLDPEAVLPTVGSKELIAWLPTLLGLGAGDVVVFPATAYPT +YAIGAQIAGAEAVAADTLAELDDDVRSRVRLVWTNSPANPTGAVLDAAELRAIVDDARAL +GAVVCGDECYAELGWDEWEDRVVPCILAPEVSGGDLTGLLSVYSLSKQSNLAGYRAAFVG +GDPELIAPLTNTRKHAGMIVPGPVQHAMAVALRDDAHVAAQRDLYRERRAALKAALESAG +YAVDHSEAGLYLWTRRADLAPGQGTAQDSWDLLGELAELGIVAGPGVFYGAAGHGHVRVA +ITASDEAVAAGAARLTARGPLPR +>GCF_023573625_PROKKA_01488 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG +TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT +YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV +GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG +HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFY--GGDGYVRVA +ITATDEAVARAAARLTARGPRTG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001277.fa new file mode 100644 index 0000000000000000000000000000000000000000..c322621fe077798a0a762f21f3ade470cbe6ed2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001277.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01562 +MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD +TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA +>GCF_003691675_PROKKA_01272 +MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD +TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA +>GCF_005280335_PROKKA_01364 +MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD +TPEEWADYYKANVEFFDDLGSPGGAAKLGMIAKDHPIIAALPPQNADA +>GCF_020097155_PROKKA_01255 +MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD +VPEEWADYYKANVEFFDDLGSPGGAAKLGQIAKDHPLISALPPQGEGA +>GCF_023573625_PROKKA_01489 +MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD +TPDEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001280.fa new file mode 100644 index 0000000000000000000000000000000000000000..122dd6ec02a6ece6e848f50686832889b7485e93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001280.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01566 +MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEEAGGSARISDA---DEDGQ----R----------------- +--- +>GCF_003691675_PROKKA_01276 +MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEAAGGSARISDA---DEDGQ----R----------------- +--- +>GCF_005280335_PROKKA_01360 +MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT +TAGGLGTAPTARDGEA-------DDLIADP---DAPEH----RRGGAGGPAG-------G +VGQ +>GCF_020097155_PROKKA_01251 +MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL +AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT +STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA +KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA +FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT +TAGGLQASPASAPAGH-------ADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEG +DAR +>GCF_023573625_PROKKA_01493 +MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEEAGGSARISDA---DEDGQ----R----------------- +--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001282.fa new file mode 100644 index 0000000000000000000000000000000000000000..d0f9e0eec8c4ad7b915fc5f47badf18817edc769 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001282.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01568 +MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASG-------ASQGGDSGAGNVIEGDKGQKLTAEASGPGKADL +GDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWYFGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDD +AKWSDGTPVTAGDFIVHWAANNDTIKAE--------GAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEI +LISTALPAHIVAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQSITLE +ANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGEDVNVQTGDQLTWEHVDYNRGEGSVFA +DSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLREVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVR +LGYQAGNQRRTETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQSYNNP +EVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRDTAAQSGALWNVEQWVRVQE +>GCF_003691675_PROKKA_01278 +MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASG-------ASQGGDSGAGNVIEGDKGQKLTAEASGPGKADL +GDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWYFGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDD +AKWSDGTPVTAGDFIVHWAANNDTIKAE--------GAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEI +LISTALPAHIVAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQSITLE +ANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGEDVNVQTGDQLTWEHVDYNRGEGSVFA +DSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLREVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVR +LGYQAGNQRRTETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQSYNNP +EVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRDTAAQSGALWNVEQWVRVQE +>GCF_005280335_PROKKA_01358 +MKYTKLSAAAALAAGSALILSACAPGGGDDADNTASSGNG--GASGSASQGGEAGAPEVTEGDKGQKLTAPVDGPGMADL +GDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWYFGTDGSIIPNKDFGTYEKTSDDPLTVKYTISDD +AKWSDGTPVTAGDFIVHWAANNETVKAE--------GSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEI +LISTALPAHIVAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQSITLE +ANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGDDVNVQTGDQLTWEHVDFNRGEGSVFA +DSPELREAFALCLPRQQIVDNLIKPIYADAQVMNAREVFPFQENYQEVVDAAFPEEMDQPNIEKAKELVEKSGVSKPTVR +LGYQAGNQRRTETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDGAQNQQSYNNP +EVDAAWDKLATSLDEDEQLEQVKTIERLLWEDFQAIPLYAHPGLVGHKADVANVRDTAAQSGALWNVEQWVRVQE +>GCF_020097155_PROKKA_01249 +MKHTKLSAAAALAFGSALVLSACAPAGPAASGSSSN-GGGSSAASGSSAASGSDAAGGVTTGEKGEKLTAPADGPGMADL +GDVKTEEGSVAYSVGKDDFLSYNGVQANTYSTYNSAIVDRLFSGFYYFGTDGTIVRNEEFGTFEKISDDPLKVKYTINED +ATWSDGTPVTAADFIVQWAADNPNIVDESGKADPKTGQKPQLFESITSEPGKYIPEAPEGDPKGKEFTVTYAEPYADWEI +LITTALPAHVIAKGADMSLDDLVAAAKAKDSTKLVPAAKFWNNGWDFNPGELPSADMIPSMGPYKIKDGGWVAGQSITLE +ANDKYWGTPAATKNLVIKFAAPETHVQALQNKELDVIEPQATVDTVSQLEGLGDSVNIQKGDQLTWEHLDFNRGTGSTFA +DSKELREAFALCVPRQQIVDNLVKPINPDATVMNAREVFPFQDNYQEVVDAAYPKEMDQPNIEKAKELVAKSGVSKPTVR +LGYQAGNQRRAETVKLIKASCDQAGFDVQDANSNVFFKEVMPTGDYDVALYAWSGSGQKASGANIYQSDGEQNQQSYSNK +TVDEAWDKLAGSLDEKEQLEQVKVIEKALWEDFQAIPLYAHPGVVAHQADLANVRDTVAQQGALWNVEQWKRVS- +>GCF_023573625_PROKKA_01495 +MKYTKLSAAAALAAGSALILSACAPGGGNADDSSSN-GSG-------ASQGGDSGAGNVVEGDKGQKLTAEASGPEMADL +GDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVVDRMFSSFWYFGTDGSIIPNEDFGTYEKTSDDPLTVKYTISDD +AKWSDGTPVTAGDFIFHWAANNDTVKAE--------GSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEI +LISTALPAHIVAEEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGSYKFKDGGWQAGQSITLE +ANPEYWGTPPATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGDDVNVQTGDQLTWEHVDYNRGEGSVFA +DSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLREVFPFQDKYQEVVDEAYPKEMDEPNIEKAKELVEKSGVSTPTVR +LGYQAGNQRRTETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDGAQNQQSYNNP +EVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRDTAAQSGALWNVEQWVRVQE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001284.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b372038d5796489acb6436a302cd28084f5116a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001284.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01571 +M-TPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMV-DVAADSAPTVPAAEA +P---AREAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTG +TGTGMVLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSD +LPVASVSLDPVRRGDQVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLI +QTDADVVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLTGEE +TDTVSIGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASR +MSRLVNDHNVGDRITVQWRTADGEVREAEAVLQPALVN +>GCF_003691675_PROKKA_01281 +M-TPPGWPPRARRAPLAFVIALFGVLGALVLAGGLTALLAGRMV-DVAADSAPTVPAAEA +P---AREAGELAAGLTHVHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTG +TGTGMVLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSD +LPVASVSLDPVRRGETVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLI +QTDADVVPGYSGGPVVDDAGQVVGVTVAASDGTTAEEVDGFAIPLDVAFDVVDQVLSGEE +TDTVSIGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRPVGDDAFR +MSRLVNDHNVGDRITVQWRTASGEVREAEAVLQPALVN +>GCF_005280335_PROKKA_01353 +MSVPPGWPPRRRRSPLALAISFFGVLGALVLAVGVTLLVAGRMV-DVVGAPDPVVSARES +A---PPDAGALAQELAGAHEGVAVDWDAPAHAGSELDPGLAVDHAPGILLVETVLGQRMG +TGTGMVLTPEGLALTNYHVVEDSSEVFVVEADTGERHTATVLGRDAEHDVAVLDVHGVTD +LPVASVSLDPVRRGDEVAAVGNGRGQGHLTAVRGTVLGTDRSIMAASQGSDEYARLTGLI +QTDADVVPGYSGGPVVDDDGQVVGVTVAASDGTGAQEVDGFAIPLGVALGVVDQVLSGEE +TDTVSIGADGALGIMVAADPEAGVVVMQVDADSAAEAIGLVPGDVVLAVDGQAVEGNASR +MSRLVNDHNVGDRITVTWRTASGEVREAEAVLQEAVVN +>GCF_020097155_PROKKA_01246 +-----------------MAIAVFGVLGAVVLAVGLTLLAGGRLIAAVGAGSSSSAAAPSG +PQVTTRSLDALAASLDHAHAGIAVPAADAPPADGSLDPGERVRRAPGVLLVETRLEAMQG +TGTGMVLTSDGLALTNYHVVEDSTAVSVVVADTGARHAATVLGRDAKNDVAVLQIDGVSG +LTTTSVSRDPVRPGEAVAAVGNGGGQGYLTSVGGEVLRVDQSILAATEGTDDFERLTGLI +QTDADVVPGYSGGPLVDGEGQVVGVTVAASEGRTAAQVDGYAIPLSTAFDVVAQVLSGEE +TDSVSIGADGSLGISVAGSRD-GVEVLSVDRGSAGEELGLRPGDVITAIDGRTLDGNATA +MSRLVNDHEVGDRLSVQWRTADGEARQGEAVLQKARHN +>GCF_023573625_PROKKA_01498 +M-TPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMV-DVAADSAPTVPAAEA +P---AREAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTG +TGTGMVLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSD +LPVASVSLDPVRRGDQVAAVGNGGGQGYLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLI +QTDADVVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLSGEE +TDTVSIGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASR +MSRLVNDHNVGDRITVQWRTADGEVREAEAVLQPALVN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001285.fa new file mode 100644 index 0000000000000000000000000000000000000000..89bf7eaa7a53230ea06c621f26d297b994843459 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001285.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01572 +MATTHMKSTPVHTVGELPQVGSPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGGDYGVRM +TDGPLEGLLARAVVMVDADGVVRHAQLVPEISEEPDYEAALAAARG +>GCF_003691675_PROKKA_01282 +MATTHMKSTPVHTVGELPPVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLEDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM +TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG +>GCF_005280335_PROKKA_01352 +MATTHMKSTPVQTVGDLPEVGAPAPDFTLTGADLSPVTLQELRGRRVILNVFPSLDTGVC +AASVREFNSRATDLEDTTVLAVSADLPFAAARFCSAEGIENVRSGSVFRSSFGDDYGVTM +VDGPLEGLLARAVVVVDAEGVVRHAQLVPEITEEPDYEAALAAAQA +>GCF_020097155_PROKKA_01245 +MATTHFKGTSVHTVGELPEVGSAAPEFTLTGSDLSSVTLADLKGRTVVLNIFPSLDTGVC +AASVRRFNQEAAGLEDTTVLAVSADLPFAAGRFCSAEGIENVVTGSVFRSDFGTAYGAEL +ADGPMRGLLARAVVVVDAEGTVAYTELVPEITTEPDYEAALAVVRG +>GCF_023573625_PROKKA_01499 +MATTHMKSTPVHTVGGLPQVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM +TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001286.fa new file mode 100644 index 0000000000000000000000000000000000000000..071fe5059a8b90ccfcd4f2d847f93926a84098ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001286.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01573 +M-------TEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNA +VNYLSRDPARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATF +RANPARLVLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDG +ALGVDGGIPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRW +RRYNATRERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAF +LGLPASR +>GCF_003691675_PROKKA_01283 +M-------TEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNA +VNYLSRDPARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATF +RANPARLVLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDG +ALGVDGGIPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRW +RRYNATRERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAF +LGLPASR +>GCF_005280335_PROKKA_01351 +M-------RTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNS +VNYLARDPERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATF +QANPARLVLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDG +ALGVDGGIPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRW +RRYNETRERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREF +LGL---- +>GCF_020097155_PROKKA_01244 +MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA +VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY +RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG +ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW +QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF +LGL---- +>GCF_023573625_PROKKA_01500 +M-------TEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNA +VNYLSRDPARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAF +RANPARLVLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDG +ALGVDGGIPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRW +RRYNATRERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAF +LGLPASR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001289.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3a08f59c73ea5501efc048b6de076bc8bf77834 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001289.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01576 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV +LLVGRLRGNKAAPAH +>GCF_003691675_PROKKA_01286 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV +LLVGRLRGKKAAPAH +>GCF_005280335_PROKKA_01348 +MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL +PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS +-PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAIL +ITAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWV +GGHIVLVELAALGVPWPYDVQHGIVHAV-EAAGGFVAWLVETLTSALWGLIWGSLALGVV +LVVNRLRGKKDTLAH +>GCF_020097155_PROKKA_01241 +MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL +PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH +EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV +ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV +GGHIVLMELATLGLPWLYELQHTIVHAV-EGAGSVIAWLVETLTSAIWGLVWGSLVVAVV +GLVRRLRT------- +>GCF_023573625_PROKKA_01503 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV +LLVGRLRGKKAAPAH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001290.fa new file mode 100644 index 0000000000000000000000000000000000000000..db0e1981c6db1033cb64ff8657e8f89230142e91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001290.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01577 +MN-----------------TT---AAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNF +TGPAKELGDDFTVELIDLPDHGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSM +GGKVAMVLALRHPELVDRLIVEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAA +MAEHVHDARVRGFLLQNLRRTAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHP +VLWLAGAESDYVQDEDVPRMKELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>GCF_003691675_PROKKA_01287 +MN-----------------TT---AAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNF +TGPAKELGDDFTVELIDLPDHGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSM +GGKVAMVLALRHPDLVDRLIVEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAA +MAEHVHDARVRGFLLQNLRRTAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHP +VLWLAGAESDYVQDEDVPRMKELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>GCF_005280335_PROKKA_01346 +MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF +TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM +GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV +MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP +VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>GCF_020097155_PROKKA_01239 +M-------PTWSRASLSRVNT---TAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNF +TGVATALADDFTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSM +GGKVAMVLALRHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAA +MAEHVHDARVRGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRP +VLWLGGADSDYIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD +>GCF_023573625_PROKKA_01504 +MN-----------------TT---AASA-PSDAPLASTRIGEGPRRVAFLHGLMGRGRNF +TGPAKELGDDFTVELIDLPDHGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSM +GGKVAMVLALRHPELVDRLIVEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAA +MAEHVHDARVRGFLLQNLRRTAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHP +VLWLAGAESDYVQDEDVPRMKELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001291.fa new file mode 100644 index 0000000000000000000000000000000000000000..73c8c0e147481f8425fe80eb9839ecba31195892 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001291.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01578 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DAR---R +>GCF_003691675_PROKKA_01288 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DAR---R +>GCF_005280335_PROKKA_01345 +MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD +AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD +VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR +AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGA--PPPAAP +DDPGDLS +>GCF_020097155_PROKKA_01238 +MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP +DAS---R +>GCF_023573625_PROKKA_01505 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DAR---R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001292.fa new file mode 100644 index 0000000000000000000000000000000000000000..065164b55fc9b10b4e8ef51a075d9f586cc94647 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001292.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01579 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART +ALERMLAVAPK----QSAAQSAGAGT +>GCF_003691675_PROKKA_01289 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART +ALERMLAVAPK----QSAAQSAGAGT +>GCF_005280335_PROKKA_01344 +MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA +PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL +EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL +FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA +QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA +ALERMLAVAPR----QSVAQGAGA-- +>GCF_020097155_PROKKA_01237 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART +ALERMLAVAPKQSAAQSAAQSAGAGT +>GCF_023573625_PROKKA_01506 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART +ALERMLAVAPK----QSAAQSAGAGT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001294.fa new file mode 100644 index 0000000000000000000000000000000000000000..e892825b64309bb44141119a16b3055fdc8b3db9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001294.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01587 +MSRSHSDALDASGPDSGGAV-------AVPR---RRFGLLPRILVAIVAGVLVGLVAPTW +LVQAFATFNGLFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFG +ALLVCLLVFPLILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTML +PRGALHESFDQLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVF +GLTVVLLLLQYVVAGTIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRR +PIASFVVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMIAAPGVP +GGAIVAASGLLTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLI +EDSEDEGLERLDDEGAATGADAG +>GCF_003691675_PROKKA_01298 +MSRSHSDALDASGPDSGGAV-------AVPR---RRVGLLPRILVAIVAGVLVGLVAPTW +LVQAFATFNGLFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFG +ALLVCLLVFPLILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTML +PRGALHESFDQLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVF +GLTVVLLLLQYVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRR +PIASFVVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVP +GGAIVAASGLLTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLI +EDSEDEGLERLDDEGAATGADAG +>GCF_005280335_PROKKA_01335 +MSHASSGAAAPSDRAPQGAVS-----ESCRR---RRFGLLPRILVAIVAGVLVGLVAPTW +LVQAFATFNGLFSNVLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLFGGFG +ALLVCLLVFPLILTPGSFEAMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTML +RRGALHEGFDQLRSIIERVVMGLI------------------------------------ +------------------------------------------------------------ +------VPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVP +GGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLI +EDSEDEGLERLDDEEAATGADAG +>GCF_020097155_PROKKA_01233 +MSHAAPSSSVPPAPPSSSATDGTAAPEKAPRRGLRRLGLLPRVLLGIVLGVVVGLVSPEW +LTRTAVTGTSLFSAFLGFIVPVLIVALVAPAIAELGRGAGRWLSVTAAIAYGSTLFGGFL +SLGVALALFPRILTPGSISGVTDPSEGGATPFFEIAMDPPFGVMTALLLSFVLGIGMTLI +PRGVLQQGFEELRTIIERVVTGIVVPLLPFYIFGIFLAMAASGGVFEVIGTFLGVILIVF +ALTVVLLLVQYAVAGVIAHRNPLTALKAMMPAYATALGTSSSAATIPVTLRQVVSLGVRQ +PIAAFVVPLAATIHLAGSTVKIVAFSTAVIILTGGQVDVGLMVGFIFMLGITMVAAPGVP +GGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDGAIALIMDRIAGDRIA +ADP-----------GVAEESPAA +>GCF_023573625_PROKKA_01514 +MSRSHSDALDASGPDSGGAV-------AVPR---RRFGLLPRILVAIVAGVLVGLVAPTW +LVQAFATFNGLFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFG +ALLVCLLVFPLILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTML +PRGALHESFDQLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVF +GLTVVLLLLQYVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRR +PIASFVVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVP +GGAIVAASGLLTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLI +EDSEDEGLERLDDEGAATGADAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001296.fa new file mode 100644 index 0000000000000000000000000000000000000000..b095a67456f220bbd0f8412fbfad2e718ea655f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001296.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01591 +MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS +ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA +TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD +>GCF_003691675_PROKKA_01303 +MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS +ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA +TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD +>GCF_005280335_PROKKA_01300 +M-----ADLRVEPGPGAPRGLVIPAAELMERFSHASGPGGQGVNTADSRVQLSLDLATTT +ALDESQRARALAVLGPRLAGTVLTVAAEEHRAQRRNRVAARERLAAMLREALIPETPRRA +TRPTRGSRRRRLEAKRQRSETKQLRRRPGV- +>GCF_020097155_PROKKA_01219 +M-----DDLRVPPGPGVPRGLRIPAAELSERFSHGSGPGGQGVNTADSRVQLSLDLAATT +ALTDAQRIRLLEGLAPRLAGTVLTVDAAEHRAQRRNRTAARERLAALLREALVPETPRRA +TKPTRGSQRRRLQAKARRSEVKQSRRRPRMD +>GCF_023573625_PROKKA_01518 +MAEPRPGDVRVTPGPGAPRGLIIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS +ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQWRNRVAARERLAALLREALAPPTPRRA +TTPTRGSRRRRLEAKRRRSEVKRTRRRPGLD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001302.fa new file mode 100644 index 0000000000000000000000000000000000000000..1f428053bc39741bf9a8725544ede855285496ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001302.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01600 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAEGDASAE +TEASTPD-AGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR +>GCF_003691675_PROKKA_01312 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAESDASAE +TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR +>GCF_005280335_PROKKA_01293 +MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRIGLTYPQYLVMLTLWQVEGDASAE +TEAPTPG-AGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPADALTRIPLDATERQVLMCLLNRITEAVGPR +>GCF_020097155_PROKKA_01202 +MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRLGLTYPQYLVMLTLWQVEGDASAE +TDAPTPG-AGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRESARTVPADALTRIPLDATERQVLMGLLNRITEAAGPR +>GCF_023573625_PROKKA_01527 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQVESDASAE +TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001307.fa new file mode 100644 index 0000000000000000000000000000000000000000..4479eeb071b513ac0c113b36277e05130932536d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001307.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01612 +MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR +REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH +VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL +DDGIFPAPSGLTPAVPWPLF +>GCF_003691675_PROKKA_01323 +MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT +ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH +VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL +DDGRFPAPSGLTPAVPWPLF +>GCF_005280335_PROKKA_01286 +MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR +REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH +VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL +DDGVFPAPSGLTPAVPWPLF +>GCF_020097155_PROKKA_01191 +MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT +ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH +VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL +DDGIFPAPSGRTPAVPWPLF +>GCF_023573625_PROKKA_01538 +MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR +REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT +ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH +VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL +DDGTFPAPSGLTPAVPWPLF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001308.fa new file mode 100644 index 0000000000000000000000000000000000000000..848d5bd2d4184e34f061965b31416bcbb70f309b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001308.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01620 +M---ARRAAKAKPAKT---LEQTLWDAADKLRGNQEPSEYKHVVLGLVFLKYVSDRFEERREQLKDELAAEGIKPERIES +FLEDR--------DEYASQNVFWVPSLARW-------GYVQSVAKQPEIGQQIDQAMDLIEKENPSLRGVLPRNYGRDGL +DKRRLGELVDLIGSIGFTETDDHGADDVLGRVYEYFLGQFAGKETGKDAGAFYTPRSVVKTLVEMLE----------PFK +GRVYDPAVGSGGMFVQSAEFVKAHGGKRTDISVYGQEFTDTTWKLAKMNLALRGVEADMGSHSADSFTEDLHLDLRADYV +IANPPFNVSDWWDAKLADDP---------RWKYGTPPKGNANFAWVQHFLHHLAP----HGTAGFVLANGSLSSKSSGEG +--EIRQRLVEAGLVDCIVAMPDKLFFNTGIPVSLWFISKGRDGNGHRARKGEVLFIDARKLGAMQSRRL----RVLSDDD +IAQIADTYHEWRNHDGCYEDVPGFAKSATIGEIEKHEFVLTPGRYVGAAEAEVDDEPI-----DEKIERLTNELLAEFE- +-----RGRELENE----------------------VRLRMGSLS------------------------------------ +---------------------------------------------------------------- +>GCF_003691675_PROKKA_01648 +MTIPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPHREFFA-ELAAKGHPDFVLDN +LVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTY-YEFDKTVAKLDEHD---------------- +---RLFLVLQQFASIDLSP--ETVSNAEMGTLFEDLIRRFAAA-SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVR +-TVYDPTAGTGGMLSVLDERLR-RMNPNAEVRLFGQELNDQSYAICKSELLGKGQAAD-GIARGDTLKNDAHMTERFDYV +LSNPPYG-GDWKASRAAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSG +PSEIRRWLLESDLVDVIVALPTDMFYNTGIATYVWVL----DNNKPADRRGRAQLIDARTFFTKLRRNVGSKNKELSKAD +RQRVLDIY---RDFDAQSEANAEFSKVLTAQDFGYREITVERPLQL---RFEVEDATIAAALATKPADKLPDDGRSALEA +ALASLRGRVWDHQPTFVLDLKKALKEHGVTAGAPLVKALTGAIGVHDPKAEVVTNKKGEPEPDTSLRDTELVPFGRDIHE +YFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDADLKQLTAEIIELLQEVER +>GCF_005280335_PROKKA_00900 +MTTPATPGAASAARRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPHREFFA-ELAAKGHPDFVLDN +LVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTY-YEFDKTVAKLDEHD---------------- +---RLFLVLQQFASIDLSP--DTVSNAEMGTLFEDLIRRFAAA-SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVR +-TVYDPTAGTGGMLSLLDERLR-RMNPNAEVRLFGQELNDQSYAICKSELLGKGQDAD-GIARGDTLKNDVHLTERFDYV +LSNPPYG-GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSG +PSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVL----DNNKSAERRGRVQLIDARTFFTKLRRNVGSKNKELSKAD +RQRVLDIY---RDFDAQSEANAEFSKVLTAQDFGYREITVERPLQL---RFEVEDATIAAALATKPVDKLPDDGRSALET +ALASLRGRVWDHQPTFVLDLKKALKEHGVTAGAPLVKALTGAIGVHDPEAQIVTNKKGEPEPDTSLRDTELVPFGRDIHE +YFAAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLDEIDAELKQLTAEIIELLQEVER +>GCF_020097155_PROKKA_00838 +MP-------------SPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAQHREFFA-ELAAKGHPDFVLDN +LVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTY-YEFDKTVAKLDEHD---------------- +---RLFLVLQQFASIDLSP--ETVSNAEMGTLFEDLIRRFAAA-SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVR +-TVYDPTAGTGGMLSLLDERLR-RMNPNAEVRLFGQELNDQSYAICKSELLGKGQDAD-GIARGDTLKNDAHLTERFDYV +LSNPPYG-GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSG +PSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVL----DNNKSAERRGKVQLIDARTFFTKLRRNVGSKNKELSTAD +RQRVLDIY---RDFDAQSEANAEFSKVLTAQDFGYREITVERPLQL---RFEVEDATIAAALATKPADKLPVDGRSALGA +ALASLRGRVWDHQPTFVLDLKKALKEHGVTAGAPLVKALTGAIGVHDPKAEVVMNKKGEPEPDASLRDTELVPFGRDIHE +YFEAEVVPHVSGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIELLQEVER +>GCF_023573625_PROKKA_01879 +MTTPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMDPHREFFA-ELAEKGHPDFVLDN +LVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTY-YEFDKTVAKLDEHD---------------- +---RLFLVLQQFASIDLSP--DTVSNAEMGTLFEDLIRRFAAA-SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVR +-TVYDPTAGTGGMLSLLDERLR-RMNPNAEVRLFGQELNDQSYAICKSELLGKGQDAD-GIARGDTLKNDAHLTERFDYV +LSNPPYG-GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSG +PSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVL----DNNKPADRRGRVQLIDARSFFTKLRRNVGSKNKELSTAD +RQRVLDIY---RDFDAQSEDNAEFSKVLTAQDFGYREITVERPLQL---RFEVEDATIAAALATKPVDKLPDDGRSALES +ALASLRGRVWDHQPTFVLELKKALKKHGVTAGAPLAKALTGAIGVHDPDAEVVKDKKGEPEPDTSLRDTELVPFGRDIHE +YFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIELLQEVER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001309.fa new file mode 100644 index 0000000000000000000000000000000000000000..87ed8a8f2e579f95b0fa3980e48be63601069efb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001309.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01626 +MARPID-------PFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASI +DVDVEERTLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVL +TLTIPVAEQAKPRKISVTHGGAA-PVAGQTVEGE-TAET----------TGE-------- +-- +>GCF_003691675_PROKKA_01332 +MARPID-------PFREMERLMTGFA-RTSGAASMPMNLYREGDVFVAEVELPGVDPSSI +DVDVEERTLTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVL +LLTIPVAEQAKPRKIQVKHTGSAAQVEGEAVEGE-AVEGSAA-----EASGE-------- +-- +>GCF_005280335_PROKKA_01271 +MARPIDPFREMERPFREMERLVNGLT-RTSGTASMPMNLFREGDRFVAEVELPGVDPASI +DVDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVL +TLTIPVAEQAKPRKISVKHSGAG-AGAGQTVPGE-TAEVEER-----SAEQEAAQNGGAP +QA +>GCF_020097155_PROKKA_01181 +MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI +DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL +VLSIPVAEQAKPRKIQVKHSAAD-QVEGQEVAGQESVQDSAAVEAPQQPSGE-------- +-- +>GCF_023573625_PROKKA_01555 +MARPID-------PFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASI +DVDVEERTLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVL +TLTIPVAEQAKPRKISVTHGGTA-PVAGQTVEGE-TAET----------TGE-------- +-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001310.fa new file mode 100644 index 0000000000000000000000000000000000000000..8079ca708a54e098eaf331489c078fb5789ad1ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001310.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01628 +MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT +DDEG-DTGR +>GCF_003691675_PROKKA_01333 +MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG--- +--------- +>GCF_005280335_PROKKA_01268 +MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL +PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI +SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALD------AP +DETGAPAAS +>GCF_020097155_PROKKA_01176 +MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI +SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT----- +--------- +>GCF_023573625_PROKKA_01557 +MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT +DDEG-DTGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001312.fa new file mode 100644 index 0000000000000000000000000000000000000000..3f2666247e65f02d627722edec0a226e522bfbff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001312.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01630 +MEILSLLLALTLGLVLGALLGAWLMWRRAADGGEEARRAQAELAALRTEHQGAREALAAA +RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL +RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD +GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR +HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGSV +ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAG-VEEDELRRRRAESARE- +-------------------------------A +>GCF_003691675_PROKKA_01335 +MEILSLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA +RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVGVLERDRASQFGRLGEQL +RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGKD +GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAGQHAAAVRR +HVDQLSAKSYWAGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV +ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAG-VEEDELRRRRAESARE- +-------------------------------A +>GCF_005280335_PROKKA_01266 +MDILSLLLALALGLVVGALTGAWLMWRRAAGGGEEARRAEQELAALRVEHQGAREELAAA +RAEHRAVAAARAEDVERQRSEARVLSTLTPLGQQLTALQEQVGVLERDRAAQFGRLGEQL +RAAAATDRDLLNQTTSLMATLRSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQSTLSGRD +GERLRPDLLVSLPGGKSMAVDAKAPIGDALAAEALADEPGEEAWERRQALAAQHAAAVRR +HVDQLSAKAYWAGLEHSPELVLCFLPAESLLAAALDADGGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTTVDRYNQLVGNV +ESRVLPAARKLREADPGLAPTPDIRTLESAPRVLSAPELVEG-VEQDELRRRREDPAREE +AVREDPARE----------------------A +>GCF_020097155_PROKKA_01174 +MDFLTLVITLALGLLVGAAVGAWLMWRRMDGAADGS--AGAELDALRREHAAVREELAGA +RAESRALTQQRAEDAERARTDARVLETLAPLGRQLGALQEQVGVLERDRAAQFGRLGEQL +RTAAANDRDLLNQTASLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQTTMTGRD +GERLRPDLLVSLPGGKTLAVDAKAPIGDALAAGALAEEPGEEAAERRAALNARHAAAVRR +HVDALSAKAYWTGLERSPELVLCFLPAESLLAAALDADGALLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQERLAENAQLIVSGARELYDRLGTMGSHLDRMGGSLRAAVDGYNRLVGNV +ESRVLPAARTLREADPGLPALADVRSVDNAPRPLTAPELVDGDGPVDEGWTPAGSAAAED +RPEPAPAFEESPLWEDDEWTEDAAWDTDRRTA +>GCF_023573625_PROKKA_01559 +MEILNLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA +RAEQRALTAARAEDAERRRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL +RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD +GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR +HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKELYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV +ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAG-VEEDELRRRRAESARE- +-------------------------------A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001313.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001313.fa new file mode 100644 index 0000000000000000000000000000000000000000..db6148ea011870d5009a885e97119f8770fd0327 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001313.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01631 +MESRPLPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLPGGENVKRIIGLVVGPLLAVALFLLMPGDLGVWPRLVAA +TAVLMAVWWMTEALPIPATALLPLVVFPLGVPAEESDGGITFDAVGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGV +LKFMGARTVNLILGFMIATGFISMWVSNTATAVMMLPIGVSILVLVQRYGTDGALTADEGADQVDRPAAPASAAGEAPTQ +AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVQIGFGQWMLVGVPIAVVLLFACWFLLTRVL +FRPEIDEVPGGRDLIATELARLGRMSAPEAKVLAVFVLAALAWITVPLISEY--VLDLESPL--LSDAAIAIVVGLILFL +LPA--GGGAGRGVRLLDWEAAKDLPWGVLLLFGGGLALSGQFSKSGLSTWLGEQVKGFGDIPVWVLVVIASVGILLLTEM +TSNTATAATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKGGVWLNIIAAVLISI +ASMTLLVWVFGL +>GCF_003691675_PROKKA_01336 +MESRSIPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLTGGENVKRIIGLVAGPLLAVALFLLMPGDLGVWPRLVAA +TAVLMAVWWMTEALPIPATALLPLVIFPLGVPAEESDGGITFDSIGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGV +LKFMGARTVNLVLGFMIATGFISMWVSNTATAVMMLPIGVSILVLVQRYGTDDALTGDEAAGQVDRPAAPASAPGEAPTQ +AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVEIGFGQWMLVGVPIAVVLLFACWFLLTRVL +FRPEIDEVPGGRDLIATELARLGRMSAPEAKVLAVFVLAALAWITVPLISEY--VLDLKSPL--LSDAAIAMVVGLILFL +LPA--GGGAGRGVRLLDWEAAKELPWGVLLLFGGGLALSGQFSKSGLSTWLGEQVKGFGDIPVWVLVVIAAVGILLLTEM +TSNTATAATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKGGVWLNIIAAVLISL +ASMTLLVWVFGL +>GCF_005280335_PROKKA_00143 +------------------------------------------------------------------MSSSLAFEGRAVAG +AAVWMAVWWMTEAVPIPVTSLLPIVRFPLF-------GMGTMAEVASPYANSVVFLVMGGVILGLATEK----------- +-------------------------------------------------------------------------------- +-----------------------------------------AYLLENHDDDMQFGRWMLVGVPWAIVMLLIAWVVLTKLV +FRAEVDRIPGGAEMIRGELAKLGPMTTPERRIALIFATAIFFWVAVPFIADIPAVADVAPWLGTIDDTQVAIAAAIACFI +VPARRRGEDASQTALLQWSASKEIPWGLLLLFG---------------------------------VVVG----LALTEL +TSNTATEAAFFPIFGAVALGLGMDPIFMTIAVTLAVCSAYMLPVATPSNAVAFGSGEVSIKQMVRAGVGLNVVSIGLIML +VMYTLVPAVFG- +>GCF_005280335_PROKKA_01265 +MASRPVPPPSNVNEHVSRFAPQAAAQEFEHETSPGMRDQPLTGGEHTKRIIGLVAGPLLAIGLFLLMPGDLGVWPRLVAA +TAVLMAVWWMTEALPIPATALLPLVVFPLGVPAAESDGGVTFDSIGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGV +LKLMGAKTVNLVLGFMIATGFISMWVSNTATAVMMLPIGVSILVLVQRYGTEDALAADA------VPAAEQSAPGEAPTQ +AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMATEHGIEIGFGQWMLVGVPIAVVLLLACWLLLTRVM +FRPEIDEVPGGRDLIAAELARLGRMSAPEAKVLVIFVLAALAWITVPLLSEY--VLGLDSPL--LSDAAIAMVVGLVLFL +LPA--GGGAGRGVRLLDWEAAKELPWGVLLLFGGGLALSGQFSKSGLSTWLGEQVRSLGEIPVWVLVVIAAIGILLLTEM +TSNTATAATFLPVASGVALGTGVEPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKGGVWLNITAAVLISV +ASMTLLVWVFGL +>GCF_023573625_PROKKA_01560 +MESRPLPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLPGGENVKRIIGLVVGPLLAVALFLLMPGDLGVWPRLVAA +TAVLMAVWWMTEALPIPATALLPLVVFPLGVPAEESDGGITFDAVGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGV +LKFMGARTVNLILGFMIATGFISMWVSNTATAVMMLPIGVSILVLVQRYGTDGALTADEGADQVDRPAAPASAAGEAPTQ +AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVEIGFGQWMLVGVPIAVVLLFACWFLLTRVL +FRPEIDVVPGGRDLIATELARLGRMSAPEAKVLAVFILAALAWITVPLISEY--VLDLTSPL--LSDAAIAMVVGLILFL +LPA--GGGAGRGVRLLDWEAAKELPWGVLLLFGGGLALSGQFSKSGLSTWLGEQVKGLGDIPVWVLVVIAAVGILLLTEM +TSNTATAATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKGGVWLNIIAAVLISL +ASMTLLVWVFGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001320.fa new file mode 100644 index 0000000000000000000000000000000000000000..e799059d8e0fde80e147bf64e2b330ce7c4fc8cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001320.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01639 +MSRPAHRRPT-----ALAASALALSLALGAC-ARQADAPPTPSASGTPITVVHGGEGLEG +AVAAVLARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPP +--PPTSTPSSTPTGTEAG--PSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLE +TLLAEETA-------------AAGTPQ-DEAPAVLSSSAGVLRLTAVVTQTTAARLELES +ITDLNGWCESLTAVAPPPLTAAADPDAATALRARLDRLAGCRPETWLADTEDPSAALVAD +EAQVALLTDTDPEIDANTLVPLEDDGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDG +DGLRELERLTTGADPLPAAEAAQYWLVDHGLEDAPEDWFVPRGSWF +>GCF_003691675_PROKKA_01344 +MSRPAHRRPT-----ALAASALALSLALGAC-ARQADAPPTPSASGAPITVVHGGEGLEA +AVAAVLARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPP +--TPTPTP--TPTGTEAG--TSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLE +TLLAGQTA-------------AAGTPQ-DEAPAALSSSAGVLRLTAVVTQTTAARLELES +ITDLNGRCESLTAVAPPALTSA--ADAATALRARLDRLAGCRPETWLADTEDPTAAVVAD +EAQVALLTGTDPEIDANTLIPLEDDGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDG +DGLRELERLTTGADPLPVAEAAQYWLVDQGLEDAPEDWFVPRGSWF +>GCF_005280335_PROKKA_01256 +------------------------------------------------------------ +------------------------------------------------------------ +----------MPTASESS-----------DAADASATPEPTPLPDGEPAADAAEAGRVVE +RLLQGDAE-------------AGASPEPGDAVAVLGSSAGVLRLSAVVTATTAARLELDA +LEDLNGRCEGLTAALPAGLAG--DPQANAALHARLDRLAGCRPGTWREEDASAAAVVVAD +QAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAAVGAPDALDDDAQRRIEEVLSALDE +DGLRELERITTGADALPPAEAARYWLVDQGLEDVPEGWFMPRDSWF +>GCF_020097155_PROKKA_01165 +MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADP--TGAPVTVVHTSDPLDS +AVAAVVARHLRHRGHPVTLED--AGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEP +EDAAASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVD +AALSRVAAGADAAAPTPAASRSAATPT-GPSPRVLADSAGTLRLAAVVTATTASREGLDS +IDDLDGRCGDLTLAVPAALAA---AVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVAD +AAQVGLTYRTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDD +DGIAELARLTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF +>GCF_023573625_PROKKA_01568 +MSRPAHRRPT-----ALAASALALSLALGAC-ARQADAPPTPSASGTPITVVHGGEGLEG +AVAAVLARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPP +--SPTSTPSSTPTGTEAG--TSADAVP----TASTAAPSPTALPVGDPAADAPAAGRVLE +TLLAEETA-------------AAGTPQ-AEAPAVLSSSAGVLRLTAVVTQTTAARLELES +ITDLNGRCESLTAVAPPTLTAAADADAATALRTRLDRLAGCRPETWLADTEDPTAAVVAD +EAQVALLTGTDPEIDANTLVLLEDDGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDG +DGLRELERLTTGDDPLPVAEAAQYWLVDHGLEDAPEDWFVPRGSWF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001321.fa new file mode 100644 index 0000000000000000000000000000000000000000..9eaa18309e3859d7164a77748841f0ec35cee55b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001321.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01640 +MSTTPAAPDAAGAH---PAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIEL +GESPEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGG +VLRPEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT-------- +>GCF_003691675_PROKKA_01345 +MSTTPAAPDAAGAH---PAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIEL +GESPEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGG +VLRPEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT-------- +>GCF_005280335_PROKKA_01255 +MSPTP-VPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIEL +GESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGG +VLRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA-------- +>GCF_020097155_PROKKA_01164 +M--SAASPTAASTA---P-GPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIEL +GESPEEACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGG +VLRPEADGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR +>GCF_023573625_PROKKA_01569 +MSTTPAAPDAAGAH---PAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIEL +GESPEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGG +VLRPEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT-------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001324.fa new file mode 100644 index 0000000000000000000000000000000000000000..f426d478d8ed54425da593347530fe0422196974 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001324.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01643 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARAA-RGRTGLHIRWGRTALFLAALVALLVFLV +AGLAAAFGAGTLALAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPAAPAAEER +QAPPA--DPERDRRVLETVLAFETEAPR-PAAAPAAPRVEPVVVTASAA-APAADRVVTI +PAVPRPTYLDAPEMARPLPAPLETPAPTGA-DTRLTDAARTADDQ--ISAAAEQDIAA-- +LDLDNVLARRRAC +>GCF_003691675_PROKKA_01348 +MDETTPPTTAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLGAAADAARAA-RGQTGLHIRWGRTALFLAALAALFVFLV +AGLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAADVVPARPAAPAAEER +QAPPA--DPERDRRVLETVLAFETEAPR-PAAAPAASRVEPVVVTASAA-APAADRAVTI +PAVPRPTYLDAPEMARPLPAPLETPAPTGA-DTRLQDAASTADDR--ISAAAEQDIAA-- +LDLDNVLARRRAC +>GCF_005280335_PROKKA_01250 +MEDTTAPASAGRAALDALADARVSASFVILALVAYFAWRLVVRRRRVESAPARPTMLRST +MHRLQSSPAVRALTERLSGRVSGLADSARAAGRRTAGLQVRWGRTALFLAALAALAVALV +AGVAAAFGAGTAGLAGACLLFAVAAVAGLRALAVRDRARRAPAAVVEAPA-EAAPHAAP- +EAPRV--DPERDRRVFETVLGLEDEAARVSAAAPAAPAAAPTVVAASAVRAPEATDTVTL +PVVPRPTYLDAPEMLRPAPAPLTAPEAAGS-DVRLKDAARAAEHEEALSATAEQDVAA-- +LDLDHVLARRRAS +>GCF_020097155_PROKKA_01161 +------------------------------------------------------------ +------------MTETPSPREDARLDA--EPGHADSGFHVHWDRASLFLVGVGALAVALV +TALCALAGLPTAGLAGWSLLVTVGAVVGLRVLAARDQREHHDDLADDADEPNLAEEDLDT +HELPVVPDPERDRRVLAAALSLTDEAEDEEPAAEPVPVVVDALQRRRAPRIPLG--GIVI +PEVPRPTYLDAPE-APAAEAQAEYPAEDDAVATRPEAEEQAASAE--VVEIPEPAARAVV +LDLDGVLARRRAS +>GCF_023573625_PROKKA_01573 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARTA-RGRTGLHIRWGRTALFLAALVALLVFLV +AGLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPTAPAAEER +QAPPA--DPERDRRVLETVLAFETEAPR-PAAAPAAPRVEPVVVTASAA-APAADRAVTI +PTVPRPTYLDAPEMARPLPAPLETPAPTGA-DTRLTDAARTADDQ--ISAAAEQDIAA-- +LDLDNVLARRRAC + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001325.fa new file mode 100644 index 0000000000000000000000000000000000000000..b44f3bdba8e351bea8dc0f7171e4a50fbb2c6ce7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001325.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01644 +MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ +MVRWHGRQGRDGSAYTWGMAL-DDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA +GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA +WRDHRTFAVTAEEVPDGLLAGWLATRPRP------------------------- +>GCF_003691675_PROKKA_01349 +MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ +MVRWHGRQGRDGSAYTWGMVLDDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA +GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA +WRDHRTFAVTAEEVPDGLLARWLASRPRA------------------------- +>GCF_005280335_PROKKA_01249 +MSWQRSPWPVTLRHGTLSLRPLRRRDRDAWEAQRAHNHAWLTPWDATSPVPGAGPSSFGQ +MVRWHGRQGREGSSFTWGVAL-DDDAPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA +GRGLTPTAVAMAADWAFRSAGLHRVEVNIRPENAASLRVVEKLGLRDEGVRRSYLHVDGD +WRDHRTFAITAEEVPEGLLARWLASRPRA------------------------- +>GCF_020097155_PROKKA_01160 +MDVSGSLWPVALRHGTLTLRPLRRGDRRAWEEQRAANRDWLTPWDATSPVPGAAPASFAQ +MVRWQHRQARAGTSYTWGMAL-DDDAPGRDRLIGLLSLGGVQHGSVMSGAVGYWIDRRQA +GRGLTPTAVAMATDWAFHGLGLHRVEVNIRPENTASLRVAEKLGLREEGLRRAYLHVDGA +WRDHLSFAVTAEEVPEGLLPRWLARREAAAGTAEPRDTAHTPGVAGDVPGPSGR +>GCF_023573625_PROKKA_01574 +MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGVGPASFGQ +MVRWHGRQGRDGSAYTWGMVL-DDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA +GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA +WRDHRTFAVTAEEVPDGLLARWLATRPRP------------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001328.fa new file mode 100644 index 0000000000000000000000000000000000000000..9fe40c041c0cc2a08359773aea132b404a3554a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001328.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01647 +M------PADGAPRRRGPRRADAPGTGPASADGREPRLPGMPRLIGQAGTSPATAPTG-- +----------------DVAGVESGPAEAERDRWLREQRPPHWG +>GCF_003691675_PROKKA_01352 +M------SADGAPRRRGPRRADAPGTGPAAADGREPRLPGMPRLAGQAGTSPVTAPTG-- +----------------DVAGVESGAAEAERDRWLREQRPPHWG +>GCF_005280335_PROKKA_01246 +MGAE---VPDPAPRRRGPRRADAPGTGPASADAPEPRLPGVG-----AGTDGARGAEGVR +GAGGVRGAV----GVRGAAG---EPTADERDRWLLEQRPPHWG +>GCF_020097155_PROKKA_01157 +MRTTPTASPEPG-RRRGHRRADAAGTGPASADGPEPTLP-EPTLPG----PALPGAQTAG +DATPSRPAVSRGRAVTSAAGADRPQPADELGRWLLEQRPPHWG +>GCF_023573625_PROKKA_01577 +M------SADGAPRRRGPRRADAPGIGPAAADGREPRLPGMPRL---AGTSPATAPTG-- +----------------DAAGVESGPAEAERDRWLREQRPPHWG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001330.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5c1a51e3d2d048e61e24ae9bf50f0a1e3218718 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001330.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01649 +MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILERKPAALILSGGPSSVYEPGAP +QLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYGSTRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAV +TASTAGAPVAAFEDRERRIYGVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTVSNVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFLSALAGVTDPEAKRKIIGERF +IRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESGGGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAV +GAELGLPEGIVHRQPFPGPGLGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>GCF_003691675_PROKKA_01354 +MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILERKPAALILSGGPSSVYEPGAP +QLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYGSTRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAV +TASTAGAPVAAFEDRERRIFGVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFLSALAGVTDPEAKRKIIGERF +IRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESGGGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAV +GAELGLPEGIVHRQPFPGPGLGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVISEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>GCF_005280335_PROKKA_01244 +MTENAPHSDAPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILERRPAALILSGGPSSVYEPGAP +TLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYGSTRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAV +TASTAGAPVAAFEDAERRIYGVQWHPEVGHSSHGQQVLEHFLHQGAGLGSDWTASNVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESAEIEQAFGEAHGGARLVMVDAREDFLSALAGVTDPEAKRKIIGERF +IRTFEKAQADIVLESEHDPEATEVRFLVQGTLYPDVVESGGGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAV +GAELGLPEGIVHRQPFPGPGLGIRIIGEVTQERLDLLRSADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPIVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>GCF_020097155_PROKKA_01155 +MTQNEPTRDQPAPLHDVLPTVLVMDFGAQYAQLIARRVREANVYSEVVPSSTPAQEILDRRPAALILSGGPSSVYEAGAP +QLDPALLEAGVPVLGLCYGFQSIAHALGGTVARTGTREYGSTRLESADGGSVLLAGQDAAQVVWMSHGDAVTEAPEGFAV +TAVTAGAPVAAFEDRERRIFGVQWHPEVGHSERGQEILANFLTEGAGLSQDWTAENVIEEQVARIREQIGDARAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESDEIERAFGEAHGGAKLVMVDAREDFLAALAGVTDPEAKRKIIGERF +IRTFEKAQADIVLESAHDPNAPEVRFLVQGTLYPDVVESGGGDGTANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAV +GAELGLPEGIVHRQPFPGPGLGIRIIGEVTQERLDLLRQADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPSEVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE +>GCF_023573625_PROKKA_01579 +MTQNAPHPDTPTPLSDVMPTVLVLDYGAQYAQLIARRVREANVYSEVVPASTPAAQILEREPAALILSGGPSSVYEPGAP +QLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYGSTRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAV +TASTAGAPVAAFEDRERRIYGVQWHPEVGHSSRGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFLSALAGVTDPEAKRKIIGERF +IRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESGGGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAV +GAELGLPEGIVHRQPFPGPGLGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001334.fa new file mode 100644 index 0000000000000000000000000000000000000000..9df55dcb0a5c537d7a42a786c1b884263b362002 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001334.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01653 +MARTRVAGLTPGHRIAETPVPKGVFVTTTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPNATDVIPADADPGTRLTRNIR +LNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVS +GLPVVAEDMTLLGIITNRDTRFIPREEWATRTVDTAMTRMPLVTAQEGVSRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIG +GQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGA +DSVMLGSLLAGTAESPGDLVFYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA +SVVHQLVGGLRQTMFYTGASTVTDLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>GCF_003691675_PROKKA_01358 +MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPNATDVIPADADTGTRLTRNIR +LNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVS +GLPVVAEDMTLLGIITNRDTRFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIG +GQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGA +DSVMLGSLLAGTAESPGDLVFYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA +SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>GCF_005280335_PROKKA_01240 +MARTRVAGLTPGHRIAETPVPKGAFVTTTSTGPSSEPVHSSADPFGFFGLTYDDVLLLPSATDVIPAEADTSTQLTRNIR +LNIPVVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQARHVDTVKRSESGMIKDPVTIGPKATLADLDELCAQYRVS +GLPVVAEDMTLLGIITNRDTRFIPHEEWETRTVDTAMTRMPLITAREGISREETIRLFSQNRVEKLPLVDEAGRLTGLIT +IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIG +GQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGA +ESVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGKRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA +SVVHQLVGGLRQTMFYTGASTVDELKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>GCF_020097155_PROKKA_01151 +--------------------------MSTSTGPSSDPVYASEDPFGFFGLTYDDVLLLPNATDVIPADADTSTQLTRNIR +LNIPVVSAAMDTVTEAPLAIAIARQGGMGIIHRNLSIEDQAKHVDTVKRSESGMISDPVTIGPKATLAELDELCAQYRVS +GLPVVAEDMTLLGIITNRDTRFIPHEEWDTRTVDTAMTRMPLITAQDGISREEVLHLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMTLVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIG +GQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGA +DSVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPYRGPIA +SVVHQLVGGLRQTMFYTGAPTIVDLKENGRFVRITTAGLKESHPHDIMMTVEAPNYRSK +>GCF_023573625_PROKKA_01583 +MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPNATDVIPADADTGTRLTRNIR +LNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVS +GLPVVAEDMTLLGIITNRDTRFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIG +GQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGA +DSVMLGSLLAGTAESPGDLVFYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA +SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001339.fa new file mode 100644 index 0000000000000000000000000000000000000000..b748a9e67928f00058cfff904e97fe7c094c544e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001339.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01661 +MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>GCF_003691675_PROKKA_01366 +MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>GCF_005280335_PROKKA_01233 +M-TDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGL +GKDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNL +PWVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG +>GCF_020097155_PROKKA_01144 +MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>GCF_023573625_PROKKA_01591 +MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001340.fa new file mode 100644 index 0000000000000000000000000000000000000000..06975bb4521ddafd8c0b0446f039293c99b5f952 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001340.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01662 +MPRSVSAPRLA-RLALTSVAALALVGCSAGGAATGSS----------SASASGESSASAS +AAGGSSAASG-GIAAGVTVTDMSGAEVTLPEEVDSVIATDNRAFRTLDDWGVELSAAPKQ +IMYKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAA +VVDTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMG +LIASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIV +MDRDAAIGEENATAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAK +AFEGAQ +>GCF_003691675_PROKKA_01367 +MPSSARAPRLA-RLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGESSASAS +AAGGSSAASG-GIATGVTVTDMSGAEVTLPEEVDSVIATDNRTFRTLDDWGVELSAAPKQ +IMYKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAA +VVDTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMG +LIASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIV +MDRDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPTDFYVAEDIQNHTTVMEDLAK +AFEGAQ +>GCF_005280335_PROKKA_01232 +MQRSPRTPRLK-ALALASVAALALVGCSAGGAAEGPA-------------SGSADTGSAA +GSGSASAPAGDGVAAGATVTDMSGAEITLPEEIDSVITTDNRTFRTLDEWGVELSAAPKQ +LMFKGEGGPGYLQDDEVADIGNHREPDMEVFVTAEPDVVFNGQRFNERKAEIDELTGDAA +VIDTDFDPKQKPMDEGLKELTTLLGEATGHQDDAAALNKEFDDAVAKAKGAYDSEQTVMG +LISTGGELSYVAPGTGRSIGPMFDILGLTPALEQAGSDNHQGDDISVEAIAQSNPDWLIV +MDRDAATGEANATAAELIERSEALKDVTAVKEGNIVYLPQDFYVAEDIQNYTTVMDDLAK +AFEGAR +>GCF_020097155_PROKKA_01143 +M----RTARLSTAAALASLAALTLAGCGAGGPAAEGS----------SPASSAASSSPAS +SAASSSATAG-GVAAGVTVTDMSGTEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQ +IMYKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAA +VVDTNFDVTQTPMDEGLKKLTTLLGEATGHEADAEKLIADFDAATQLAKDAYDPEQTVMG +LIASGGELSYAAPSTGRSIGPFFDMLDLTPALDQSGTDNHQGDDISVEAIAKSNPDWLIV +MDRDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPADFYVSEDIQNHTTVMEDLAK +AFEGAQ +>GCF_023573625_PROKKA_01592 +MPRSARAPRLA-RLALTSVAALALVGCSAGGAATGSS----------SASASGESSASAS +ASGGSSAASG-GIATGVTVTDMSGAEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQ +IMYKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAA +VVDTNFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMG +LIASGGELSYVAPSTGRAVGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIV +MDRDAAIGEENATAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAK +AFEGAQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001341.fa new file mode 100644 index 0000000000000000000000000000000000000000..9417f54bce6728e50a5efca7c45ce33f8cfbb4a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001341.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01663 +MA-----------RPRPAARPSRPSAAASEEDDTALAPVLESEGRALLDSLAGYREADAL +AVSSRLRAAGHPPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHA +DRLAAAGARRVADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAG---HRGARV +VHGDAVAWARAHVPAEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPV +GVKLGPGLPHEAVPAGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVHGGKTTTA +QLVSGADFGDSPEVEAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAVSWPVPTRQLDPH +LAYLVAPEPVHDGLARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRA +VLGGAKPGRRGGAGRHATLVLARVGRSRFALEVTPL--D +>GCF_003691675_PROKKA_01368 +MA-----------RPRPASRSPRPTAAASEADDTALAPVLEPEGRALLDSLAGYREADAL +AVSSRLRAAGHPPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHA +DRLAAAGARRVADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAG---HRGARV +VHGDAVAWARAHVPAEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPV +GVKLGPGLPHEAVPEGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTA +QLVSGADFGDSPEVEAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPH +LAYLVAPEPVRDGLARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRA +VLGGAKPGRRGGAGRHATLVLARVGRSRFALEVTPL--D +>GCF_005280335_PROKKA_01231 +------------------------------------------------------------ +------------------MLTQADLRARAVPRLGPDARGMLFTRDGLEQATRPVVAALHA +QRMAAAGARTVADLGCGLGLDARAFADAGLGVVAVERDAVVAAAAEVNLTD---RPGARV +VHGDAVPWAREHVPAQADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVEELAATGVPV +GVKLGPGLPHEAVPAGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVIDTRGGQATTA +ELVSGADFGDSPGVEAVGEEGMPGLVG-----------RCSTSRTAPSSGPGSSRTWR-- +-------SPGRRRPASWTRTWPIWWPPSTRPTRWPGRTGSTRSTISTSSL---------- +CAGGRR--RRGSAAW-----------------------T +>GCF_020097155_PROKKA_01142 +MARSQRPARPSRPRPRPADRPGRPRAAESAADATRLEPVLDPAGRVLLDGLGDVSGQDPL +ALSSRLRAAGHDADTVAAALTQAGLRHAGRAKLGALADGMLLTRDGLEQATRAVVAEHRA +RRLQEAGVRSLADLGCGIGADALVYARAGLDVTAVERDPTVAAAAAANLATLAPAGAASV +VTGDAEAWAAAHAD-EVDALWLDPARRRLGSSGTARVFDPEAFSPPLSFVLGLADGGRPV +GVKLGPGLPHEHVPAAAEAEWVSVDGDVVEVTLWFGPLAQAPGRRTATLLDTRG--SAVH +RLVPAA--ASSPAVEAVGEEGVDGLVGQVLLEPDGAVIRAGLVTDLAVELGPAVRLLDPH +LAYLVAPDAAPHPLARGYRVLAVHEFRTKALARWARETGVGRLDVKKRGVRETPEQVRAA +VLGRGTPG-----GRHATLVLARVGERRVAFEVEPLPAG +>GCF_023573625_PROKKA_01593 +MA-----------RPRPASRSPRPTAAASEADATALTPVLEPEGRALLDSLAWYREADAL +AVSSRLRAAGHPPERVAAALTQAALRSRAEARLGRQARRMLFTRDGLEQATRPLVAGLHA +DRLAAAGARCVADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAG---HRGARV +VHGDAVAWARAHVPAEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPV +GVKLGPGLPHEAVPAGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTA +QLVSGADFGDSPEVEAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPH +LAYLVAPEPVHDGLARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRA +VLGGAKPGRRGGAGRHATLVLARVGRSRFALEVTPL--D + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001342.fa new file mode 100644 index 0000000000000000000000000000000000000000..26e7144db28b57ea820003d8bde45d7a33902e0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001342.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01664 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG +>GCF_003691675_PROKKA_01369 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG +>GCF_005280335_PROKKA_01230 +MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL +QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER +YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD +TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT +VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD +ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA +LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG +>GCF_020097155_PROKKA_01141 +MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL +QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR +YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD +TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT +VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE +ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA +AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG +>GCF_023573625_PROKKA_01594 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001343.fa new file mode 100644 index 0000000000000000000000000000000000000000..12cf3b4a52d25f33df15daa916c419fb64c6c21a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001343.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01665 +MRALTWQGKRNVVVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGCGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLD-ADG---GEAEVL +RERTGGRGPDAVLDAVGMEAHASPVGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAI +DAVRRGGTVSISGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLG +VLDLTTHTAPLEDAPALYETFQKKEDGCVKVVLKP +>GCF_003691675_PROKKA_01370 +MRALTWQGKRNVAVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLD-ADG---GEAEVL +RERTGGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAI +DAVRRGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLG +VLDLATHTAPLEDAPALYETFQKKEDGCIKVVLKP +>GCF_005280335_PROKKA_01229 +MRALTWQGKRNVAVEDVPDPRIQEPTDAIVEITSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGAEVTHIKPGDRVVVPFNIACGRCWMCERGLQSQCETTQVREQGSGAALLG +YSRLYGSVPGGQAEYLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYAQVPRGG +TLAVIGLGPIGQLAARIGVHQGLRVIGVDPVPERRAMAARHGVEVLDSSDG---GVAELL +RECTQGRGPDGVVDAVGMEAHGSPVAKAAHTVVGLLPDALGRAAMKTAGVDRLDALHTAI +DAVRRGGTVSLSGVYGGMQSPMPLLTMFDKQVTLAMGQCNVRRWVDDLLPLLDDPSDPLG +VLDLTTHTAPLEDAPALYETFQKKEDGCIKVVLKP +>GCF_020097155_PROKKA_01140 +MRALTWQGKRSVSVEDVPDPRIQEPTDAIIKVTSTGICGSDLHLYEVLGPFMDKGDVIGH +EPMGIVEEVGSAVTNLSPGDRVVIPFNISCGHCWMCQHGLQSQCETTQVKEQGSGAALLG +YSRLYGSVPGGQAEYLRVPHADYGPIKVPHTGPDTQWLFLSDVVPTAWQAVQYANVSKGD +TLAVLGLGPIGQMSARIGVHLGCRVIAVDPVPERRHMAARHGVEVLD-MEGSGTGVPDLL +RQATGGRGPDGVVDAVGMEAHGAPVAAAAQTAAGMLPGPLARAAVKTSGIDRLTALHTAI +ESVRRGGTVSLSGVYGGMQDPMPLLTMFDKQIQFTMGQCNVRRWVDDLLPLMDDPSDPLG +VLDLVTHTAPLEDAPAMYEKFQKKQDGCIKVVLTP +>GCF_023573625_PROKKA_01595 +MRALTWQGKRNVTVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLD-ADG---GEAEVL +RERTSGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAI +DAVRRGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLG +VLDLTTHTAPLEDAPALYETFQKKEDGCIKVVLKP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001345.fa new file mode 100644 index 0000000000000000000000000000000000000000..150877d6d8d611d71fce1c4cb1930b6c6f10df24 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001345.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01667 +MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV +SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA +SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR +>GCF_003691675_PROKKA_01372 +M---TITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDA +SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA +SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR +>GCF_005280335_PROKKA_01227 +M---TITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDA +SGAEPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHA +SLTRDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR +>GCF_020097155_PROKKA_01138 +M---QTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDA +AGAEPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDA +GLTRPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA +>GCF_023573625_PROKKA_01597 +M---TITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDA +SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA +SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001346.fa new file mode 100644 index 0000000000000000000000000000000000000000..061cc1f972dbbeda2f3bfac70a74f74cd44fef1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001346.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01668 +MTRR-DTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAFVMGSSQA +MRAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV +GDSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRV +LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAILVGVSIVLDGWKNLKEAVTNLA +DRRAATIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVA +RCCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQT-GEE +>GCF_003691675_PROKKA_01373 +MTRQ-DTRETGPSGRRFGATELPPEIERVVQQAKRLEWVTLGVIVVTIVLVAIVMGSSQA +MRAAWIEDLLSLIPPIAFLIALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV +GDSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLTLAEQLHDRV +LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLA +DRRATTIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVA +RCCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQT-GEE +>GCF_005280335_PROKKA_01226 +MTHHASTTHRSPGGRRFGATELPPEIERALRRAVRLEWATLAVLAVTIALVAVVMGSSQA +MRAAWIEDLLSLVPPIAFLVAVRVTRRHPTRARPYGSHRSVGVGHLVAAVALSVMGVILV +ADSALGLVTGEHPPIGTLDLFGHTVWQGWFMMAVMALSIPGPVLLGRAKLKLAEQLHDRV +LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWRNLREAVGNLA +DRRATTIDGDRPHPLIDRAERVAWAQPWVRHAGTRVRDEGHVLHVEMFVVPHEGAGATVG +RCAQLREEIVALDWKLEDVVVVPVAELPAEVHGGASGDEQS-GEE +>GCF_020097155_PROKKA_01137 +MSEK----------RTIGRAELPDDVARAAHQAVVLEWVSLGWLVLTVSLVAVVMGSSQA +MRAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV +GDSLLGLLTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRV +LYADADMNKADWQTGVATIVGVAGIGLGWWWADAAAAIFVGVSIVLDGWKNLKEAVTNLA +DRRATTIDGARPHPIIDRAERVAWAQPWVRHAGARVRDEGHVFHLEMFVVPRHGADVTVG +RCADLRERIEELDWKLEDVVVVPVAELPEEVHGGRSGDEQSKGSE +>GCF_023573625_PROKKA_01598 +MTRR-DTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAIVMGSSQA +MRAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV +GDSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRV +LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLA +DRRAATIDGARPHPLIDRVERVAWAEPWVRQAGARVRDEGHVFHVEMFVVPHEGADVTVG +RCCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQT-GEE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001349.fa new file mode 100644 index 0000000000000000000000000000000000000000..47eb0a8bd45d8c234e7a6bbb7faa19814d79d6f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001349.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01672 +MALLLAIDSSAAASVAVLRDGEELARWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWESATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRA---GA +>GCF_003691675_PROKKA_01377 +MALLLAIDSSAAASVAVLRDGEELAHWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHAAGVDAFRHGIEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRA---GA +>GCF_005280335_PROKKA_01206 +MALLLALDSSAAASVAVLRDGEALARWATEDTHAHAEVLAPAVRAVLAEAGVAGAGLDAV +AVGVGPGPFTGLRAGLATAAALGLAWDVPVRGVRSLDALAHDAAVDAFRHGAEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPAYGAGAGLYPEALRAVPGWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRA---GA +>GCF_020097155_PROKKA_01134 +MPLLLALDSSSAASVALLRDGEPLAAWSTADTTSHAEVLAPAVRQVLAEAGVAGGDLDGI +AAGVGPGPFTGLRAGLATAEALGFAWDVPVHGIRSLDALAHRAGTDAFAHAVEEFVVVTD +ARRREVYWAHYAQVGGQPTLLHGPFVTPAAEVTPLPAYGAGAGLYPEALHAVDGWEGAVP +DAVSLGRVDELALRRGRGVLPPTPLYLRESDATVPAPRTPARPAGA +>GCF_023573625_PROKKA_01602 +MALLIAIDSSAAASVAVLQDGEELARWATDDTHAHAEVLAPAVQAVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVIATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRA---GA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001352.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b111e86f1024c2a6b676e3a5b1ce08c1da34215 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001352.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01675 +MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGTTVAALVGPGNNGGDALFALAFLR +RRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAVPPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDV +PSGVDADTGEVRGEALRAAATVTFGALKSGLVLGEGAGRAGTVHVADIGLGPHLPTSPAARLGVMDEAAARAAHPAPAAA +AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSAEGPEPSRADAWVAGPGLDTE +HDARRRWAGVLAAL------EERPEAALLADASALDLVTAAELRSLRAAGTPVVLTPHAGEWSRLRERVPADGADAAD-- +-----PLAALRAWTAEHGATVLLKGPRTLVVAPDGEAWAVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRA--RRAG +EDPGPAPT-ARLAAAAAWLHAQAGAEQARAGRITTATLPAALGARVARLWWPDDAEPEAVR +>GCF_003691675_PROKKA_01380 +MTADDLTRIAVTGSAVRTAEEPLLTAGRGPELMRAAAWALAEHAAALLRERGPVAGATVAALVGPGNNGGDALFALAFLR +GRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAVPPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDV +PSGVDADTGEVRGEALRADTTVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE +AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSAEGPEPSRADAWVAGPGLDTE +HDARRRWAGVLAAL------EERPEAALVADASALDLVTAAELRSLRAAGTPVVLTPHAGEWSRLRERVPADGADAAD-- +-----PLAALRAWTSEHGATVLFKGPRTLVVAPDGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRA--RRAG +EDPGPAPT-ARLAAAAAWLHARAGADQARAGRITTATLPTALGARVAHLWWPDDAEPEAVR +>GCF_005280335_PROKKA_01203 +MSVEELRRVAVAGSAVRAAEAPLLAAGRGPAMMRDAAWALAEHAAALLRARGPVAGTTVAALVGPGNNGGDALFALAFLR +RRGVAAVAVPVRHDDDGAPRWHAEGWAALRAAGGRRADAVPAAAALVIDGMLGTGFAGELTLPPAARALPRDAVVLACDV +PSGVDADTGEVRGEALRADATVTFGALKTGLLVGEGAALAGEVHPVDIGLGPQLPTSPAARLYLADEAAVRAAHPAPAPD +AHKYTRGLVAVAAGSPRYPGAAVLSCSGALHAGAGMVHHAGPEATRDRVLAEHPEALVSAEGPAPDRADAWVAGPGLDTQ +DDARRRWEGVLSAL------AERPEAALVADASALELVTAAQLRALREGGTPVVLTPHAGEWARLRERLPADGADAAD-- +-----PLAALRSWSAAHGATVLLKGPRTLTVQPDGEAWLVADGGPELAMGGTGDVLAGALGAVLAADVARRSRA--RRAE +QAPGPVPT-AALAAAAAWLHARAGAEQARAGRLTTRTLPAALGAVTARLWRAGDENGRTRG +>GCF_020097155_PROKKA_01131 +MR-------AHTGTDVRAAERPLLDEGRGEALMRTAAWGLAEHVAAELRARGPVAGATVAALVGPGNNGGDALWALAFLR +RRGVEAVAVPVRRNEAGEPVWHAAGWAALQAAGGRRSTAVPARAAVVVDAMLGTGARGGFTLPEPARHLPSGAAVVACDL +PSGVDADTGAVPGEALAADLTVTFGASKTGLLLGAGPGRAGRVVCVDIGLGPHLPADPAAGLHVVDDDAVARLHPVPARD +AHKYTRGVVGVVAGSERYPGAAVLAVGGVLAGGAGMAHHGGPARAGDLVLAAHPAALTSADGPAPERADAWVLGPGLGDG +DGARERVRATVAAVLASGADGDRGPAALVVDASALDLVTGEDLAALAAVDARTVITPHAGEWARLRDRLPVPAADAVDVD +EDGAGELARLRAWTAARGVTVLLKGPASLAVAPDGQAWLMRDGGPQLGVAGTGDVLAGALGAVLAAETARARRGGDERHG +AARGGRPSPAALAAAAAWLHARAGVRQAADGRATADTLPAALGDVVARRWWENDAHGR-RP +>GCF_023573625_PROKKA_01605 +MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGATVAALVGPGNNGGDALFALAFLR +RRGVAAVAVPVRRDDDGAPRWHAEGWAALQAAGGRRADAVPPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDV +PSGVDADTGEVRGEALRADATVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE +AHKYTRGVVAVVAGSERYPGAAVLASAGALQTGAGMVHHAGPQTTRDLVLAAHPEALVSAEGPEPSRADAWVAGPGLDTE +HDARRRWAGVLAAL------EERPEAALVADASALDLVTAAELRSLRAAGTPVVLTPHAGEWSRLRERVPADGADATD-- +-----PLAALRAWTAAHGATVLLKGPRTLVVAPDGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRA--RRAG +EDPGPAPT-ARLAAAAAWLHAQAGADQARAGRITTATLPTALGARVARLWWPDDAEPESVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001353.fa new file mode 100644 index 0000000000000000000000000000000000000000..79566ef4309016c82789f58f96d1cb4f177c7945 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001353.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01676 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA +>GCF_003691675_PROKKA_01381 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA +>GCF_005280335_PROKKA_01202 +MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA +GED-GA +>GCF_020097155_PROKKA_01130 +MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP +GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERH- +-----D +>GCF_023573625_PROKKA_01606 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001355.fa new file mode 100644 index 0000000000000000000000000000000000000000..568bf2b0ae8e7682af72d6aa9c2a2a3a2fe61b7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001355.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01678 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHAHVAGIGHGQRYGYRVHGPWD +PARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPDRIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYE +THVKGMTKLHPAVPEELRGTYAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP +KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGL +WSEWNGMYRDAVRDFWRGEPGTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAMDDSLV +AFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVWLEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPY +RDFYVLMNAWWEPVPYTLPGPTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQV--PEGA +>GCF_003691675_PROKKA_01383 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHAHVAGIGHGQRYGYRVHGPWD +PARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPDRIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYE +THVKGMTKLHPAVPEELRGTYAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP +KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGL +WSEWNGMYRDAVRDFWRGEPGTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAMDDSLV +AFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVWLEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPY +RDFYVLMNAWWEPVPYTLPGPTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQV--PEGA +>GCF_005280335_PROKKA_01200 +MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHVHVAGVGHGQRYGYRVTGPWD +PSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPDRMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYE +THVKGMTMRHPAVPEELRGTYAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA +SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEADERHYMDYTGTGNSVDLSSP +KALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGI +WSEWNGMYRDTVRDFWRGEPGTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG +ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAVDDSLV +AFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVWLEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPY +RDFYVLMNAWWEPVPYTLPGPLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQV--PEGA +>GCF_020097155_PROKKA_01128 +MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHVHVAGIGGGQRYGWRVHGPWD +PARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPDRMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYE +THVKGLTALHPDVPEELRGTYAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS +ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP +KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGI +WSEWNGMYRDTVRDFWRGEPGTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG +DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNVYCQDNELSWIDWSTRDDALI +AFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVWLEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAF +RDFYVLMNAWWEPVPYTLPGPLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG +>GCF_023573625_PROKKA_01608 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHAHVAGIGHGQRYGYRVHGPWD +PARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPDRIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYE +THVKGMTKLHPAVPEELRGTYAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP +KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGL +WSEWNGMYRDTVRDFWRGEPGTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAMDDSLV +AFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVWLEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPY +RDFYVLMNAWWEPVPYTLPGPTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQV--PEGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001359.fa new file mode 100644 index 0000000000000000000000000000000000000000..3dea7b9916a976b27417d8d3723f1d5891a33bf9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001359.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01685 +MTSDAAPR--PRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDS +EVAPDAGSSADRTTSRP +>GCF_003691675_PROKKA_01389 +MTSDAAPR--PRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDS +EVAPDAGSSADRTTSRP +>GCF_005280335_PROKKA_01193 +MSSEAVPR--PPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDP +DVAPQR----------- +>GCF_020097155_PROKKA_01123 +M----SPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDR-GGPADWLPCVDPGRSVP +--APGA----------P +>GCF_023573625_PROKKA_01614 +MTSDAAPR--PRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDS +EVAPDAGSSADRTTSRP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001360.fa new file mode 100644 index 0000000000000000000000000000000000000000..b03287444bcfbdd730ef7b3b2e0318650e12415a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001360.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01686 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD +>GCF_003691675_PROKKA_01390 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD +>GCF_005280335_PROKKA_01192 +MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI +AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL +DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP +LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAEALADVVQRELRLHV +>GCF_020097155_PROKKA_01122 +MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI +AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL +DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA +HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG +IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP +LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETARREAEALAEVVQRELRLHD +>GCF_023573625_PROKKA_01615 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001365.fa new file mode 100644 index 0000000000000000000000000000000000000000..72070e57f88ab84b4b7793761d6cb0e506ecc132 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001365.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01692 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAA---PA-ESTPVEAVDPAATEEVTVAESQETAAEID +GAVPTTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE +AAQKMA- +>GCF_003691675_PROKKA_01399 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAA---PA-ESTPVEAVDPAATEEVTVAESQETAAEID +GAVPTTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE +AAQKMA- +>GCF_005280335_PROKKA_01186 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKSIVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +IMEPISGKQAVVREAEQAAASAPAAETAPVQETAPVEAVDPAAAEDVTVAESQEAAAEID +GAVATTEDGSAPEGASIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE +AAQKMAD +>GCF_020097155_PROKKA_01116 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPHAERLITIAKKGDL +PARRKVQGIIAAKSRTNKSIVHELFTVIAPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +VMEPVSGKQAVVREAEQAAASAPAA--APV-EETPVEVVDPAATEEVTVAESEETAAEID +GAVATTEDGSAPEGATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE +AAQKMA- +>GCF_023573625_PROKKA_01621 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAA---PA-ESTPVEAVDPAATEEVTVAESQETAAEID +GAVPTTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE +AAQKMA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001367.fa new file mode 100644 index 0000000000000000000000000000000000000000..343fdd2c93f5a25ff865caf35b91cbdf147e5e31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001367.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01694 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>GCF_003691675_PROKKA_01401 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>GCF_005280335_PROKKA_01184 +MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>GCF_020097155_PROKKA_01114 +MPPKTR-SAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +QAHNGARPAKRRRV +>GCF_023573625_PROKKA_01623 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001369.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001369.fa new file mode 100644 index 0000000000000000000000000000000000000000..3562a0e3aaf5dfbd2a59618d008d46a265c3792b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001369.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_01696 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG +>GCF_003691675_PROKKA_01403 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG +>GCF_005280335_PROKKA_01182 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG +>GCF_020097155_PROKKA_01112 +MKVQPSVKRICDKCQVVRRKGRVLVICENPRHKQRQG +>GCF_023573625_PROKKA_01625 +MKVQPSVKRICDKCQVVRRKGRVLVICSNPRHKQRQG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001370.fa new file mode 100644 index 0000000000000000000000000000000000000000..40ebabdcefd79cab9293d6e4cbb09b9f0f21c890 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001370.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01697 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>GCF_003691675_PROKKA_01404 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>GCF_005280335_PROKKA_01181 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>GCF_020097155_PROKKA_01111 +------MAKKEGVIEVEGTVTEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>GCF_023573625_PROKKA_01626 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001371.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e4292b7401cf5befe6cb6bc56f1d98247bc7a00 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001371.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01698 +MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +EAGTAGPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE +>GCF_003691675_PROKKA_01405 +MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE +>GCF_005280335_PROKKA_01180 +MVGRRSLELKTTPQLQTMRRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAEHGATS +NFLGYYDFPATICASVNEEVVHGIPGDRVLQAGDVLKVDGGAIVDGWHADSARTLVLGSS +EAGTADEGDERLSAITREALWVGIAAFATAKHVGDIGDAIDDFVSAQPGEPLGILEEYVG +HGIGSSMHMPPDVFNYRTGHRGPKVRPGLALAVEPMLVRGGIETRVLEDDWTVVTVDGAR +ASQWEHSVCRHAGGLWVLTAPDGGASELERFGVVPVPPGE +>GCF_020097155_PROKKA_01110 +MFSRRSIELKTTPQLQTMQRAGVVLSEALDAAVAAAAPGVTTAEVDAVFADVLAQHGATS +NFLGYYGYPATVCASVNEEVVHGIPGERVLQQGDVLKIDGGAIVDGWHSDSARTLILGSS +EAGTADPEDERLSEITRQALWVGIAAFAQARHVGEIGDAVDDFVTSQPGAPLGILEDYVG +HGIGSAMHLAPDVFNYRTGHRGPKVQHGMALAIEPMLVRGGIETRTLEDEWTVVTTDGAR +ASQWEHTVCRHPGGVWVLTAPDGGAAELAAHGVVPVPPGE +>GCF_023573625_PROKKA_01627 +MIGRRSLELKTAPQLQAMQHAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVTAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001372.fa new file mode 100644 index 0000000000000000000000000000000000000000..b82d9db431d9c612dd08a61f96dd553488ff0386 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001372.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01699 +MTRMLLMGPPGSGKGTQATRIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGLSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>GCF_003691675_PROKKA_01406 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAESGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>GCF_005280335_PROKKA_01179 +MTRMLLMGPPGSGKGTQATRIADKLGIVAISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDDVTNRMVADRIAQPDAEHGFLLDGYPRTKGQVEALDAMLTEAGLALSAVVELEVPDAE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETEAVIQEYVERGIVARVDGTGQIDDVTE +RLLQSVYAVRAATGSLPVIAPDTES +>GCF_020097155_PROKKA_01109 +MTRMLLMGPPGSGKGTQATRIADKLGIVAVSTGDIFRHNVKNMTELGKEAKRYMDAGDFV +PDEVTNRMVADRLSQSDAETGFLLDGYPRTAGQVDALDAMLKDTGQALSAVVELEVPDAE +LVARLLKRAEIEGRADDTEEVIQHRLDLYHRETESVIESYAERGIVARVDGTGQIDDVTE +RVLQSVYSVRAATGTLPIITPDTQA +>GCF_023573625_PROKKA_01628 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKRYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001383.fa new file mode 100644 index 0000000000000000000000000000000000000000..a20cd13f03284fb8efa2420c53103aefa674e782 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001383.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01710 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>GCF_003691675_PROKKA_01417 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>GCF_005280335_PROKKA_01168 +MTEQTPAVSEERGYRKALRGVVVSDKMDKTIVVEVEDRKKHSLYGKVMKTSKRVKAHDED +NTAGIGDRVRIAETRPLSASKRWRLVEIVERAK +>GCF_020097155_PROKKA_01098 +MTEQTAAPVEERNYRKSLRGVVVSDKMDKTIVVEVEDRKKHALYGKVMKTSKRVKAHDED +NTAGVGDRVLIVETRPLSADKHFRLVEIVERAK +>GCF_023573625_PROKKA_01639 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001385.fa new file mode 100644 index 0000000000000000000000000000000000000000..791e2692e89541f4a94937d06ecf7b8311060cf2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001385.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01712 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE +>GCF_003691675_PROKKA_01419 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE +>GCF_005280335_PROKKA_01166 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL +AIHKLPLKARVIRREGGE +>GCF_020097155_PROKKA_01096 +MLIPRRVKHRKQHHPKRSGMAKGGTTVTFGEWGIQALSPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL +AIHKLPLKARIIRREGGE +>GCF_023573625_PROKKA_01641 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001390.fa new file mode 100644 index 0000000000000000000000000000000000000000..ce626424026c0373fd595d1123088e9d72e72416 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001390.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01717 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDG-TIDIFGGPLA- +>GCF_003691675_PROKKA_01424 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDG-TIDIFGGPLA- +>GCF_005280335_PROKKA_01161 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDG-TIDIFGGPLA- +>GCF_020097155_PROKKA_01091 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKTEIKQAIERIFDVSVASVN +TLNRPGKRRRTRFGWGQRKSTKRAIVSLKDGATIDIFGGPLAS +>GCF_023573625_PROKKA_01646 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDG-TIDIFGGPLA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001391.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a96fd4005252b4374ee6bc021e1c5f528fd7180 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001391.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01718 +MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ +>GCF_003691675_PROKKA_01425 +MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ +>GCF_005280335_PROKKA_01160 +MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ +>GCF_020097155_PROKKA_01090 +MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ +>GCF_023573625_PROKKA_01647 +MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001393.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f8bb51eb078cd9cecd471e36f60ce0c6252a3bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001393.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01720 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>GCF_003691675_PROKKA_01427 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>GCF_005280335_PROKKA_01158 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>GCF_020097155_PROKKA_01088 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>GCF_023573625_PROKKA_01649 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001395.fa new file mode 100644 index 0000000000000000000000000000000000000000..6957915fac89ba8e817bf3fdcdf9895cc98be374 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001395.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_01722 +MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER +>GCF_003691675_PROKKA_01429 +MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER +>GCF_005280335_PROKKA_01156 +--------------MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR +>GCF_020097155_PROKKA_01086 +M---------------EWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER +>GCF_023573625_PROKKA_01651 +MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001396.fa new file mode 100644 index 0000000000000000000000000000000000000000..8275f3062cdb39f2860a2d6b000aff71a91b6cd2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001396.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01723 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>GCF_003691675_PROKKA_01430 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDPQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>GCF_005280335_PROKKA_01155 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDDAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVAPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MTVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>GCF_020097155_PROKKA_01085 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEKRDFASIDSAPEERQ +RGITINISHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRPVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVQPGS +ITPHTDFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKINK +>GCF_023573625_PROKKA_01652 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001400.fa new file mode 100644 index 0000000000000000000000000000000000000000..96c5cfa2a26e64f6e440fe62de3add992fa986ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001400.fa @@ -0,0 +1,90 @@ +>GCF_002008305_PROKKA_01727 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECACGKYKRVRFKGIICERCGV +EVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETR +VLADQRDSDIAAVAADLEKDLAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVNAFLTTDNSPEGMVLDAVPVI +PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLK +SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQMAVHLPLSPEAQAEARLLML +SSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGNLYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPE +GWSEGEIALIETTLGKVLFNELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLPELNTINRMVSSGARGNWLQV +RQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATHGARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTE +RGLSVTIAAPNADGELVAHEQVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQELFEARTPKGVAPISEVAGR +VTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEHVPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQS +QGVGIHDKHVEVIVRQMLRRITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFASPAGFADFDYPGLDQSLGEN +DFHAVSLDDYGRGGDFRA +>GCF_003691675_PROKKA_01434 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECACGKYKRVRFKGIICERCGV +EVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETR +VLADQRDSDIAAVAADLEKDLAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVNAFLTTDNSPEGMVLDAVPVI +PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLK +SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQMAVHLPLSPEAQAEARLLML +SSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGNLYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPE +GWSEGEIALIETTLGKVLFNELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLPELNTINRMVSSGARGNWLQV +RQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATHGARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTE +RGLSVTIAAPNADGELVAHEQVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQELFEARTPKGVAPISEVAGR +VTIEDTEASVRLLLTPDDGSEEIAYPVLRRARILVADGEHVPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQS +QGVGIHDKHVEVIVRQMLRRITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFASPAGFADFDYPGLDQSLGEN +DFHAVSLDDYDRGGDFRA +>GCF_005280335_PROKKA_01151 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECACGKYKRVRFKGIICERCGV +EVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITSVDEEGRHRDLANLQAEYDQETR +VLADQRDADIAAVAADLEKDLAKLESEGAKAAEKKKARDAADKTMSQIRKRADAELDRKEQVWDRFKNLKVADLEGDEGL +YRTMRDKYGQYFEGSMGAEAIQRRLQTFDLAAESEMLRETIKTGKGQRKTRALKRLKVVNAFLTTDNSPEGMVLDAVPVI +PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLK +SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQMAVHLPLSPEAQAEARLLML +SSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDAVGAGNAYATVGEAVMAFDGGDLHLNAPVKIGVDGFVPSTAVPAPE +GWSEGELAVIETTLGKVLFNELLPADYPWLDTQATKGSLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQALRVQQQYEKGLIADDERRSELIDIWNKATDEVAAAMKDGLPELNTINRMVSSGARGNWLQV +RQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATHGARKGLADTALKTANSGYLTRRLVDVSQDVIVREEDCGTE +RGLSVTIAVPNADGELVAHEQVENSAFARTLAQDVTGEDGSVLASGGADVGDVLIDQLVGAGVSEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQELFEARTPKGVAPISEVAGR +VTIEDTDASVRLLLTPDDGSEEIAYPVLRRARILVADGEHVAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQS +QGVGIHDKHVEVIVRQMLRRITVIESGETDLLPGELTDRARFVAANRSAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFASPAGFADFDYPGLDQQLGES +DFHAVSLDDYGRGGDFRS +>GCF_020097155_PROKKA_01080 +MTTENPFGLMRIGLATADDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECACGKYKRVRFKGIICERCGV +EVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITSVDEEARHRDLPNLQAEHDQETR +VLEDQRDADIAAVAADLEKDLAKLEAEGAKAAEKKKARDAADKTMAQIRKRADAELDRKAQVWDRFKNLKVADLEGDEGL +YRAMRDKFGAYFEGSMGAEAIQRRLQTFDLAAESELLRETIKTGKGQRKTRALKRLKVVNAFLTTDNSPEGMVLDAVPVI +PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLK +SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNVKSAKRMVERFR +PQVWDVLEEVISEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQMAVHLPLSPEAQAEARLLML +SSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRAEGKGAGRQFATVGEAVMAFDNGELHLNAPATIGVEGFVPSAAVAAPE +GWTEGEVALIETTLGKVIFNDLLPADYPWLDTQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKASIMQGYEDQAQRVQAQYDKGLIADDERRSELIDIWNKATDEVAAAMKAGLSELNTINRMVSSGARGNWLQV +RQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATHGARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTG +RGLSVTIAEPNHDGELVVREQVENSAFARTLAQAVTAEDGTVLAEAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQELFEARTPKGVAPISEVAGR +VTIEDTDASVRLILTPDDGSEEIAYPVLRRARLLVADGEHVAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVQEVQDVYQS +QGVGIHDKHVEVIVRQMLRRITVIESGETDLLPGELTDRSRFVAANRAAVAEGKQPAAGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKEDPLLGLKENVIIGKLIPAGTGLDRYTQTTVEPTEEAKANLFAAPVGFADFDYPGLDQPLGEA +EFHAVSLDDYGRGGDFRA +>GCF_023573625_PROKKA_01656 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECACGKYKRVRFKGIICERCGV +EVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETR +VLADQRDSDIAAVAADLEKDLAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVNAFLTTDNSPEGMVLDAVPVI +PPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLK +SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQMAVHLPLSPEAQAEARLLML +SSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGNLYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPE +GWSEGEIALIETTLGKVLFNELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLPELNTINRMVSSGARGNWLQV +RQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATHGARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTE +RGLSVTIAAPNADGELVAHEQVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQELFEARTPKGVAPISEVAGR +VTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEHVPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQS +QGVGIHDKHVEVIVRQMLRRITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFASPAGFADFDYPGLDQSLGEN +DFHAVSLDDYGRGGDFRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001402.fa new file mode 100644 index 0000000000000000000000000000000000000000..8054497f2e13bc1a6c631278c45f694ef3bf7334 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001402.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01729 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>GCF_003691675_PROKKA_01436 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>GCF_005280335_PROKKA_01149 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGG-DAAAAEEK +DEFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>GCF_020097155_PROKKA_01078 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGG-DAAAAEEK +DEFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>GCF_023573625_PROKKA_01658 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001403.fa new file mode 100644 index 0000000000000000000000000000000000000000..9da4362a9dc3d85c8d1f51b07fe9d54f4c0f88e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001403.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01730 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KQLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA +>GCF_003691675_PROKKA_01437 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA +>GCF_005280335_PROKKA_01148 +MATSAKESAVAELTDLFRESNAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKEAGVEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKIADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAQQGEAA +>GCF_020097155_PROKKA_01077 +MATSAKESAVAELTDLFRSSSAAVLTEYRGLTVSELKQLRDSIRQDATYSVAKNTLTEIA +AKEAGVEGLDAHLAGPTAIAFVTGDPVTVAKALRDFAKDHDKLVLKGGYMDGQPLDEAGI +EKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTARTVEALRAQQDQAA +>GCF_023573625_PROKKA_01659 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001405.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001405.fa new file mode 100644 index 0000000000000000000000000000000000000000..798cfdaacbc6910e4962f4e833a94c96d699d1b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001405.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01732 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG +>GCF_003691675_PROKKA_01439 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG +>GCF_005280335_PROKKA_01146 +MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA +NDVKAAAKIIAGTARSMGITVEG +>GCF_020097155_PROKKA_01075 +MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI +TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA +NDVKAAAKIIAGTARSMGITVEG +>GCF_023573625_PROKKA_01661 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001406.fa new file mode 100644 index 0000000000000000000000000000000000000000..19caa3cc318f8659e123f9cbd1501d2ea81c1dcb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001406.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01733 +MSEQELDRQPAEESVPMSEDAVAEETAETAQDAGTPVEDALDEVAGSGDETA---EATVQ +EADLAVAEGE----DAPTPVE----EQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGY +EKRVKTNLEARILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDA +SWGVVRHTPGVTGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESG +APAAPAIHVDFEVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQ +VTKAI +>GCF_003691675_PROKKA_01440 +----------------MSEDAVAEETAETAQDAGTPVEDALDEAAGSGDETA---EATVQ +EADLAVAEGE----DAPTPVE----EQADDEPAVDPAEELRTRLRRQPGDWYVVHTYAGY +EKRVKTNLEARILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDA +SWGVVRHTPGVTGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPALVESG +APAAPAIHVDFEVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQ +VTKAI +>GCF_005280335_PROKKA_01145 +MSEQELDRQAAEESVSVQEDGAVEETVETAQDAPAPAEDAAGETAVDGEEAAEATEATAQ +EADPAAV------------------EQAEEEPAVDPGEELRTRLRRQPGDWYVVHTYAGY +EKRVKTNLEARILSQDMEDAIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDA +SWGVVRHTPGVTGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPASAESG +AAAAPAIHVDFEVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQ +VTKVI +>GCF_020097155_PROKKA_01074 +MSEQELDRQD------VEETAVAEDS--TALEA--PVED-------TAAEEA---EQTVQ +EADLAIAEGDQDAAEAPSAEELDAAGQAPAQPDVEAAEQLRTRLRRQPGDWYVVHTYAGY +EKRVKTNLEARIQTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDA +SWGVVRHTSGVTGFVGNDAHHPQPLTLDEVYDMLAPSVVQEAVREAEKAGLVPVAVAESG +AAGAPAIHVDFEVGESVTVDDGPFETLPATISEIKPETQQLVVLVSIFERETPVTLSFNQ +VTKVI +>GCF_023573625_PROKKA_01662 +----------------MSEDAVAE---ETAQDAGTPVEDALDEPAGSGDETA---EATVQ +EADLAVAEGE----DAPTPVE----EQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGY +EKRVKTNLEARILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDA +SWGVVRHTPGVTGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESG +APAAPAIHVDFEVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQ +VTKAI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001410.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5854267a4c3b4677abdfd6e51b9f1ea79da381c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001410.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01738 +MP---------------------------------TPSAPAPA---PRPPLMRHGADRPV +SGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALYVWLWLLVPEEGPDGAPAADAPTLR +GRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLGLAVDWALVGPVAVLVIGLGLAWMQ +LDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGAVSSGELWRALLAAVAMLAGAALVA +MPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAQDADAVARVARAQE +RELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGARVEVVAVGRAAGAWLEPLAAAAREA +MQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGPGFDLPTVPADRLGVRESILGRMGR +AGGTARIRSGPGGTEVHLTLAEP--EGARARTGQEHP +>GCF_003691675_PROKKA_01445 +MP---------------------------------TPSAPAQA---PRPPLMRHGADRPV +SGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALYVWLWLLMPEEGPDGAPAADAPTLR +GRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLGLAVDWALVGPVAVLVIGLGLAWMQ +LDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGAVSSGELWRALLAAVAMLAGAALVA +MPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVLQSLALIQRRAHDADAVARVARAQE +RELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSRVEVVAVGRAAGAWLEPLAAAAREA +MQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGPGFDLHTVPADRLGVRESILGRMER +AGGAARIRSGPGGTEVHLTLTEP--EGARARAGQEHP +>GCF_005280335_PROKKA_01140 +MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASG---TRAPLMRHRADRPV +SGVAAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLR +GRAPEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQ +LDLAGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVA +MPYALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQE +RELRRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREA +MLNAARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMER +AGGAARIRSGPGGTEVHLTLTRP--DRVPPHAAQERP +>GCF_020097155_PROKKA_01069 +MP---------------------------------APAIPPPADLSARPALLRHAADRPV +SGVAGGVARHLGLDPRLARAGFAVLALAGGAGIALYAWLWLLMPEEGPDGAPAGPAPTLR +GRAPEVLERLREGGWPILLAVVVLGVGVLTVADGLGVPVDWALVGPVAVLVIGLGLAWMQ +LGAADGPEGGRWARRARLGLGTALVLLGVLAIVVGAVTAGDLWLGLLVAVALLAGGALVA +MPFVLARRRRRDEERTGAAVRAQRDEIAAHLHDSVLQSLALIQRRADDPETVARVARAQE +RELRQFLALDSARAHGTLAEAVEDHAAAVEDAFGRRVEVVSVGEASGPWLEPLASAAREA +MVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRDRGTGFDLADVPADRLGVRESILGRMRR +AGGTARIRSGPSGTEVQLSLADPGAPGVGLREGRGRA +>GCF_023573625_PROKKA_01667 +MP---------------------------------TPSAPAPA---PRPPLMRHGADRPV +SGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALYVWLWLLMPEERPDGAPAADAPTLR +GRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLGLAVDWALVGPVAVLVIGLGLAWMQ +LDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGAVSSGELWRALLAAVAMLAGAALVA +MPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAQDADAVARVARAQE +RELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGARVEVVAVGRAAGAWLEPLAAAAREA +MQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGPGFDLHTVPADRLGVRESIVGRMER +AGGTARIRSGPGGTEVHLTLTEP--EGARARTGQEHP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001415.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a2c71e9cd8ae599faaed41938cd2b9c634ca928 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001415.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01743 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG +LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV +ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQ----S +>GCF_003691675_PROKKA_01450 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG +LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV +ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQ----S +>GCF_005280335_PROKKA_01134 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSDGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRERRDGDVGPGMRPADIVPAFRSAEDVESLRAGDEGFG +ITATITHPGSLAELYYGRIKGPQLQLVTDAVLRGSAAGDYHRATRMAGLVNGQLFWRWDS +SGSEGAELEAHASAILDRMPSESEGRLAPGAPRPRGAGGAEPGERP +>GCF_020097155_PROKKA_01063 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSEGTDIFYQRVDFVEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARQDGDVGPGMVPADIVPAYRSAEDVEALRSEDGAFR +ITATITHPGSLAELYYGRIKGPQVQIVMDSLLRGAAAGEYARATRMAGLVNGQLFWRWDS +SPAVEGPMEVHASAILDRMPDPSEGRLAPGAPRPRGERGRAPEQGA +>GCF_023573625_PROKKA_01672 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG +LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV +ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQ----S + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001416.fa new file mode 100644 index 0000000000000000000000000000000000000000..a0b3eed23d385008904c0ee76309aea6f2e46de1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001416.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_01744 +MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR +>GCF_003691675_PROKKA_01451 +MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR +>GCF_005280335_PROKKA_01133 +MDTLLALEIFFLALVVLAGLGMAAVAAVVVGGLFKGQR +>GCF_020097155_PROKKA_01062 +MDSIVALEIFFLVLVVLAGLGMAAVAALVVGGLFKGQR +>GCF_023573625_PROKKA_01673 +MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001417.fa new file mode 100644 index 0000000000000000000000000000000000000000..03bac58a3aa21ff288b172816a35f0a51b4462b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001417.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01745 +MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI +LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW +STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV +TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL +VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA +>GCF_003691675_PROKKA_01452 +MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI +LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW +STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV +TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL +VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA +>GCF_005280335_PROKKA_01132 +------------------------MMRLSMALSAAVAALVLGGATLLGPVPAAVAAMAVI +LVIAWGWPRQMGAPARLSLSVTLAAVGLVAVLLMLLWPPIEDGRSGAWTLFEPLAVALAW +STMASFVVQLVRGTGRPLRLESTVATMGGGLIAVMTACWVAVSRWTDAPAVAGLVLTLAI +SVAAFSLIGLIPGVQGRPGVLALVVVPLGALLAWPVSALLGVGPQDRAAVVAAVVAVATL +VSLTAATAPSARPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA +>GCF_020097155_PROKKA_01061 +------------------------MMRLSMALSAALAALVLGGAALLGPVPAAVAACLVI +AVIAFGWPRQMGAPARLSLTLTMLVAGVLGVLVMVLWPRGDAGPRGAWALFEPLAVVLAF +GTMASFIVQLVRGTGRPLRLESTVTTMGGVLVCLLAASWVPLAHHREAPGATGLVVTLAA +TLIVTSLIGLTPFMQGRPRVLALVMVPASGVVAALVSLLLGAPAHTAWVYAAAALGTAGL +VSLTAAAAPSSRPLPEDRVVGTTLSPRRAGYALAMAPVGAAGVVGHVMLGFLA +>GCF_023573625_PROKKA_01674 +------------------------MMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI +LVIAWGWPRQMGAPARLSLSVTLAVAGGIAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW +STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWSDTPAVAGLVITLAV +TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL +VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001419.fa new file mode 100644 index 0000000000000000000000000000000000000000..4bba3bfe462555248e803179cdce9c0cdf4bbf84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001419.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01747 +---------------------MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPG +G-LEVMVIHRPRYDDWSWPKGKLDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPG +KRG-ARQSKEVWYWAAEVDGQRALPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRA +ASRGRLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSS +PWRRCVETLAPLVKSSRLALKTKGAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPV +LPTLFEVVEDAAAGRTDRVLRALPTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD +>GCF_003691675_PROKKA_01454 +---------------------MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPG +G-LEVMVIHRPRYDDWSWPKGKLDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPG +KRG-ARQSKEVWYWAAEVDGQRALPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRA +ASRGRLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSS +PWRRCVETLAPLVKSSRLALKTKGAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPV +LPTLFEVVEDAAAGRTDRVLRALPTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD +>GCF_005280335_PROKKA_01130 +---------------------MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPG +GRLEVLVIHRPRYDDWSWPKGKLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSG +KRG-ARLTKEVWYWAADAGAQRAVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRA +DSRGRLRTLPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSS +PWRRCVETLAPLVKSSRLPLKTKGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPV +LPVLFEVVEDAARR-QERVLRAMPREDPWLRPGAVLVVHRS--LDGDVVAVEAYDPWDD +>GCF_020097155_PROKKA_01058 +MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE +G-LEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPD +RKGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERA +DARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSS +PWRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPV +IPSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD +>GCF_023573625_PROKKA_01676 +---------------------MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPG +G-LEVMVIHRPRYDDWSWPKGKLDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPG +KRG-ARQSKEVWYWAAEVDGQRALPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRA +ASRGRLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSS +PWRRCVETLAPLVKSSRLPLKTKGAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPV +LPTLFEVVEDAAAGQADRVLRALPTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001422.fa new file mode 100644 index 0000000000000000000000000000000000000000..afec59429e91dd35e9f564d968be06b1eaddf428 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001422.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01750 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>GCF_003691675_PROKKA_01457 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>GCF_005280335_PROKKA_01127 +MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>GCF_020097155_PROKKA_01052 +M-ARHHDDGARPRQ-TIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRR +TWDSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDL +VWVIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAG +PRRRDERWERD +>GCF_023573625_PROKKA_01679 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG +PRHRFERWERD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001423.fa new file mode 100644 index 0000000000000000000000000000000000000000..b84783492add7be5abbc89cb6470429b4b6fd866 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001423.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01751 +MA--PTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVF +AVGGLIAWNRRKRAQQGR +>GCF_003691675_PROKKA_01458 +MA--PTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVF +AVGGLIAWNRRKRAQQGR +>GCF_005280335_PROKKA_01126 +MA--PTDPQDRLFTPQAVTFLALVACPVLAFVCAVMGLILVLQGKTIAGLVFLIVLTQVF +AVGGLIAWNKRKRAQQGR +>GCF_020097155_PROKKA_01051 +MADLPSDEKAPLLDAQAVTFLTLIAFPVLAFVCAVMGLILVLQGKVVAGVVFLVVLTQVF +AAGGLITWNRRRRDRSGR +>GCF_023573625_PROKKA_01680 +MA--PTDSDQRLLSPQAVSFLALVVLPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVF +AVGGFIAWNKRKRAQQGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001425.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001425.fa new file mode 100644 index 0000000000000000000000000000000000000000..0123cc0c416e71bd760d14bda3e6a591535e3ea4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001425.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01753 +MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP +GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA +HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY +RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL +AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG +TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN +RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL +>GCF_003691675_PROKKA_01460 +MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP +GTVVRLAFEGIHVLDGPLPGEGETPPAGDGARSADHEGEAVVVRIAAGHPWDDAVAWTVA +HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY +RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL +AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG +TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN +RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL +>GCF_005280335_PROKKA_01124 +MSERLAEHTTTRVGGPARAWETARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADAGFP +GTVVRLAFEGIEVRAGD-EAHGGDADDQDPAAGGDRAGEAVVVRVAAGHPWDDAVAWTVE +HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAWDREAGQVVELGAEELEFDY +RDSIIKRSMLETGAPSPRWIVLSIDLRLRRASGAAEPTAPVRYGQLASALDVAEGTHAPL +AVVRREVLALRAAKGMVSDPQDPDTWSTGSYFTNPIVPAAVRASLPEGAPAFAAGRAADG +TELVKLSAAWLIDHAGFAKGFGLPDVAPREGGPDGRGADGAGLAGGRASVSTKHTLAMTN +RGDASTEDVLTIARTVRDGVKARFGVDLHPEPMIIGTSL +>GCF_020097155_PROKKA_01049 +MSERLSDHTTTRVGGPARAWVEARTEAEAVAAVRAADAAGEPLFVLGGGSNTLMADAGFE +GTVVHMGFTGVEVL----PAEGAADGAGD-----------VVVRVAAGHVWDEAVAWTVE +HGLAGVEALSGIPGSAGATPVQNVGAYGADVSQVLVSLRAFDRAAGQVVELSAEDLRFGY +RDSVIKRSMFEDGSPSPRWIVLSIDLRLRRAEEGAEPTAPVRYAQLARALEVEEGADVSL +AQVREHVLALRASKGMVSDAADHDTWSTGSYFTNPIVPATVRVTLPEGAPAFAAGTDEDG +TPLVKLSAAWLIDHAGYGKGFGLPDAPRREGDADGSGPDGRGLAGGRAALSTKHTLAVTN +RGGASTEDVLTVARAVRDGVKARFGVDLHHEPMIIGTRL +>GCF_023573625_PROKKA_01682 +MSERLADHTTTRVGGPARAWVTARTEAEAIEAVRAADAAGEPLFVLGGGSNTLMADSGFP +GTVVRLAFEGIGVLDGPVPGEGEAPPVGDGARLADHEGEAVVVRVAAGHPWDDAVAWTVA +HGLGGIEALSGIPGSAGATPVQNVGAYGADVSQVLVALRAWDREAGDVVELTPADLRFGY +RDSVIKRSMLETGAPSPRWIVLSIDLRLRRASSDAEPTAPVRYGQLAAALDVEEGAHAPL +AVVRREVLALRAAKGMVSDPADPDTWSTGSYFTNPIVPASVRASLPDGAPAFAAGQAEDG +TPLVKLSAAWLIDRAGFAKGFGLPEVAPREGGPDGRGADGTGLAGGRASVSTKHTLAMTN +RGDATTEDVLTVARTVRDGVRERFGVELHPEPMIIGTSL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001427.fa new file mode 100644 index 0000000000000000000000000000000000000000..efb00558b6ebbfb1271fd321e0772a5e67f5e644 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001427.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01755 +MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA +VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM +VTTVTEIADLDGAAVSTVTSTLLVRGEES +>GCF_003691675_PROKKA_01462 +MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA +VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM +VTTVTEIADLDGAAVSTVTSTLLVRGEES +>GCF_005280335_PROKKA_01122 +MSVNPDVAGRSYPPAPPFQVGREAVRAFASAVQAQHPAHHDVEAARALGHADLLAPPTFA +VVIAQRAEAAAVNDPEVGIDFSRVVHADERFVHHRPLVAGDEVVATVRIASVKSLGGNDM +VTTVTEIADADGAPVSTVTSTLLVRGEES +>GCF_020097155_PROKKA_01047 +MSETESLVGRTYPPAPPYQVGREAVRAFADAVQAAHPAHTDVDAARALGYADVVAPPTFA +VVVAQRAEAAVVADPEAGIDFSRVVHADERFTHHRPIVAGDELTATVLIEAVKELGGNRM +VTTVTEIVDAAGAPVSDVASTLLVRGEES +>GCF_023573625_PROKKA_01684 +MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA +VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM +VTTVTEIADLDGAPVSTVTSTLLVRGEES + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001429.fa new file mode 100644 index 0000000000000000000000000000000000000000..72a4a0f82a5cb3e3f55fede420660eb9a1677514 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001429.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01759 +M-------SDILDPQTTAEV---APELAEAEQEAT-GTVPQV------------DAAPEAPAEPAAPEAPAEPAGPTFLD +LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRADTPQVLVLAPTR +ELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM +GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEE +HDGVIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISHVVNYDIPQ +DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPSVADVNAARKRRFADGITRTLERASEEELA +VFGEIVAAYVDEHEAEPARVAAALGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPARE +PAAGNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAEINGRRLGLRKDT +GRPTRAERDGE--------DRGER------RGGFRKDRGERG------ERGGFRGDRDG-GQRGGYRKDRDDRG------ +-----------SREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR +>GCF_003691675_PROKKA_01466 +M-------SDILDPQTTAEV---APELAEAEQEAT-GTVPQV------------DAAPEAPAEPAAPEAPAEPAGPTFLD +LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRADTPQVLVLAPTR +ELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM +GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEE +HDGVIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISHVVNYDIPQ +DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPSVADVNAARKRRFADGITRTLERASEEELA +VFGEIVAAYVDEHEAEPARVAAALGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPARE +PAAGNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAEINGRRLGLRKDT +GRPTRAERDGE--------DRGER------RGGFRKDRGERG------ERGGFRGDRDG-GQRGGYRKDRDDRG------ +-----------SREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR +>GCF_005280335_PROKKA_01118 +M-------SDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAET-AEEPEAPAEPAGPTFLD +LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALARLAETADVNGRADTPQVLVLAPTR +ELALQVADAFDSYAKHLEDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM +GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKLEAFTRILETED +HDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISLVVNYDIPQ +DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELA +VFGEIVAAYVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIP-TGPRGRKERD----GGRDGGREHGTADGRGSRGPARE +PAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTPAQLEAAANIEISGRRLGLRKDT +GRPTRAERDGDERRGGFRKDRGERGGHGGHRGGFRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDR +EDRGDRGGFRKDREDRGGFRKDRDERG--GFRGGKAGGRKPRWGAQERSDRGPRR +>GCF_020097155_PROKKA_01043 +MTPHETIPADDQAPVDLTEF---DPELAETTAE-----------------------APAAEQDADDAEADAEPAGPTFLS +LGLDARVLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNGRSQAPQILALAPTR +ELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVVGTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRM +GFAEEVDRILAETPDSKQTALFSATMPPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETED +HEGVIAFVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLDVERISLVVNYDIPQ +DAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEEMQVPTVAQVNEARTRGVVAGIGRTLETASEADLD +TYARMVAEYVEANDVDPARAAAALALMAQGGRPLLTEADEVP-AGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRRE +PAAGNATYWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANTEINGRRLNLRKDT +GRPTRAERDGD---G----ERGHRGPRED-RGGFRRD---RG------DRGGFRRDRGERPERGGFRKDRDDRG------ +-----------PREDRGGFRHDRDDRG------GRPGARKPRWGSDDRRDRGPRR +>GCF_023573625_PROKKA_01688 +M-------SDILDPQTTAEA---APELAEAEQEAT-GTVPQV------------DA-----AEPAAPEAPAGPAGPTFLD +LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRADTPQVLALAPTR +ELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM +GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEE +HDGVIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISHVVNYDIPQ +DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPSVADVNAARKRRFADGITRTLERASEEELA +VFGEIVAAYVDEHEAEPARVAAALGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPARE +PAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAEINGRRLGLRKDT +GRPTRAERDGE--------D----------RGGFRKDRGERG------ERGGFRGDRDG-GQRGGYRKDRDDRG------ +-----------SREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001433.fa new file mode 100644 index 0000000000000000000000000000000000000000..eba2a6a7c5190f884d24caea7b75677c451d4606 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001433.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01763 +M---------------QYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGLLGPGG +TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAVDPTSEESYYGVADRLVREIPGAYQP +NQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGAGTGGTITGTGRYLKEVSADRPSGAVRVIGADPSGSVYSGGAGRPY +FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPDSGRGY +LAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPVEALEHADAEPATRAG----APAEAD +RWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVATMNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGR +ATAQTPVADVMGPVLPCLGARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA +>GCF_003691675_PROKKA_01470 +M---------------QYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGLLGPGG +TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAVDPTSEESYYGVADRLVREIPGAYQP +NQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGAGTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPY +FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPDSGRGY +LAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQMDDDGATGAAGGAGTPVEVLEHADAEPATRAG----APAEAD +RWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVATMNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGR +ATAQTPVADVMGPVLPCLGARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA +>GCF_005280335_PROKKA_01114 +M---------------QYAENVLELIGHTPLVKLNSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEDAEKAGKLAPGG +TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLTAYGAEIVVTPTSVAPESEESYYGVANRLERDIPGAYQP +NQFFNPAAPASHYETTGPEIWEDTAHRVTHVVIGAGTGGTITGTGRYLKEVSADRESGPVRVIGADPSGSVYSGGTGRPY +FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARDLGPKDVMVIVLPDSGRGY +LAKIFNDPWMDERGFDYDVQDTVLPEWARGRTRSAAPEADDDGAQGAAGGAGTPVEALEQADAAAGADAGQVADAPAEAD +RWAATAGELLAEKADLFPGSVPTLVTASPTTSVADAVATMNRYGVDALPVVAEPRHDLRIGEVRGTVSAAALGEALAAGR +VHPGTPVAEAMGPVLPCIGARTPLRAVARRLAQDPTLLVLSAGRVAGVVTLHDVLAHVTA +>GCF_020097155_PROKKA_01039 +MGAVNEINPAPAHGQPRWAENVLDLIGRTPLVKLNRVTEGVEATVLVKVEYLNPGGSVKDRIALRMLEEAERDGKLAPGG +TVVEPTSGNTGVGLALVAQQKGYRAVFVTPDKVGQEKRDVLTAYGAEIVVTPTSVEPSSDESYYGVANRLEKEIPGAFQP +NQFFNPAAPASHYETTGPEIWEDTAGTVTHVVIGAGTGGTITGTGRYLKEVSADRASSPVRVIGADPEGSVYSGGTGRPY +FVEGVGEDMWPGNYDPSVPDEVIAVSDDAAFEMTRRLAAEEGLLVGGSSGMAVVAGLQAARELGPDDVMVIVLPDSGRGY +LAKIFNDDWMDERGFHYAQEETVLPAWAQGRTRSAVATAPSDSREGARGGVGTPVEAPGEGSPQDGAATA----TPAPGS +RWDASLADVLADKEDLFPGSVPTLVTASPDTTVADAVATLARYGVDALPVIAEPRHDLRINEVRGTVSAPALAAALAAGR +VQPGSAVSDVMEPALPSVGAAMTLRAAARRLQEDPILLVMDAGIVQGVVTLHDVLVYATA +>GCF_023573625_PROKKA_01692 +M---------------QYAENVLELIGRTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGLLGPGG +TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAVDPTSEESYYGVADRLVREIPGAYQP +NQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGAGTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPY +FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPDSGRGY +LAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPVEVLEHADAELATRAG----APAETD +RWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVATMNRYGVDALPVILEPRHDLRIGEVRGTVSTAALADALAEGR +ATAQTPVADVMGPVLPCLGARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001435.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e806f129d42c12f7cbb4f5c581f5a1b182a27ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001435.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01765 +MTTAFEPRPHTAAAPREPD---PHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWI +TAFEEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWR +LRDADPRA--------WSTTYRATILGAAPEAVCTIWDVFPLPAA- +>GCF_003691675_PROKKA_01472 +MTTAFEPRPHAAAAPREPD---PHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWI +TAFEEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWR +LRDADPRA--------WSTTYRATILGAAPEAVCTIWDVFPLPAA- +>GCF_005280335_PROKKA_01112 +MTTAFEPRPHTGLAPREPE---PHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWI +TAFEDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWR +LREPDARA--------WSTAYRAAILGAAPHAVCTVWDVLPLPAA- +>GCF_020097155_PROKKA_01037 +MTAQH-------AEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWI +TAFEDDCGLVLDRDATSLYAVSPA----DGLRREGDVPSDGGIAE---HLDFVLAGDVWH +HRGTCPPAPAGSDVDGWALLVHRLQREAPRGALGTVWDVFPLPAAG +>GCF_023573625_PROKKA_01694 +MTTAFEPRPHTAAAPREPD---PHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWI +TAFEEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWR +LRDADPRE--------WSTTYRAAILGAAPEAVCTIWDVFPLPAA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001436.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c3f2e6c133e5288d963a976f5400644f3581230 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001436.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01768 +MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMRASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR +>GCF_003691675_PROKKA_01475 +MASDSTFDIVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR +>GCF_005280335_PROKKA_01109 +MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEASMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQEVIAMLKDFEDADLQFVNFR +>GCF_020097155_PROKKA_01035 +MASDSTFDVVSKVDKQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKANSEERVK +AVLDVFESKLVKRGISLKSLDCGEPFASGKETRMEASIKEGIDQPTAKKITKLIRDEAPK +SVKAVIQGDELRVSSKSRDDLQETIALLKTFEDADLQFINFR +>GCF_023573625_PROKKA_01697 +MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001440.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa8f6694070daec24920a678505e0db1b1dba41c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001440.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01773 +MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW +RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDGEGLDR +>GCF_003691675_PROKKA_01480 +MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW +RRSAGADAPEGEWQDEGGTFSEFLTDLLAWTFEDPEDDDEGPDR +>GCF_005280335_PROKKA_01104 +MPAKPPAPVHLPAFQRLVPDLLGDAWAEDDGLSPADVEARLGQSPAAGQLGAGFMVPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDAEETVVWGLPVDNLALPDPLVW +RRSSGAEAEEGDWQDEGGTFSEFITDLLAWTFEDPEDDDGRDER +>GCF_020097155_PROKKA_01029 +MPAKPPAPVYLPGFQRLVPDLLGDTWAKDDGLAPADVEARLAESPAAEQLGTGFMVPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDEGETVVWGLPVDNLALPDPLVW +RRDTGADAEEGDWQDEGGTFSEFITDLLVWTFEDPEDDAAEDAR +>GCF_023573625_PROKKA_01702 +MPAKPPAPVYLPAFQRLVPDLLGDAWAEDDGLAPADVDARLAQSPAAEQLGAGLMIPAAL +REFYLALGNCGDLMETDHYVWDPEDLEVRDGFLMFLEDADETVVWGLPVDNLALPDPLVW +RRSAGADAPEGEWQDEGGTFSEFLTDLLAWAFEDPEDDDEGPDR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001443.fa new file mode 100644 index 0000000000000000000000000000000000000000..7cea204ba15b6f1654732c4117a6db65323c24a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001443.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01776 +MTDTPT-SPAPDSTSAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC +GDGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALT +RTRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFT +APIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGA-AVDGAIPAPPGDRGEWMES +WLRLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWG +IAEQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADL +AVQAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPP +LLRAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR +>GCF_003691675_PROKKA_01483 +MTGTPT-SPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC +GDGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALT +RTRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFT +APIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGA-AVDGAIPAPPGDRGEWMES +WLRLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWG +IAEQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAAEL +AVQAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPP +LLRAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR +>GCF_005280335_PROKKA_01101 +MTAAPSSSPSESAPPPVVRRADVLISGGGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC +GDGLTPQAVRELQLLGVPHRGEPGDDGGWQVIRGLRLRAGERSVDVPWPETRSWPDYALT +RTRRDFDALLADLARERGAEVRERHAVTSVVRDDAGRVCGLDAELIAPNGRKTGETARFE +APVVLSCDGVSARAAVSAGIHRREDRPMGVAVRAYYTAGP-AADGAVPAPPGDRGEWMES +WLRLPDAQGRPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWSGALTPDWG +ISEQTRVSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADL +AVQAHAAGSDAAADTVLSRYPVITQHLWGRHFALGARFARLIGDPRVMRASLGAGMAVPP +LLRAVVKVMGNTVDPERGDAVDRAVRVLEALTPALTTADSAPLGRLAR +>GCF_020097155_PROKKA_01025 +MTEHPT-----PAAAPVVRRADVLISGAGPAGATAAAHLAAAGLDVVVLEKSAFPREKVC +GDGLTPQAVQEIRNLGIEHQGGPGDDGGWHAVRGLRLRAGERSVDVPWPATQSWPDYALT +RTRKDLDALLADTARARGAEVRERHAVTGVTRDDAGRVDGLEAELIAENGRKTGERVRFA +APLVLACDGVSARAAVSMDVHRRTDRPMGVAVRAYYTAGPVGADGAVPRPPGDRVDWMES +WLRLPDEHGNPLPGYGWLFPLADGTVNVGLGILDTSPLFGKLDYRALLKQWSGALSEDWG +ISEETRTSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADL +AVQAHAAPNTPAADAVLARYPVITQHLWGRHFRLGTVFARLIGEPRVMRAALATGMAVPP +LLRTVARVMGNVVDPSGGDAVDRAVRILESVTPSLTTADAPGVGRLAR +>GCF_023573625_PROKKA_01705 +MTGTPT-SPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC +GDGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALT +RTRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVIGLDAELIAPNGRKTGETARFT +APIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGA-AVDGAIPAPPGDRGEWMES +WLRLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLRSWTGALTADWG +IAEQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADL +AVQAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPP +LLRAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001446.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b9b713e496bd67275c2313780dd67ae3674c517 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001446.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01782 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLHGAEGETMDVGSPLITIGAAG +ES-GEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEEMAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHR +ATSRSRPSKRGRGAARPT-----PAPTAGA------GAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEG +-SAPQAAPAQAPLVAAVPAAEA--AAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL +RASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKLSADE +LTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF +DHRVTDGATASAFLTFVADCLHDPTAALARI +>GCF_003691675_PROKKA_01489 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLHGAEGETMDVGSPLITIGAAG +ES-GEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEEMAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHR +ATSRSRPSKRGRGAARPT-----PAPTAGA------GAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEG +-SAPQAAPAQAPLVAAVPAAEA--AAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL +RAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKLSADE +LTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF +DHRVTDGATASAFLTFVADCLHDPTAALARI +>GCF_005280335_PROKKA_01096 +MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLHGAEGQTMEVGRPLITVGAAG +ES-GEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEEMAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHS +ATSRTRPSKRGRRGAGTTTAGGSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQG +GDAPQAAAAPAAQPAATAGAAS--TVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL +RAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADE +LTAAINETVTRAREGKAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF +DHRVTDGATASAFLTFVADCLNDPQSALARI +>GCF_020097155_PROKKA_01019 +MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLHGAEGETMEVGAPLITVGAVG +ESAGDAPPPSSAADAGTAP------AADGAVPGALSYREEERAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHT +ATSRSRPSKRARGGAGTTQAAAGAAPAASG------RAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGG +ASAPQDAQAPAPVQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDVDVTALLEL +RAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKMSADE +LTRAINDTVSRAREGRAAPAELTRGTFTLNNYGPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF +DHRVTDGATASAFLTFVADCLNDPQAALARI +>GCF_023573625_PROKKA_01711 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLHGAEGETMDVGSPLITIGAAG +ES-GEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEEMAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHR +ATSRSRPSKRGRGATRPT-----PAPTAWA------GAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEG +-SAPQAAPAQAPSVAAVPAAEA--AAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL +RAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKLSADE +LTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTF +DHRVTDGATASAFLTFVADCLHDPTAALARI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001447.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bba5e317af1f42dc4f4f4a10a0a438bc5ddd36c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001447.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01783 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>GCF_003691675_PROKKA_01490 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>GCF_005280335_PROKKA_01095 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK +AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA +EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>GCF_020097155_PROKKA_01018 +MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK +ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA +>GCF_023573625_PROKKA_01712 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001448.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ade6e9a180d3ce0fbaf74f4c2d9359630e188f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001448.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01784 +M--SDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQG +TEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC +LGEDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHA +VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA +KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAH +TNTDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAM +NAETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA +>GCF_003691675_PROKKA_01491 +M--SDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQG +TEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC +LGEHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHA +VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA +KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAH +TNTDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAM +NAETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA +>GCF_005280335_PROKKA_01094 +M--SDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQG +AEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC +LGKQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHA +VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA +KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAH +TNTDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAM +NAEAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA +>GCF_020097155_PROKKA_01017 +MTSTRPGPATP--------DTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQG +TAPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC +LGQDDWLFPTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHA +VGMAKAARLRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFA +KQSAAPSLAHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAH +TNTDDPTRYREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAM +NADVELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA +>GCF_023573625_PROKKA_01713 +M--SDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQG +TEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVS +LGEDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHA +VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA +KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAH +TNTDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAM +NAETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001451.fa new file mode 100644 index 0000000000000000000000000000000000000000..14450bade00c983590c161bae55973ebb60fbb0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001451.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01798 +MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLREAIVGEIKARTVETD +RSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADWTPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPD +ATRVAYAVDHTGDERFTLRVREIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLADVEPVTDADGVRRLLVVHDRA +L-----DDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQ +AAHWREPAFDEELYACHLSATAAESPFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPS +SVTGEDVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGGGELGRRWYEDGKKLA +KRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTTILDPELPLSALEWEEW +GNPIEDAAVYAAMRAYTPYENVRAVDYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDG +GHGGASGRYQGWEDTAWEYAFLLTALGATARIV +>GCF_003691675_PROKKA_01495 +MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLREAIVGEIKARTVETD +RSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADWTPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPD +ATRVAYAVDHTGDERFTLRVREISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLADVEPVTDADGVRRLLVVHDRA +L-----DDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQ +AAHWREPAFEEELYACHLSATAAQSPFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPS +SVTGEDVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGGGELGRRWYEDGKKLA +KRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTTILDPELPLSALEWEEW +GNPIEDAAVYEAMRAYTPYENVRAVDYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDG +GHGGASGRYQGWEDTAWEYAFLLTALGATARID +>GCF_005280335_PROKKA_01078 +MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLRAAIFGEIKARTVETD +RSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADWTPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPD +STRVAYAVDHTGDERFTLRVREIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE +ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLADVEPVTGADGVRRLLVVHDRT +VARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGE +AADWREPAFEEELYACHLASTAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS +SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVAHVRGGGELGRRWYEDGKKLA +KRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEW +GNPIEDPEVYAAMRDYTPYENVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG +GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD +>GCF_020097155_PROKKA_01013 +MYE--TSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQADLRAAIYGEIKAHTVETD +QSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTPPVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPD +GALAAYAVDLAGDERYTLRVREIATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYE +ESDPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVD-ASPLPAPRVLVPRTARMLADVEPF-DMDGRRRLLIVHDRL +A-----DG----TTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTRTHVGLAVRRDTTPRVLIAPLEGLREGS +APAWTEPSFDEELYMCRLAGVNLDSPFLRLSYASWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPS +SLTGEQVRIPLTVIRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWYEDGKKAA +KRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTSILDPDLPLSALEWEEW +GNPIEDPEVYATMKAYTPYENVRAVDYPAIAAVTSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDG +GHGGASGRYQGWEDTAWEYAFLLTALGATARVD +>GCF_023573625_PROKKA_01717 +MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLREAIVGEIKARTVETD +RSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADWTPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPD +ATRVAYAVDHTGDERFTLRVREIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLADVEPVTDADGVRRLLVVHDRA +L-----DDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQ +AAHWREPAFDEELYACHLSATAAESPFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPS +SVTGEDVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGGGELGRRWYEDGKKLA +KRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTTILDPELPLSALEWEEW +GNPIEDAAVYAAMRAYTPYENVRAVDYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDG +GHGGASGRYQGWEDTAWEYAFLLTALGATRRVV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001454.fa new file mode 100644 index 0000000000000000000000000000000000000000..b75d1d151b3fd986420acb19074cfa08658fc1fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001454.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01801 +MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLISLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVPAADGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAALEAHPGVAAAHVAGVPDPEWGARLCAAVVPVRPAAAPDEAVLRAHVRAALGA +AAVPKTWLLLEALPLLSTGKTDRQALAARFTAG- +>GCF_003691675_PROKKA_01498 +MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDNAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVTAVDGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA +AAVPKTWLALDALPLLSTGKTDRQALAARFTAAG +>GCF_005280335_PROKKA_01072 +MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGIAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDHAGPRLVSLVPTQLARLLAADTDPAGRTALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV +AVGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA +AAVPKTWLALDALPLLSTGKTDRQALAARFAAAG +>GCF_020097155_PROKKA_01008 +MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHPAAAPDEAVLRAHVRAALGA +VAVPKTWLVLDALPLLSTGKTDRQALAARFTAG- +>GCF_023573625_PROKKA_01722 +MPATADALARATDALAAAFDGGAPVELTADGAALPRPEARDPRRCGDPDAVAVVRSSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAAAVAPDDPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVTAADGTRAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHEAAAPDEAVLRAHVRAALGA +AAVPKTWLVLEALPLLSTGKTDRQALAARFTAG- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001455.fa new file mode 100644 index 0000000000000000000000000000000000000000..8019e38e61cdc6d6c1a3c398614fb927f29cc334 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001455.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01802 +MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG +LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL +>GCF_003691675_PROKKA_01499 +MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV +GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG +LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL +LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL +>GCF_005280335_PROKKA_01071 +MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG +LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL +>GCF_020097155_PROKKA_01007 +MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN +DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV +GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG +LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL +WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL +>GCF_023573625_PROKKA_01723 +MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN +DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV +GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG +LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL +LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001456.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001456.fa new file mode 100644 index 0000000000000000000000000000000000000000..52f5889405f599218c82dd29bdf4a18f799ee429 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001456.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01803 +MRIFFYGLVRVVLFVALWALFYYVMDLWMIFAVIAAAILAFAVSYLFLDRLRTGATEDLS +AAWEGRPGRRGRTETADADAEDAYTEGRFRE +>GCF_003691675_PROKKA_01500 +MRILYYGLLRVALFFVLWWVGLQ-LGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLS +AAWEGRPGRRGRTEAADAEAEDAYTQGRFRE +>GCF_005280335_PROKKA_01070 +MRILYYGLLRVALFFVLWWVGLQ-LGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLS +AAWEGRPGRRGRTEAADAEAEDAYTEGRFRE +>GCF_020097155_PROKKA_01006 +MRLFLYGLVRVVLFFVIWALCYYVFGLGMLFSTLAAVILTFAVSYLFLTRLRLDASTDLQ +NAWEGRPSRRGRTEAADAAAEDAYTDGRFPG +>GCF_023573625_PROKKA_01724 +MRIFFYGLVRVVVFVALWALFYYVMDLGMIFGVIAATILTFAVSYLFLGRLRAGATEDLS +AAWEGRPGRRGRTETADADAEDAYTEGRFRE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001467.fa new file mode 100644 index 0000000000000000000000000000000000000000..ddf9858f2f5cf7b0ced775b4523377f80fe91f08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001467.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01818 +MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV +REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV +RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVPEDPPSPKAVK +KLRKHVEKRLEEAYTVFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL +HLWVNRLAAMTIAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTRDGLPGVGHVNLNPDTLLPGLSLGVR +>GCF_003691675_PROKKA_01515 +MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV +REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV +RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVK +KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL +HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR +>GCF_005280335_PROKKA_01052 +MRLGVLDIGSNTVHLLLVDAHPGARPSAYAEHKRSLPLIRYQDAEGAITEEGQHELVDFI +REAVAFAEEHRAEDMISFCTSAIRESANGAEVLARVDREAGVHLAELSGDQESAMTYFAV +RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWLPEDPPSPKAVK +KLRKHVEKRLEEAFAAFPPVEAPVAVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL +HLWVNRLAAMTAAERADLPGVSEVRAPQVLAGAIVALAAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTHDGLPGVGHVNLNTDTLLPGLRLGVR +>GCF_020097155_PROKKA_00990 +MRLGVLDIGSNTVHLLLVEARAGARPTPYAEHKRSLPLIRYLDESGAINEEGQDELVGFI +GEAVAFAEEHRAEDMISFCTSAIREAENGPAVLARVEAETGVHLSELSGEQEASMTYFAV +RRWQGWGVGSILNFDIGGGSFEIAYGQDELPSHAVSLPLGAGRLTRERLPDDPPSPKAVK +KLHKHVSREIEAVFADFPPLEAPYVVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL +QLWVNRLAAMTWEQRAELPGVSEVRAPQVLAGALVALAAMRTFGVAQLEICPWALREGLI +LNRLDALMLEGHLTREDGLGVGHVNLNTDSLLPGLSLGVR +>GCF_023573625_PROKKA_01739 +MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV +REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV +RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVN +KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL +HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001468.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba85423760abdf79cde97280fba75bde28448489 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001468.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01819 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLPADMKKGPFGKFAVDTEHGFT +PYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIAWHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTAL +VDAQETRRILDRLFGYELSPVLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVEDKPYTRRPAAPFTTSTLQQEA +ARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQAARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAG +DSFRTPAQVKAELRPDEFRLYELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTYAPTISTIMDRGYVSKRGTAL +VPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGELGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARA +VNSLPITEDITLRVGQYGPYLERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTIVA +KDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSVDTVTLEQALQLMSLPRVVGA +DAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRF +GPYITDGVTNITVPRGRRPEELTAEEAYQLLADKRAKGPATRGG-AKKPAARKAPAKK----TTARKKA +>GCF_003691675_PROKKA_01516 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLPADMKKGPFGKFAVDTEHGFT +PYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIAWHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTAL +VDAQETRRILDRLFGYELSPVLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVEDKPYTRRPAAPFTTSTLQQEA +ARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQAARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAG +DSFRTPAQVKAELRPDEFRLYELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTYAPTISTIMDRGYVSKRGTAL +VPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGELGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARA +VNSLPITEDITLRVGQYGPYLERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA +RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSVDTVTLEQALQLMSLPRVVGA +DAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRF +GPYVTDGVTNITVPRGRQPEELTAEEAYQLLADKRAKGPATRGG-AKKPAARKAPAKK----TTARKKA +>GCF_005280335_PROKKA_01051 +MPTTPASVTASVPEGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLPADMKKGPFGKFAVDTENGFA +PYYVVHPDKKKKVTELKRELKDAVALYLATDADREGEAIAWHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHL +VDAQETRRILDRLFGYELSPVLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAAYWGVEGTFTVAPGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGALKASAGKKVTHLDEAAASSLAQGLRGADFTVDAVEDKPYTRRPAAPFTTSTLQQEA +SRKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQAARRQATELYGQDAVPAQPRVYAKRNESAQEAHEAIRPAG +DSFRTPAQVKAELRPDEFRLYELIWKRTVASQMADAKGYTATLRFSATAQDGRAAQFSASGTVITFKGFLDAYEEGKDAE +TEDEKAEAKDRRLPQVAEGERLVGEPIEATGHETSPPARYTEASIVAELERREIGRPSTYAPTISTIMDRGYVSKRGNAL +VPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGELGREAWLQTFYFGAPASETGKGVEGLQQVVENLGEIDARA +VNSLPITDEITLRVGQYGPYLEKPLPADAEAGSTPPRANVPEELAPDELTPAKAEELFATAKPSERELGTDPETGRAVVA +KDGRYGPYVTEVIPEMTEEQLQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFSSMSVDTVTLEEALRLMSLPRVVGA +DAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTITQEQALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRF +GPYVTDGVTNITVPRGRQPEELTAEEAYQLLADKRAKGPATRKAPARKPAARKAPAKK----SAPKKKA +>GCF_020097155_PROKKA_00989 +MPTASASTSSSVPQGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLPADMKKGPYGKFAVDTEHGFT +PYYVVHPDKKKKVTELKRELKDAEALYLATDADREGEAIAWHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHL +VDAQETRRILDRLFGYELSPVLWRKVSRGLSAGRVQSVATRLVVERERERMAFVAAQYWGVEGTFTVGPDAKADGAAGSS +FTARLSTVDGARVATGRDFDDAGRLKESAGKKVAHLDEAAAASLAEGLDGKDFTVDSVEDKPYTRRPAAPFTTSTLQQEA +SRKLRMSARVTMQVAQRLYENGYITYMRTDSVNLSQEAVQAARRQATELYGQESVPTQPRVYAKRTENAQEAHEAIRPAG +DSFRTPAQVKAELRPDEFRLYELIWKRTVASQMADAKGYTATLRFSAQAEDGRTAQFAASGTVITFKGFLDAYEEGRDAE +PE-EEKDAKDRRLPQVAEGETLTGAPIQPTGHETTPPARYTEASIVAELERREIGRPSTYAPTISTIMDRGYVSKRGSAL +VPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGELAREAWLQTFYFGADSADTQKGVEGLKHVVENLGEIDARQ +VNSLPVTEDITLRVGQYGPYLERRLPEGAAEGTAPERANVPEDLAPDELTPAKAEELMAAGGADERELGVDPETGRTVVA +KDGRYGPYVTEVIPEMGEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFKTMSVDTVTLEQALQLMSLPRIVGA +DAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTVTQEQALEIYAQPKQRGRGTAKPPLAEFGEDPVSGKKVTVKEGRF +GPYVTDGVTNITVPRGRAPEELTAEEAYQLLADKRAKGSAKKPA-AKKPAARKPAAKKTTTSTTTRKKA +>GCF_023573625_PROKKA_01740 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLPADMKKGPFGKFAVDTEHGFT +PYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIAWHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTAL +VDAQETRRILDRLFGYELSPVLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVEDKPYTRRPAAPFTTSTLQQEA +ARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQAARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAG +DSFRTPAQVKAELRPDEFRLYELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTYAPTISTIMDRGYVSKRGTAL +VPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGELGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARA +VNSLPITEDITLRVGQYGPYLERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA +RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSVDTVTLEQALQLMSLPRVVGA +DAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRF +GPYVTDGVTNITVPRDRQPEELTAEEAYQLLADKRAKGPATRGG-AKKPATRKAPAKK----TTARKKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001469.fa new file mode 100644 index 0000000000000000000000000000000000000000..a2d5f68d758765494154203ea487a941c161d4c5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001469.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01820 +M---SPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRVVAGHL-AGPGRHDDA-- +-------------AGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAGLVV-EGPDG---RVRGAVDLS +PYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGATQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSE +RALAFTRFNLLLNADVLGLDRERLEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVA +ELIAALPDVLAEGGTAQLLANWEIPAG---------DTADADTA------PWDARPRSWVASGMQAWFIQRDRQDPAGYA +ETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVAEELTQAVDEALGTAWAAAVARR +DRLTAG--AGAGDAV--GDPALAALRGLHLRVAADVTEERHQRFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGE +LSVGQLVGAVAALLELDDVGRAGLLAALRELYEDGFLVE---G +>GCF_003691675_PROKKA_01517 +M---SPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRVVAGHL-AGPGRHDDA-- +-------------AGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAGLVV-EGPDG---RVRGAVDLS +PYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGATQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSE +RALAFTRFNLLLNADVLGLDRDRLEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVA +ELIAALPDVLAEGGTAQLLANWEIPAG---------DTANADTA------PWDARPRSWVAPGMQAWFLQRDRQDPAGYA +ETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVAEELTQPVDEALGAAWAAAVARR +DRLAAG--AGAGDAV--GDPALAALRGLHLRVAADVTEERHQRFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGE +LSVGQLVGAVAALLELDDVGRAGLLAALRELYEDGFLVE---G +>GCF_005280335_PROKKA_01049 +MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPARRVVARVLTAAPGDHTQALY +DDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADAADVAAALPALGLDGAREAGLVA-EEGGG---TVRGTVDLS +PYEADEPGRMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSE +RALEFTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVA +ELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLADTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYA +ETWLQDSSLELDPHRYEAAYRGYLEDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARR +DRLA----AGAPDGA--GDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGE +LSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED +>GCF_020097155_PROKKA_00988 +M----------SLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVL-AAPAARDAA-- +-------------------AASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAERARATVDLS +PYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARALDLGVGCGVQTLHLLAHAEHVTATDLSE +RALDFTRFNLLLNADVLRLDRERLEDRVRLAAGDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVA +ELIAALPEHLVEGGTAQLLANWEIPAGAAEIPAGAAEVPAGDDA----PPAWDARPRSWVGPGMQAWFVQRDRQDPAGYA +ETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWTVAEELTQPLDEALGTAWAAAVARR +DRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDVTEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGE +LSVGQLVGAVAALLELDDAGRAGLLAAVRELHEDGFLLE---A +>GCF_023573625_PROKKA_01741 +M---SPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRVVAGHL-AGPGRHDDA-- +-------------AGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAGLVV-EGPDG---RVRGAVDLS +PYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGATQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSE +RALAFTRFNLLLNADVLGLDRERLEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVA +ELIAALPDVLAEGGTAQLLANWEIPAG---------DTADADTA------PWDARPRSWVAPGMQAWLLQRDRQDPAGYA +ETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVAEELTQPVDEALGTAWAAAVARR +DRLAAG--AGAGDAV--GDPALAALRGLHLRVAADVTEERHQRFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGE +LSVGQLVGAVAALLELDDVGRAGLLAALRELYEDGFLVE---G diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001470.fa new file mode 100644 index 0000000000000000000000000000000000000000..95f2fe4766440450298d8a45c66e31c01676e312 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001470.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01821 +M------------STAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGI +NGTVGGPVDAVKRYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVT +VDADGVVGTGERLTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTR +DLLAAVDSGALDHLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGD +AGLWRGELAVFDRRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVD +DPERRCPVCVHHPHPAERTEA +>GCF_003691675_PROKKA_01518 +M------------STAPLSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGI +NGTVGGPVDAVKRYMRGTREHPAFRDLEVKWSDGSAADFPRLSVKVKPELVAFGAPERVT +VDADGIVGTGERLTPVQVDALVAERAGTANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTR +DLLAAVDSGALDHLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGD +AGLWRGELAVFDRRLSTRFTADAETIGRCVTCHAPTSALRNCADPACTTLEVRCAACAVD +DLEHRCPFCAHRPHPAERTEA +>GCF_005280335_PROKKA_01048 +M------------SPAPVSRIALYYRFAPLADPEAVRLWQRTLAASLGLTGRIIVSPQGI +NGTVGGPVDAVKQYVKGTREHPALKDLEVKWSDGSAADFPRLSVKVRPELVAFGVPERIT +VDEHGVVGTGERLTPERLEALVAERAGTENPVRFLDGRNTVEAQIGRFDGAVVPAAHTTR +DLLAAVDSGSLDHLRDAPLVTYCTGGVRCEVLSALLKDRGFREVYQLDGGIVRYGEAFGD +AGLWRGELAVFDRRIALRFSEDAETIGRCVTCEAPTSALRNCSDPACTTLEVRCAACAAA +DPDRRCPVCT------ERSAA +>GCF_020097155_PROKKA_00987 +MTAAAPAAPTPLPAPGGPGRIALYYRFTPLADPEAVRLWQRTLAVSLGLAGRIIVSPQGI +NGTVGGPAEAVKRYVRGTREHPAFRGLEVTWSDGSAADFPRLSVKVRPELVAFGAPERIR +VDEHGVVGTGEHLPADQLHALVAERAAQGRPVRFLDGRNSVEAAIGRFEDAVIPAAHTTR +DLLEAVDSGSLDHLKDQPVVTYCTGGVRCEVLSALLKDRGFSEVYQLDGGIVRYGEAHGD +AGLWHGRLAVFDRRLSLAFTDGAETLGRCVTCGGATSHLANCADPACTTLQVRCPDCVAA +HPDHVCPRCL------ERTPA +>GCF_023573625_PROKKA_01742 +M------------STAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGI +NGTVGGPVDAVKRYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVT +VDADGVVGTGERLTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTR +DLLAAVDSGALDHLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGD +AGLWRGELAVFDRRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVD +DPERRCPVCVHHPHPAERTEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001472.fa new file mode 100644 index 0000000000000000000000000000000000000000..47330378811a553a3d837ad6e57e5db7c6fb530b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001472.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01823 +MTG---HLPEH-------DPWADPAGGWGPPGTA-----DAAPPVD--DAAPDSSGP---EPQPVGEVVADVVAGLSVTA +PGDLCPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGVERPWLHQVRAAALAGAGTHT +VLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALAADQLTSWRALERDGAPGLRSAPYDGDTAPQDRIWAREHAS +VLMTNPDMLHVGILPHHERWATFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAP---AAAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLALQQVRTLAFIRSRRGAE +AIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ +QIGRAGRGGQDALAFFVASDDPLDTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVR +ALLDVLVDQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQAHPGAVYVHQDRTYLVE +ELDEDAHAVVVTRAWPDFTTQARDVTEVEIVAVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALASGEVLGEEPLDLPA +RDLFTSAVWFQAASDELIAAGLTTDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG +FAERGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADHLVPADASTDGSGGGASG +GSSGGATDAAPGA------ +>GCF_003691675_PROKKA_01520 +MTG---HLPEH-------DPWADPAGGWGPPGTA-----DSAPPVD--DAAPDFSGP---EPQPVGAVLADVVAGLSVTA +PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGVERPWLHQVRAAALAGAGTHT +VLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALAADQLTSWRALERDGAPGLRAAPYDGDTAPQDRIWAREHAT +VLMTNPDMLHVGILPHHERWAAFFRNLTFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAP---ATAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLALQQVRTLAFIRSRRGAE +AIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ +QIGRAGRGGQDALAFFVASDDPLDTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVR +ALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQAHPGAVYVHQDRTYLVE +ELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPA +RDLFTSAVWFQAASDELIAAGLTTDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG +FAERGFEQARRWVEATAGAIAACECTEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADHLVPADASTDGSG----G +GASGGSADPAPGA------ +>GCF_005280335_PROKKA_01046 +MST---PPPEPAAAGVAFDPWADPAAGWGAPDDGPSDRRDAPADVDETDHPGDEAHP-WDEPAPLADAVADVVAGLSVSR +PGDPVAGGEAADVLRGALGRHGLPEQIRHVVTLPAREARHADWPSEAPEALVGAFAGRGIERPWAHQVRAATVAGAGTHT +VVATGTASGKSLAYQLAAGIRLSGDPHATVLHLSPTKALAADQLLAWRALERDGATWLRAAPYDGDTAPPDRIWAREHAN +VLMTNPDMLHVGILPHHERWARFFRHLAFVVVDESHSYRGVFGSQVGILLRRLRRVAAHWRGDRPEPVFIGASATSADPA +GHFSRLIGAP---ATAVAEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAASADLLTDLALQQVRTLAFIRSRRGAE +AIASAARRQLEELEAGLGSRIAAYRSGYLPEERRALEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ +QIGRAGRGGQDALAFFVASDDPLDTYVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPLTPEAFERFGDPERVR +ALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGTLLGTMDSPQTHYQAHPGAVYVHQDRTYLVE +ELDEDAHAVIVTRAWPDFTTQARDVTEIEIVDVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLELPA +RDLFTSAVWFQASSEELIAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG +FAERGFAQARRWVEATAGAIAACECEAGCPSCVQSPKCGNRNSPLDKAGALTVLRFLLGQADHLVPVVAEGSGETDGGTD +DGVGVDGEDASGSGSSGTA +>GCF_020097155_PROKKA_00985 +MTGGPVPWPDD-------DPWA----ARGPAEDRSA--RDVP--------TPAPGGPGWEPPQELAT------------- +-GDP----EARAAFAAALGRRSLPAQIRHVTTIPARTPRSAPWPAGTPAGLVRAFAARGVQAPWEHQARGTAAALAGRHT +VLATGTASGKSLAYQLAVGATLAADPRATVLYLAPTKALAADQLASWRALERDGAAWLRAAPYDGDTAPQDRIWAREHAN +VLLTNPDMLHVGILPHHERWAVFFRNLAYVVLDESHTYRGVFGSQVGILLRRLRRVVAHYRGERPETVFIGASATSAAPA +EHLATLIGAAPGEVEAVTEDASPHGAVHVAFWEPELTDRRGENGAPVRRSATATAADLLTDLALQQVRTLAFIKSRRGAE +TIAGAAKRQLEEVEAGLGSRIAAYRSGYLPEERRALEEALRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ +QIGRAGRGGQDALAFFVASDDPLDTFVVEHPGAVFDLGVEDTVLDPANPHLLGPQLCAAAAELPLRPEDLPWFGGPERVR +ELLDVLVEQGLLRRRPAGWFWTHTEHAASLVSLRDDGGGPMDIIDVESGALLGTMDSPQTHYQAHPGAVYVHQDRTFLVE +DLDEDAHAVLVQRAWPDFTTQARDVTEIEIVAVHRRLDAAGSSLRWCLGDVQVTTQVISFQRKALLSGEVLGEEPLDLPA +RDLFTSAVWFQAASEELVAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGVPTVFVYDGRPGGAG +FAERGFAQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLAERFDGLIEVPAHLPDV------ +-----------------TA +>GCF_023573625_PROKKA_01744 +MTG---HLPEH-------DPWADPAGGWGPPGTA-----DAAPPVD--DAAPDSSGP---EPQPVGEVVADVVAGLSVTA +PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGVERPWLHQVRAAALAGAGTHT +VLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALAADQLTSWRALERDGAPGLRSAPYDGDTAPQDRVWAREHAS +VLMTNPDMLHVGILPHHERWAAFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAP---ARAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLALQQVRTLAFIRSRRGAE +AIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ +QIGRAGRGGQDALAFFVASDDPLDTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVR +ALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQAHPGAVYVHQDRTYLVE +ELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDARAGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPA +RDLFTSAVWFQAASDELIAAGLTTDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG +FAERGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADHLVPADASSDGS-----G +GASGGATDAAPGA------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001473.fa new file mode 100644 index 0000000000000000000000000000000000000000..058195b5d462d6df5931f04928e02ea114a6f06b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001473.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01824 +MTRGRAP------ARGERGSGTVSVLGTAALGAGLLLAVAALGQASATGSRAAGAADLAA +LAASDARRGLSD------HEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPA +ATADAVAGPPRSQAPGAASVAP------PEDPPEAPPP-------EPSVEASAGTR +>GCF_003691675_PROKKA_01521 +MTRGRAP------VRGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGARAAGAADLAA +LAASDARRGLSD------HEPCVLAGRTAERNGAAVVACEAREDGTVRVAVELARAPLPA +ATADAVAGPPRSQAPGAGSADP------PE----APPP-------EPSVEASAGTR +>GCF_005280335_PROKKA_01045 +MT-GRAPGGVPRGAASETGSGTVSVLGTAALGAGLLLAVAALGQASVAGAQAAGAADLAA +LAASDARRGLSA------GEPCLVAGQTAARNRAVVVECEVRENGTVRVSVERGRAPLPP +ALAAAVAGPPRLQAPQAVPEDPLPDASSPS----TPTPSSVPPSVSPDPSATTGTR +>GCF_020097155_PROKKA_00984 +M------------------SGTATALGTALLGAGLLTGVLAVGHASATAARASGAADLAA +LAASDARRGLGAVPDAGVLEPCPLAEESARRNGAEVTECVLLPDGSVRVAVVIAADPLPA +STAVAVAGPP--VGPRGPVAGPGRDDA-PE----DAPD-------TPGAPPEAATP +>GCF_023573625_PROKKA_01745 +MTRGRAP------ARGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGSRAAGAADLAA +LAASDARRGLSD------HEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPA +ATADAVAGPPRSQAPGAASVAP------PE-----APP-------EPSLEASAGTR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001474.fa new file mode 100644 index 0000000000000000000000000000000000000000..aaca583b1abe39d0e700047abf9bf75c14cd591a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001474.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01825 +MTEHPTSASPSGRRTGAR-----TAGRPRALRG-GETGAVTAEYAVLLPVIAFVLVSVLL +AGAAAVQQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQ +PGPGPLAWAEVLTLTAHAAAPDQ--RPGTPAAGP-------EDRS +>GCF_003691675_PROKKA_01522 +MTEHPTSAPPSARRTGAR-----TAGRPRGLRG-GETGAVTAEYAVLLPVIAFVLVSVLL +AGAAAVQQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQ +PGPGPLAWAEALTLTAHAAAPEQ--RPGTPAAGP-------EDRS +>GCF_005280335_PROKKA_01044 +---------------------------------------MTAEYAVLLPVIAFVLAAVLL +AGAAAVQQVRGQDAATAAARILARGDGEAEARRAVARMAGDDAALAHTADGGWVAVEVSQ +PGPGPLAWAEALTLTARAAAPQQ--HPGAAVDPD-------GGRT +>GCF_020097155_PROKKA_00983 +MADLPAEAPRPGRLRGARAGASGTVAFRDAERGEGERGAVTAEYAVLLPAAVAVLVAVLL +AGVAAVHQVRAQDAAASAARILARGDAESLARDAVGRMAGGDAALEARTAEGWVTVTVTR +PGPGPLA---AVTLSAEAVAPVQATSPTPPGRTPGITAPTGEAAP +>GCF_023573625_PROKKA_01746 +MTEHPTSASPSGRRTGAR-----TAGWPRALRG-GETGAVTAEYAVLLPVIAFVLVSVLL +AGAAAVQQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTIKGGWVTVEVVQ +PGPGPLAWAEALTLTAHAAAPDQ--RPGTPAAGP-------EDRS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001476.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcac0151120a1152e4538c144dd51689cf309018 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001476.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01827 +------------------------------------MLVGALRRWAALVAAGLTEEQAWR +ETACTLPACGSGPGEAGAACCAHHRARRRAEALAWDVPA--------------------- +--SHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADV +DAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWLA +GRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAA +LLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERA +AEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG +>GCF_003691675_PROKKA_01524 +MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR +ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPA--------------------- +--AHAPTGEAARRGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADV +DAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLA +GRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAA +LLLWGRDWDEAWVGLDTDPVWAETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERA +AEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG +>GCF_005280335_PROKKA_01042 +MS-TAA------------------------PEDATEELVVVLRRWAALVSAGLTEEAAWR +ETVRMLPDDDGH---------ARHAARLRAERLAWDAAGDLSTGRDAPDVRGLRRDEHPP +GDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAALAAGARAGAAPAVVVRRLAESLEADV +DAARARRSAAAGPAATARLLQWLPLGGVGLAWLLGSSPWETVSTPFGAVVAAVGLLFWLA +GRSWTRLLLRSAAREPAALTAPVVLDVLAALLGAGRSLPAALDDLARTLPGARGLRVTSA +LLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRSGMAGARTLAESAAAARQQGRRADERA +AEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLGAG-A +>GCF_020097155_PROKKA_00981 +MI------------------ALPGRAEER-AEERAQEVVEALRRWAGLTAAGMTPAEAWT +AVAQASSPCG----RPTPGCCPRHEALRRAALARWGGPG-----------RGAEGGQPRP +GE-----------------RSP-----WDLADAALAAAARAGASFSRTAARLADALEADV +DASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGVLTAA +GRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLRVVAV +LLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRADERG +AEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGA--R +>GCF_023573625_PROKKA_01748 +------------------------------------MLVGVLRRWAALVSAGLTEEQAWR +ETACTLPACGPGPSEAGTACCAHHRARRRAEALAWDVPA--------------------- +--SHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADV +DAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWLA +GRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTAT +LLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERA +AEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001477.fa new file mode 100644 index 0000000000000000000000000000000000000000..94c2ac6c0d02795c4e5ebb0c59e60acf2f98c1fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001477.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01828 +MRPFVPAAPARPPRGRRRRPAPPEGGRRFPWP------RTGPAEPERTQVAAPPLAAPA- +AGPDGLDAAVVRRRVAEARASAADGAEPPLAPLIAEALDVPIDD---------PRVAALV +D------ELDGFGPLAPWVRTPGVTDVLVDGAGAVWTDGDGGLVRRPDRLDPETARALAV +RLLHRAGRRLDAAVPLADARVGGVRVHAVLPPVSGGGTLLSLRIPAAATPSLAALADGWP +DGALWADALEALVRDRATVLVSGATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHP +HVVALQCRAANAEGAGEVGLAELVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAW +GTLHANAAAEVPARLTAMASLAGWRPETVAAQARAGVDAVLHIARDGHGRHPVELAVPDL +RAD---GFALLPALTWRPGTEATGGRTVEGPGMPALAARLAGRSGR +>GCF_003691675_PROKKA_01525 +MRPFVPAAPARPPRGRRRRPAPPEGSRRFPWP------RTDPAEPERTQVAAPPLAAPA- +AGPGGLDAAVVRRRVAEARASAADGAEPPLAPLIAEALDAPIDD---------PRVAALV +D------ELDGFGPLAPWVRTPGVTDVLVDGAGAVWTDGDEGLVRRPGRLDPETARALAV +RMLHRAGRRLDAAVPLADARVGGVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWP +DGALWADALEALVRDRATVLVSGATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHP +HVIALQCRAANAEGAGEVGLAELVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAW +GTLHANAAAEVPARLTAMASLAGWRPETVAAQARAGVDAVLHVARDGHGRHPVELAVPDP +RAD---GFALLPALTWRPGTEATGGRTVEGPGVPALAARLAGRSGR +>GCF_005280335_PROKKA_01041 +------------------------------------------------------------ +----------MRRRVAEARAAAAEGQEPALAPLVAEAIGVSATD---------PRVAALV +D------ELDGFGPLAGWVRAPGVTDVLVDGSGAVWTDGAEGLLRRPQRLDPHAAQALAM +RLVHRAGRRLDAAVPLADARVDGVRVHAVLPPVSGGGTLLSLRIPAARTPSLAELAAGWP +DGDLWGEALEALVRDRASVLVSGATGTGKTTLLAAALGCVPGDERILTVEDTAEAAPEHP +HVVALQCRAANAEGAGAVGLAELIRHALRMRPDRLVVGECRGAEVADFLTALNTGHQGAW +GTLHANGAADVPARLTAMGSLAGWGPDTVAAQARAGVDAVVHLVRDRHGRHPVELAVPDP +DAR---GFALLPALTWTPGPGPGDGSTAEGPGLRALAARLAGRGSR +>GCF_020097155_PROKKA_00980 +MPAWVPDAP-RPA----RRPALLPAGLSLPAPLLPDLRRVGRRRPGSDR------GEPAH +VGPD--PDARLRRAVAEAQARADPHAPPPLRETVSRALADLAAEDGDTPPSGCPRPAGLR +DPDAVLEELVGFGPLAPWVRRTGVTDVLVDAAGSVWTDGVEGLVRRPLILPEPTARALAV +RLIGLAGRRLDPACPVADARVDGVRVHAVLPPVSGGGTVLSLRVPAAEPPSLDALAADWP +DGERWRDAVVALVRGRASVLVSGATGTGKTTLLAAALGLAGADERIVLVEDTAEAAPAHP +HVISLQARAPTADGAGEVTLAELIRQALRMRPDRLVVGECRGPEVADLLTALNTGHQGAW +GTLHANAAADVPARLAAMGALAGWSASAVAAQARAGVDAVLHVRRDGRGRHPVELAVPAP +AAHPDAPLSVLPALTWD------GGGTRAGPGLEVLEARLSGRGHG +>GCF_023573625_PROKKA_01749 +MRPFVPAAPARPPRGRRSRLAPPEVGRRFPWP------RTGAAEPERTQVAAPPLAAPA- +AGPCGLDVAAVRRRVAEARASAADGAEPPLAPLIAEALDAPIDD---------PRVAALV +D------ELDGFGPLAPWVRTPGVTDVLVDGVGAVWTDGDEGLVRRPGRLDPETAGALAV +RLLHRAGRRLDAAVPLADARVGGVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWP +DGALWADALEALVRDRATVLVSGATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHP +HVVALQCRAANAEGAGEVGLAELVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAW +GTLHANAAAEVPARLTAMASLAGWRPETVAAQARAGVDAVLHLARDGHGRHPVELAVPDP +RAD---GFALLPALTWRPGTEAAGGRTIEGPGVPALAARLAGRSGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001478.fa new file mode 100644 index 0000000000000000000000000000000000000000..a5cbe4224b19a24d7cfd134f14106c309a28d6ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001478.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01829 +M---PETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVP +PEAVPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAER--VHPHVDVLLTQRAATLRQ +HAGQIAFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVL +GWWRDPSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGF +TAALLDRVLGLLGWDVPWDDSRVRDARTHEILRD +>GCF_003691675_PROKKA_01526 +M---PETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVP +PEAVPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGR--VHPHVDVLLTQRAATLRQ +HAGQIAFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVL +GWWRDPSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGF +TAALLDRVLALLGWDVPWDDSRVRDARTHRILRD +>GCF_005280335_PROKKA_01040 +M-------------------------AAVRDRLAALVERHGVPADQAPRD----ALTEIP +ASAVSTWGFDWPRAQRARPSAVLILFGSLDDVPAHHADDR--VHPDVDVLLTQRAATLRT +HAGQIAFPGGRVDPEDADVVATALREAEEETDLDPDGVEVLGVLPPVPVVVSGHVVHPVI +GWWRDPSRVAVVDQAEAAAVFRMPVGDLVDPANRCRVARPGGRRGETPGFLVGERLVWGF +TAALLDRILTLLDWDTPWDSGRVIDAHTHAPLRG +>GCF_020097155_PROKKA_00979 +MSIPPLPPSSP---------------SSARADLQRIVAEHGVAPVAG---DDEAGLTTIP +ASSVRVWGFDWPQAARPRASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRT +HAGQVAFPGGGVEAQDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVI +GWWRDPSRVAVVDHNEATAVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGF +TAALLSRVLELAGWDEPWAGAPLIDAGSRAVLEG +>GCF_023573625_PROKKA_01750 +M---PETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIP +PEAVPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAER--VHPHVDVLLTQRAATLRQ +HAGQIAFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVL +GWWRDPSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGF +TAALLDRVLALLGWDVPWDDSRVRDARTHEILRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001483.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001483.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f028e60e128d306f7eac06410ca7dc8a52d73ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001483.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01835 +MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLIALLTAGIPLLFFDYAIGHRF +RGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWAIMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSG +VFWPMLAVWVITLLIMGFGVRRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVSVSEVAGSGIGLAFIAFPTLI +SQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKLGWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFAN +NFGIVGAALLSVLLVTGALGSARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPVATTRKEL +>GCF_003691675_PROKKA_01532 +MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLIALLTAGIPLLFFDYAIGHRF +RGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWAIMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSG +VFWPMLAVWVITLLIMGFGVRRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVSVSEVAGSGIGLAFIAFPTLI +SQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKLGWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFAN +NFGIVGAALLSVLLVTGALGSARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPTAATRKEL +>GCF_005280335_PROKKA_01033 +MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLIALLTAGIPLLFFDYAIGHRF +RGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWAIMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSG +VFWPMLAVWVITLLIMGFGVRRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVSVADVAGSGIGLAFIAFPTLI +SQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKLGWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFAN +NFGIVGAALVSVLLVTGVLGSARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY +GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPADHTRKEL +>GCF_020097155_PROKKA_00974 +M-STSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVALLTAGIPLLFLDYAIGHRF +RGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSIMYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPG +VFWPMVAVWGVLLLIMGLGIRRGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQI +FFSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQVSEVAGSGIGLAFIAFPTLI +TQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLGWGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFAN +NFGIVGAALVAVIAVMWIARRGGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVY +GWGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEI-----------DHTAPVAS----------KES +>GCF_023573625_PROKKA_01756 +MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLIALLTAGIPLLFFDYAIGHRF +RGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWAIMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSG +VFWPMLAVWVITLLIMGFGVRRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVSVSEVAGSGIGLAFIAFPTLI +SQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKLGWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFAN +NFGIVGAALLSVLLVTGALGSARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPAATTRKEL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001485.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ffb6011bd5cd5b6c26b8fb671cf176be17819e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001485.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01838 +MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV +LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH +VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGP---AGAEGTAP +FDQVATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDD----GTPRMR +VKRATR-D +>GCF_003691675_PROKKA_01535 +MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV +LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH +VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGP---AGAEGTAP +FDQVATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDD----GTPRMR +VERATR-D +>GCF_005280335_PROKKA_01030 +---------------------------------------MVLVRDGEDGPEVFLRHRPGR +TPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTDRRCARQQVVAAVRELHDEAGV +LLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAARGLGLRTDLLRPVARWHSAPH +AHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRAVAGPVPLPGP---AGEEGVAP +LDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYRLVTEAGDD----GAPRMR +VERVTR-D +>GCF_020097155_PROKKA_00971 +MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR +TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV +LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH +SPRRFDTVVFAAALPPQQELVHRPE-GPVLQGWFSARRLLSEPAALPGPDGWLGESGVVA +LEEVSTPMTQLVLRRVAEHRTAAGFLLSPAGC--RGPVPVVKLRTEAEHDDLATGTLYTV +AERVDPVG +>GCF_023573625_PROKKA_01759 +MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV +LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH +VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGP---AGAEGTAP +FDQVATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDD----GTPRMR +VERATR-D + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001487.fa new file mode 100644 index 0000000000000000000000000000000000000000..4bce90c854a1e4e80c9fbbdd5750c9aa186a07c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001487.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_01840 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA +>GCF_003691675_PROKKA_01537 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA +>GCF_005280335_PROKKA_01028 +MTEQTKWEYATIPLLIHATKQILDQWGEDGWELVAVVPGPDGPNPVAYLKRPKAA +>GCF_020097155_PROKKA_00969 +MTQRIQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGANPVAYLKRPKDA +>GCF_023573625_PROKKA_01761 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001489.fa new file mode 100644 index 0000000000000000000000000000000000000000..b75aa5b8a0bdfb465f6c6e30b751e4207298948c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001489.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01842 +MPPAASPT-RRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRV +LHLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVF +VPGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPT +RAGTTLEVLAAGTDDPHLGLDAWAGFPGAAP------------------DENAGRPGDDG +RFRLGVTHAPYRRVLDAMTADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVST +WTAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLDLVPRG +>GCF_003691675_PROKKA_01539 +MPPAASPT-RRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRV +LHLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVF +VPGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPT +RAGTTLEVLAAGTDDPHLGLDAWAGFPGAAP------------------DENAGRPGDDG +RFRLGVTHAPYRRVLDAMTADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVST +WTAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLDLVPRG +>GCF_005280335_PROKKA_01026 +MRPSATAP-RRLVRAGSRAAVGMGTAAALGLAWGLVEAEARVVRTHRLAVLPAGADPVRV +LHLSDIHLLPRNRSRMAWLRGLDALEPDLVVNTGDNISAAASVPLVLDALGPLLRRPGVF +VPGSNDYYEPKPANPFRYFAGPSRMDEDRARLPTEALFGAFRAAGWADLTNRGSVLSVPT +RAGTVLEVLAAGTDDPHLGLDAWGGFPAPAPAPAPAPGDAAASGPASAHDDGAARPGGDG +RFRLGVTHAPYRRVLDAMTVDGADLLLAGHTHGGQVCLPGFGALVTNCDLPRAQASGVST +WTAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLELLPCA +>GCF_020097155_PROKKA_00967 +MTDAPGPRLRRLTHTAAWAAGGASALGAGALVWGRVEAEARVVRTHTVPVLPAGARPLRV +LHLSDIHLLPRHRRRLEWLCSLADLEPDLVVDTGDNISSAASIPLLLDALAPLLAVPGVF +VPGSNDYFTPKPANPLRYLRGPSELEASRSRLPTEDLFSAFRAAGWTDLTDRAADVVVGS +-GPDAVRIRAAGTDDPHLGLDRWPGF--------------------DLADEGAA--GDAP +LLRLGVTHAPYRRVLDAMTADGADLLLAGHTHGGQVCLPFAGALVTNCDLPRSQASGLSS +WTAAGRTVPLEVSAGIGTAPSAPVRTFCRPEAVVLDLVPRA +>GCF_023573625_PROKKA_01763 +MRPAASPA-RRMFCAAAPAAAGLAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRV +LHLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVF +VPGSNDYYAPKAANPLRYFAGPSRMDADRPRLPSDVLFGAFRAAGWADLTNRGAALAVPT +RAGTTLEVLAAGTDDPHLGLDAWAGFPGSAP------------------DGGAGRPGDDG +RFRLGVTHAPYRRVLDAMTADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVST +WMAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLDLVPRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001490.fa new file mode 100644 index 0000000000000000000000000000000000000000..0361e941a246e9e6497c4bb133d3c1708b4394da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001490.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01843 +MTRATSP-DASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFTQ-TVLAGPSSPDSRADVWR +AAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVML +VVDVVTIAVGLVLLFLLSWQLALLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHA +LDGFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYFATAAVLAGPVESVGQLMG +MTLSARTAIDRHVDVLATPVDIASPTGEAAV--------------------------VPPATGALAFRGVRFRWPDADPG +RGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSVCVDGVDVRRMPLEELRRRVSVAFEDATLFSAT +IRQNVLLGAPADVLADGLHSPAADALLDLALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVL +DDPLSALDVRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVYRHIISSRPEEQA +------------------------------------------- +>GCF_003691675_PROKKA_01540 +MTRATSP-DASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFTQ-TVLAGPSSPDSRADVWR +AAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVML +VVDVVTIAVGLVLLFLLSWQLALLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHA +LDGFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYFATAAVLAGPVESVGQLMG +MTLSARTAIDRHVDVLATPVDIASPTGEAAV--------------------------VPPATGALAFRGVRFRWPDADPG +RGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSVCVDGVDVRRMPLEELRRRVSVAFEDATLFSAT +IRQNVLLGAPADVLADGLHSPAADALLDLALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVL +DDPLSALDVRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVYRHIISSRPEEQA +------------------------------------------- +>GCF_005280335_PROKKA_01025 +MTRTAT--RPLPLREALQVVAPYLQGVRGRWVLGLLSAMAAGLVALAIPQVVQVLVNTVFAE-AAPGTAGTADPAAGVWW +AAGALALFGLAEALFIWLRRFFILPPAADVENRARISIYRRLQRLPVAFHDAWASGQLLSRAQGDLALLRRWIAFGSVML +VVETVTIVVGLVLLFVMSWQLALLYLVAAVPIMIRSFRFRTDFRAASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPDA +LDGFRGEAETLQGTEVHKASVLAKFISLTVSLPELVLGVALGLGLYLVAVGDLTVGALAAYFATTAVLARPVEGVGQLMG +MTLSAKTAIDRHLEVMRVPVAVASPAGTDAAEEEATSRAVASS---AAEDSPVVTDGLPPSSGRLAFRDVVFRYPDAP-- +EDSRPLLAGVDLELTPGETMALVGVTGSGKSTLVQLVPRLLDVTAGVVEVDGTDVRAYPLDELRRRVSIAFEDATLFSDT +VRANVLLGAPAEVTADGLDSPRAQALLDLALDTAQAGFARDLPAGVDTEIGEEGLSLSGGQRQRIALARAIAARPDVLVL +DDPLSALDVRTEEAVTGRLREVLAGTTTLIVAHRPSTVALADRVAVLQDGAIHDVGTHAELLARSAAYREIITTGAAEDR +SLAGLADAAHDDAALAAATDAARPPAGAARPPAGRTAGREETR +>GCF_020097155_PROKKA_00966 +MTRTTTAAAPLPLRDAVRGIAPYLEGVRTRWVLGLLSALAAGLVALAIPQVIRLLVNTVFAAPTTPGAPAAEDATASVWW +AVGGLALLGAAEALFIWLRRFFILPPAADVENRARIAVYRRLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVML +VVETVTLVVGVGLLFWLSWPLALVYLAAALPIMWRSYGFRNDFRTASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPHA +LEGFRGEAQTLQGTEVHKAGVLASFIAFTVSLAEVMLGVALALGVWLVATGQMTVGALAAYFATTAVLARPVEGIGQLLG +MTLSAKTAIDRHLEVMRQPVSIASPPGTDPAEEAATGASVGEDPDPAVADAPVDVSALPPSRGGLAFRGARFRHPDTP-- +DDAPDLLAGVDLELVPGETMALVGLTGSGKSTLLQLVPRLRDVTGGVVEVDGVDVRDYPLEELRRRVSIAFEDATLFSDT +VRANVLLGAPAAEVADGPDSPAAEALLELALDTAQAGFVADLPQGVDTPIGEEGLSLSGGQRQRLALARAIAARPDVLVL +DDPLSALDVRTEEAVTARLREVLAGTTTLIVAHRPSTVALADRVAVLQDGRIADVGTHADLLARSGAYRQIITTDREDAR +------------------------------------------- +>GCF_023573625_PROKKA_01764 +MTRATSP-AASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFTQ-TVLAGPSSPDSRADVWR +AAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVML +VVDVVTIAVGLVLLFLLSWQLALLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHA +LDGFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYFATAAVLAGPVESVGQLMG +MTLSARTAIDRHVDVLATPVDIASPTGEAAV--------------------------VPPATGALAFRGVRFRWPDADPG +RGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSVCVDGVDVRRMPLEELRRRVSVAFEDATLFSAT +IRQNVLLGAPADVLADGLHSPAADALLDLALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVL +DDPLSALDVRTEEAVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVYRHIISSRPEEQA +------------------------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001494.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2b9d7cacacefcc5e45957385ab20fcf4f9fc40c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001494.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01850 +M-SVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPA +TTLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWV +AFPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAG-GVRVPAVIGPLVG +AAVAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLT +QGLASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGT------- +---GAPSLIEALERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLA +NVGAHAGARRARVTLGYLGDELTVDVADDGAGFDPAVVAA-------------RPRAG-A +AGADPGA------GTGVGLASVRERLAAVGGEATVESAPGEGTVVALRVPLVAAGAGRSA +DPEQTESEETA +>GCF_003691675_PROKKA_01546 +M-SVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDA-SGPFPA +TTLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWV +AFPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAG-GVRVPAVIGPLVG +AAVAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLT +QGLASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGT------- +---GAPSLVEALERAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLA +NVGAHAGARRARVTLGYLGDELTVDVADDGAGFDPAVVVA-------------RARAG-A +AGADPGA------GTGVGLASVRERLAAVGGEATVESAPGEGTVVALRVPLAAAGAGRSA +DPEQTESEETA +>GCF_005280335_PROKKA_01018 +MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAP-AV +LALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWV +AFPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVG +AAVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLT +QGLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRAT------- +---GGASLVAAVERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLA +NVAAHARATRARVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAG-R +A-SRPGA------GTGVGLASVRERLAGVGGHASVESAPGEGTVVALRVPLPAA-AGRAE +EDEGRER---G +>GCF_020097155_PROKKA_00960 +MRTSDPADGPRGA---NGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPA +LALVGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWV +AFPLFFVALHAVHVI----LGRPRLALACVAAMTVVVV---VASLERGTAPGAVLGPAVG +AAVAVVVFHACRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLT +QGLASIVLVSRAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGG +ADRAGSALEAALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLA +NVDQHARTDRCRVTLTWMDGEVALDVADDGVGFDPEAA---------------RARASRA +AVSDPAAPRPAEEGTGVGLAGLAERVAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA +----------- +>GCF_023573625_PROKKA_01770 +M-SVAPRAA---APTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPV +TTLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWV +AFPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAG-GVRVPAVIGPLVG +AAVAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLT +QGLASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGT------- +---GAPSLIEALERAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLA +NVGAHAGAHRARVTLGYLGDELTVDVADDGAGFDPAVVAA-------------RPRAG-A +AGADPGA------GTGVGLASVRERLAAVGGEATVESAPGEGTVVALRVPLVAAGAGRSA +DPEQTESEETA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001496.fa new file mode 100644 index 0000000000000000000000000000000000000000..f48c55bd6b5e04f3ebe01887d57f31c80b94ec37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001496.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01853 +MTHATVAPAGETLALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP +RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALQCPPA +WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA +>GCF_003691675_PROKKA_01549 +MTHATIAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTSPDGRVLAGLGPADALIYP +RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA +WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPTFEARA +>GCF_005280335_PROKKA_01015 +MTQT---PSA-TFALADAVELVHVVRNGFVESRTPGAAVVTGPDGTVLAALGPVDALIYP +RSTLKPFQAIASLRHGARLEGQEVAIACGSHRGTAAHRELAARILAEAGLSAADLQCPPD +YPADAAEIVRFAQDLEHGAEKTPLAYNCSGKHAGFLAACVAAGHEVGTYLEPDHPLQAEV +ERVIEEYCGEPVAHTGTDGCGAPAAVLSLTALARGIGKVASAPSRRDAEIHAATVANAML +EHPWAVHGQSSSNTVVMRELGLLAKLGADGVMVMAAPDGTAVAVKALDGGTRAGNLVALA +LLAQFAPDHVDADRLPAVLETVAPKILGKGEPVGAVRLARPVLDLLD---------- +>GCF_020097155_PROKKA_00957 +MTQTSAAPAGQTFALADAVELVEVVRGGFVESRTAGAAVVTGPDGEVLAALGPADALVYP +RSTLKPFQAIASLRHGARLEGEALAIACGSHTGSEAHQQLAARVLADHGLAPEALQCPSA +LPEVAGEVARLAAQAGTAEIATPLAYNCSGKHAGFLAACAASGHDVGTYLDPEHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVVSLAGLARGIGAVSKAPGREGAEPHAAAVARAML +AHPWAVQGPGKANTVVMEELGLVAKLGADGVMVMGAPDGTAVAVKALDGGTRAGNLVALA +LLGRFAADQVDAGRLAEVSARVAPSILGRGAPVGEVRLAAPVRQLVG---------A +>GCF_023573625_PROKKA_01773 +MTHATVAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP +RSTLKPFQAIASLRHGAALAGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA +WPADTSEVVAQVRRDGEAAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001498.fa new file mode 100644 index 0000000000000000000000000000000000000000..568a9536890a089a523f012da307b8a0706d8ad1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001498.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01855 +MTSAPEPT----PDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYS +GIPLSFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDR +VDAGAPPARTT--PTE-RTPEQ +>GCF_003691675_PROKKA_01551 +MTSAPEPT----PDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYS +GIPLSFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDR +VDAGTPPARTT--STE-RTPEQ +>GCF_005280335_PROKKA_01009 +MTTGPERS----QHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYS +GIPLSFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDR +SAADALRSRTA--PTE-RTPEQ +>GCF_020097155_PROKKA_00953 +MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS +GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR +PEAVAPAARPAADPSDGRTPEQ +>GCF_023573625_PROKKA_01775 +MTSAPEPT----PDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYS +GIPLSFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDR +VDAGAPPARTT--PTE-RTPEQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001499.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3304829a89b3544a0c24a10bc61781f82fe0b42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001499.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01856 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAVSDGGRIAVYKDIGLVSQ +VFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNT +TDTALVTALLHGAPGDRLEETALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRLALEQPVEADVVIPVPESGTP +AAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGA +AEVHVKISSPPVKWPCFYGIDFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL +>GCF_003691675_PROKKA_01552 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAVSDGGRIAVYKDIGLVSQ +VFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNT +TDTALVTALLHGAPGDRLEETALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRLALEQPVDADVVIPVPESGTP +AAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGA +AEVHVKISSPPVKWPCFYGIDFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL +>GCF_005280335_PROKKA_01008 +MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAASDGKRIGVYKDIGLVSQ +VFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATAGGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNT +TDTALVTALLHGEEGRKLEETALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRLALEGPVDADVVIPVPESGTP +AAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGA +AEVHVKISSPPVKWPCFYGIDFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA +DESERGKSVLETDAGSAAVT-VMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL +>GCF_020097155_PROKKA_00952 +MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAGIAASDGKRIAVYKDMGLVSQ +VFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNT +TDTALVTALLHGEKGVSVEETALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRLAQEHPVDADVVIPVPESGTP +AAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGA +AEVHVKISSPPVKWPCFYGIDFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA +DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL +>GCF_023573625_PROKKA_01776 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAVSDGGRIAVYKDIGLVSQ +VFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNT +TDTALVTALLHGAPGDRLEETALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRLALEQPVDADVVIPVPESGTP +AAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGA +AEVHVKISSPPVKWPCFYGIDFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001501.fa new file mode 100644 index 0000000000000000000000000000000000000000..4cc6741446e78c15062f04b57a88b755b69b94eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001501.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01858 +MA------------------TSSLPLSDIVETGRP---FTRGDLRAAGVSERLVRGGDVR +RVTHGVHRLRSDHLGSWADLGYVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPP +FLAEDGTVHVSRPHPRGASVRPEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRP +GMLEPVVAAGDALIHRPWSPEGRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGA +DSPQETALRLALLHAGLPEPELQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQL +AVDSWRDEGWARAGWTQIWATVDDARDDFRRVVAEVQTHRARLGGRVFAS +>GCF_003691675_PROKKA_01554 +MV------------------TSSLPLSDIAEAGRP---FTRGDLRAAGVSERLVRGADVR +RVTHGVHRLRSDHLGSWADLGYVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPP +FLAEDGTVHVSRPHPRGASVRPEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRP +GMLEPVVAAGDALIHRPWSPEGRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGA +DSPQETALRLALLHAGLPEPELQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQL +AVDSWRDEGWARAGWTQIWATVDDARDDFRRVVAEVQTHRARLGGRIFAS +>GCF_005280335_PROKKA_01006 +MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPL---FTRADLSAAGLPADRLRAADVR +RVTHGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPP +FLVDDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRP +GHLDPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGA +DSPPETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQ +AVDAWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA +>GCF_020097155_PROKKA_00950 +MALESLADV-----------LGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVR +RVTHGVHRLATDPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPP +FLAEDGTVHVSRPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPP +GLVDPVVAAGDAVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGS +DSPQETALRLALVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQR +AVDARRHEGWERAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC +>GCF_023573625_PROKKA_01778 +MA------------------TSSLPLPDIVETGRP---FTRGDLRAAGVSERLVRGGDVR +RVTHGVHRLRTDHLGSWADLGYAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPP +FLAEDGTVHVSRPHPRGASVRPEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRP +GMLEPVVAAGDALIHRPWSPEGRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGA +DSPQETALRLALLHAGLPEPELQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQL +AVDSWRDEGWARAGWTQIWATVDDARDDFRRVVAEVQTHRARLGGRIFAS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001510.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0c06950069a8bead0e5f6df46b8a0c91977c16e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001510.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01867 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDIARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL +>GCF_003691675_PROKKA_01563 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL +>GCF_005280335_PROKKA_00993 +MAQQTPQP----AASAVDAAGVHVADLNKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGRITVGEFDVTDEDVDLDALRRHVGMVFQQFNLFPHLSVLENCTV +AQVKVLKRSKAEAAEVARRQLARVGLAELEDRFPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGEVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVSMDAGVVVETGPA +AALIADPQQPRTQDFLRRVLHPTEIDL +>GCF_020097155_PROKKA_00931 +MTEQTASP---RPSDAGTAAGVHIAGLHKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEVPDSGGVQVGEFTVTDPDVDLDRLRQHVGMVFQQFNLFPHLTVLENCTV +AQVKVLKRSAAEAADTARRQLARVGLGELEGRYPDQLSGGQQQRVAIARALSMDPRLMLF +DEPTSALDPETVGDVLAIMRKLAREGMTMLVVTHEMGFAREVADRVVFMDGGVVVEQGPA +SAVITDPQEPRTQDFLRRVLNPAGVDI +>GCF_023573625_PROKKA_01787 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLGIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001512.fa new file mode 100644 index 0000000000000000000000000000000000000000..2ebb939c44bf0e1e2e52eec94f867736968681bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001512.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01869 +M--------------------LPLVA--PLTVAAA---APTDYGWLGNIVVDIMEAVGPI +GVGLAVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALVWATVGSIVGALALYGLGAWL +GRHRMYRLADRMPLVDMEDVAKTERWFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLA +KFTLFTALGSLIWNAIFVYGGYALGERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRR +DARRRNDPDWRPPTADEMAARVEAILESSDHRK +>GCF_003691675_PROKKA_01565 +M--------------------LPLVA--PLTVAAA---APTDYGWLGNIVVDIMEAVGPI +GVGLAVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALVWATVGSIVGALALYGLGAWL +GRHRMYRLADRMPLVDMEDVAKTERWFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLA +KFTLFTALGSLIWNAIFVYGGYALGERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRR +DARRRNDPDWRPPTADEMAARVEAILESSDHRK +>GCF_005280335_PROKKA_00991 +M--------------------LPAVT--PLTLAASTVTADTDYGWLGNVVVDIMEAVGPV +GVALAVFAENIFPPIPSELILPLAGFTAAGGAFSPLAALLWATVGSVTGALALYGIGALL +GRRRMYRIADRMPLVDVEDVAKTERWFARYGYWTVFLGRMVPVFRSLISIPAGIERMHLG +MFTLFTTLGSLIWNAIFVYGGYALGERFHLVSDYADVFSNVVVVLVLAFLVVWVVLRLRR +NARRAKDPDWHQPTADEMAARVDALLESSDHRK +>GCF_020097155_PROKKA_00929 +MIRRGRTTSDAAAVVVVENGGMSALSTLPLLAAAG---TP-DYGWLGNTIVAIMEAIGPV +GVGLAVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALIWATVGSVVGALALYGLGAWL +GRRRLYRIAAWMPLVDVSDVERTEKWFARYGYWTVFVGRMVPVFRSLISIPAGIERMNVA +KFTLFTALGSLLWNAIFVYGGYALGENFHVISDYADMFSNIVMVLILVFLAVWVVLRLRR +NRGRAADPAVDHEDPEAAAARVEAEIKALQHRK +>GCF_023573625_PROKKA_01789 +M--------------------LPLVA--PLTVAAA---APTDYGWLGNIVVDIMEAVGPI +GVGLAVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALVWATVGSILGALALYGLGAWL +GRHRMYRLADRMPLVDMEDVAKTERWFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLA +KFTLFTALGSLIWNAIFVYGGYALGERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRR +DARRRNDPDWRPPTADEMAARVEAILESSDHRK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001518.fa new file mode 100644 index 0000000000000000000000000000000000000000..b57131783afd023cb56d07fd8beaa2ec747da7b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001518.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01875 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPR--------VSAESAAEQAED- +GDALAQAERILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEYVNYKRRVDRDRDLAR +DAGVLKAVTALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVE +FDPAVHEAVMRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>GCF_003691675_PROKKA_01571 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPR--------VSAESAAEQAED- +GDALAQAERILDEAGAEAGTQAPQPAASDREAELETDLRRLQAEFVNYKRRVDRDRDLAR +DAGVLKAVTALLPVLDDIDAARAAGDLTDGPFAAIATKLDTVLAGLGLERHDQAALAGVE +FDPALHEAVMRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>GCF_005280335_PROKKA_00984 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPR--------VSAESAAEQAED- +GDALTQAERILDEAGAQAGTEAPQPAASDREAELETDLRRLQAEYVNYKRRVDRDRALAQ +DLGVLKAVTALLPVLDDLDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVE +FDPSVHEAVMRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>GCF_020097155_PROKKA_00922 +MSENQN--------ETPSPEEPVI-RDRRRIDPETGQARTPGAGEDTVPAQEQGQAPQDS +GDALSQAEQILDEAGAAAEAEALPAAGSDREAELLEDLRRLQAEYVNYKRRVDRDRDVAK +EQGVLKAVTALLPVLDDLDAARAAGDLEDGPFAAIAAKLMTALEGLGLEREDQEALAGVE +FDPVRHEAVMRQPHAEVPADHVVQVFRNGYARDGRVLRAAQVMVSAGQD +>GCF_023573625_PROKKA_01795 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETDEPR--------VSAESAAEQAED- +GDALAQAERILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEFVNYKRRVDRDRDLAR +DAGVVKAVTALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVE +FDPAVHEAVMRQPHAEVPADHVVQVFRNGYLRDGRVLRAAQVMVSAGDE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001521.fa new file mode 100644 index 0000000000000000000000000000000000000000..daf8e7a24697977f8f292696570bb0bc9802d363 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001521.fa @@ -0,0 +1,75 @@ +>GCF_002008305_PROKKA_01881 +MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLKEEFPEASRGRGQVVFTTEDG +SPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDARTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEAD +AAEQRLAEAAAQLEEGQAKLDAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA +QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQVTEQFADQEAQLAAAEAQLA +AGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAARLAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQ +QQKIDEGRAEYERGVAELEDGRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV +TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVLVVMLGTLVGAGLPLVNALVG +VGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFIVNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVAL +VGLNVTGIPFLGLMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSA-------------- +---AVRRAGRRSTMSTPAAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVVTVD +LPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVSTEELVRDLRATEPAGEASNLGVAG +MTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRSILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPV +LSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPMGFG +LAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQPSVPAP----------DGGAHRA +>GCF_003691675_PROKKA_01577 +MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLKEEFPEASRGRGQVVFTTEDG +SPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDARTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEAD +AAEQRLAEAAAQLEEGQAKLDAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA +QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQVTEQFADQEAQLAAAEAQLA +AGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAARLAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQ +QQKIDEGRAEYERGVAELEDGRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV +TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATVSSLLGPGEVVGLVVAAIVLVVMLGTLVGAGLPLVNALVG +VGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFIVNRHRHELRRGTSLHESIALATGTSGNAVVFAGITVIVAL +VGLNVTGIPFLGLMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSA-------------- +---AVRRAGRRSTMSTPAAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVVTVD +LPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVSTEELVRELRATEPAGEASNLGVAG +MTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRSILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPV +LSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPMGFG +LAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAAEAASAPAPEAGRTPAVDGGAHRA +>GCF_005280335_PROKKA_00977 +MAKLLYRLGLGAARRPLTVILAWVLALALAVGGFLAFGGTLSTNVTIPGTPTAQVTDRLQDEFPEASRGMGQVVFTTEDG +QPFTDAQRDAVAALLDEVAGQDAVDAVVDPFEVQAQQDDARTALADGRQEIADGEQALVDGREQVDAGRAEIEEGRAQAD +AGEQELADAAAQLEDGQVQLDAARADIEARGLDALPAEALAPLREAEQQIADGQAELDAGRAEIEEQAARLAAGQAEIDA +NREQLEAGQAELDARWGELDAAQAQLDAQREELEAGRAQLEQALAAALEQAEAAGIPAEQVTAQFAEQQAQLEAGQAQLD +AAQEQADAGREQLVAAQAEADAGAEQLAEAQAQADAGAEQLAAGREQLEAAEAELESGREQLAAGRQQALDAAAAELDAQ +QARIDEGRAQHEQGVADLEAGRAELAAGAERLDQAEADLATGRTELEDGRVAAERGERSLALVGGYRSVSEDGSTAVGIV +SFSQPSLDVTAEEKEAVTGALTGADIDGVAVHPSQELNATVPSILGPGEVVGLIVAAIVLVVMLGTLVGAGLPLVNALVG +VGVGAAGALAFSSVVEMISVTPVLGVMLGLAVGIDYALFIVNRHRQELKRGTALHEAIALANGTSGNAVVFAGITVIIAL +VALNVTGIGFLGLMGTVGAVCVAVAVLVAVTLTPALLSLAGTRILSRKERARLADEGPASAAEGSA-------------- +---AVRRAGRRSTMSTPAAIASALAAIALLVLVALPFGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVVTVD +LPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVSTEELVRELRATEPAGEASNLGVAG +MTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGSVFGVHNPGPV +LSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPIGFG +LAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAAEAASAPAPEAGRTPAVDGGAHRA +>GCF_020097155_PROKKA_00915 +MATLLHRLGLASARRPWAAILAWLIALALAVGAFLAFSGTLTTAVTIPGTPTAQVTDRLKEQFPDAAKGTGQVVFATEDG +SAFTEAQRRAVSDALRGVEGQDAVDSVVDPFDVARQQDEARTALEDGRRQIAEGEQKIAENEKALEDGRAQLAEAKDKAE +AGQKELDAAAAQLDAGQEKLDAARADLEARGLDALPAEATAPLTEAQQKLDAGQAEYDAGVAALEEQRPALEAAEAEIAK +QEAALEQAQA---------------------RFEAGRAQ-------AIAQAEAAGATPEQAA---AAVDARLAPEREKLD +AGAAQLEEARARTEAGRAEFDAGEEKLAAAA---------------------AELEQGRAQLAAGREKALTAARAELDAQ +QQKIDAGRAEHEQGVRELEAGRAEIAQNEAKLADGPAQLEQARKDLAAGREKADRGQRMLTLTDGYRVVSEDGSAALGTV +AFDRPSLDVTTEQKTAVIDALADADIPGVRAIPTQALNATMPSLIGPGEVVGLAVAALVLVLMLGTLVGAGLPLVNALIG +VGVGAAGALAFSGVVEMMSVTPVLGIMLGLAVGIDYALFIVNRHRLELKRGTPLHASIALANGTSGNAVVFAGITVVIAL +VALNVTGIPFLGLMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSRKERARRAAEA-APVADDAAAPSGSHAAAPVSRS +AARAVRDARRRRRMSTPAAVATVLASAAALIVVAIPFGSMRLGLPDGASEPVGSDSQVSYELIADEFGEGYNGPLVVTVD +LPSGLDETTAEDAQVQVGEQLKGLEHVAAVVPAGFNQDRTTAMFQVLPEEGPNAISTGDLVHTLRDTEPAGEASNLGVAG +VTSGFIDVSEKLSAALPLYLGVVVGLSLLIMILVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGGLFNVHAPGPV +LSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGQPARDAVMTGLRAGRAVVTAAAIIMISVLGGFVFSHDAMIRPIGFG +LAFGVLLDAFVVRLLLMPALMHLLGDAAWWLPKWLDRILPDVDVEGAGLER-HGAAGEAADAAPV----------GADRA +>GCF_023573625_PROKKA_01801 +MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLKEEFPEASRGRGQVVFTTEDG +SPLTDAQREQITALLDDVAEQPAVEGVVDPFEAQAQRDDARTRLDEGRAELADGEQRLADGRQEIEDGRAELERRTAEAD +AGEQRLAEAAAQLDEGQAALDAARADLEERGLEALPADALAPLREAEQKVADGQEQLDAGRAELEEQAERLEAGQAEIDA +QRQELEAGQAELGDRWTELEAGQAELDAQAEQLAAGRAELEQARDAALAEAEAAGIPAEQVAAQFADQEAQLAAGEAQLA +AGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAARLAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQ +QQKIDEGRAEYERGVAELEDGRAQLAAGAERLDQAEADLADGRAELDDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV +TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVLVVMLGTLVGAGLPLVNALVG +VGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFIVNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVAL +VGLNVTGIPFLGLMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSA-------------- +---AVRRAGRRSTMSTPAAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVVTVD +LPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVSTEELVRDLRATEPAGEASNLGVAG +MTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRSILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPV +LSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPMGFG +LAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQPSVPAP----------DGGAHRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001525.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b83224330a528dbad3acd664c767ffd1401e179 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001525.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01885 +-MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRH +THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR +>GCF_003691675_PROKKA_01581 +MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAAHRH +THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR +>GCF_005280335_PROKKA_00973 +MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAIATDVLLVVLSSGLILDMAVRRH +TDNVVLVVLAATVGFVGSVTVARFVEDRRPDHSMEDQARVPGTSDVPGGEEGR +>GCF_020097155_PROKKA_00911 +MSLPLTLAAWIGGAMLFVGAVGALYRIARGPSLLDRAAATDVLLVVLSGALLLDMGVHRR +TDTVVLVLLAAAVGFMGSVMVSRFVEDRRPEHPQEHEALVPGTSDVPAPREDA +>GCF_023573625_PROKKA_01805 +-MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRH +THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001526.fa new file mode 100644 index 0000000000000000000000000000000000000000..b4e6f4df757ea548354126f76d2d05ce1129c841 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001526.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01886 +MPGSDSARRGV-----VRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALL +IIGLFPMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLR +SHDDLIITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGII +RAVGTREDLELVRRFPSSAPPAARPPKEEA------------------------------ +---- +>GCF_003691675_PROKKA_01582 +MPGSDSARRDV-----VRPDRVRGIVAQWPLILVMVAVWCALWQDFAPHVALAGLAFALL +ILGLFPMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVTGVVLLRGRRARGSIVGVPLR +SHDDLIITLVSHALVLVPGSIVLDVDRVRSVLYLHVLDATTDEDVEGFRAKALDVEAGII +RAVGTREDLELVHRYPDTAPPEEESAERRR---------PAAPRPGGTAPIGSTADHAKE +GT-- +>GCF_005280335_PROKKA_00972 +MPGTDPARDAAGAERPARPHRVRDMVGQWPLIAVLVLLWCAVWEDYSLHVALAGLAFSLL +VMVLFPMPRIPFSGRLNPWWFLVFTAQFLGDVVRSSVEVSKVVLLRGRAARSSIVGVRLR +SHDDLVITLVSHALALVPGSIVLDVDRARSILYLHVLDATTDEDIEDFRAKALRVEAGII +KAVGTREDLELVHRYPDTAPPEEESAERRR---------PAAPRPGGTAPIGSTADHAKE +GT-- +>GCF_020097155_PROKKA_00910 +MPAAETTSPASAPTRPA-PGGVRSVLRQWPLLLALVLMWCAVWQDFSAHVALTGLLFSLL +VVVLFPMPPIPFGGRFHPGHALVFTGRFLADVVASSLSVTRVILTRGRTVRSSVVRVPLR +SHDDIVLTLVSHALALVPGSIVLDMDRANGVLYLHVLDATTDADVADYRAKALRVEADII +RAVGTRADVAVLRDHPDSAPDPEGVEERRRHPAYRAELLPDTPGPVAPAPVDARPEPDAP +GGDR +>GCF_023573625_PROKKA_01806 +MPGSDSARRGV-----VRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALL +IIGLFPMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLR +SHDDLIITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGII +RAVGTREDLELVRRFPSSAPPAARPPKEEA------------------------------ +---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001527.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001527.fa new file mode 100644 index 0000000000000000000000000000000000000000..5cbcc0f6895122d342bb0a13af96c94ba0b6c181 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001527.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01887 +MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWDTGVAAVHLGGWPAPLGISLV +VDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIFHPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTM +GGTAQRIRAGVTYVVVSVLSSVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALAQTDIKRILSFILVSHIGYMI +FGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAGTANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGK +VGLLRGGVEQATPLAYTLVGVSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHDARK +>GCF_003691675_PROKKA_01583 +MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWDTGVAAVHLGGWPAPLGISLV +VDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIFHPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTM +GGTAQRIRAGITYVVVSVLSSVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALAQTDIKRILSFILVSHIGYMI +FGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAGTANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGK +VGLLRGGVEQATPLAYTLVGVSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHDARK +>GCF_005280335_PROKKA_00971 +MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWEGGVASVHVGGWPAPLGITLV +VDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIFHPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTM +GGTAQRIRAGITYVVVSVISSVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALAQTDIKRILSFILVSHIGYMI +FGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAGTANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGK +VGLLRGGVEQGTGLSYTLVGVSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT +AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHDARH +>GCF_020097155_PROKKA_00909 +M-LGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTGGVAVVELAAWPAPVGITMV +VDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFHPTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTL +GGTEARIRAGITYVVVSVISSVLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQSGLKRILSFILVSHIGYMV +FGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGTASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGK +VGLIRGGVEDGGVLAWVLVGVSLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPT +AGLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDAGR +>GCF_023573625_PROKKA_01807 +MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWDTGVAAVHLGGWPAPLGISLV +VDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIFHPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTM +GGTAQRIRAGVTYVVVSVLSSVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP +DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALAQTDIKRILSFILVSHIGYMI +FGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAGTANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGK +VGLLRGGVEQATPLAYTLVGVSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT +TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHDARK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001528.fa new file mode 100644 index 0000000000000000000000000000000000000000..a084ec201ffb2b5a190794d1f824fee9b5cc20db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001528.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01888 +MM-TVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLF +VRGRDPHEYADTLPQALILTAIVIGFAVIAFLTAMIYRSWLLVREDEVEVDAEDVKIARM +PAWDAEDDAELVEESSEFLDDAADPNAHYEHATESRPHVRHASPTPPAHPGPASAVRAHR +ADGGPRP +>GCF_003691675_PROKKA_01584 +MM-TVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLF +VRGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARM +PAWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRR +PEGGERA +>GCF_005280335_PROKKA_00970 +MM-TVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLF +VRGRDPHEYADTLPQALILTAIVIGFAVTAFLTAMIYRSWLISREDEVEVDAEDVKIASQ +GAWDAEDDSELVEEHSEFMDASTDPNAHYEHTTEARPQVQHVIPAPPTAAGSREAARGRR +PEGGERA +>GCF_020097155_PROKKA_00908 +MTPTVDLALLAVMGVLFATGIYLLLERSLTRILVGVMLINNAAVVLLFLTSGGAGLAPLY +DADTAPEDYADMLPQALILTAIVIGFATTAFLTAMIYRSWQLRREDDVATDVEDVKIAAQ +SGWDAEDDSVLTEEDSEFMDDASDPNAEYEFATAAAPRARAVRPGRATVQG--------- +--GGGRP +>GCF_023573625_PROKKA_01808 +MM-TVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLF +VRGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARM +PAWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRR +PEGGERA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001530.fa new file mode 100644 index 0000000000000000000000000000000000000000..c03dbe9444276e80c06b7bc08daf2b82963f773d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001530.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01890 +-----------------MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTY +LASDAFGPDERGTAWLSTAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTA +ACFWVTPEESSLLLGVTLIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLG +GILLLLIVFVGFVSGDAHWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPA +ADGGPRRESVLGSYRELGATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVY +GLAASDVILFAIAANVVAALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLA +FWVGGLALCLFVGPVQSASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALAL +HPDNRVVIPVIAVVLVAGGLLFARVTEPITRSAESVR--------- +>GCF_003691675_PROKKA_01586 +-----------------MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTY +LASDAFGPDERGTAWLSTAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTA +ACFWVTPEESSLLLGVTLIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLG +GILLLLIVFVGFVSGDAHWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPS +PGGGPRRESLAASYRALGSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVY +GLAASDVILFAIAANVVAALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLA +FWVGGLALCLFVGPVQSASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALAL +HPDNRVVIPVIAVVLVAGGLLFARVTEPITRSAESVR--------- +>GCF_005280335_PROKKA_00968 +-------MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTY +LASDAFGPDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTT +ACFLVTPQESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLG +GILLLLIVFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPT +PGGGPRRESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVY +GLAASDVILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLA +FWIGGLALCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAA +VPDNRVVIPVIVLVLIVGGVLFARVTDPVTRSAEPAP--------- +>GCF_020097155_PROKKA_00906 +MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY +LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA +ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG +GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG +ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY +GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA +FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV +WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR +>GCF_023573625_PROKKA_01810 +-----------------MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTY +LASDAFGPDERGTAWLSTAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTA +ACFWVTPEESSLLLGVTLIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLG +GILLLLIVFVGFVSGDAHWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPA +ADGGPRRESVLGSYRELGATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVY +GLATSDVILFAIAANVVAALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLA +FWVGGLALCLFVGPVQSASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALAL +HPDNRVVIPVIAVVLVAGGLLFARVTEPITRSAESVR--------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001531.fa new file mode 100644 index 0000000000000000000000000000000000000000..af9bc64edfcb47d57250a84ef8fec7610751ed0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001531.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01891 +---MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQKQ +DELTRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGF +IDPGFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGP +TASRAHRDFHLTRIER +>GCF_003691675_PROKKA_01587 +---MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQ +DELTRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGF +IDPGFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSAAQSPYGTGANQNRYQGQRGP +TASRAHRDFHLTRIE- +>GCF_005280335_PROKKA_00967 +---MLLSDQDIRAELASGRVGLDPLDEAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQ +DELTRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGF +IDPGFTGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSPAASPYGTGANQNRYQGQRGP +TASRAHLDFHLTRIDR +>GCF_020097155_PROKKA_00905 +MASVLLSDRDIRAELSSGRIGLDPLELSMVQPASVDVRLDRFFRLFDNHRYAHIDPAQPQ +EELTRLVEVEPDQPFVLHPGEFVLGATYEQITLPDDVAARLEGKSSLGRLGLLTHSTAGF +VDPGFTGHVTLELSNVATLPITLWPGMKIGQLCFFRMSSPAESPYGSGGNLNRYQGQRGP +TASRSHQDFHLTRIPR +>GCF_023573625_PROKKA_01811 +---MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQ +DELTRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGF +IDPGFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGP +TASRAHRDFHLTRIER + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001532.fa new file mode 100644 index 0000000000000000000000000000000000000000..a55de1061c7ba01ca4be739936b5295f9bb3ffc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001532.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01896 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTT---------AGRRRAVRRSPGRA +VADQVRHTVTNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGS +RPLERAGGRRADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFV +TAVRYDTGLRVSKDTILVTTIVAIPAMIAVALLLA +>GCF_003691675_PROKKA_01592 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTT---------AGRRRAVRRSPGRA +VADQVRHTVTNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGS +RPLERAGGRRADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFV +TAVRYDTGLRVSKDTILVTTIVAIPAMIAVALLLA +>GCF_005280335_PROKKA_00962 +MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV +LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG +DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARA----------AGGRPAVRRSRGQA +LAAQLRQTGTNPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGS +RPLERAGGRRADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFV +SAVRYDAGLRVAKDTILITTIVAIPAMIAVALLLA +>GCF_020097155_PROKKA_00901 +MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV +LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG +DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVR--PRNP +VLAQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGS +RPLARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYV +SAVRYRAGETVSKDTILVTTIVAIPAMIAVALLLA +>GCF_023573625_PROKKA_01816 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTT---------AGRRRAVRRSPGRA +VADQVRHTVTNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGS +RPLERAGGRRADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFV +TAVRYDTGLRVSKDTILVTTIVAIPAMIAVALLLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001533.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a118087b30789c1a43984dfa3ca80a8993d9ec3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001533.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01899 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG +SFAADARAFLDTRRAELTDLPLVILASGGAPELARPVREKLESYGPREVAYFRGALFEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLPGAGVR +>GCF_003691675_PROKKA_01595 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG +SLAADARAFLDTRRAELADLPLVILASGGAPELAPPVREKLESYGPREVAYFRGALVEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR +>GCF_005280335_PROKKA_00959 +MTTLIVTSSAHGSTREIAERVAEVLRTSQSVETVVEDVAGAAAWLATADAVIVAAPVYEG +SLAAEARHFLDSRRAELADKPLLFLASGGGYELDPKVREKLESYGPREIAFFRGALVEER +LGWLEKLKLKVSRNENYGDYRDWDAIEAWAKSLSGHGVR +>GCF_020097155_PROKKA_00899 +MTALIVTASRHGSTREIAERVAEVLRTTAQTDTVVEDVAGAAAWLDTADAVVVAAPVYGD +KLEKSAKAFLDSRRAELSQKSLVILYSGASPVPNRALADQLGTYGARDVKYLRGALVEER +LGALEKLQIKLVKGR-YGDFRDWNAVEHWAKGLSAHGVN +>GCF_023573625_PROKKA_01819 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVKGAAAWLATADAVIVAAPVYTG +SLAADARAFLDTRRAELADLPLVILASGGAPELARPVREKLESYGPREVAYFRGALVEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001534.fa new file mode 100644 index 0000000000000000000000000000000000000000..9504decf8b21b7154353512b4d192afbc353a128 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001534.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01900 +--------------MMVGMTAPQT-----PNPVPSADAPAAVPRAATRVRASELVGRGWLNTGGEQVTLEDLRGKVVLLD +FWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPVLDDPELTTWQAYSARAWPTLV +VVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLHRGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGSFLVSDTG +HHRLLEVAEDLTTVLRAFGGGDPATADAGQAELAFPTPGEKGHADGGPDEALFNEPQGLALLPEDVAERVGYDVVVADSV +NHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDIAVDLADLPGEPTAISLSSPWDVVWHPALGRVVIAMAG +THQLFDFDPVTGALAVHAGTALEGLLDGDAGRAWFAQPSGLSVGADGALWVADSETSAVRWVRTGEDGRREVGTAVGAGL +FDFGHVDGEADRARLQHPLGVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADGN +DTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKLDDRWGDPTQLKISSSPEELLL +EGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQPIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRG +IH +>GCF_003691675_PROKKA_01596 +--------------MMVDMTAPQT-----PNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLLD +FWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPVLDDPELTTWQAYSARAWPTLV +VVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLHRGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTG +HHRLLEVAEDLTTVLRAFGGGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADSV +NHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISLSSPWDVVWHPALGRVVIAMAG +THQLFDFDPVTDALAVHAGTALEGLLDGEAGRAWFAQPSGLSVGADGTLWVADSETSAVRWVRTGEDGRREVGTAVGAGL +FDFGHVDGEADRARLQHALGVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADGN +DTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKLDDRWGDPTQLKVSSSPEELLL +EGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQPIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRG +IH +>GCF_005280335_PROKKA_00958 +--------------MMVGMTDPQTPPAVSPDAAPSDAAPAAVPRAASRVRASELVGRGWLNTGGEQVTLEDLRGKVVILD +FWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYTIEHPVLDDPELTTWQAYSARAWPTLV +VVDPEGYIAAHLSGEGHVAGLYSLVRELVAEHEAKGTLHRGSGPYVPPAPVARDLKFPGKAISLAGRGTAPGTFLVADTG +HHRLLEVAEDLTTVLRAVGGGDPAGAGEEQAGLAFPTPGEKGHADGGPEQALFNEPNGLALLPEDVAERVGYDVVVADTV +NHRLRGLRLADGGVSTVAGNGVQKLIDSERAKEASAGDAE-DVAVDLSDLPGEPTAISLSSPWDVAWDPAAGRVVIAMAG +THQLFDFDPVAGALAVHAGTGLEGLLDGDAGSAWFAQTSGLSLGPDGTLWAADSETSAVRWLRTGEDGRREVGTAVGTGL +FDFGFVDGEAAQARLQHPLGVTALPDGSVLIADTYNGAVRRYAPAGEDAAGRPVAAAVSTVARGLQEPSDVLVEHDADGA +PAAIVVVETNAHRLVRLAVPEEYLTVDEGARQTQRPRTPMVAGDVDLAIGFAAPSGQKLDDRWGDPTQLKVSSSPEELLL +EGAGTSTGLSRTLRLNPAVAEGVLHITARAAACDGEKGQPIPDHAACHLYQQDWGIPVTVHAPEGAPEGAETRLDLDLRG +IH +>GCF_020097155_PROKKA_00898 +MRRPLPADARRAWAMMEGMTEQQT-------SAPS------VPRSGSRVRASSLVGRRWLNTGGTEVSLEDLRGKVVILD +FWTFCCINCLHVADELRPLEEEFSDVLVTVGVHSPKFEHEADPDALDAAVERYDIAHPVLDDPTLVTWQAYSARAWPTLV +VVDPEGYIVAHLSGEGHVAGLYSLVRELVAEHEAKGTLHRGSGPYVAPAPVARDLKFPGGAVSLEGRGSRPGSFLVADTG +HHRIVELAADLTTVLRAIGGGDPAEAPAEAADLAFPTPATRGHRDGGPETALFSEPNGLLLLPEDVAARAGVDVVVADTV +NHRLRGIDLATGEVTTLAGNGVQKLIDSERVREAAAGDES--AAADLSDLPGDPTGISLSSPWDVAWDAAAGRVIVAMAG +THQLFSYDPVARVLAVHAGTGLEGLLDGPADTAWFAQTSGLSFAQDGTLWLADSETSAVRWLRTAEDGTRQVGTAVGTGL +FDFGYVDGAPEQARLQHPLGVTALPDGSVLVADTYNGAIRRYAPAAEDAAGRPVEAAVSTVTRELKEPSDVLVEPGEDGA +PAEIVVVETGAHQLVRISVPAEYLTVDEGARQTARPSTDVAAGDLDLSVGFAAPAGQKLDDRWGDPTQLKVSSSPEELLL +DGAGTSVGLTRTLRLNPAVAEGVLHITARAAACDGEKDGPIPDSAACHLYQQDWGIPVRVHAADQAPDGAETRLDLDLRG +IH +>GCF_023573625_PROKKA_01820 +--------------MMVDMTAPQT-----PNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLLD +FWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPVLDDPELTTWQAYSARAWPTLV +VVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLHRGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTG +HHRLLEVAEDLTTVLRAFGGGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADSV +NHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISLSSPWDVVWHPALGRVVIAMAG +THQLFDFDPVTSALAVHAGTALEGLLDGEAGRAWFAQPSGLSVGADGTLWVADSETSAVRWVRTGEDGGREVGTAVGAGL +FDFGHVDGEADRARLQHALGVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADGN +DTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKLDDRWGDPTQLKISSSPEELLL +EGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQPIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRG +IH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001535.fa new file mode 100644 index 0000000000000000000000000000000000000000..119131abd1dfc4d98aa011706beecb58afa27980 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001535.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01901 +MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDND-PAAASVPADGVHDDAGT +AVHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADA +DRTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVER +HIQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQ +LTAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAA-LAAD +>GCF_003691675_PROKKA_01597 +MSADRLPPLGRPAAPRRGRLRLAAAVAAGLLALTGCGAGDGD-PAAASASADGVHGDAGT +AAPTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADA +DRTTVQPAQCKAPLTALDFSPIALDEAEATRVDVGADTFTGTGTVEVARLTGQGRQDVER +HIQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQ +LTAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAA-LAAD +>GCF_005280335_PROKKA_00957 +-----------------------------MLALTGCGAGDEPAPEQPSAPADALHGDVGG +AAPAPEEGAEGLGLGDRQDERMAAAAAERAVGFGFVRQRAAAPEEIDAAREDSRARRSDA +DRTTVQPAACKAPLTALDFSPISLDEGEATRVDVGADTFTGTGTVEVARLTGSGRQEVER +HLQTVNGLLADCREMTMTVQDGDASVDYRLAVSEAPLSEGTPAQSALVWERSLASADGPQ +LTAQVLTAVTADAVVMVSFVGQPEAGRKEFTLIAEEMLAAA-LAAG +>GCF_020097155_PROKKA_00897 +MSADRTRP--RPAVRRLAVASSGAALAAVLLA--GCASGGDA---AASSGAQA------- +AGPSSSAATGGLDLGDRVDQRRAEAAAARAASFGFTRQDAVGADQIAAARGDAADRAADD +GRTTVEPARCQAPLAALDFSPILLDQEEVSRVDVGTDSFAGTGTVEVATLDGPGRQRVEE +HLQTVNTLLADCRDMTVTTRDADGARTYRLQMSAAGLSDGSPAQSGLVWTQTPAGRDEPA +TAAQILTAVGPEDVVMVSFTGQPQAAERQFTVMAEEMLAAAGTVTR +>GCF_023573625_PROKKA_01821 +MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDND-PAAASVPADGVHDDAGT +AVHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADA +DRTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVER +HIQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQ +LTAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAA-LAAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001542.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa6dbdb9a75358ab8417fe76bb045f797544a952 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001542.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01908 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>GCF_003691675_PROKKA_01604 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>GCF_005280335_PROKKA_00950 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>GCF_020097155_PROKKA_00890 +MAKKSKIAKNEQRKVMVARNAEKRLELKKTLIDPNASDEAREAARVGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFREMAHRGELPGVTKSSW +>GCF_023573625_PROKKA_01828 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001545.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001545.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1429c53b4e1ca79e5ad9f06543e1cf309337b97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001545.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01911 +MSHTSEQSSPLA--DQVPPGGPD--EPHAAEGVHARLNWLRAGVLGANDGIVSVAATVVG +VAGATTALTPVLLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGEL +EELVQLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLSFL +VGALLPFLTVVLAPVDFRIPLTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALAL +GLTLAVGSLLGASVA +>GCF_003691675_PROKKA_01607 +MSHTSEQSSPLA--DQLPPGGPD--EPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVG +VAGATTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGEL +EELVQLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFL +VGALLPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALAL +GLTFAVGSLLGASVA +>GCF_005280335_PROKKA_00943 +MNESTAPSEPTVRDDVAASSGHDRPEPHAGGGLHERLNWLRAGVLGANDGIVSVAATVVG +VAGATTAVAPVAIAGVAAVVGGAVSMALGEYVSVSSSSDSQKALIAKERRELAEDPEGEL +EELVGLYEAEGLSRATAENVARELTEKDALKAHLRAELGMDETGVVSPWSAAGASFVAFL +LGALLPFLTIILAPVDIRVALTFVTTLVALAGTGYAGAWLGGAPPVRAMLRVVIGGALAL +ALTFAVGAWLGTTVA +>GCF_020097155_PROKKA_00884 +MSHSTAPAAPSS--------YPD--EPHAQTGVHARLNWLRAGVLGANDGIVSVAATVVG +VAGATTAVTPVLLAGTAAVVGGAVSMALGEYVSVSSSSDSQKAMIAKERRELAEDPEGEL +EELVGLYEAEGLSRDTAEQVARELTANDPVTAHLRMELGMAEEDVVSPLAAAGASFIAFL +VGALLPFLAILLSPVGVRVPVTFGVTLVALAVTGYLGAWLGNAPAVRAMVRVVVGGALAL +ALTFGVGTWLGVGVA +>GCF_023573625_PROKKA_01831 +MSHTSEQSSPLT--DQVPPGGPD--EPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVG +VAGATTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGEL +EELVQLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFL +VGALLPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALAL +GLTFAVGSLLGASVA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001546.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7f873cadd5cba161000c1a31ac9699289c5e03f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001546.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01918 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEEGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMSALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>GCF_003691675_PROKKA_01614 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLSTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>GCF_005280335_PROKKA_00942 +MENQQTGQAADRGTIDTREGLKGNYVQSGAEFTRDTNYITDRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRAIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERLQENYFARFPDYPRGITVPAVVDVPTGDVVTNDYPQMTLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIKRVFTEVNNGVYRCGFAGSQEAYDAAYDR +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGEEVEPAHTPLR +>GCF_020097155_PROKKA_00877 +MEDQQTGQAADRGTIDTREALTGNYVQSGAEFTRDTDYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDAGGKDPVLGTERLQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWAAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPDLSGWTTEHGRADLGGDPW +GGGTAPGPVRDDERVDPEHTPLR +>GCF_023573625_PROKKA_01838 +MENQQTGQAADRGTIDSREGLKGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFVQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001550.fa new file mode 100644 index 0000000000000000000000000000000000000000..d37d0c2b7669d0d3f4ca357cbe020157a8b037a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001550.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01923 +M-------SGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVR +QDGRERILEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQL +DALRGR---DRR +>GCF_003691675_PROKKA_01619 +M-------SGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVR +QDGRERILEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQL +DALRGR---DRR +>GCF_005280335_PROKKA_00937 +MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR +KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL +DELRGRASDERS +>GCF_020097155_PROKKA_00872 +M-------GAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVR +QDGRERILEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQL +DALRGRASTGRG +>GCF_023573625_PROKKA_01843 +M-------SGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVR +QDGRERILEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQL +DALRGR---DRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001551.fa new file mode 100644 index 0000000000000000000000000000000000000000..3972a53f6d287f7c13080a1df4ac0d5c8d4737f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001551.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01924 +M----------------------------------------------------------- +----------TLVE------------------------------YTRRHPDADHLDPEKE +SVLEEAVGTGTQQITVDAQQGAVLRVIVLCP-SDATGETEILTSRGGGGTKTWMAGSEAL +CGGWSAAT-PPVDEAGPMTFTVTVDNDKPFRMVLTAPSA +>GCF_003691675_PROKKA_01620 +M----------------------------------------------------------- +----------TLVE------------------------------YTRQHPDADYLDPEKE +SVLEEAVGTGTQQITVDAQQGAVLRVIVMCP-SDATGETEILTSRGGGGTKTWMAGSEAL +CGGWSAAT-PPVDEAGPMTFTVTVDNDKPFRMVLTAPSA +>GCF_005280335_PROKKA_00936 +MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP +TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPV-PDGA +SILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPG- +CGHWSAGL-PAREADGPLTLTGVVPDGGPFRMVVYRSEG +>GCF_020097155_PROKKA_00868 +M----------------------------------------------------------- +----------TLEE------------------------------YTRQNPDSDYLHPETE +SVLQEKVGTGTQQITVDAQEGAVLRVILLCP-SDATGKTDIHTSRGAEGEKTWMAGSEAL +CGGWSAAT-PPVEKAGPMTFSATVDNDKPFRMVLTAPAA +>GCF_023573625_PROKKA_01844 +M----------------------------------------------------------- +----------TLVE------------------------------YTRRHPDADHLDPEKE +SVLEEAVGTGTQQITVDAQQGAVLRVIVLCP-SDATGETEILTSRSGGGTKTWMAGSEAL +CGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001556.fa new file mode 100644 index 0000000000000000000000000000000000000000..674ebe6adc014a6d9c23d94b7cafe64e0829a29a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001556.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01930 +-MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDA +MVRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDG +DVAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSART +PLPHTWDLDTVRRG +>GCF_003691675_PROKKA_01626 +-MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDA +MVRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDG +DVAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSART +PLPHTWDLDTVRRG +>GCF_005280335_PROKKA_00928 +-MHLIPRTLWVLARARRRPPLSIWDSASLPMRALPTDVDIAGHVNNGQYFGLFDLGRFDL +MARSGLMRAVRRRGWLPVVQAEQIAFRRSVTLGTAFTLETRIIGLDERAVWFEQRVVVAG +DVAVRGYVCTRLRGRDGTPVGNDEVRALAVELGHDPAAEPELPGWLHDWREQVALPSART +PLPHAWGR------ +>GCF_020097155_PROKKA_00862 +MLHLLPRTALVVVRARRRPRLGIWEASTLPLRALPTDVDFAGHINNGQYFGLFDLGRFDL +MVRAGVWDGAKRRGWLPVVQAEQIAFRRSVTLGTRFTVESRIIGLDERAVWFEQRAVVDG +DVAVRAFICTRLRAKDGTPVSNEDVRDLARELGHDLAAEPVLPEWLHGWRSDIALPSART +PLPHAWGTPAPAGV +>GCF_023573625_PROKKA_01849 +-MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDA +MVRTGLWDEIRRRHWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDG +DVAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSART +PLPHTWDLDTVRRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001557.fa new file mode 100644 index 0000000000000000000000000000000000000000..66daac677b9b66ce42c680e718984d419866fafc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001557.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01932 +MAA-VDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETL +AAVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRP---EGLAAVAWR +SAAGLTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRIN +GAWTPGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPG----HLASWVRLQGDGEAAVH +WRGDRFNPEHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLP +LG-AAVLRPAFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQP---- +----------------RP +>GCF_003691675_PROKKA_01628 +MAA-VDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETL +AAVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRP---EGLAAVAWR +SAAGLTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRIN +GAWTPGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPG----HLASWVRLRGDGEAAVH +WRGDRFHPEHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLP +LG-AAVLRPAFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQP---- +----------------RP +>GCF_005280335_PROKKA_00927 +MPA-AETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETL +AEVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRP---EGLAAIAWR +PAAGAGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTN +PAWTPEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAG----HLGAWVRLLGGGEAAVH +WRADRFHPEHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVP +LG-SAVLRPAFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQP---- +----------------HP +>GCF_020097155_PROKKA_00861 +MSTPAVPEP----------PRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETL +GAHAPVAVLTDPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWR +LPSDAAGTAGRAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSA-ALLDPAVN +EGWTRAQAEDALAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVH +WQPGRLHPDHAASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLP +LAPGVVLRPAHADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGAR +TRRPSPAPAHPEGPRAAP +>GCF_023573625_PROKKA_01851 +MAA-ADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETL +AAVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRP---EGLAAVAWR +SAAGLTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRIN +GAWTPGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPG----HLASWVRLRGDGEAAVH +WRGDRFHPEHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLP +LG-AAVLRPAFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQP---- +----------------RP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001558.fa new file mode 100644 index 0000000000000000000000000000000000000000..0fc9c9dfa992f394779df6374603abf78133dfac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001558.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01933 +MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLR-------------PAAWRSDAHGKDEDRAPTDG +GDDDGPATDEVTG--GAGA----------------------------------------- +-APGR +>GCF_003691675_PROKKA_01629 +MSAAQPAGVTPPSASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAILGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLR-------------PAAWRSDAHGGDEDRASADG +GDDDGPATDEVTG--EAGA----------------------------------------- +-APGR +>GCF_005280335_PROKKA_00926 +MSAAQPVGAAPTPSAAGPVSDWDIRRPHRMWPRMLVIVLTLAGLVLLVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGVHPVLGAAASVVVVVAVLGAFVGMIVWSGLELVAELPK +YSGQFQQIVLDVSNWLNARGVTPDMVSQQLASIDVSAVTSAAVSALTKIATNLYAVLGLL +VTVVMGMFFLAMDSMDVERRVRLLSTARLELGEALIDFAHGVRRYWVVTTVFGLIVAALD +VIALVLIGVPLALVWGVLSFLTNYIPNVGFIIGLIPPAILGLAAGGWTSFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +SRWVNSLIASDLKGMERRQHSLLERLR--------------VGRRGEGRAGKADAEAVAG +ADVAAAGVEAALDVDDAAAGARRPEAAPTGSTLTEPARTEPGPAAPADAADGPGLTGGAA +PAPGR +>GCF_020097155_PROKKA_00860 +MSASAPPAVT---GTSTPATEWDNRRPHRMWPRMLVIVLTLAGLVVLVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVVVVCAVIAAFLGMIAWSGMELLTELPK +YAGQFQQIMHDASQWLSDHGVTPDMVNQQLASVDMSAVTGAAVSALTTIASNLYAVLGLL +ITVIMGMFFLAMDSMAVERRVRLLSTARHELGQALIDFADGVRRYWIVTTVFGLIVAVLD +MVALVIIGVPLALVWGVLSFLTNYIPNVGFIIGLVPPAILGLAAGGWPAFLWVVVSYSVL +NFVLQSIIQPKVAGDAVGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLVKAVLIDADPN +SRWVNSLIASDLKGMERRQSSMLERLRLPRELIRHGGSTASHATAADVQ-GDDDVAPERT +AEDAAPAQDRRRV--RAAAQEARLEGPPP-STLRAPRVDLPGEPEPATADGSAPPEAGA- +-APGR +>GCF_023573625_PROKKA_01852 +MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSTVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLR-------------PAAWRSDAHGGDEDRASADG +GDDEGPAADEVTG--EAGA----------------------------------------- +-APGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001559.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c6808948f6dbacde78df078732d490462334351 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001559.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01934 +MSRTPHR---------ALAALSVAALALTGCSVS----GSSGDGASSSAA---------- +-----GA-GGEPTTVTIMTHDSFNLPQELVQKFEQESGYTLKTTAPGDAGSVVNQLLLAK +DEPTVDGVYGVEDHSAHRLVREGVVAEYTPQDLPASAQDRMVEDRMTPVDQGQVCFNTDP +AWFEAHDVEAPTSIDQLDDPEYAKLTVATSPVASSPGLALLAATTEKYGDDGWQDWWRGL +KENGGKVADSWSDAYNSDFSGGEGKGRFPVVLSYSSSPAFAPETEVIEDSCTPQVEYAGV +LEGAKNPEGAQAFVDFMLTEEVQSALPESMYMYPIDESVQLPEEWAQNAPLVEDAITPDP +ARIDERREDLLKEWTALAEASRR- +>GCF_003691675_PROKKA_01630 +MSRTPHR---------ALAALSVAALALTGCSVS----GSSGDGASSSAS---------- +-----GAGGGEPTTVTIMTHDSFNLPQELVQKFEQESGYTLKTTAPGDAGSVVNQLLLAK +DEPTVDGVYGVEDHSAHRLVREGVVAEYTPQDLPASAQDRMVEDRMTPVDQGQVCFNTDP +AWFEAHDVEAPTSIDQLDDPEYAKLTVATSPVASSPGLALLAATTEKYGDDGWQDWWRGL +MENGGKVADSWSDAYNSDFSGGEGKGRFPVVLSYSSSPAFAPETEVIEDSCTPQVEYAGV +LEGAKNPEGAQAFVDFMLTEEVQSALPESMYMYPIDESVQLPEEWAQNAPLVEDAITPDP +ARIDERREDLLKEWTALAEASRR- +>GCF_005280335_PROKKA_00925 +MTTAPHRVRTRPRRHGALAALSVAALALTGCSVA--DRGGSGDQGSSSA----------- +----------EARTVTIMTHDSFSLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAK +DAPTVDGVYGIEDHSAHRLVSEGVIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDT +PWFQEQGLAAPTTLEQVAAPEYAELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTA +LQGGMQVDASWSDAYNTSFSGGEGTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGV +VEGAENPEGARAFVDFLLTEDVQAAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDA +GLLDSRREDLLKEWTALHEEAAS- +>GCF_020097155_PROKKA_00859 +MSV--HR--TATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSST +SASGTAA-AGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSK +DAPVADGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDP +AWFTEHGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDL +LKGGAKVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGV +LTGAENPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDP +AEIDTEREGLLKEWTALSESAGSR +>GCF_023573625_PROKKA_01853 +MSRTPHR---------ALAALSVAALALTGCSVS----GSSGDGASSSAA---------- +-----GA-GGEPTTVTIMTHDSFNLPQELVQKFEQESGYTLKTTAPGDAGSVVNQLLLAK +DEPTVDGVYGVEDHSAHRLVREGVVAEYTPQDLPASAQDRMVEDRMTPVDQGQVCFNTDP +AWFEAHDVEAPTSIDQLDDPEYAKLTVATSPVASSPGLALLAATTEKYGDDGWQDWWQGL +MENGGKIADSWSDAYNSDFSGGEGKGQFPVVLSYSSSPAFAPETEVIEDSCTPQVEYAGV +LEGAKNPEGAQAFVDFLLTEEVQSALPESMYMYPIDESVQLPEEWAQNAPLVEDAITPDP +ARIDERREDLLKEWTALAEASRR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001560.fa new file mode 100644 index 0000000000000000000000000000000000000000..db046c6407be2802a3d3a8cd06ff3fcd6e67cee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001560.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01935 +M---------------SALTEV----AAPGTDLP------RRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWR +GIGG--DADAFTGAVDLTAFGETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRAVLRALVLVPFVLP +TVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVGALWNALDPRQTEAARTLGASPWRAFRTVTLPQL +APAIAASAALVFLFCASAFGIVQTLGRPGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLVAVVVSGVTAARTQRALR +LRETPPARLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTPARALEQSLRVAVD +ATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTVGFGFVVSLRAAFPELAASGVLVPLAQAVVALPL +AVRALVPVLAAVDPRLREAARTLGAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLL +GRPGADNYGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL +>GCF_003691675_PROKKA_01631 +M---------------SALTEV----AAPGTDLP------RRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWR +GIGG--DADAFTGAVDLTAFGQTLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRAVLRALVLVPFVLP +TVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVGALWNALDPRQTEAARTLGASPWRAFRTVTLPQL +APAIAASAALVFLFCASAFGIVQTLGRPGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALR +LRETPPARLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTPAQALEQSLRVAVD +ATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTVGFGFVVSLRAAFPELAASGVLVPLAQAVVALPL +AVRALVPVLAAVDPRLREAARTLGAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLL +GRPGADNYGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL +>GCF_005280335_PROKKA_00924 +MDGPARGGGLLTVGLTSVPAPVGGPGAPPGAPGPAASGGRRRRRTAGGDGIGAWWLLAAVVPVAFLLVFFAWPVGAMLWR +GVSA-------EGVLDLGAFAEVLGRERTWRIVGQTLGMAAAGTVLAVALGLPAAFVLHRRAFPGRAALRAVITVPFVLP +TVVVGVAFRALLAPGGPFGWTGLDQSTAAVVLAMVFFNVSVVVRQVGALWASLDPRQAEAARTLGSSGWRAFRTVTLPQL +APALASSAALVFLFCASAFGIVQTLGRPGVGTLESEIWVQTVVYFDLGTAAVFSTLQFLVVLAAVLVSGATARRTRRALR +LRDAPVRRLTRADAAPVAVTLATALLVLAPLATLLVRSFHSSEGWGLRNYRLLASSPGAGFSGGVTPAQALEHSLRIALD +ATLLTLLIGVPLALLLTRPVRSAAGRRAQRGLDGALLLPLGVSAVTVGFGFVVSLRAEAPALAASGALVPIAQAVVALPL +VVRSLVPVLGAVDPRLREAARTLGAGPLRVLATVDGPFLLRGLGVAAGFAFAVSLGEFGATSFLSSPDYQTLPLLIVKLL +GRPGADNYGMALAAATVLAVLSAGTMMACERLGPRAAASRGGI +>GCF_020097155_PROKKA_00858 +M---------------PTPAPA--RGRRRATLRP------PRGRRAAGDGLAPLWLLSAAVPVAFLLVLFAWPVAAMLWR +GVASVDAAGDPTGGLDLSAFAQTLGAPRTWRILGNTLGLAAAGTAASVALGVPTAFALHRRAFPGRGLARAVVTVPFVLP +TVVVGAAFRALLAADGPLGWTGLDQTSTAVVMAMVFFNVSVVVRQVGGLWAALDPRQAEAARTLGASPWRAFRTVTLPQL +APAVAGAAALVFLFCASAFGIVQTLGRPGPGTLETEIWAQTTVYLDLRTAAVLSTVQLAVVLAAILASGAAAARARRALR +LGEAPARPLTRADAVPAAVTLAVLALVVAPILALLAGSLHSAEGWGLRNYRLLATSPGTGFAGGVTPAQALEQSLRTAVD +ATVVTLVVAVPLALVLTRPVRSRAGRAAQRALDGALLLPLGVSAVTVGFGFIVSLRATAPDLAASGALVPLAQSVIAVPL +AVRALVPVLGAVDPRLREAARTLGAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLAAADRPTLPVLIARLI +GRPGADNHGMALAAAVVLAVLSAGALLACERLRPRGAAPSGGL +>GCF_023573625_PROKKA_01854 +M---------------SALTEV----AAPGTDLP------RRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWR +GIGG--DADAFTGAVDLTAFRETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRAVLRALVLVPFVLP +TVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVGALWNALDPRQTEAARTLGASPWRAFRTVTLPQL +APAIAASAALVFLFCASAFGIVQTLGRPGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALR +LRETPPARLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTPAQALEQSLRVAVD +ATLVTLVVAVPLALLLTRPFRSRAALVAQRALDGALLLPLGVSAVTVGFGFVVSLRAAFPELAASGVLVPLAQAVVALPL +AVRALVPVLAAVDPRLREAARTLGAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLL +GRPGADNYGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001562.fa new file mode 100644 index 0000000000000000000000000000000000000000..67b8202fe8d3a6c0f07f774280d802a4b59c9b68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001562.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01937 +M-TPP---APRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQS +LLARVADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH +RLLTEAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL +>GCF_003691675_PROKKA_01633 +M-TPP---APRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQS +LLARVADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLH +RLLTEAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL +>GCF_005280335_PROKKA_00922 +MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT +LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH +ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL +>GCF_020097155_PROKKA_00856 +M-STS---SARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQT +LLARVADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLH +RLLVDAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL +>GCF_023573625_PROKKA_01856 +M-TPP---APRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQS +LLARVADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH +RLLTEAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001568.fa new file mode 100644 index 0000000000000000000000000000000000000000..f1f11dc6b556caa94c0bef78258d9749bcf70d2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001568.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01947 +MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGTEAVGWGLATEAAAGDAFAARLAELEDELVAGPAHTYGPTKALTRGADVEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR +>GCF_003691675_PROKKA_01641 +MTTAPTPSPHDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGNVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGTEAVAWGLATEAVAGGAFAARLAELEDDLVAGPAHTYGPTKALARGADVEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR +>GCF_005280335_PROKKA_00911 +MS---GDGGAADVATVRVEARPGVVRLTLDRPAQGNALSLAMARELTAAVRASEADPDVH +VLTLTGAGRFFCGGGDLAAMGAASPA-ERPAVLRELADAASEVALALVRSRLLVVAGVNG +TAAGAGLGLVLNADVVLVGDDALLLAAYAGIGLVPDTGVSWWLPRAVGPVRAAELTLRGR +RLTGAEAVEWGVASEAVSGDEFEARLAALEDELAAGAVHAYGPTKALLRGPEIVGYAEHL +DRETAAISAASGHPEAVRRVDAFLRR +>GCF_020097155_PROKKA_00847 +MTTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEAAVALTGSRLLVLTGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGAEAVAWGLATEAVAGDAFAARLTELEDELVAGPTHTYGPTKALARGADAEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR +>GCF_023573625_PROKKA_01866 +MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGDVQAMAASPAGPERRAMIQELGEAAGEVAVALTGSRLLVLTGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGAEAVAWGLATEAVAGDAFTARLAELEDELVAGPAHTYGPTKALARGADVEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001569.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec979e823ad4fca7676cdab68338dd1f09404658 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001569.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01948 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFK +>GCF_003691675_PROKKA_01642 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFK +>GCF_005280335_PROKKA_00907 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFR +>GCF_020097155_PROKKA_00846 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFK +>GCF_023573625_PROKKA_01871 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAARNAVYKRTTFG +LGDVLRMFR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001570.fa new file mode 100644 index 0000000000000000000000000000000000000000..c87804623b158e93736a55356f2ba202594261c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001570.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01951 +MINSAEPRHVHELFSSQTKAHYVVPPYQREYSWHRAQWEALFADLVESEDE--------HFLGTIITLSRTKDSLSGPVL +E--VIDGQQRLTTLTILLAAVHSHLQDAEDLDEDARFERMTLRRELVRDEAKAPRLTPQVQGANRADYQAMLADAGLPVK +SEKKAYYPSRKVAKAFWFFRAAITELAEER--GESLSTTALSVLAAARRAL-IVNIEVASAADAFVLFESLNNRGVPLTP +VDLIKNSFLARAEHRA----------------GMEVEEAFEL---WSDTLAHLGDSYATHERFLRHF----YNAFRGDLP +PVKLAPVATRKNLIRIYETLLDQDLEGTVRSLERAAQVYGRIAGGGDVDEPTSLDQELTALRRAQAAPSYVLVMWLLVRQ +EK-------------AGWSEEDLAAVARLLVSFFVRR----NLTGFPATYALPRLFMDVIDQVAAGEPDRLL-TIVRGSL +VAASASDATFRER-LEGPVYEENRDVTRFLLATLAEDAMTKETRVDLWAQSGKTFVWTIEHILPQGENLPQEWVDALGGP +EAA----AETQNRFVHTLGNLTITGFNSTLGNQTFLRKRDRIDHQGRAIGYRNGLALNAELAEKEAWSSADIEARTVRLV +ERALE--------------------------------------------------------------------------- +----------------------------------RF-------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------AL +>GCF_005280335_PROKKA_00906 +MV-AAREVTLQELLGGSYQ--YTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIGSLV-LAGFRDNGPGGVQ +RWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVNKWEDGDLRYKVLPTQ---ADRAAYRGRIEHA--PDA +AE------GSRISEAHQFFLTKLFGLSQPSADGEEEQLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQ +GDLLRNYLFMQLPTRADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRGL----QDESQ---- +--VRAEVERFLALGRLYDVMLRPE-------KEKDAAVRFRLA----------------RLRAWRTTTTFPITLHLMERR +SL-------------GDIDSDELARALLYLESYLVRR----LVFGRYSDGLNTTLLAATADIQGQDDPADAL-QRFLSSG +RKHFASDDQIRQAVITAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSA-------TIEHVMPQ--TLTEEWERALAGQ +LEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELA--------KSGIRMNQEISTVPVWGPAQIRARAERLA +DRIVGIWPGPS----------AEAASGVAHTA--WQTLTDAVEAIPAGSWTSYGELARLIGSHPVPVGTYLARTAL-PHA +HRVLQAGGTVSPSFRWTDVHRKDDPHDVLAAEGVRFSEDGRAYGGQRLVAEQLAELIDVDVDLTDPRSLAAPGNDPALRD +RWVDRLHDHNDPESARALIEVQRGWVERGGRAEFADNAAGGCFLVVPRASARAIWPVILYPTYGVEVVFYHLAKWPPFTD +EALLDDFRGRLNLIPGVEFGPEALRRRPSIRPQILQPAAAQEAFLDALEWFLHTIQEDDRSA +>GCF_020097155_PROKKA_00292 +MS------------------------HERVYRIGSP-------------------------------------------- +------GAEPLVPVSFAEAGLRERQD----------------LQEWV--------------------------------- +-------------------------IAHPEILGEDIR---------------IV-------------------------- +--------------------------------------AFEFD--------RWEDADGGRQRDRLDVLGLDQSGCL---- +--VLAELKRDAAPD---TVEMQAI-------KYAAMASRFTEE----------------KLVAWHAA-----MLGRLENR +PVSEEEAREALTDHAGELDVEQLRRPRIVLVAGAFTRSTTAAVVWLTEMGLDITLQRVQAYRMGGDDVVITVSQLFPVPD +VEEFTVSPMRMESTARRTSSTRSPSTVRRLV-----------KAGTLPDG-------TVLTLVPT--------------- +-------TEVNAETREAIADW--------ISDDPRRGRATWWN--------DPTKPMEWELDGNR-YRPSRIVQQALREA +TGITRSPRGPAWWVTESGMSLTELAGDVENGAFDWTQLHRLLCELPAGRWTTYGEVARLIGTAPQPLGGHFRTCTLCRNA +YRVLDANGAVSSGFTWGDPQETRTQQEVLEAEGISF-DGGRAAPSQRLQPSELESVWKV--------------------- +-------------------------------------------------------------------------------- +---------------------------------------AQAAL----------------GE +>GCF_020097155_PROKKA_00845 +MV-AAREVTLQELLGGSYQ--YTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIGSLV-LAGFRDNGPGGVQ +RWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVNKWEDGDLRYKVLPTQ---ADRAAYRGRIEHA--PDA +AE------GSRISEAHQFFLTKLLGLSQPSAAGEEEPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQ +GDLLRNYLFMQLPTRADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRDL----QDESQ---- +--VRAEVGRFLALGRLYDVMLRPE-------KEKDAAVRFRLA----------------RLRAWRTTTTFPITLHLMERR +SL-------------GDIDSDELARAFLYLESYLVRR----LVFGRYSDGLNTTLLAATADVQGQDDPADAL-QRFLSTG +RKHFASDDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSA-------TIEHVMPQ--TLTEEWERALAGQ +LEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELA--------KSGIRMNQEISAEPVWGPAQIRARAERLA +DRIVDIWPGPS----------AEAASGVAHTA--WQTLTDAVEAIPAGSWTSYGELARLIGSHPVPVGTYLARTAL-PHA +HRVLQAGGTVSPSFRWTDVHRTDDPHDVLAAEGVRFSEDGRADGGQRLVAEQLAELIDVDVDLIDPRSLAAPGNDPALRD +RWVDRLHDHNDPESARALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWPPFTD +EALLDDFRGRLNLIPGLEFGPEALRRRPSIRPQTLQPAAAQEAFLDALEWFLHTVQEDDRSA +>GCF_023573625_PROKKA_01872 +MV-AAREVTLQELLGGSYQ--YTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIGSLV-LAGFRDNGPGGVQ +RWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVNKWEDGDLRYKVLPTQ---ADRGAYRGRIEHA--PDA +AE------GSRISEAHQFFLTKLLGLSQPSADGEEEPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQ +GDLLRNYLFMQLPTRADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKIRQTEIYAGQQRRMRGL----QDESQ---- +--VRAEVERFLALGRLYDVMLRPE-------KEKDAAVRFRLA----------------RLRAWRTTTTFPITLHLMERR +SL-------------GDIDSDELARALLYLESYLVRR----LVFGRYSDGLNTTLLAATADIQGQDDPADAL-QRFLSSG +RKHFASDDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSA-------TIEHVLPQ--TLTEEWERALAGQ +LEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELA--------KSGIRMNQEISAEPVWGPAQIRARAERLA +DRIVGIWPGPS----------AEAASGVAHTA--WQTLTDAVEAIPDGSWTSYGELARLIGSHPVPVGTYLARTAL-PHA +HRVLQAGGTVSPSFRWSDVHRTDDPHDVLAAEGVRFSEDGRADGGQRLLAEQLAELIDVDVDLTDPRSLAAPGNDPALRD +RWVDRLHDHNDPETARALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWAPFTD +ETLLDEFRGRLNLIPEVEFGPESLRRRPSIKPQTLQPAAAQEAFLDALEWFLRTVQEDDRTS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001571.fa new file mode 100644 index 0000000000000000000000000000000000000000..d43df7de190abe9938713239a2ae5a5cf620fb95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001571.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01963 +MTSHTDPSHPAAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAA-TGPTP-----FTLGVASGDPWPDGVVLWTRLAVDP +LALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRAQGYAVHVTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPAR +GSNPSRLTMTVASCANWEHGYFTAYGHMAAERP-DLMVHLGDYYYEIMPYGYPVS------SGVPRAHRNGESRTLAQYR +ARMAQYKTDPHLQDAHAAAPWLVIFDDHELENNW--ADETPEIWDPSFLARRAAAFQAYYENMPLRASSVPRGIDMQLYR +RIHWGDLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGFETSVARWDLITQQVPFVQYDRTSGP +LLWGDMDTWDGYVASRDRVVSAWTAAGVRNPVVLTGDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEA +LAWNPH--IKFNNDLRGYLRVDLSAQLLEARFRVVDYV-SELGSSVRTRAVFGVGDGEHRLHRIA +>GCF_005280335_PROKKA_00894 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +--------------------------------------------------------------MPLRASSVPRGIDMQLYR +RIHWGDLATFHLLGTRQYRSDQANLDLVKVVDADARDPRRTITGAAQEAWLREGFETSVARWDLITQQVPFVQYDRISGP +LLWGDMDSWDGYVASRDRVVSAWTAAGVRNPVVLTGDIHEAFASDIKRDFNDLSSESVGVELITTSITSGGDGSDAAAEA +LAWNPH--IKFNNDLRGYLRVDLSAHMLEARFRVVDYV-SELGSSVRTRAVFGVGDGEHRLHRIA +>GCF_020097155_PROKKA_00439 +MSS---PS-PT---LSRRRLLGLSG---ASAAVLALGVNAPDAAHAEPLPQRDGLFGLGVASGYPRPDGAVLWTRLAPEP +LAENGHGGMPLRSVPVKWEVARTADFRRIVARGTALAQPELAHSVHPRVEGLAPGTEHFYRFVVGPQTSPVGRFVTLPAA +GAATDDYTVGLISCQAWYHGHFAAHRHLAQEEDLDLTVFLGDYIYE---YGITAANLWRQGAEVTPAHAV-EIETLEQYR +LRYALTKSDPHLQALHARAAAVAIWDDHEVQNNYVGAASSTGIPEELFAHRIAVAYRAFYENLPVDIDALPEGPESDIVA +GLDVGALARISLLDTRQFR------DAPPADAADRERENRTMLGAAQERWVTERLRTSQSQWNVLAGGVVL-------AP +ISDDRTDQWDGYPAARRRLLTEMKRAG--NAVMLTGDIHKHVAAELRGESAGLPAGPAGVELVTTSAASDGDGAKTDKYT +PDWVRHDYVRHYDGRRGYLHLRFTPAQLTSSFWVVPWVESDDTAPKELSARFTTPAGSSRLIE-A +>GCF_020097155_PROKKA_00834 +M---------------------------AAAALISTPAGTAHAA-AGPNP-----FTLGVASGDPWPDGFVIWTRLATMP +LNRDGFGGMPDASFTVEWQVSRHADFRSTVRTGTTTTSRAQGYAVHVTLTGLRAGTEFFYRFRCNGHLSRTGGAVTAPAL +GSMPGHLTATEAE------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------RLIRA---AGF-APVRL-GGIDESIRMEVTGE------------------------------- +--------LHPFGGLDGTLPTTANVEQLR-----------------------------------G +>GCF_023573625_PROKKA_01889 +MSSHTDPAHPTAHPVSRRTLLGGAGLVVASAALLSTPAGTAHAA-TGPTP-----FTLGVASGDPWPDGVVLWTRLAVDP +LALDGLGGMPDQSFRVEYQVATDEGFRKVVRSGAVTTDRTQGYAVHVTLTGLRPGTEYFYRFRALGHLSRVGRTVTAPAR +GSNPSSLTMTVASCANWEHGYFTAYGHMAAERP-DLMVHLGDYYYEIMPYGYPVS------SGVPRAHRNGESRTLAQYR +ARMAQYKTDPHLQDAHAAAPWLVIFDDHEVENNW--ADETPEIWDPNFLARRAAAFQAYYENMPLRASSVPRGIDMQLYR +RIHWGNLATFHLLDTRQYRSDQANLDLVKVVDADARDSRRTITGAAQEAWLREGFETSVARWDLITQQVPFVQYDRSSGP +VLWGDMDSWDGYVASRDRVVSAWTTAGVRNPVVLTGDIHEAFASDIKQDFNDLSSESVGVELITTSITSGGDGSDAAAEA +LAWNPH--IKFNNDLRGYLRVDLSAQLLEARFRVVDYV-SELGSSVRTRAVFGVGDGEHRLHRIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001572.fa new file mode 100644 index 0000000000000000000000000000000000000000..b399f4c4f18dd66b06b56236411c679784065833 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001572.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01966 +------------------------------------MHEDEGRRRHYGHFYGLEDLPEDD +LLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVPPAFEAQPDEVAHLERLLPRVKALV +TQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYDVSRFPWQVTLRNWKFAPGAAERPG +EDPPVVPYHDLRVLAEAA----------------------TGRRREVAPAAIREAAAASV +QALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPVPA +SRVLLGGVRAPLEAPVVEALDLDAAPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVEVG +MRKYADQLRLLGLTG +>GCF_003691675_PROKKA_01660 +------------------------------------MNEDEGRRRHYGHFYGLEDLPEGD +LLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVPPAFEAQPDEVEHLERLLPRVKALV +TQPIPHDYRGMPIGTDQLVARLPKDAAVVRIPVVYDVSRFPWQVTLRNWKVAPGAAERPG +EDPPVLPYHDLRVLAEAA----------------------TGRRRQVAPAAIREAAAASV +QALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAGHLPGDVAVQPVPA +SRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTIPAEQLRQTHLDWYAQNPQAVEVG +MRKYADQLRLLGLAA +>GCF_005280335_PROKKA_00893 +------------------------------------MHEDEGRRRHYGHFYGLEDLPEGD +LLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVPPAFEVQPDEVEHLERLLPRVKALV +TQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYDVSRFPWQVTLRNWKFAPGAAERPG +EDPPVVPYHDLRVLAEAA----------------------TGRRREVAPAAIREAAAASV +QALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTVLTRVAERVAEHLPGDVAAQPVPA +ARVLLGGVRAPLEAVVVEALDLDAEPTEDWTVGGETIPAEQLRQTHLDWYAQNPQAVEVG +MRKYADQLRLLGLAA +>GCF_020097155_PROKKA_00833 +MSEETPMDDQTRTAGAEPGDEGVQVRGAAERAPSSDLPADEGRRRHYAHFYGLEPLPEGE +LLTVMGGCQAEATRLLLCGEPGRA-EGGTPASVRVPPMFELGPDDLPHLLALLKRTTVLV +VKPVRDDYQGLPLGLGQLESLLPAGARSIRVPALYDSSRFPWLVTLRH-------PTRPW +EDPPVVPYHDLRTVAEAAAEAGLIPWPAALGGPGEAGAYDAGPRLPLSAEALRGLAAESV +ARLRAREEHFGTVRVSDAVADERGVGFHTVNHPDNPLLEALARTVLAELGVDKEVH--AP +DRLLLGHVLAPIEEQVVDALGLQTAPRAAWRVGGAEVSDAEVRRAHLGWFRANPEALAPG +LERHGALMRELGLLA +>GCF_023573625_PROKKA_01892 +------------------------------------MNEDEGRRRHYGHFYGLEDLPEGD +LLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVPPAFEVQPDEVAHLERLLPRVKALV +TQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYDVSRFPWQVTLRNWKFAPGAAERPG +EDPPVVPYHDLRVLAEAA----------------------TGRRREVAPAAIREAAAASV +QALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPVPA +SRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVEVG +LRKYADQLRLLGLTG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001573.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5b1b393996a1585c1cefbf80eaa0e5caee781a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001573.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01968 +MSAA-------------------VSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVAD +DGSPVPPRVDPGLPFDVVTVRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLA +AALAAVAEAPRDAAVVGRRRHLAEAWLERAWADGWRPGHEVPADALLAEPAWLRDGYRAT +DDLRRADSTGYRYVISAVLTVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHA +PDAVAWQAGADFGGRGDAAEAARVKAREALVLVSRIPATTSRGHGLSLAGPLRAEARVRV +PEGADGAAAAVVAVDAVLRAAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAAPED +LPPTPARGDLDAVRSVPDWSVDVQVPLRPAAAGARPDTDAVAAWLLRLERAGVERVEVLG +------EPGE--RAERDVLAVLTCARARWRPRRGGTARVWRVPASRLGWAPVAAVPDLEA +WWGGWG +>GCF_003691675_PROKKA_01662 +MSAA-------------------VSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVAD +DGSPVPPRVGPGLPFDVVTVRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLA +AALAAVAEAPRDAAVVGRRRHLAEAWLERAWVDGWRPGDEVPADARLAEPAWLREGYRAT +DDLRRADSTGYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGAALRHA +PDAVAWQAGADFGGRGDAAEAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRV +PEGADGAAAAVVAVDAVLCAAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQD +LPPTPARGDLDAVRSVPDWSVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLG +------EPGE--RAERAVLAVLTCARARWRRRRGGTARVWRVPASRLGWAPVATVPDLEA +WWGGWG +>GCF_005280335_PROKKA_00891 +MSAA-------------------VSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVAD +DGSPVPPMVGPDLPFDVVTVRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLA +AAVAAVAEAPRDAAVVGRRRHLAEAWLERAWADGWRPGHEVPADARLADPAWLREGYRTT +DELRRADSTGYRYVISAVLTVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHA +PDAVAWQAGADFGGRGDAAEAARVKAREALALASRIPATTARGHGLSLAGPLRVEARVRV +PERADGAAAAVVAVDAVLRAAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQD +LPPTPARGDLDAVRSVPDWSVDVRVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLG +------EPGE--RAERAVLAVLTCARARWRRRRGGTSRVWRVPASRLGWAPVAAVPDLEA +WWGGWG +>GCF_020097155_PROKKA_00832 +MTAPVAGREAAAETAGPEASVPEVSVVVPHYRAPADLERVVAALAAQDHPASRLQLVVAD +DGSPEPPVLPAGLPFEAVVVAQEDHGFRASAARALGASAAEGRILAFLDGDMLPEPGYLT +AACAAPA-ASVDAVVVGRRRHLDPALLE----SGWRPGEPVPEAARLPEPAWLAEAYQRS +GDLAAADSTSYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGGAFRHQ +PAAVAWQAGEDFGGRGDAAERTAVKQREALRLAARITATTARGHGLSLPGPLRVGARVRA +E--ASGDAAAVVGVDALLAAAPGARVGVTGLGSGAARAALADPRVWIMD--GGGEAARAD +LPPAPARGDLGAVRGIPDWSCDVRTPLRPAAPGARPDAARAADWLLRLERAGVERVEVLG +EPQAAEEPGEAGRGERPVLAVLTCSRALWRSRRGGDSRVWRVPAARLGWAPVARDVDLEA +WWGGWG +>GCF_023573625_PROKKA_01894 +MSAA-------------------VSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVAD +DGSPVPPRVDPGLPFDVVTVRQPDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLA +AALAAVAEAPRDAAVVGRRRHLAEAWLERAWAHGWQPGHEVPADARLAEPAWLREGYRAT +DDLRRADSTGYRYVISAVFTVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHA +PDAVAWQAGADFGGRGDAAEAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRV +PEGADGAAAAVVAVDAVLCAAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAADED +LPPTPARGDLDAVRSVPDWSVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLG +------EPAE--PGERAVLAVLTCARARWRHRRGGTARVWRVPASRLGWAPVATVPDLEA +WWGGWG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001574.fa new file mode 100644 index 0000000000000000000000000000000000000000..081128874addae59ad5dae68abc1f158bfdc1ad0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001574.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01969 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV +PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA +GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR +YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARML +FDVLRRVHRWT--- +>GCF_003691675_PROKKA_01663 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV +PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA +GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR +YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARML +FDVLRRVHRWT--- +>GCF_005280335_PROKKA_00890 +------MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLV +PLMAEARSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR +RGEAYARLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMA +GLDQDVVLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR +YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARML +FDVLRRVHRWT--- +>GCF_020097155_PROKKA_00831 +------MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLA +PVLARAREARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLE +RAEAYVRIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRR--AAREAVRLPEALE +GLDRDVVIFGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELT +ARAEVSGLQFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGR +YTQEMARLRPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARML +AAALADVHGWAWPR +>GCF_023573625_PROKKA_01895 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV +PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA +GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR +YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARML +FDVLRRVHRWT--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001575.fa new file mode 100644 index 0000000000000000000000000000000000000000..af9864deb7ce786c302124238d705c90884804c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001575.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01970 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFSPAQLAA +ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQ +GDDDAPGAEPGLLPPDASDDGD--GAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDED +ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLTPDS +LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPGVSVLVITGHRDEHLARVI +AGLERSHRRPDQVVVVFMGQPDGRVPATDLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLAT +EVAAHPGSVVMGRPRYLRPGWTRDVGE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI +GGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG +LIAWDPEGERLELLRHPTEAELTAARRDDAAY +>GCF_003691675_PROKKA_01664 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPDAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFSPAQLAA +ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQ +GDDDAPGL----LPPDASDDGD--GAPVPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDED +ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLSPDS +LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPSVSVLVITGHRDEHLARVI +AGLERSHRRPDQVVVVFMGQPDGRVPATDLPVTVGHVAADAGLPLAQARNRAAELAIGEILVFLDVDCIPAAETVGVLAT +EVAAHPGSVVMGRPRYLRPGWTRDVGE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI +GCFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG +LIAWDPEGERLELLRHPTEAELTAARRDDAAY +>GCF_005280335_PROKKA_00889 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFNPAQLAA +ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVSQ +GDDDAPGL----LPPDASD--D--GAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQATVQDED +ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLAPDS +LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPSVSVLVITGHRDEHLARVI +AGLERSHRRPDQVVVVFMGQPDGRVPATGLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLAT +EVAAHPGSVVMGRPRYLRPGWTRAVEE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI +GGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG +LIAWDPEGERLELLRTPTADELAVARRDDAAY +>GCF_020097155_PROKKA_00830 +MSLTVQHVPAGHPYARSVRPLDGAAAPDVEFWPDPPVPGAAEGVWWPPRALDPAWIAEHRPDVLHVHFGFEHFTPEQLRA +ALDAQHAHGGAVVVTVHDLQNPHLQDQDPHRARLRVLLDAADAVITLTPGAAAAVEAASGRAPLVLPHPHVVPLDA---- +------------LPDDGAADGERPGVDRPARLLMHAKDLRAQVDPVGLLPVLAAARDALAARGLAVEVTVDVQDGVRDEA +ALAELEAGAEAHGFALWRHARLDDAELHAALRDADVSVLPYRVGTHSGWVEMCRDLGVPVAVAEVGHIADQARAWTTPEL +LAAFDPDDPASLADALAALLTAAPDARAAAPAARAAQRRRVAAAHVAVYRQALAVRRGTAATVSVLVITGHRDAHLARVL +AGLERSHRRPDQVVVVFMGQPDGAVPATDLPVTVGHVAADHGLPLATARNRAAELATGEVLVFLDVDCIPAADTVGVLAA +EVAAHPGSLVMGAPRYLAPDWTAALAAEGVDADAAPTDGDLRRHAVPHRARTHLRPGPSEEWALVWTLVMAIGAADLARI +DGFDEGFAGYGAEDTDLAFRARDAGLTLRISPAEAFHQHHGVHRPPLHHVADIVVNARRFRTLHGTWPMGGWLAAFAERG +LIRWDPDGDLLELVREPTPDDVAAARVDDAAY +>GCF_023573625_PROKKA_01896 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFSPAQLAA +ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQ +GDDDAPGA----LPPDASDDGD--GAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDED +ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLSPDS +LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPGVSVLVITGHRDEHLARVI +AGLERSHRRPDQVVVVFMGQPDGRVPATDLPITVGHVSAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLAT +EVAAHPGSVVMGRPRYLRPGWTRDVGE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI +GGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMVPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG +LIAWDPEGERLELLRHPTEAELTAARRGDAAY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001577.fa new file mode 100644 index 0000000000000000000000000000000000000000..dfc2f14c24b0a569a5895c377111b400717ea792 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001577.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01972 +MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRVPG-DVVAVLPA +EGAGPGRAGARVREEAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATL +AEVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHQWVSDAVPVRGR +AVWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHH +ALPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHT +AQELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDP +HGVPRPSADAADLESL +>GCF_003691675_PROKKA_01666 +MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPG-DVVAVLPA +EGAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATL +AEVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGR +AVWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHH +ALPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHT +AQELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDP +QGVPRPSADAADLESL +>GCF_005280335_PROKKA_00887 +MRISVLTHMLHPIRSPYAGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPA-DVVPVLPA +EGAGPGKEGDRLREEATRRACEMVLADDSDAVLNNSLSPAPLELLRERPMITVLHTPATL +AEVLAVVDHPDWRAPQHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGR +AVWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHQ +TLPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHT +AQELAVSIRHARRKDRGRVRAWACRFSAETMVEGYLDLLEQAAEDARD-GEL-------- +---------------V +>GCF_020097155_PROKKA_00828 +MRIDVLTHPLHPIRSPYEGGLEMHTAMTVEHLVAAGHQVRVHARAGTRIPGADVVSLLAA +APDAPGAEGQAVREGALAGACQRILADAPDAVLNNSLSPQPLIRLRSLPMLTVLHTPATL +EPVLEVTDAPGWTPPAHHRWASVSVSNALAWRHRLPSVDVVPNGIDLDRWVSDRAPVPGR +AVWSGRITPEKGLHMAIDAARAVGMELHAAGPVSDPAYYAERVAPRLGEDVVHHGHLDHT +ALPDLLATGEVFLSTPLWAEPFGLATVEAMALGVPVAALLTGAMGEIVAPQAGALAVHHS +VEALADAIRYARRKDRARVADWARRFSADTMVAGYLDLLEQAVADHADDAEL-------- +RKVP-----------A +>GCF_023573625_PROKKA_01898 +MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPG-DVVAVLPA +EGAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATL +AEVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGR +AVWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHH +ALPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHT +AQELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDP +QGVPRPSADAADLESL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001580.fa new file mode 100644 index 0000000000000000000000000000000000000000..e836774c22eb33ee8e50fd8cde8e7963189731ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001580.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01979 +MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAGVVEELPDWQELRAAGSALKQ +SVMADLPALLERLESEVTARGGVVHWARDAAEANRIITELVTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAE +LIVQLGHDRPSHILVPAIHRNRREIRDIFRREMPDTDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGVTEGDGPQEFHLVLLDNGRSA +VLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAID +IPSILIHLRDEDVQATHAARKALRTEKDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEHVEEDGR--- +>GCF_003691675_PROKKA_01673 +MSTAPTRVRLGMPTVRPVHGEGEVLLKTPFPESAREQLGNDQMRANIRRATHTIRAKRAGVVEELPDWQELRAAGSALKQ +SVMADLPALLERLESEVTARGGVVHWARDAAEANRIITELVTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAE +LIVQLGHDRPSHILVPAIHRNRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGVTEGDGPQEFHLVLLDNGRSA +VLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAID +IPSILIHLRDEDVQATHAARKALRTEKDAAGGPLARAKTAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEHVEEDGR--- +>GCF_005280335_PROKKA_00879 +M----TRTALGMPAVRPAHGHGNIVLDEPFPSAARTQLGNAQMRANIHHATHTIRGKRARVVGELPDWAELRQAGSALKQ +QVMADLPALLEQFEQRVTERGGVVHWARDAEEANRIITGLVKAKGVDEVIKVKSMATQEIDLEHALQAEGIAAVETDLAE +LIVQLGHDKPSHILVPAIHRNREEIREIFVREMPETDESLTSDPSALADVARVHLREKFLTTSVAISGANFGVAETGTLT +VVESEGNGRMCLTLPETLITVMGIEKIVPTFQDLEVFLQLLPRSSTGERMNPYTSMWTGVTPGDGPQEFHLVLLDNGRSA +VLSDPEGRPALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGAILSPQLTGVQEGANGSLPYASSLCGACYDVCPVAID +IPSILVHLRDQDVRATH-----------------ARKKEETRVPLPSQMDLMMKGARTVMSSGTAMSLAERGLPLGRLAA +GRDATLGWLPGIAGGWTDQRDVPSPPRQSFRNWWRGNAEHTEERVARDGGRRDVAAEDETTTTDGQEQR +>GCF_020097155_PROKKA_00814 +MSTAPTRVRLGMPTLRPVHGEGEILLKTPFPESAREQLGNGQMRANIRRATHTIRAKRAGVVGELPDWQELRAAGSALKQ +SVMADLPALLERLESEVTARGGVVHWARDAAEANRIITELVTAKGVDEVIKVKSMATQEIGLDAALAQAGVAAVETDLAE +LIVQLGHDRPSHILVPAIHRNRREIRDIFLREMPETDESLTSEPADLAEASRRHLREKFLSTKVAISGANFGVAETGTLA +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGVTEGDGPQEFHLVLLDNGRSA +VLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGAILSPQLTGVDAGENGTLPYASSLCGACYDVCPVAID +IPSILIHLRDEDVQATHAARKALRTEGDGDAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEHVEEDGR--- +>GCF_023573625_PROKKA_01905 +MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAGVVEELPDWQELRAAGSALKQ +SVMADLPALLERLESEVTARGGVVHWARDAAEANRIITELVTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAE +LIVQLGHDRPSHILVPAIHRNRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGVTEGDGPQEFHLVLLDNGRSA +VLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAID +IPSILIHLRDEDVQATHAARKALRTDEDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRVAMDGVAGLDRPEDEHVEEDGR--- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001583.fa new file mode 100644 index 0000000000000000000000000000000000000000..5f2b6ca340b0992bffeabc8332b6d67e4fe18d5b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001583.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01982 +MTA---------------APAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRAS +VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL +LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV +VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH +VLGFAALAQAGRVPAGG +>GCF_003691675_PROKKA_01676 +MTA---------------APAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRAS +VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL +LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV +VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH +VLGFAALAQAGRVPAGG +>GCF_005280335_PROKKA_00876 +MTARPPTPPAEPEPGRRRAPGHAVILDWLEGELRSGRIQVGDKLPSERTLAERFGMSRSS +VREAGRVMDAMGLVRSATGSGPRAGAIVVSEPSAALAWALRMHVATRALPVADLVTTRVL +LETEAA-LEAAEHDVPGRGAILATAHAHLDRMDVPDFPAREFHRLDAEFHVLLSTLSGNV +VLETILRSLREATIGYVEEAMAGVEDWGAVRDELQRQHRDILAAAVERDGPRAAQAVREH +IHWFSRFTTAGPDAAGG +>GCF_020097155_PROKKA_00811 +MTA---------------APAYTIVLDWLEAELRSGAVAVGDKLPGERTLAERFGISRAS +VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL +LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV +VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH +VLGFAALAQTGRVPAAG +>GCF_023573625_PROKKA_01908 +MTA---------------APAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRAS +VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL +LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV +VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH +VLGFAALAQAGRVPAGG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001588.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf93753f828c6a9c4787d9876cff9577038d3bc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001588.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01990 +MRNL-----RDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIAS +DLMTRFGTESLQYGPGQGTEEMRAAAATVMAADGIPDADPDLVVITPGSQAAIDTACRAF +ANPGDVVVVEDPTFVGALTTFATWQLEAVATGTDDQGLVPAALDETLTRLAAEGRRVAFL +YTIPSFANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNV +VHLGTMSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGH +VRHVTGLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGA +VFVPGAAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR +>GCF_003691675_PROKKA_01684 +MRNL-----RDHLSQRAVGVKQSAVRDVFDIAMDPNLISLAGGNPWLADLPLDELGRIAS +DLMTRFGTESLQYGPGQGTEAMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAF +ANPGDVVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFL +YTIPSFANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNV +VHLGTMSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGH +VRHVTGLYRERAAALVDAVREHWDPAVEFITPQGGFFLWATLPVGVDTLEVMHRGIEAGA +VFVPGAAFTPVEGTHSTLRLAYSFVAAEKLVEGVRRLAPAVNESIARAR +>GCF_005280335_PROKKA_00867 +MRHL-----RDHLSHRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIAS +DLMTRFGTESLQYGPGQGTEEMRAAAAAVMAADGIPDADPELVVITPGSQAAIDTACRAF +GNPGDVVVVEDPTFVGALTTFNTWELDAVATGTDEHGLVPAALDETLTRLAAEGRRVAFL +YTIPSFANPSGALLPADRRAEVAAICERHGVLIVEDNPYGQIAFDGDPVAPIAAEHRDGV +VYLGTMSKIFSPGVRIGWALVPAELKREFYLSAESAFIHASTYSQMLSTAFVTQLDWQGH +VRHVTGLYRERAGVLVDAVREHWDPGVEFITPRGGFFLWATLPGGVDTIELMHRGIEAGA +VFVPGGAFTPVEGVHSTLRLAYPFVEAERLVEGVRRLAPVVNDAVARAR +>GCF_020097155_PROKKA_01757 +MSTLDPAGARAHLARRATTVQQSAVRDVFDIAMDPDLVSLAGGNPWLAGLPLEELGATAA +RLVAEQGTASLQYGPGQGLECMRVAACAVMAADGIPDADPELVVITPGSQAAIDTACRAF +ADPGDVVVVEDPTFVGALTSFQTWELEAVATPTDEHGLVPADLDATLARLEAEGRRVAFL +YTIPSFANPSGLLLPADRRDDVAAVCERHGVLIVEDNPYGQIAFDGAPVAPIAAAHRERT +VYLGTMSKIFSPGVRVGWALVPEALHREFYLCAESAFIHASTTSQMLSTAFVTEYDWQDH +VRGVTGLYRSRAQALQAAIAEHWDPGFTFTPPAGGFFLWGSLPAGVDAVELMHRGIAAGA +VFVPGAAFTPVPGTHSTLRLAYSFVDEETLAEGVRRLAPVVNTAVEGAR +>GCF_023573625_PROKKA_01916 +MRNL-----RDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIAS +DLMTRFGTESLQYGPGQGTEEMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAF +ANPGDVVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFL +YTIPSFANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNV +VHLGTMSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGH +VRHVTGLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGA +VFVPGAAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001589.fa new file mode 100644 index 0000000000000000000000000000000000000000..25305fdc8850c733477167b28eee954961cfab35 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001589.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01991 +MTQSTPEPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRPPQAPGYFLKAGTSLARSGDTIERPAGTELLAYEGEI +ALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIV +QDDTTEGLVFPFGRLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHALAPF +GAQPQVDDVQREEAWGSREAAGLAP-------QAEAASSSAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL +QKRGVQNATIDGPRPVHRGRRVLGYAKTLRYVPKREDLAKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA +LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSL +LQEVVDDAYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA +>GCF_003691675_PROKKA_01685 +MTQSTPDPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAGSGDTIERPAGTELLAYEGEI +ALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIV +QDDTTEGLVFPFGQLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHSLAPF +GAQPQVDDVQREEAWGSREAAGLAP-------QAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL +QKRGVQNATIDGPRPIHRGRRVLGYAKTLRYIPKREDLAKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA +LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSL +LQEVVDDAYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA +>GCF_005280335_PROKKA_00866 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------------------------MDENGHWVASAPQPDRSLLTPELRAKIDAVAVATLTAQL +QKRGIQNATIDGPRPIHQGRRVLGYAKTLRYVPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA +LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDVIVGDDDGVVVIPPSL +LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKATFDEYRKTLPDAPAPEGDA +>GCF_020097155_PROKKA_00804 +MTQNTSPATPSVTEHDFTVRQNRPGKVLALHLNYPSRIAQRGRSPQFPGYFIKAGTSIARSGDAVERPAGTELLAYEGEI +ALIIGRTARRVRPEEGWSYVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVIAAANLDPAALRVRTWVNGALV +QDDTTEGLVFPFGQLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPTAPGAPSTGRLITHVTDSDIPMADY +GHGPRVDDLQREEAWGSREAAGLAPVEDAPAQDDAAPASTAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL +QKRGIQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA +LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVVPPSL +LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAKFDEYRKTLPDAPAPEGDA +>GCF_023573625_PROKKA_01917 +MTQSTPDPTPTVTEHDFTARENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLARTGDTIERPAGTELLAYEGEI +ALIIGRTARRVSPKEGWSHVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIV +QDDTTEGLVFPFGQLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVESEHALAPF +GAQPQVDDVQREEAWGSREAAGLAP-------QAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL +QKRGVQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLAKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA +LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSL +LREVVDDAYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001591.fa new file mode 100644 index 0000000000000000000000000000000000000000..07f4524927742f763c1c3c29763631e46121a5ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001591.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01993 +MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDRAVAAAKRAFESGEWSQALPR +QRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG +LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY +AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKTEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF +GPVVAITPFDTEEEALQLANNTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG +>GCF_003691675_PROKKA_01687 +MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDRAVAAAKRAFESGEWSQALPR +QRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG +LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY +AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKTEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF +GPVVAITPFDTEEEALQLANNTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG +>GCF_005280335_PROKKA_00864 +M---TEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVAAAKAAFESGVWSQALPR +ERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG +LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLI +SFTGESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAGSRILVAREVYDEFVERY +AAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAHLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF +GPVVAITPFDSDEEALELANNTKYGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG +>GCF_020097155_PROKKA_00802 +MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDAAVAAAKRAFESGEWSQALPR +QRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG +LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY +AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKAEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF +GPVVAITPFDTEEEALQLANNTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQESKETG-DA +>GCF_023573625_PROKKA_01919 +MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDRAVAAAKRAFESGEWSQALPR +QRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG +LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY +AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKTEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF +GPVVAITPFDTEEEALELANNTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001592.fa new file mode 100644 index 0000000000000000000000000000000000000000..77843674b7176b6637a99a03c32658588905bcfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001592.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01994 +MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRSASMELVVTDLAQSREFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL +GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD +GFSYTREGQGEESLPEWKQGEYKLGNQL +>GCF_003691675_PROKKA_01688 +MTNLESRQKTSSGFFVTKEAPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL +GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD +GFSYTREGQGEESMPEWKQGEYKLGNQL +>GCF_005280335_PROKKA_00863 +MSNYAGRTRTSVGTYVGQEGPVKTDNPIPTPKAEAPDVLRCASMELVVTDLEKSRQFYVD +VLDLVVTEEDEDTVYLRSMEEFIHHNLILRKGEIAAVAAFSYRVRTPEDLDKAVAFYTEL +GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFYEVDHVERLAWRYDLYSPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVAF +ATHEKHNILAICDKLGSLRMSDAIERGPGRHGVSNAFYLYLRDPDGHRVEIYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASLVLDLDGNVKEVVARTDDSEMAVTIGAD +GFSYTRAEEGEDSMPEYKKGEYKLGNQL +>GCF_020097155_PROKKA_00801 +MSNLESRKKTSSGFFVTEEAPITPANPLPTPKAEAPDILRCASMELVVTDLAASRHFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLILRKGETAAVAAFSYRVRTPEDLDKAVAFYTEL +GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFFETEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAAKFMQDLGFRVTEDIQDEQGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVARTDDSEMAVTIGAD +GFSYTREDEGEESMPEYKQGEYKLGNQL +>GCF_023573625_PROKKA_01920 +MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL +GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPIVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD +GFSYTREGQGEESMPEWKQGEYKLGNQL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001600.fa new file mode 100644 index 0000000000000000000000000000000000000000..770ee3dc5f918094a1b7ffb90b063de2c51c8f00 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001600.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02007 +MPPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRAALGG +LVSAATDVRSAIQTGWRGEAAGAYGEAVRRAAALAAELEREAGEWLALRATAERDAEDAR +RNAEARQRAAEETALAVLRSLAVAA +>GCF_003691675_PROKKA_01717 +MSPLIGPQQIATALRAVGLDDDAARLAAWADPARREREAAEQALADLAAAQTQLRTALGG +LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR +RNAEARQRAAEETALAVLRSLAVAA +>GCF_005280335_PROKKA_00835 +MLQLIGPQHLAAALQAAGLDDDAARLLAWADPARRDRDAAQAALDELAVAQESLRGALAG +LVAAARDVRAGAAVAWRGPAAGEYADAVAEAVGAAEGLEREAGEWLALRATAEREAEDAR +QDAEARLRAAEETARAALRALAVAA +>GCF_020097155_PROKKA_00772 +MLLPPTAQALLRTLVAAGLDDDAARLAVGLTDAHADLQAARAAQDALADAAEDLRDLLAL +LEELTRGVAAALDVDWRSEAGAEYGERTDGLHRTATDRQDEAREWAGLLGRARSEAEQAE +RDAELRVRRAEEGASALLRAMAAA- +>GCF_023573625_PROKKA_01945 +MSPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRTALGG +LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR +RDAEARQRAAEETALAVLRSLAVAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001605.fa new file mode 100644 index 0000000000000000000000000000000000000000..71510281233cbc8285dd919c8dc68c0413983b92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001605.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02012 +MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA +>GCF_003691675_PROKKA_01722 +MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA +>GCF_005280335_PROKKA_00830 +MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS +HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD +EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI +EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA +LEKDEVEAGYVLTCQTRATSDSITVDYDA +>GCF_020097155_PROKKA_00767 +MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT +NVTSMNDPEAVAAEAVKQDQ-THLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRS +AMDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTD +EWFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTI +EFNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYA +LEKDEVEQGYVLTCQTRPTTDSIKVDFDA +>GCF_023573625_PROKKA_01950 +MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001607.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e9c48dd7c5aa89dc5475e13a02441016ffc620d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001607.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02016 +M---SAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILG +NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG +GVESMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVG +EVDGITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGST +PEVLASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA +PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAI +ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV +>GCF_003691675_PROKKA_01725 +M---SAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILG +NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG +GVESMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVG +EVDGITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGST +PEVLASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA +PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAI +ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV +>GCF_005280335_PROKKA_00805 +MTTPSPQPQALLVGGKRTAVGRYGGALSAVRPDDLAALTIKQVIEDAGIDPAAVDEVILG +NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG +GVESMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVG +EVDGITREDADAFAARSHGRAIAAIEAGRFKDEIVPVTVKGRKGAETVVDTDEGPRPGST +PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA +PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPEIVNADGGAI +ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV +>GCF_020097155_PROKKA_00764 +M---SAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILG +NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG +GVESMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVG +EVDGITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGST +PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA +PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAI +ALGHPLGSSGSRLVVTLLGRMEREGADKGLATMCVGVGQGSAMLVEKV +>GCF_023573625_PROKKA_01953 +M---SAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILG +NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG +GVESMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVG +EVDGITREDADAFAARSHARALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGST +PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA +PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAI +ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001608.fa new file mode 100644 index 0000000000000000000000000000000000000000..df2c96bc42c8e19a6adcb4b7e2b44313c6bb2742 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001608.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02017 +MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA +ILFESDAKFERMQAFLDRKKK +>GCF_003691675_PROKKA_01726 +MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA +ILFESEAKFERMQAFLDRKKK +>GCF_005280335_PROKKA_00804 +MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA +ILFESEAKFDRMQAFLDRKKK +>GCF_020097155_PROKKA_00763 +MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA +ILFESQAKFERMQAFLDRKKK +>GCF_023573625_PROKKA_01954 +MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA +ILFESEAKFERMQAFLDRKKK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001613.fa new file mode 100644 index 0000000000000000000000000000000000000000..088c9fbac8ceb4c8ee5240fd3e634583724e65f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001613.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_02023 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHARTVGQQALGALTIHERALKLKE +LALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGV +AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVEA +VTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGAVQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFED +ARTPEVHSVEAFGPVTSVIGYTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV +GDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI +TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>GCF_003691675_PROKKA_01732 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHARTVGQQALGELTIHERALKLKE +LALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGV +AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVEA +VTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGAVQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFED +ARTPEVHSVEAFGPVTSVIGYTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV +GDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI +TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>GCF_005280335_PROKKA_00796 +MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHARTVGRKSLGELTIHERALKLKE +LALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGV +AVQINAFNFPVWGMLEKFAPSFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF +TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVDA +VVEALSARL-GKVVLGDPRVEGTTMGALASKEQQGEVRGAVQRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFED +ARTPEVHAVEAFGPVTSVVGYTDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGA +PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV +GDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI +TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>GCF_020097155_PROKKA_00757 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHARTVGQRNLGELTIHERALKLKE +LALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTFSGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGV +AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPEAMVED +VTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKAVQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFAD +ADTPQVHSVEAFGPVTSVIGYTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATREDVEAGKAKHPFYKALDELQI +GDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFI +TPVTYDDAIRVTLTAKRITPRVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAE-PKA +>GCF_023573625_PROKKA_01960 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHARTVGQQALGALTIHERALKLKE +LALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGV +AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVEA +VTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGAVQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFED +ARTPEVHSVEAFGPVTSVIGYTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA +PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV +GDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI +TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001615.fa new file mode 100644 index 0000000000000000000000000000000000000000..d041996920ee0cb05e87130070ce3920b18f7adf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001615.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02025 +MT------TSRLPLLGALAVGALALAGCA-GGGAEPSSPAP----SSASSTTTAASSA-- +SPAASSSTAPTSPAASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSE +VGLSAASPLERQTELRQRAA----GLEQTVDAGASPASTRSAEQQACLDATRSDLERDAE +AGAADLGLTAQPETAATTGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALED +ARAAAQACTGVDLAG-LGVESVTR-TEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAV +AQADADGGVPADAEDRAASIVADVLAALDGEG +>GCF_003691675_PROKKA_01734 +MT------TSRLPLLGALAVGALALAGCAGGGGAEPSSPAP----SSASSTTTAASSAPT +SPAASSSTESTGAA-----ESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSE +VGLSAASPLERQTELRQRAA----GLEQAVDAGASPASTRSAEQQACLDATRSDLERDAE +AGAADLGLTAQPETAATTGGGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALED +ARAAAQACTGVDLAG-LDVESVTR-TEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAV +AQADADGGVPADAEDRAASIVADVLAALDGEG +>GCF_005280335_PROKKA_00794 +MT------PSRLPLLGVLAVGALALAGCA-GGGAEPSSPAPSPASSSASPTTTAASSAST +SPAASASASSTPTA--------------TALSLDLPEELSGESATRLRAVVQDAAGPAAE +LGQTFSSPLERRAALEEDAAIV-DALEE--DAG------DDAGRRACVDATRAAREADQA +SGAAQAAWYAQPQTASTTGG---STDGTAASGRPGLQVEPLGVQVAVYPDEATARSVAEA +ARDAAEACEGQEMSS-MGVSSVEPLTGAPGETAFTVVPVSGSIIYAVSTVVQVGDRVYAV +SQGEDGAGVPEGAEERAVALVEDLEAALEG-- +>GCF_020097155_PROKKA_00756 +MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSST------AAGSPTAGGAGSSVT +SPAASSSAAS-----------------SSALSLSMPDRFGNEARTGLTEAVTAAAPEGFE +VTTRSVSPLERKTDLEDQATILTDGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAA +AGGAQLRSDAMPTVA---GGGYTSVRA----------------DVVAYPDVSAAVAALAD +GSAPIELCTDVQVPGAEQPTDIAPVTGIGDEA------VGGELAGGRWLAVRRGTDVVSV +MVAGPGETAPAGAADQARALAEQVLEAVPA-G +>GCF_023573625_PROKKA_01962 +MT------TPRLPLLGALAVGALALAGCAGGGGAEPSSPAP----SSASSTTTAASSAST +SPAASSSTAPTSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSE +VGLSAASPLERQTELRQRAA----GLEQAVDAGASPAPTRSAEQQACLDATRSALERDAE +AGAADLGLTAQPETAATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALED +ARAAAQACTGVDLAG-LGVESVTR-TEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAV +AQADADGGVPADAEDRAASIVTDVLAALDGEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001622.fa new file mode 100644 index 0000000000000000000000000000000000000000..1ed34613500737fe3accee5515871aee6a84ead7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001622.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02036 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV +ERTLERRLRSPGAP--------------------------------------AFPDDDAD +G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF +DDPEHDWIADDPEDE-KG +>GCF_003691675_PROKKA_01743 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAP--------------------------------------AFPDDDTH +G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF +DDPEHDWIADDPADP-RD +>GCF_005280335_PROKKA_00780 +MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT +RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL +IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM +NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV +ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP +GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY +DDPEHDWIADDAEDDARG +>GCF_020097155_PROKKA_00747 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRAPGAP--------------------------------------AFPDDDTH +G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF +DDPEHDWIADDPEDS-RD +>GCF_023573625_PROKKA_01971 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAP--------------------------------------AFPDDDTH +G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF +DDPEHDWIADDPADP-RD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001624.fa new file mode 100644 index 0000000000000000000000000000000000000000..945f6469aa7afb8c3d61918b656e2864deda3e2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001624.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02045 +MTTSETTSETTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAATAGWLRHRGVGPG +DRVAVMLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELGYFLEDSGARMLWAMPGLPAVDEVAGNVDV---EVVTLDLE +AVGRECAAEGIAPVTEITPRDPDD-DAVLLYTSGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFG +LSVVLNGAVFAGSTLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGAEPADFSRLRMPLSGGASLPV +ETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRIVAMDGTEVPEEDLETSGELRIRGEGIMA +GYWGRPEDTEAAFDEDGWFRTGDIARRDEAGYVMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGE +EIAAFVSLAPGSTATGEELQAFAAERLARYKQPREVTIMDGLPKNATGKILRRELRQG +>GCF_003691675_PROKKA_01751 +M--------TTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAATAGWLRHRGVGPG +DRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGARVLWAMPGLPAVDEVAGNVDV---EVVTLDLE +AVGRECAAEGIAPVTEITLRDPDD-DAVLLYTSGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFG +LSVVLNGAVFAGSTLSLMPRFVPEAAYDQLQDHGVTFLPGVPTMHGAFLSVARARREAGAEPEDFSRLRMPLSGGASLPV +ETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRIVAMDGTEVPEEDLETSGELRIRGEGIMA +GYWGRPEDTAAAFDQDGWFRTGDIARRDEAGYVMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGE +EIAAFVSLAPGSAVTGEQLQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELRQG +>GCF_020097155_PROKKA_00735 +M--------TTSETPDTSTTTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAATAGWLRHRGVGPG +DRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELGYFLADSGARMLWAMPGLQAVDEVAGNVDV---EVVTLDLE +AVGRECAAEGIAPVTEITPRDPDD-DAVLLYTSGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFG +LSVVLNGAVFSGSTLSLMPRFEPEAAYDQLQDHGVTFLPGVPTMHGAFLTVARARREAGAEPADFSRLRMPLSGGASLPV +DTLHAAEKLYGVPVFEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRIVAMDGTEVPEEDLETSGELRIRGEGIMA +GYWGHPEDTVAAFDADGWFRTGDIARRDEAGYVLIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGE +EIAAFVSLAPGSTVTGEELQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELR-G +>GCF_020097155_PROKKA_00741 +M---------NSALPATDP--------HRGDVCALLEAGHDRDPRAVAWREDGVDTTYAELLELVQATAGVLRRQGVGPG +DRVALLMPNTLAFPAVYYGALWLGAVVVPLNPLSTDRELEYFLTDSQAVLLWSMRGTSAAAEAAQAVGVPHLQSSPADLR +DV-----VAGAEPVRERTPRTSEEADAVVIYTSGTTGQSKGARLSHRTVASSAVLTSEALDWLQAGHTVLGVLPFFHVFG +MSAALNMPLYTGCRNSVVTRFAPHTALEQVVRDEVRALPAVPTMIGALLRALRSARAKG-DDVDLSALRYILSGGAPLPV +ETLHEAEEEFGVPVREGYGLTESCGPVSFNPMLRPSRAGTVGQPLPGVEFRLVTTDGVEVPAGDTETPGELRIHGPVLMT +GYLGEPQADAASFDDEGWLRTGDVATRDEEDYYRIVGRLKDIIIHGGYNVYPREVEEAFYEHPAVSEAAVLGVPDERFGE +KVVAYVALQDGPEVEVAELNAFVRERLASYKWPSQVTVMDALPKNTTGKIVKDLLR-- +>GCF_023573625_PROKKA_01979 +M--------TNSETPDTSATTVGRPTERRGHVAELLSATVARQPDAVALRIGEASMTYRELDQVTAATAGWLRHRGVGPG +DRVAMMLPNIPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGARMLWAMPGLPAVDGVAGNVDV---EVVTLDLE +AVGRECDAEGITPVTEITPRDPDD-DAVLLYTSGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFG +LSVVLNGAVFAGSTLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGTEPADFSRLRMPLSGGASLPV +ETLRAAETLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRIVAMDGTEVPEEDLETSGELRIRGEGIMA +GYWGRPEDTEAAFDEDGWFRTGDIARRDEAGYVMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGE +EIAAFVSLAPGSAVTGEELQAFAAERLARYKQPREVTILDGLPKNATGKILRRELRQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001628.fa new file mode 100644 index 0000000000000000000000000000000000000000..21f7d29a89f7d1ec4be1ae3c40e31e148cd3db1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001628.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02056 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSRWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLHALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMAG +VAEAMLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID +>GCF_003691675_PROKKA_01762 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG +VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID +>GCF_005280335_PROKKA_00764 +MISLYVPGDSPLHRAPAGLKLALFAAWALAVTLAPPTPWTAGAAVGMALAAYLTGFGPRR +GAAMLGRDLRALWVFYAFLFAAQWLFADLTAAALMVGRVLGLVLAAQVLTRTTRIAELVG +VAEAVLAPVERIPWLGPRLARVGLRPERVGLAMGLVLASIGHLRSVAEQVRQAQASRGVR +MAPWAWVLPLLVLSVKHADDVGDALAARGIE +>GCF_020097155_PROKKA_00728 +MLSLHVPGDSPLHRCPAGAKVAALAVWALVVTLAPVSALTAGASVVVGVGAYLLGFGLRR +GVRLLAADLRGLWVFYAVLFAAQWLFTDLPTAALTTARVLGLVLAAQVLTRTTRIAEMAG +VAEAVLGPVTRIPWLGPRLARAGVRPDRVGLAMGLVLASVGHLRGLAEQIRAAQAARGVR +MAPWAWVLPLLVLSLKHADDVGDALAARGID +>GCF_023573625_PROKKA_01990 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG +VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001629.fa new file mode 100644 index 0000000000000000000000000000000000000000..e589e7e0ff691f9e568eba67310669e17814f3a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001629.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02057 +M-----------SPDRSVTLTGVRVEADGPEGAVVLLDGVDLTLAAPRVAVIGENGSGKS +TLARAIAGLADVVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVK +SLRDDAGRRLTKDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLV +IADEPTSLLDGRHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHSGRVER +TGPAEEVVEAYERFLDHAVAAELR--------------------- +>GCF_003691675_PROKKA_01763 +M-----------SPDRSVTLTGVRVEADGPEGVVVLLDGVDLTLTAPRVAVIGENGSGKS +TLARAIAGLADVVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVK +SLRDDAGRRLTKDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTTGPSLV +IADEPTSLLDGRHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWVHGGRVER +TGPAEDVVEAYEHFLDHAVAAELR--------------------- +>GCF_005280335_PROKKA_00763 +M-----------EQTTGVRLRGARVEADGPEGVVALLQDVDLDLTAPRVAVVGENGSGKS +TLARAVAGLVDVVAGEVTVHGVDAVRDVKALRRVVGMVFANPAAQAVMPTVREDVELTVK +SLRDDDGRRLSKDDVAARVAAALAEHRLTELAERPCLALSSGQAQRLAMCSVMAGRPRLV +IADEPTSLLDGRHRRIIADRLLAA-----DGFQLLLVTHDLELARACDDAVWVHEGRVRA +VGPAGEVVDAYAAFLDEAVAAESAEAAAGDPAAVNPAGASAEARP +>GCF_020097155_PROKKA_00727 +MTGRTPPTRAPHDDDAAVRLAGVQVAAPGGP---VLLDGVDLHLTAPRVAVVGENGSGKS +TLARAVAGLAEVTAGEVAVHGVDAVRDVKALRRTVGMVFANPAAQMVMPTVREDVELTVK +ALTDDAGRRLSRAEVAARVDAALAEHRLTDLAERPCLSLSSGQAQRLAMCSVLVGAPRLV +IADEPTSLLDGRHRRIVADRLLGGAER--GEFQLLLVTHDLDLARACDAAVWVHSGRVER +HGPAAETVAAYEAFLDDAVARELA--------------------- +>GCF_023573625_PROKKA_01991 +----------------------------------MLLDGVDLTLTAPRVAVIGENGSGKS +TLARAIAGLADVVAGEVSVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVK +SLRDDAGRRLAKDDVAARVAAALEEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLV +IADEPTSLLDGRHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHGGHVER +TGPAEDVVEAYERFLDHAVAAELR--------------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001632.fa new file mode 100644 index 0000000000000000000000000000000000000000..969d10af7fdce36fdd39bc7c24e7efaaff813153 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001632.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02080 +------MNLDQLQALRAIADEGSFEAAAYELDVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGIGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +EDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAGPLGSMRYVPLASPALLARH +AADDVVDLGAMPMMRYNAKDDLQRLALSGAGLDIAPPTHLAPSFDGFHRSVRAGLGWGML +VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG +>GCF_003691675_PROKKA_01784 +MPKLCFMNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALRARH +AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML +VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG +>GCF_005280335_PROKKA_00704 +------MNLDQL--------------------------------------QVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDLVLDLHVEDQDHSAQLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLVAPALLARH +AAGDVVDLGAMPMMRYNVKDDLQRLALSDAGLDVAPP----------------------- +--------------------------------TLPVTRLVRLTRAVREAAQRTLEPG +>GCF_020097155_PROKKA_00614 +------MNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRMAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDTVLDLRVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH +AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML +VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQATTLPVTRLARLTQAVREAAQRTLERG +>GCF_023573625_PROKKA_02018 +MPKLCFMNLDQLQALRAIADEGSFEAAAYDLGVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH +AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML +VGAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001633.fa new file mode 100644 index 0000000000000000000000000000000000000000..106131c774288cc2d29b64fcbd244a3463536e5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001633.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02081 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>GCF_003691675_PROKKA_01785 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>GCF_005280335_PROKKA_00703 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>GCF_020097155_PROKKA_00613 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV +VDLVIAVVMAVLAVRLIAGSGVWG +>GCF_023573625_PROKKA_02019 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001634.fa new file mode 100644 index 0000000000000000000000000000000000000000..76fa62e78578eb6cc6292b0748f4dc9f00d6ebc1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001634.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02082 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG +>GCF_003691675_PROKKA_01787 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG +>GCF_005280335_PROKKA_00701 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG +>GCF_020097155_PROKKA_00611 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG +>GCF_023573625_PROKKA_02021 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001638.fa new file mode 100644 index 0000000000000000000000000000000000000000..645e1aca151c1e36e449ce424728981116c0467b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001638.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_02086 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA +PAHHRTTRARTPERTR +>GCF_003691675_PROKKA_01791 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA +PAHHRTTRARTPERTR +>GCF_005280335_PROKKA_00697 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA +PAHHRTTRVRTPERTR +>GCF_020097155_PROKKA_00607 +MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA +PAHHRTTRVRTPERTR +>GCF_023573625_PROKKA_02025 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA +PAHHRTTHARTPERTR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001642.fa new file mode 100644 index 0000000000000000000000000000000000000000..08c2f97cf5b93f8a9b3856f89d3b5c58df67ecfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001642.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_02095 +MSPSAPQRRAARAATFAATLAAAAIALTACGADAAPFSPASAPASASDGAESPAGEATAA +SSVSEEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVTGFTRLSNAGNG +KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA +DGTGAIRTFDSTHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRDALQ +VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ +RSGNLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR +AEDGSAVVLTYDGEANVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA +EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPDEAADAASGHDE--HTDHDH +------------- +>GCF_003691675_PROKKA_01803 +MSHSAPQRRSARTAALSATLAAAAIALTACGADAAPSGPTSAPAPAADGAESPSGEARAA +SSVSEGDRVDPTRTTEVSAVTPRILLSHEGGLTLLDAESGEVVREQDVPGFTRLSNAGNG +KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFG +DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ +VIDPKTSEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ +RSGNLFGLHDSPIVLGDHKVEEEPEEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR +AEDGSAVVLTYDGEVTVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA +EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGEPESVKPEEGADAESGHDE--HADHDH +GHESDE-HTDHDH +>GCF_005280335_PROKKA_00683 +MSHSAPQCRSTRTA-------------------------------ASDGAESTSGETTAA +SSVSEEERVDPTRTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVPGFTRLSDAGNG +KDVLVTTGNGWEVFSTGIQAKAHGDHVHNDESAPGMTGVTFPGEDPGHVVTHNGRTTLFA +DGTGAIRTFDATHLDKATPDLMPVMTEAETEDPHHGVALELYDGTLFTTQGTEDSRDTLQ +VIDSTTGEVTAETDDCPGSHGEAAAQPTEAGDVVVTGCENGPVVYRDGEFHKVEVETEYQ +RSGNLFGLHDSPIVLGDHKVEEEPTEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR +AEDGSAVVLTYDGEVNVIDEETGEVTAEYAVIEPWKEKDEWQEPGPILKVAGNTAYVTDA +EAQKLVVVDLETGETVLEKDLDFAPVEMAVVTGQPESVKPEEAADAESGHDE--HTDHDH +------------- +>GCF_020097155_PROKKA_00598 +------------------------------------------------------------ +-------------------MTPRILLSHEDGLTLLDAESGEVVKEQDVAGFTRLSNAGNG +KDVLVTTGNGWEVFSTGIQAKAHGDHFHNYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA +DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ +VIDPTAGEVKAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ +RSGNLFGLHDSPIVLGDYKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR +AEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAHVTDA +EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQRESVKPEEAADAESGHDE--HTDHDH +------------- +>GCF_023573625_PROKKA_02034 +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------MTGVTFPGEHPGHVVTHNGKTTLFA +DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRNTLQ +VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ +RSGKLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR +AEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA +EAHKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPEEGAHGDEDHDDDGHEGHDH +GAEPSEGHEGHDH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001643.fa new file mode 100644 index 0000000000000000000000000000000000000000..9d0b7e27b0424b3e026e5fae803b114cf76969df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001643.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_02099 +M--------------ASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRAGARNPS +DLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRIADIVGTAADTAGVAQLVYLSGLHPDT +VPVAELSDHMRSRALVAERLERAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQ +ACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLAEEAVVE +DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPSDPEWAGTTVYTDERERESDLPAQEVW +PVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGLTRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQL +STEPREGGGSVYRQRAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRLPLRRNP +LDRRARGAGGAQSRD +>GCF_003691675_PROKKA_01806 +M--------------ASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRAGARNPS +DLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRIADIVGTAADTAGVAQLVYLSGLHPDT +VPVAELSDHMRSRALVAERLERAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQ +ACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLAEEAVVE +DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPSDPEWAGTTVYTDERERESDLPAQEVW +PVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGLTRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQL +STEPREGGGSVYRQRAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRLPLRRNP +LDRRARGAGGAQSRD +>GCF_005280335_PROKKA_00680 +--------------------------------------------------------MGGRLIPELLAAGFDVRAGARNPS +DLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDT +IPVAELSDHMRSRALVAERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLYYLLQ +ACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIGTVTPIPVAVALPLAASLAEEAVVE +DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVW +PVIESVGGANGWYSTPMLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRAWLQM +STEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTTGGERRRPRSLARALVDRLPLRRNP +LDRGASA-------- +>GCF_020097155_PROKKA_00594 +MSTPSTSRGSGLTSAAASGDTPAGTGATTAS-LSPLGLALPDGHDRRVLVTGATGYVGGRLIPELLAAGFRVRAGARTPR +DLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSMGAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAG +KPVEELSDHMRSRALVAERLEAAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQ +ACALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPIPVKVALPLAASLAEDAVVE +DHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEADVYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVW +PVIESIGGRNGWYSTPLLWKVRGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQL +TTEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARRRTRGLVRALADRLPLRRSP +LDRRAG--------- +>GCF_023573625_PROKKA_02039 +M--------------ASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRAGARNPS +DLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRIADIVGTAADTAGVAQLVYLSGLHPDT +VPVAELSDHMRSRALVAERLERAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQ +ACALPEPVQLRAQIGNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLAEEAVVE +DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPSDPEWAGTTVYTDERERESDLPAQEVW +PVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGLTRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQL +STEPREGGGSVYRQRAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRLPLRRNP +LDRRARGAGGAQSRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001649.fa new file mode 100644 index 0000000000000000000000000000000000000000..8825cd794753e8f19137de0ef7d2e4ef8fdf8958 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001649.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02107 +MG--EARTGGEA----------------ALSGVTAELDAALRHAAAQAPGSAAFAELLDS +LHVHVGAGKLIRPRLVELGWRLATADP----VPPSGRA--------AVDRLGAAFELLHT +ALLVHDDVIDRDVLRRGQPAVHASARHRLEARGVPAADAAHAGVAVALIAGDVLLTQAFR +LAATCAADTARAAEAAAVVFDAAAVTAAGELEDVLLGLSRHTGEEPDPDRILAMQRLKTA +HYTVGAPLRAGALLAGADPDLARAMGEAGADLGA-AYQVIDDVLGVFGDPGETGKSADGD +LREGKATVLTAHGRRIPAVRALLDAGPAT----------PADIEAARRALEAAGAREHAL +DVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS +>GCF_003691675_PROKKA_01814 +MG--EARTGGEA----------------ALSGVTAELDAALRHAAAQAPGSAAFAELLDS +LHVHVGAGKLIRPRLVELGWRLATADP----VPPSGRA--------AVDRLGAAFELLHT +ALLVHDDVIDRDVLRRGQPAVHASARHRLEARGVPAADAAHAGVAVALIAGDVLLTQAFR +LAATCAADTARAAEAAAVVFDAAAVTAAGELEDVLLGLSRHTGEEPDPDRILAMQRLKTA +HYTVGAPLRAGALLAGADPDLARAMGEAGADLGA-AYQVIDDVLGVFGDPGETGKSADGD +LREGKATVLTAHGRRIPAVRALLDAGPAT----------PADIEAARRALEAAGAREHAL +DVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS +>GCF_005280335_PROKKA_00672 +M---------SA----------------GREGVVAELEAALSRAAGLAPESAAFAELLAG +LRTHAGAGKLIRPRLVELGWRAAADGP----VPAAERP--------AVDRLGAAFELLHT +GLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEAEAAHAGTAVALIGGDVLLVEALR +LAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLGLARHTGEEPEPERILAMQRLKTA +HYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPTRWWTTCSGCSAPRSRPASPPTAT +CARARPPCSPRTAAATPPSAPCSTPAPAT----------PEELEAARRALEAAGAREHAL +QVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS +>GCF_020097155_PROKKA_00588 +MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR +LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA +ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR +LAAASGA-RVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTA +GYSFEEPLRAGALLAGADPAHAEALAEAGALLGV-AYQVVDDVLGTAGDPAVTGKPHDAD +LREGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHAL +GVAEELVDQARALLDALPMAPAERAEFAATCGQILQREA +>GCF_023573625_PROKKA_02047 +MG--EARTGGEA----------------ALSGVTAELDAALRHAAAQAPGSAAFAELLDS +LHVHVGAGKLIRPRLVELGWRLATADP----VPPSGRA--------AVDRLGAAFELLHT +ALLVHDDVIDRDVLRRGQPAVHASARHRLEARGVPAADAAHAGVAVALIAGDVLLTQAFR +LAATCAADTVRAAEAAAVVFDAAAVTAAGELEDVLLGLSRHTGEEPDPDRILAMQRLKTA +HYTVGAPLRAGALLAGADPDLARAMGEAGADLGA-AYQVIDDVLGVFGDPGETGKSADGD +LREGKATVLTAHGRRIPAVRALLDAGPAT----------PADIEAARRALEAAGAREHAL +DVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001652.fa new file mode 100644 index 0000000000000000000000000000000000000000..d0a59f5aeb0fd939ada3b9d33073903a9105a995 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001652.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02113 +---------------------------MTGAP-I-LPLLVLNGPNLNLLGTREPEVYGTA +TLDDVRALTEARAAEHGLTVDFRQSNHEGELIDWIQEARTSHAGVLINPAAYSHTSIAIR +DALAAVDRPIAEVHISNIHRREAFRHHSHVSAVADVVIAGAGVQGYTLAVDWLAAAVRR +>GCF_003691675_PROKKA_01820 +---------------------------MTGAP-I-LPLLVLNGPNLNLLGTREPEVYGTA +TLDDVRALTEARAAEHGLTVDFRQSNHEGELVDWIQEARTSHGGVLINPAAYSHTSVAIR +DALAAVDRPIAEVHISNVHRREAFRHHSHVSAVADVVIAGAGVQGYALAVDWLAAAVRR +>GCF_005280335_PROKKA_00667 +MRETGASPRTFVRETGASVVVRSYTGPMTTAPSA-LPLLVLNGPNLNLLGTREPEIYGSD +TLDDVRSRTEARAAGHGLAVDFRQSNHEGELVDWIQEARTSHAGILINPAAYSHTSVAIR +DALSAVGRPIVEVHISNIHRREPFRHHSHVSAVADAVIAGAGVLGYELGIDWLAAAVRR +>GCF_020097155_PROKKA_00583 +-----------------------MTDSMPAATAARLPLLVLNGPNLNMLGTREPEKYGFE +TLEDVRALTAARAAEHGLEVDFRQSNHEGELVDWIQEARTGFSGILINPAAYSHTSVAIR +DALAAVPVPIVEVHITNIHAREEFRHHSVVSAVATTVIAGAGTQGYALGVEVLAARLAR +>GCF_023573625_PROKKA_02051 +---------------------------MTATP-A-LPLLVLNGPNLNLLGTREPEVYGTA +TLDDVRALTEARAAEHGLTVDFRQSNHEGELIDWIQEARTSHAGVLINPAAYSHTSIAIR +DALAAVDRPIAEVHISNVHRREAFRHHSHVSAVADVVIAGAGVQGYALAVDWLATTVRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001653.fa new file mode 100644 index 0000000000000000000000000000000000000000..d60bd9edf501cd5528ba9230708c9026e333f6f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001653.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02114 +MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAE-DGGTLWFLTRATSDVAA +DAPQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVR +VDVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF +>GCF_003691675_PROKKA_01822 +MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAE-DGGTLWFMTRSTSDVAA +DAPQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVR +VDVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF +>GCF_005280335_PROKKA_00666 +MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAE-ETGTLWFMTRAASDVAS +DASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVR +VDVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF +>GCF_020097155_PROKKA_00582 +MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ +DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR +VQADSAEYWDGGGA-ASVVEIVKAKVTGGEARPGDHDTVEF +>GCF_023573625_PROKKA_02052 +MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAE-DGGTLWFLTRATSDVAA +DAPQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVR +VDVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001654.fa new file mode 100644 index 0000000000000000000000000000000000000000..00633aafd4d9e72bee73f52b9b674bedbe0685e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001654.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_02115 +---MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGH +QLSAPKRREAAT-AERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKER +QEKAKEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMET +DRGDTIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA +EIVEQIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP +SPEGLGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKAD +EAIDAAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP +GSIWTASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD----- +>GCF_003691675_PROKKA_01823 +---MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGH +QLSAPKRREAAT-AERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKER +QEKAKEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMET +DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA +EIVEQIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP +SPEGLGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKAD +EAIDAAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP +GSIWTASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD----- +>GCF_005280335_PROKKA_00665 +---MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGH +QLSAPKRREAAT-AERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAER +QAKAKEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMET +DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA +EIVEQIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP +APEGLGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKAD +EAIDAAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP +GSIWTASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA---- +>GCF_020097155_PROKKA_00581 +MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH +QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER +QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT +DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA +EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP +APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD +EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP +GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA +>GCF_023573625_PROKKA_02053 +---MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGH +QLSAPKRREAAT-AERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKER +QEKAKEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMET +DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPA +EIVEQIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP +SPEGLGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKAD +EAIDAAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP +GSIWTASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001656.fa new file mode 100644 index 0000000000000000000000000000000000000000..f71c378730d651770de1477872b6ebe469cde91f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001656.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_02118 +-----------MSVRSLLPDLGTSATGTPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLD +GPDRLRRLSALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRD +VAQHVDADALAAAVAADRGARLLADGEVPLPADVADLAWDDAGYAAGVRELLTRMADSGG +ELAKVVISRTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGS +RVLAGSMPRGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVL +TLPNVHHLATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYA +GPVGWLDQDGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRAL +GVAED +>GCF_003691675_PROKKA_01826 +--------MGAMSVRSLLPDLGAPATGAPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLD +GTDRLRRLSALWQTAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRD +VAQHVDADALAAAVAADRGARLLADGAVPLPAGVADRAWDDAGYAAGVRELLTRMADSGG +ELAKVVISRTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGS +RVLAGSMPRGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVL +TLPNVHHLATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYA +GPVGWLDQDGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRAL +GVAED +>GCF_005280335_PROKKA_00662 +-----------MSVPTLLPELG---TAAAEAAVPPFARAVLWAHGDAAWRGDDGWTVLVD +GPDRLRRLSALWQAAVAGREDPAAPVRGWVSAPFSDDSVEPAVLRVPARLRRSTASGIRE +TPQHVDAAALADAVAADGGGRLLPDGEVPLPADTSESAWDDAGYAAGVRELLARMAASDG +ALAKVVISRTLTVPADDADLWRAIRALRREYPQTWVFAVGGLLGATPEILATRHAGLVGS +RVLAGSLPRGEDEAEDAALRARLATDPRLGEEHRWAARSVLDALAPVVDLADPDPAPTVL +TLPNVHHLATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPEAVRVISEVEPVDRGRYA +GPVGWLDQDGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKLLPMRRAL +GIDLD +>GCF_020097155_PROKKA_00579 +MPPVPSVAVAALAARALSP------SGSAAGRVPAFARAVVWAREDTVRVGVGGHTVLLD +GPDRLRRLSALWRAAVAARPEPASPALAWVSSAFDDASPVPSVLRVPARVLQAGPDGVVE +VPVAMPREALAAAVAACPGARLTEAGEVPLPADDPALAWDDAGYAAGVEEVVARMEASAG +ALSKVVVSRTETVPAGEDRLWAAVDALRAEYPQTWTFAVGGLVGATPEMLATRRDGVVAS +RVLAGSLPRGVDEGDDARLRARLAADPRLLREHHWAARSVLDALAPVVELEDAHPAPFVL +TLPNVHHLATDVRGRLRPGEGAVLDVVAALHPTAAVGGTPTAEALEVIRAVEPVDRGRYA +GPVGWLDQDGDGEIALALRCGQQVPGGVRLQAGGGIVPGAAAEEEVVEVGVKLLPMRRAL +GVA-- +>GCF_023573625_PROKKA_02056 +--------MGAMSVRSLLPDLGTPATGTPEAAVPPFARTVLWAHGDDAWRGEGGWTVLLD +GTGRLRRLSALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRD +VAQHMDADALAAAVAADRGARLLADGAVPLPADVADRAWDDAGYAAGVRELLTRMADSDG +ELAKVVISRTMTVPADDADLWRAIGALRREYPQTWVFAVGGLLGATPEVLATRHAGLVGS +RVLAGSMPRGADEEEDAALRDRLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVL +TLPNVHHLATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYA +GPVGWLDQDGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRAL +GVAED + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001658.fa new file mode 100644 index 0000000000000000000000000000000000000000..7590375bb16e11ab02a1e8cc209a48147ca517cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001658.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02120 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR +>GCF_003691675_PROKKA_01828 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR +>GCF_005280335_PROKKA_00660 +MSTLPTTTD-------AHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDE +DVYCIDILTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAA +IGRLLR +>GCF_020097155_PROKKA_00577 +MEHD----------------RHAGPGYSPQREA------YLKRLKRIEGQVRGIHRMVEE +DVYCIDVLTQVAAATKALHAVSLGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR +>GCF_023573625_PROKKA_02058 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001661.fa new file mode 100644 index 0000000000000000000000000000000000000000..cdd923e731d825f930fe2ae6258d35cfb8a103e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001661.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02125 +MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY +RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV---- +>GCF_003691675_PROKKA_01833 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY +RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV---- +>GCF_005280335_PROKKA_00655 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY +RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF +>GCF_020097155_PROKKA_00572 +-----------------------------------------------------MEDPARY +RLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV---- +>GCF_023573625_PROKKA_02063 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY +RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001662.fa new file mode 100644 index 0000000000000000000000000000000000000000..24444dd3e951bf66b4eae05fec672ceb66fcc30b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001662.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02126 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLAAWFTGHSTSPRVHA +>GCF_003691675_PROKKA_01834 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRVHA +>GCF_005280335_PROKKA_00654 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHG +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRVHA +>GCF_020097155_PROKKA_00570 +MTDTPQSSSGQSRDEILARLEEIYANDPAVREHDVTLGEVAEGRVVLHRDVTAGMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPAKLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRVHA +>GCF_023573625_PROKKA_02064 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001665.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001665.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf87847542762a71dc7b8d4826052b19343f8f57 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001665.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02129 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDIDAALDAAWKAAPAWGATSPAE +RALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVPLAIDHFRYFAGAIRAQEGRLSQVDEDTVAYHFHEPLGVVG +QIIPWNFPLLMGVWKLAPALAAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGEVCTCPSRALVQESIAEKFLD +AVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIGRQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIF +QEEIFGPVVSTTTFTDFDDAMRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>GCF_003691675_PROKKA_01837 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDIDVALDAAWKAAPAWGATSAAE +RALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVPLAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVG +QIIPWNFPLLMGVWKLAPALAAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGEVCTCPSRALVQESIAEKFLD +AVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIGRQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIF +QEEIFGPVVSTTTFTDFDDAMRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>GCF_005280335_PROKKA_00651 +MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDIDVALDAAWKAAPAWGATSAAE +RALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVPLAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVG +QIIPWNFPLLMGVWKLAPALAAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGEVCTCPSRALVQESIAEKFLD +AVVERTSRIVTGNPLDTDVMMGAQASNDQLEKIISYLDIGRQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIF +QEEIFGPVVSTTTFTDFDDAMRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>GCF_020097155_PROKKA_00567 +MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDIDVALDAAWKAAPAWGATSAAE +RALVLHRIADRMEENLEMLAVAETWDNGKAIRETLNADLPLAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVG +QIIPWNFPLLMGVWKLAPALAAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGEICTCPSRALVQESIAEKFLD +AVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIGRQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIF +QEEIFGPVVSTTTFTDFDDAMRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>GCF_023573625_PROKKA_02067 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDIDVALDAAWKAAPAWGATSAAE +RALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADLPLAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVG +QIIPWNFPLLMGVWKLAPALAAGNAVVIKPAEQTPASVMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGEVCTCPSRALVQESIAEKFLD +AVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIGRQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIF +QEEIFGPVVSTTTFTDFDDAMRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001666.fa new file mode 100644 index 0000000000000000000000000000000000000000..651bd14b2640fada62c426ab6d3f827ca22bf8de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001666.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_02130 +MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSSTAPTGADQGLRAALQGLRREVRESWLR +SLGALTPAGSALDAGASAAAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIQP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLLSTVDAVH +AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAGAPHRHDEAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPGDAPARAISLRAEVHRL +RRALRDVGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAVGPVLPRSASPGV +ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT +LERIERDLA +>GCF_003691675_PROKKA_01838 +MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR +SLGALT--------------PAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH +AAWRDLPAPSRGRPRGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRL +RRALRDVGAPVALLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSTSPGV +ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT +LERIERDLA +>GCF_005280335_PROKKA_00650 +MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSPTAPTGADQGLRTALQGLRREVRESWLR +SLGALTPAGSALDAEAAATAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIHP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH +AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPSDAPARAISLRAEVHRL +RRALQDAGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSVSPGV +ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGVALRLLPADSPRRALAVAT +LERIERDLA +>GCF_020097155_PROKKA_00566 +MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPTGADQGLRAALQGLRREVRESWLR +SLGVLTPAGSALDAGASATAPAVPGQTDPATLSDDDLAAARREQRLAVALPVVRRMLIQP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAEALGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQTTVDAVH +AAWRDLPAPSRGRSRGTVPTPGPSAPPSVSPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETVGPRSAPGDAPARAISLRAEVHRL +RRALRDVGARVELLSRPYRLVGAVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV +ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT +LERIERDLT +>GCF_023573625_PROKKA_02068 +MSSTLATSAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR +SLGALT--------------PAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH +AAWRDLPAPSRGRPRGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRL +RRALRDVGAPVALLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV +ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT +LERIERDLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001670.fa new file mode 100644 index 0000000000000000000000000000000000000000..79209e3942d85b3ac46e68d087225c88c95f260d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001670.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02134 +MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +VRGRELRGRLAEVWALA-AVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAV +ERLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRS +YRARLA---------EAAEAAP------------ATDPAGPEEAEAPEAVADEAAPADKP +RQETEK-EKKERKKAEKKAEKKARKKAEKKARKKKSDKKK-------------D +>GCF_003691675_PROKKA_01842 +MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +VRGRELRGRLAEVWALA-AGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAV +ERLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRS +YRARLA---------EAAESAP------------AADPAGPEEAEAPEAVVDSEAAADEP +RRETKK-EKKER----RKAEKKARKKAEKKAGKKKSDKKK-------------D +>GCF_005280335_PROKKA_00638 +MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA +VRARELRERLTRVWALA-ATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAV +ERLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRS +YRARLA---------EAAEAAP------------ATDPAGPEEAEGTEAVVDEAAPADEP +LQETEK-EKKER----RKAQKKARKKAEKKAGKKKSDKKKSDKKK--------D +>GCF_020097155_PROKKA_00561 +MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR +TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV +ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS +YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST +KDKKSKSEKKAR----RAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD +>GCF_023573625_PROKKA_02072 +MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +GRGRELRGRLAEVWALA-AVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAV +ERLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRS +YRARLA---------EAAESAP------------AADPAGPEEAEAPEAVVDSEAAADEP +RRETKK-EKKER----RKAEKKARKKAEKKAGKKKSDKKK-------------D + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001673.fa new file mode 100644 index 0000000000000000000000000000000000000000..00e4aaa19aec07aced689bc7d85e0ee154974dae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001673.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_02138 +M-AGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGV +GIGTTILHTLTGLMIFLAYATTPAVARLIGAGNLAAAMDRGRDGIWLGLLLGAVLAVLGW +LAAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVG +FGANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTAWAPRASGMR +ATAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQ +ALIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATV +GLWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWT +AAWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVV +>GCF_003691675_PROKKA_01846 +M-AGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGV +GIGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGW +LAAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVG +FGANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMR +ATAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQ +ALIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATV +GLWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWT +AAWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG +>GCF_005280335_PROKKA_00634 +M-AEPQGSTAAPAPQDGRALTRRILALAVPAFGALLAEPLFLLADTAIVGRLGTPELAGV +GIGTTVLHTATGLMIFLAYATTPAVARLIGAGDHAAAMDRGRDGVWLGLLLGAALAVLGW +IAAPWLTGALGATGEVQEHAVAYLRWSMPGIPALLAVLAATGVLRGLQDTVTPLVVAGAG +FAVNIGLNFALVYGAGLGVAGSAIGTSAVQWGMLLTYLAVLAPRFRRAGTSLAPRASGMR +ATAQVGSWLLLRTASLRAAILITVMAAAGAGDMTLAAHQLVFTLFSTLAFALDALAIAAQ +ALIGAELGASRPATARRLTDVMVRWGLGFGVVTGGLLALAAPWLPALFTTDPQVQAAATV +GLWVLAAGQPIAGYVFVLDGVLIGAGDARYLALAGLVNLAVYAPVLWVLAQVAAGGLGWT +VDWSDPAAHVPDAGEQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRVGAH +>GCF_020097155_PROKKA_00558 +MPSRPPHDDAAPAPEDRRALARQVLGLAVPAFGALIAEPLFLLADTAIVGHLGTAQLAGV +GVGTTVLHTVTGLLVFLAYATTPAVARMVGAGNPAGALDRGRDGMWLGLMLGFVLGAAGW +LAAPWLTGALGAAGEVHSHATEYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGGG +FAVNIGLNWALVYGAGLGVAGSAIGTAAVQWAMLAVYLAVLAPRFRAAGTRPGPRADGLR +ATAQVGSWLMLRTASLRAAILITVAAATGLGDVTLAAHQLVFTLYSTLAFALDALAIAAQ +ALIGAELGASRPRTARRLTDLMVRWGLGFGVVTGAGLAAAAWALPPLFTPDPGVHAAATA +GLLVLALSQPVAGYVFVLDGVLIGAGDARYLALAGVVNLAVYAPVLWGLARLAAGG---- +----------ADAGAQVALLWLGFAGVYLGMRAATLGLRARRDAWMRLG-- +>GCF_023573625_PROKKA_02076 +M-AGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGV +GIGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGW +LAAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVG +FGANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMR +ATAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQ +ALIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATV +GLWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWT +AAWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001674.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b74c1b138f4878aae4a0889686628effd43a806 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001674.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02139 +MSVPPSG-------PPAGP----------PAGWPPSGRPSARRAAVAPSLHGHPGAPGGV +PAGWPGRRPAARPAPDWTPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFD +LVRDGFTVNIVSYAILVVLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIV +LSLIGEAQTSANQAALEEMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWV +CAVVSVLAFTLLHFLGTGGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGI +AIAMLYLVAPLLPDTLPGPTAPTTALAPLLALLG +>GCF_003691675_PROKKA_01847 +MSVPPSG-------PPAGP----------PAGWPPSGRPSARRAAVAPSLHGHPGAPGGV +PAGWPGRRPAARPAPDWTPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFD +LVRDGFTVNIVSYAILVVLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIV +LSLIGEAQTSANQAALEEMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWV +CAVVSVLAFTLLHFLGTGGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGI +AIAMLYLVAPLLPDTLPGPTAPTTALAPLLALLG +>GCF_005280335_PROKKA_00633 +-----------------------------------------------------------M +PAGWPGRTPGPRTAPDWEPGRFHWGDAVVVLAYAGLMLFGLGLPLAMLLGLVPGDLAAFD +LVRDGFTVNMVSYAILTALVLIVAWRPLVTSLRVFRTGTWWKILLLPAVWFTCILVNVLV +LSLIGEAQTSANQAALEEMSAQAPPVLMILMTVVGAPLVEEYLFRHLLVGKLSRWVNVWV +CAVVSMLAFTLLHFLGTGGQFDLVETVPYLTLAIAITVTYILMGRSFGYAVLLHMVNNGI +AIAMLYLVAPLLPDVLPEPTAPAAALSPLLALLG +>GCF_020097155_PROKKA_00557 +MSVPPPGPHDAGALPPPGSTAPTSAAGEAPEGWPPAGWPGRASAGGAPQ--------GWP +PSGWPGRTASARTAPSWEPGRLHWGDAAVVVLYVLMMVVGLGYLLAVLLGLAPRDPAAMD +-VMDGFRVNLVSYAVLVVAVLAVSWRPLVASLRVFATHTWLKILLLPALWLVTVLVNALL +LSLIGQAQTSANQAALEEMTTQAPALGMVLMTVVGAPIVEEYLFRHLLVGKLSRWINVWV +CAAISVAAFTLLHFLGTGGDFQWVETVPYLTLAVTITVTYVLIGRSFGYAVLLHMVNNGI +AIAMLYLVAPLLP-SAPAPVGPGALLSPLLALLG +>GCF_023573625_PROKKA_02077 +MSVPPSG-------PPAGP----------PAGWPPSGRPSARRAAVAPSLHGHPGAPGGV +PAGWPGRRPAARPAPDWTPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFD +LVRDGFTVNIVSYAILVVLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIV +LSLIGEAQTSANQAALEEMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWV +CAVVSVLAFTLLHFLGTGGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGI +AIAMLYLVAPLLPDTLPGPTAPTTALAPLLALLG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001675.fa new file mode 100644 index 0000000000000000000000000000000000000000..54a37572be9de82c1c5c138cbebd8a5cf4bc4833 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001675.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02140 +----------MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTY +AMYLSPGYYTDFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDL +REEMADSGMHSREIVDPDGHQWEFVTA +>GCF_003691675_PROKKA_01848 +----------MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTY +AMYLSPGYYTDFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDL +REEMADSGMHSREIVDPDGHQWEFVTA +>GCF_005280335_PROKKA_00632 +----------MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTF +AMYLSPGYYTDFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDL +REEMVDSGMHSREIVDPDGHQWEFVTA +>GCF_020097155_PROKKA_00556 +MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF +AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL +QEDMTATGVHSRQVVDPDGHQWEFMAA +>GCF_023573625_PROKKA_02078 +----------MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTY +AMYLSPGYYTDFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDL +REEMADSGMHSREIVDPDGHQWEFITA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001676.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb871029aa0f0b97cf942319c31ac52248db7057 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001676.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02141 +M-PAP---AATTTTTPPA----TPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPRVGLFASFTMA +VTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILLGVFGVARLMRFVPRSVMVGFVNALAILVFT +SQLPELIGVPWLVYPLTALALAIVVLLPRLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTW +ETLRLILPFSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMNVKANGARTRI +STFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATLRAMPRSETAVMVVTVAATVLTHNLAIGVGV +GVLAALVLFAQRVSRLVTVVREVHDD-GDAVT-YRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALD +SVLTKYARHGIHAEVTGLNEASAAMHARLTGRLGA-- +>GCF_003691675_PROKKA_01849 +M-P-----ALPAAPPPAL----TPLQRQSVLRTLRSPRLLGTEVLAAVVVALALIPEAIAFSIIAGVDPRVGLFASFTMA +VTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILLGVFGVARLMRFVPRSVMVGFVNALAILVFT +SQLPELIGVPWLVYPLTALALAIVVLLPRLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTW +ETLRLILPFSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMNVKANGARTRI +STFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATLRAMPRSETAVMVVTVAATVLTHNLAIGVGV +GVLAALVLFAQRVSRLVTVVREVHDD-GDAVT-YRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALD +SVLTKYARHGIHAEVTGLNEASAAMHARLTGRLGA-- +>GCF_005280335_PROKKA_00716 +MTPASTASARVAAPPNSREP--SPEQLQSVRLTLRSPGRLKTEVLAGLVVALALIPEAIAFALIAGVDPQVGLFAAATMA +MTIAFVGGRPAMVSAATAATALVVAPLVASHGLDHLIAAVILAGGLQVVLGLLGVAKLMRFVPRSVMVGFVNALAILIFT +SQLPDLMGVPWLVYPLTALGLAIILLLPRVTTAVPAPLVAIVVVTVIVLLAGADVPTVGDKGRLPDSLPALLVPDVPFTL +ETLQLLFPYALGMAVVGLLESLMTAKLVDDITDTRSSKTRESWGQGVANVVSGLFGGMGGCAMVGQTMINVKASGARTRI +STFMAGVFVLILSVTLGDVVALVPMAALVAVMIFVSLATFDWHSIRPSTLAFMPKSETAVMLVTVAATVLTHNLAIGVGL +GVLAAMVMFAQRVSHLATVTRTLEGQGRDAVARYRVQGELFFASSNDLYTQFDYAGDPARVVIDFSQAHLWDASTIAALD +AVEEKYRRHGATVEITGLNVASRAMRARMSGRLGGGH +>GCF_020097155_PROKKA_00554 +M-P-----ASPAAPPPAL----TPLQRQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPRVGLFASFTMA +VTTAVVGGRPAMISAATGAVALVVAPLSHAHGLDHLIAAIILGGLIQVALGLLGVARLIRFIPRSVMVGFVNALAILVFT +SQLPELIGVPWLVYPLTALALGIVLLLPRLTTAVPSTLVAIVVVTALVMAAGWSVPRVGDRGELPDALPGLFVPDVPLTW +ETLRLILPFSVGMAVVGLLESLLTAKLVDDVTDTRSDKTRESWGQGVANIVSGLFGGMGGCAVVGQTMMNVKANGARTRI +STFLAGVLLLVLVVALGDLVGQIPMAALVGVMVFVAGAAFDWHSVRPATLRAMPRSETAVMLLTVLATVVTHNLAIGVGV +GVLTAMVLFAQRVSRLARVERVVTDDNGGTAV-YRVHGELFFASSNDLYSQFEYALDPPRVVIDLSAAHVWDASTVAALD +AVVTKYAQHGIAAEVTGLNEASAAMHARLTGRTGA-- +>GCF_023573625_PROKKA_02079 +M-P-----ALPAAPPPALTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPRVGLFASFTMA +VTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILLGVLGVARLMRFVPRSVMVGFVNALAILVFT +SQLPELIGVPWLVYPLTALALVIVVLLPRLTTAVPATLVAVVVVTSLVMAAGLTVPRVGDRGALPDALPALGLPDVPLTW +ETLWLILPFSIGMAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMNVKANGARTRI +STFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATLRAMPRSETAVMVVTVAATVLTHNLAIGVGV +GVLAALVLFAQRVSRLVTVVREVHDD-GDAVT-YRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALD +SVLTKYARHGIHAEVTGLNEASAAMHARLTGRLGA-- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001677.fa new file mode 100644 index 0000000000000000000000000000000000000000..4bafdb40f5bebb4a77bb36076216e19e3af79f87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001677.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02143 +MNLRTLLREALTAARTAPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV +LTVTDSGGTGFLTGATVATLAGLDSAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTVD +RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEALTPFEDLAD +YAIAVPAAPASLVVQQVRVLAPDTAGTRAMQDSALAVIDPDPRSSQVQTARALAAGNATI +TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA +APAVLGAVVGAGTGYAVVVGQGGALGLDFVAGVAVLAALTAVVASLLPAAFAAFRDPVRV +MRTA +>GCF_003691675_PROKKA_01850 +MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV +LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD +RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGGQWAVVGAFQAQDPFQDLDG +YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI +TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA +VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV +MRTA +>GCF_005280335_PROKKA_00629 +MNLRTLLREALTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV +LTVTDSGGTGFLTGATVTTLAGLDAAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTLD +RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEARTPFEDLDG +YALAVPATPASLVVQQVRVLALDTAGTRAMQDSALAVIDPDPRSSQVQPARALAAGNETI +TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA +APAMRGAAVGAGAGHGLVLAQGSALGSAFVVGAAVLAVLTAVVASLLPAAFAAFRDPVRV +MRTA +>GCF_020097155_PROKKA_00553 +MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV +LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTWIGRGGARVAVTNVVGTLD +RGIELTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG +YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI +TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA +VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV +MRTA +>GCF_023573625_PROKKA_02080 +MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV +LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD +RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG +YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI +TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA +VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV +MRTA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001678.fa new file mode 100644 index 0000000000000000000000000000000000000000..16332888503051f52c91fd997b625e0ac518bf1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001678.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02144 +--------------MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPSAGVVRLGDVDASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVV +EPGLYAGLSRRELEGRARILLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLA +DEPTGNLDPDNASLVLDALAEAAGEGRTVVVATHDPAVVARADEVVRL +>GCF_003691675_PROKKA_01851 +MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL +>GCF_005280335_PROKKA_00628 +--------------MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPSAGVVRLGDVEASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVV +EPGLYAGLERRVLEERARALLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLA +DEPTGNLDPDNASLVLDALAETAAEGRTVVVATHDPAVVARADEVVRL +>GCF_020097155_PROKKA_00552 +MTGPATPGTPAAPGTPAALAVEDLRFAYTRAAEELFDGLTHAFTPGGVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL +>GCF_023573625_PROKKA_02081 +MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPVVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001680.fa new file mode 100644 index 0000000000000000000000000000000000000000..85d3de31a073ba189358f5d484dc2bf026130685 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001680.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02146 +MVGL----------VGALLLAGCASGADAGASAHAETGSTPS----KVWDAATWKPTEVI +EPVLATEPEKEAAYREQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPV +EVSPTG-GLRYSTPPAAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLI +PCLEAQGFTVDTSTRPSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPP +QDVFWGTSG +>GCF_003691675_PROKKA_01853 +MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI +EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN +SVGPTG-GIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLI +PCLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPP +QDVFWGSSG +>GCF_005280335_PROKKA_00626 +MKTKFAAVTAAAVTAV-LTLSGC------ATTAPSTSAAATGSPTEKVWDPETWTPTEKI +ERRMTEADERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPA +TYNEVMVGVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAI +PCLEDHGITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPP +DSMLFGYSE +>GCF_020097155_PROKKA_00550 +MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI +EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV +EVTPTG-GLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLI +PCLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPP +PDVFWGTAP +>GCF_023573625_PROKKA_02083 +MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI +EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN +SVGPTG-GIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLI +PCLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPP +QDVFWGSSG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001681.fa new file mode 100644 index 0000000000000000000000000000000000000000..798a27b6e4646abb21d9382319549d7626389546 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001681.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_02147 +MS---------------EHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLVAVVLN +VWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTPGEGIDFTELGRLILIVLGMYLVAQT +FMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSYFDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMM +FWLSWQLALIALIALPVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNEELYEA +AFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQIAGMSNMLISGVASAERIFE +LLDEPEETPDGTPARTPARTFVRETAPSEGTFVRETAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLV +AEPGQTVAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYGRLDAT +DEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL +RSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHAELLAAKGAYHRLYMSQFKGGE-----DDDGA-ASRDDAR +>GCF_003691675_PROKKA_01855 +MS---------------EHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLVAVVLN +VWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTPGEGIDFTELGRLILIVLGMYLVAQT +FMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSYFDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMM +FWLSWQLALIALVALPVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNEELYEA +AFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQIAGMSNMLISGVASAERIFE +LLDEPEETPDGTPARTPDGTFVWETAPSESAFVRETAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFV +AEPGQTVAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYGRLDAT +DEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL +RSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGSHDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR +>GCF_005280335_PROKKA_00622 +MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFAPERTGLILVSLMVLVAVVLN +VWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQGQGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQL +FMWLQGRVLNDLVMRIVFRLREDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM +FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVFGRQADMAERFDERNEAMYEA +SFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFE +LLDEDEQDSDAEVARRASDDDVAEPADAS---VRET---GASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLV +AEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGGTIRENIRYGRQDAT +DEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL +RSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGNHAELLAARGAYHRLYMSQFKGGE-----DDGGGAASGEDAR +>GCF_020097155_PROKKA_00547 +MS---------------EQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLVAVVFN +VWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTPGQGIDFDALARLILTVLGMYVVAQG +FMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSHFDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMM +FWLSWELALIALIALPVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERNDAMYEA +SFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFE +LLDEPEEEPDDVVAAR--------------------------ADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLV +AEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEAT +DEEVLAAAKATYVDRFVHTLPDGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAAL +RNDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGE--DEHHDDGAPASR---- +>GCF_023573625_PROKKA_02085 +MS---------------EHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLVAVVFN +VWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTPGEGIDFTELGRLILIVLGMYLVAQT +FMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSYFDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMM +FWLSWQLALIALVALPVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNEELYEA +AFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQIAGMSNMLISGVASAERIFE +LLDEPEETPDGTPARTPDGTFVWETAPSESAFVRETAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFV +AEPGQTVAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYGRLDAT +DEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL +RSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGSHDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001683.fa new file mode 100644 index 0000000000000000000000000000000000000000..aeb07d206a0a5c347f951ecefae2afbdfd726f1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001683.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_02149 +MRRPSLPS--LSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPN +PGVFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRA +AARGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMV +VDDEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPD +TWDPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGV +DVQVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANV +DRLSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPL +RPLL +>GCF_003691675_PROKKA_01862 +------------------------MAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPN +PGVFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRA +AARGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMV +VDDEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPD +TWDPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGV +DVQVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANV +DRLSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPL +RPLL +>GCF_005280335_PROKKA_00613 +M--SPLPASPLHRIPVRRIVRGAALAAGTGLVGVPMAVAAGLTGVDMVKRRGRRRRPAHN +PGVFDAPVKDCHLRIFTSGEDLYEEMLAAIDSAERIVKFETYIWKADPTGQRFIEAFNRA +AARGVEVYVSYDGFGNLVVPRAFYRQLDPRIRVFRLPAFARPFWRGPVRNTGFNHSKIMV +VDDEIGFVGGFNIGDDYATFWRDTHVCERGPAVWALDQSISIKWNAHHREGEQMSWRPPE +SWDPRVTVSANQPPLLVYPIRLTYLEAIQRAQHRILINTPYFIPDQQVLQALLHAARRGV +DVQVMVPRDSNHIVADWASRGFYAGMLEAGITILLYEASMIHAKTATVDGIWSTVGTANI +DRLSLGFNYESNVVVVDRDFAARMEEIFAIDAEQSERVESPRWQDRHGVARMVERLLVPL +RPLL +>GCF_020097155_PROKKA_00537 +M---------------GYALRRAAVAGTTAFVGVPLATAVAVSAYDAFKHRGRKLRPAER +PGTFQAQVGPDALTIYTAGDDVYDAMIQAIDDARETVKFETFIWKDDATGQRFVDALNRA +AARGVQVWASYDGFGNLLIPPSFYRQFDPRVRVFRLPAFARPLWRGVVRYSGFNHSKILT +VDGRVGFVGGYNVGDLYAAHWRDTHLRVEGPAVWGLEHSLSVLWNEGYTDMAEMPWTRPE +EWEERTVVAANLPTQLVYPIRNTYLNAIARAQDHIYISTPYFVPDRQVLDALKEAARRGV +DVQVLVPKDSNHVVADWVSRGFYSEMLDAGITILLYAAGMIHAKTATIDGRWATVGTANI +DRLSLSFNYETNVSVVDRDFAARMEDVFRADAARSERIQSPRWKDRHGLARVVEKLLVPL +RPLM +>GCF_023573625_PROKKA_02092 +MHRPPLPS--LSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRRGRVRRPAPN +PGVFDAHVKGSELRIFTSGEDLYEEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRA +AARGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMV +VDDEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPD +TWDPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGV +DVQVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANV +DRLSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPL +RPLL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001684.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a2ef8f476869eafc7087f5c0dca99ba8bcf5ec6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001684.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02150 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>GCF_003691675_PROKKA_01863 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>GCF_005280335_PROKKA_00612 +MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT +VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT +VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT +TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA +VQLVRLRSEVGAAWTETRRSPESR +>GCF_020097155_PROKKA_00536 +MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH +PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ +VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS +VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT +SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA +VELVRLRSEAGAVWSD------PS +>GCF_023573625_PROKKA_02093 +MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT +VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA +IELVRMRSEVSAAWTETRRSTDPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001685.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8a774002985f8287f803728ddbfaf29c213c2be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001685.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02151 +MTAFDRFPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>GCF_003691675_PROKKA_01864 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>GCF_005280335_PROKKA_00611 +MTAFDRLPLPAEPQTPHDRLRRRVAAAVAERGEAAVAGLAVRLLTGSVTPADVTSGAARA +LTGDDGDLTAGATGALALGHAWHRSALPALTSALSAPEPDVRSAAHLVLAARAGSLRADV +AVDRALVDAVRAGCADPDPQVRASAASALGALAGPQDLEAALPVLTGMVMDVDADLATAA +ELALDHLAERLDRPDLRVGAEG +>GCF_020097155_PROKKA_00535 +MTSRD-LPLPVEPQTPHTRLARRVEAAVSARGEAAVAGLAVRLLTGAPTPEDVTSGAARD +LIGDDGELTPGATGALALGVVWHRGAAGALAAALDAPEPEVRAAALLVLAARADRLRADA +QAGRALVEAVTARASDADPQVREAAASALGALARAEDLSAVEPVLSALVMDVDPELATAA +ELALAHLAARLDRPELDPTPQA +>GCF_023573625_PROKKA_02094 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPEDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVIASRAGSLRRDA +AVDRALVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001686.fa new file mode 100644 index 0000000000000000000000000000000000000000..a04d3cc61c5d10ba4fa822430ff53f96b2c97700 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001686.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_02152 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEG----GVPA-SAWDLYCGVGGFAFHLAR------AGVRDVWGMESSAEAVAAARETA +AELGLADRARFSAGDATSALSFEKRRAPEALSFEKRR--------SR------------- +-----PDAVVVNPPRRGIGAELADALEDSGAPTVLYSSCNPTTLAQDLARMPSYRVARVQ +LFDMFPQTLHAEVLTLLTRR +>GCF_003691675_PROKKA_01865 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEG----GVPA-SAWDLYCGVGGFAFHLAR------AGVRDVWGMESSAEAVAAARETA +AELGLADRARFSDGDATSALSFEKRRAPEALSSKKRR--------PR------------- +-----PDAVVVNPPRRGIGAELADALEDSGVPTVLYSSCNPATLAQDLARMPSYRVARVQ +VFDMFPQTRHAEVLTLLTRR +>GCF_005280335_PROKKA_00610 +MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEA-WLPPQASAESGFRNK +AKLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLE +PYDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVV +TANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAW +LAEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTA +AELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDA +APAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQ +VFDMFPQTGHAETLVLLSRA +>GCF_020097155_PROKKA_00534 +MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK +AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE +PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV +TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW +LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA +AELGVAERVRFTAGDATTALA--------------------APGGTR------------- +-----PDAVVVNPPRRGIGAELAGRFEESGVPFVLYSSCNAATLATDLTAMPSYRVARAQ +VFDMFPQTGHAETLVLLARR +>GCF_023573625_PROKKA_02095 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEA----GLPA-AAWDLYCGVGGFAFHLAR------AGVRDVWGMESSAEAVAAARETA +AELGLADRARFSAGDATSALSFEKRRAPEALSSKKRR--------PR------------- +-----PDAVVVNPPRRGIGAELADALEDSGVPTVLYSSCNPATLAQDLARMPSYRVARVQ +VFDMFPQTRHAEVLTLLTRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001689.fa new file mode 100644 index 0000000000000000000000000000000000000000..d055b27c2c5cdaa9730c994844494e1cbe965c51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001689.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02158 +M---TQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQ +MRAQVDALRALL--------GAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVA +AYRAG---LTAD--------------GAADLPAVADVVPDPDAERADFEAMLVAAEEQAW +PLVSFTFGLPAADVFARLAAAGVPAGATVTDAAEARAALEHGAAFLVVQGHRAGGHRGTS +DPAAEPTRAELPTVLAAVRDVVGTGAASAAPVVAAGGVGTAEDVRALLTAGADAVSAGTA +FLLTPEAGTSAAHRAAVAACAAGTRFS-ADDGRARTALTRAYTGRWARSLATAFMAEHPD +APAAYPEVNVLTKGLRAAAAAVGDLERVHLWAGTEAHRVREAPAADVLASLTP---- +>GCF_003691675_PROKKA_01871 +M---TQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQ +MRAQVDALRALL--------GAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVA +AYRAD---LTAD--------------GAADLPTAADVVPDPDAERADFDALLTAAEEQAW +PLVSFTFGLPAADVFARLAAAGIPAGATVTDATEARAALEHGAAFLVVQGHRAGGHRGTS +DPAAEPPRAELPAVLPAVRDVVGTGATSAVPVVAAGGVGTAEDVRALLTAGADAVSAGTA +FLLTPEAGTSAAHRAAVAACAAGTRFS-ADDGRARTGLTRAYTGRWARSLATAFMAEHPD +APAAYPEVNVLTKGLRAAAAAAGDLERVHLWAGTEAHRVREAPAVDVLASLTP---- +>GCF_005280335_PROKKA_00600 +M---SAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQ +VREQVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVA +AYRER---LAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAW +PLVSFTFGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTL +DPAADPVERELPSVLAQVRAVVGT----RVPVVAAGGVGAAAHVRSLLAAGADAVAAGTA +FLLAAEAGTSVAHRAGIRRCAAGEGFV-GPDGAARTVLTRAYTGRWARTLATDFAAAHPD +APAAYPELNALTTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP---- +>GCF_020097155_PROKKA_00522 +MSSTTVPSVPAPVP-APLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQ +VREQVDGLRALL-------TAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVA +SYRERLAPLAAD--------------LGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSW +PAVSFTFGLPAPDVFARLDAAGIPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATL +DPQGRPGITDLRTLVFAVRHALG---PAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTA +FLLTPEAGTSAAHRTALRQASAGVAFAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHD +APAAYPEVNGLTGPLRRAAAEEGDLEHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP +>GCF_023573625_PROKKA_02101 +M---TQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQ +MRAQVDALRALL--------GAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVA +AYRAG---LTAD--------------GAAGLPTAADVVPDPDAERADFDALLTAAEEQAW +PLVSFTFGLPAADVFARLAAAGIPAGATVTDATEARAALDHGAAFLVVQGHRAGGHRGTS +DPAAEPTRAEMPTVLAAVRDVVGTGAASAAPVVAAGGVGTAEDVRALLTAGADAVSAGTA +FLLTPEAGTSAAHRAAVAACAAGTRFS-ADDGRARTGLTRAYTGRWARSLATAFMAEHPD +APAAYPEVNVLTKGLRAAAAAAGDLERVHLWAGTEAHRVREAPAADVLASLAP---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001690.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a2571d7596e1669739e477e749425763e7b864a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001690.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_02159 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPL--AMVIMAIGCGLMVLTAWAFGDV +VRNRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGAR +YAAAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGV-TDDDARRPAA- +----------------------------------DV--------VASPDGRGTRLPPGRR +PQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIVQEALTNTLRHGGPD +ADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTALFGGTLETGPRVGA +GYRVSAHLPYSAV +>GCF_003691675_PROKKA_01872 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPL--AMVIMAIGCGLMVLTAWAFGDV +VRNRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGAR +YAAAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGV-TDDDARRPAA- +----------------------------------DV--------VASPDGRGTRLPPGRR +PQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIVQEALTNTLRHGGPD +ADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTALFGGTLETGPRVGA +GYRVSAHLPYSAV +>GCF_005280335_PROKKA_00599 +MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPG--SIVASILIALA +LIAPWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGL +VAALLGGVANGIRVGLFPDPAMRPDG--VYEPVDPSLEALLVMVFGCAAVVLTAWAFGDV +VRHRRLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGAR +YAAAAKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAG +ASDEGAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHR +PQPTLADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQ +ASAFLTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGA +GYRVSAHLPYSAV +>GCF_020097155_PROKKA_00521 +MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVG-SPAAWQTAGTVVAGLL +MTGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGL +ATGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPV--AMVVMAVLCGMAVLTAWAFGDV +VRNRRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGAR +YAAAAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGG-----PDRARRDPAA- +-------------------------------------------------------PDGHR +APPGLADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEG +AHAFLTLRWTARGLEIQADDDGR-SQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGA +GWRVWAELPYADV +>GCF_023573625_PROKKA_02103 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPL--AMVIMAIGCGLVVLTAWAFGDV +VRNRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGAR +YAAAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGV-TDDDTRRPADP +APDRADP----------------------TGTRPDV--------VAAPDGRGARLPPGRR +PQPRLADLPALVETMRLSGLEVSLLETDTPRRALPAGGELAAYRIVQEALTNTLRHGGPD +ADAFVTLAWTARGLDLQIDDDGRGAAADPATRGSGQGLRGAAERTALFGGTLETGPRVGT +GYRVSAHLPYSAV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001691.fa new file mode 100644 index 0000000000000000000000000000000000000000..5ebe3b80a674ee8dd45ff14c1ed26384664a1f45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001691.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02161 +MTGSILDH-------------PAPTTSRASDPA-AERAQRDSECVAFFVALVTAAVVMLG +LSLFTGVEGLLRLALTAGAGLLAGAVAWATARPVLEDDAPGD +>GCF_003691675_PROKKA_01874 +MTGSILDH-------------PTPTTSRASDPA-AEQAQRDSECVAFFVALVTAAVVMLG +LSLFTGVEGLLRLALTAGAGLLAGAVAWATARPVLEDDAPGD +>GCF_005280335_PROKKA_00596 +---------------------------------------------------MTAAVVILG +LSLFTQVEGLPRLLVTAASGLLAGAVTWSVTQPVLEDEVLHG +>GCF_020097155_PROKKA_00519 +MSAAPAPSPAAPAVPPVTAVPPAAREPEGTSPSDRERERGDAECLAFFLALVTAALVMAG +LALATDLGPLLRVLLSLGASGLAGALTLAFTRPSLED----- +>GCF_023573625_PROKKA_02105 +MTGSILDH-------------PAPTTSRASDPA-AERAQRDSECVAFFVALVTAAVVMLG +LSLFTGVEGLLRLALTAGAGLLAGAVAWATARPVLEDDAPGD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001692.fa new file mode 100644 index 0000000000000000000000000000000000000000..72da1b6198631e83bfd6393b2f3774a9ce24f4cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001692.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02163 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLLHCLAGLDARTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRALGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSA------------PAEGGVR +>GCF_003691675_PROKKA_01877 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSA------------PAEGGVR +>GCF_005280335_PROKKA_00594 +MSTTADSHSAHSTPPGAGASGPGMPSSSTTTTTAPAASARALTKTYGRGDAEVHALRGVD +VDFAAGAFTAIMGPSGSGKSTLMHCLAGLDTPTSGSVVLGGTEITGLGDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRKPDRAWLDEITATLGLTDRLKHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDSATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELLDPTVESVTNALAALSAPGAADAAGTFDAPADGG-R +>GCF_020097155_PROKKA_00517 +MDITSPRSAAHDAGAHALA----TPLAHAAAPPAPAVSARGLTKTYGRGDAAVHALRGVD +VDVETGRFTAIMGPSGSGKSTLMHCLAGLDTPDAGVVTLGDTVITGLSDAALTRVRRDRV +GFVFQAFNLVPTLTAEQNIVLPMELAGRTPDRAWLAEIVDRLGLSDRLAHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDSATGAQVLDLLRRATRETGQTVIMVTHDPVAAAA +ADRVVLLADGALAGELHAPTAERVAEALTALQQGRPLPQGRPL--PQDGG-R +>GCF_023573625_PROKKA_02108 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSA------------PAEGGVR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001694.fa new file mode 100644 index 0000000000000000000000000000000000000000..97c15485ed669792caa10c57569754f46ecc2814 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001694.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_02167 +MTSLLRILRFAPQLNRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAVTAVTWLAVAFLAVEVATTLV +VSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAITGRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITA +FYWWPLAILLAVVFPVYMWLTARTSTKWQVWEGEKNTEVDIASGRFAEVVSQMSVVRAYNRQDHELSGFRDRFLRTVGIT +RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSKDYFEV +LAEERERAGGAALAVAGASAESA---------------GADAPRVPAEPRADVVP-----GAP-DVPAD--VPAVRFDEV +SFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLLLGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEP +SLFSGTVRENIAYADPDASDERVRAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEA +TSALDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGGIYAQLLELQRAGTQEAR +KMLKEYGLSG +>GCF_003691675_PROKKA_01881 +MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAVTAVTWLAVAFLAVEVATTLV +VSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAITGRVVNRLNRTINEITQFLQFFANNAFTMLVTTAAMLVITA +FYWWPLAILLAVVFPVYMWLTARTSAKWQVWEGEKNTEVDVASGRFAEVVSQMSVVRAYNRQDHELTGFRDRFLRTVEIT +RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSKDYFEV +LAEERERAGGAALAAASASAESA---------------GADAPRVPAEPRADVVP-----GAP-DVPAD--VPAVRFDEV +SFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLLLGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEP +SLFSGTVRENIAYADPDASDERVRAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEA +TSALDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGGIYAQLLELQRAGTQEAR +KMLKEYGLSG +>GCF_005280335_PROKKA_00585 +-------------------------MLAAVLTLATPFLIGAATDRIVAAIAGETTVEDAVVAVTWLAVAFLAVEVTTTLV +VSVGGYWGDVMAARMRTILSTRYFDQLLHLPQRYFDTAITGRVTNRLNRTINELTQFLQFFANNAFTMLITTTAVLVITA +FYWWPLAILLAIVFPVYMWLTAKTSAKWQVWEGEKNIEVDMASGRFAEVVSQMSVVRAYNRQDHELAGFRERFTRTVGIT +RKQSRFWHGMDAWRRLALNVVFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSRDYFEV +LAEERERAGGAGPQGRGAAAVAAGQPRADDDGGTDVRWGGAAPSRPAQPRADVVPGDGTGGMP-AGPSADVVPAVRFDEV +SFAYDPDASRPVLDRVSFEIPQGQRVALVGESGGGKSTIAHLLMGLYPVTGGRIEVFGQDVAELDLAELRERIAAVFQEP +SLFSGTVRENIAYADPAASDERVRAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEA +TSALDTKSERLVQGALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAESGGIYAQLLRLQKAGTKEAR +KMLKEYGLSG +>GCF_020097155_PROKKA_00512 +MRALLRILRFAPQLNPLYLGIAVCSVLAAALSLATPFLIGAATNRIVDAIAGRSTLDDAVAAVTWLALAFLAVEVATTAV +VSVGGYWGDVMAARMRAALSGRYYDHLLHLPQRYFDTAITGRIVNRLNRSITELTQFLQFFSNNAFTMLITTAAVLVITA +FYWWPLAVLLAVVFPVYMWLTAKTSAKWQGWEGEKNTEVDIASGRFAETVAQMNVVRAYNRQDHELAGFTERFRRTVGIT +RKQSRFWHGMDAGRRLALNLVFGVMYLIVFVRTARGLFSVGDMVILLQLMNMARQPIFSMSYLVDSAQRAVAGSKDYFGV +LAEERERSGGAALPAGLGSAEA---PT-----------TTTATGVVVRDRAEAPT-----GAPVRAGAD--VPAVRFADV +TFAYDPEAERPVLDGVTFDIPQGAKVALVGESGGGKSTLAHLLMGLYPVGSGRVEVFGRDVAGLDLAVLRGQVAAVFQEP +FLFSGTIRENIAYADPDASGERVRAAAKAAFADGFVEEFEHGCEQLIGERGLRLSGGQKQRIAVARAVLKDAPVLVLDEA +TSALDTKSERLVQSALDDLMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAQSGGIYAQLLRLQKAGTKEAR +KLLKEYGLSG +>GCF_023573625_PROKKA_02112 +MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAIAGETGVAEAVTAVTWLAVAFLAVEVATTLV +VSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAITGRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITA +FYWWPLAVLLAVVFPVYMWLTARTSAKWQVWEGEKNTEVDIASGRFAEVVSQMGVVRAYNRQEQELSGFRDRFLRTVGIT +RQQSRFWHGMDAGRRLALNAAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSKDYFEV +LAEERERAGGAVLAVAS----------------------ADAPRVPAEPRADVVA-----GAP-DVPAD--VPAVRFDEV +SFAYDADASRPVLDRVSFDIPRGAKVALVGESGGGKSTIAHLLLGLYPVTSGRIEVFGQDIAGLDLAALRGRIATVFQEP +SLFSGTVRENIAYADADASDERVRAAAQAAYAHRFVAAFDDGYDQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEA +TSALDTKSERLVQAALDELMVGRSSLIVAHRLSTIASVDRIVTLRAGRVEEVGSPAELAESGGIYAQLLELQRAGTQEAR +KMLKEYGLSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001695.fa new file mode 100644 index 0000000000000000000000000000000000000000..f3cf8bfeec9acf48f4f7b076b38cc4ab412b709d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001695.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02169 +MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG +HGPDRIDLAVLTGELPLIDPVTGRLA----------EREPAGAGVGH---HDD------- +------GAPGF--------GAPSG-GGSVTVRQR----VQPRRVALDRPQTPLPRIILLA +LSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAASLVWFTALGWGGTKLAPSMDS +ARTWRIVDAVVGVLMLGIAVKVGLTLL +>GCF_003691675_PROKKA_01883 +MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG +HGPDRIDLAVLTGELPLIDPATGRLA----------EREPAGAGVGQ---HDD------- +------GAPGV--------GAPSG-GGSVAARQR----VQPRRVALDRPQTPLPRIILLA +LSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAASLVWFTALGWGGTKLAPSMDS +ARTWRIVDAVVGVLMLGIAVKVGLTLL +>GCF_005280335_PROKKA_00583 +------------MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVA +LLALGAAGIGVVAERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLA-AAAEAEGPA +VGLTDGEIAALTGELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRT +VGGIPVGNPRLCGTRPGERGADGR-SGGVAVKQR----VQPRRVVLSAPQTPLPRIVLLA +LSVSFLNPHAVLDTVVMMGTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNT +PRTWRIVDAAVGVLMLVIAAKVGLTLL +>GCF_020097155_PROKKA_00509 +------------MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIV +LLLAGAAGVGAAAERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDA +WAPTAEEVAAMTGSLPVVAAG-----------------------------PDA------- +------GADAA--------TAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLC +LSVSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNT +PRTWRIVDGAVGVVVLGIAGKVALTLF +>GCF_023573625_PROKKA_02114 +MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG +HGPDRIDLAVLTGELPLIDPATGRLA----------DREPAGAGVGR---HDD------- +------GAPGV--------GAPSG-GGSVAVRQR----VQPRRVALDRPQTPLPRIILLA +LSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAASLVWFTALGWGGTKLAPSMDS +ARTWRIVDAVVGVLMLGIAVKVGLTLL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001696.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e6bae235c0f781ee7cb70ecdc23c03597d451e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001696.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02170 +MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERMLRLARQTLALEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGR-PVADPPTHLVPSVHAYLRAVEL +GLGWGMLPSVQIPPGVLEGRHPDLETIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAA +PSAGDTAD +>GCF_003691675_PROKKA_01884 +MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERMLRLARQTLVLEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGTLPIVDYGPRDGLQHTVLRRVTRGR-PVADPPTHLVPSVHAYLRAVEL +GLGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAA +PSAGDTAD +>GCF_005280335_PROKKA_00582 +--------MNSDHLRALVSAVDHGTFDAAADALRISGSAFSQRVKALERQVGQVLLARTV +PVRPTPAGERMLRLARHTLALEEEALASLGRGDGGRVPVRVAINADSLDTWWELVLREAA +TWDDVVLQLRTEDQEHTAALLRDGTVVAAVTDDPTPVSGCTSTPLGTMRYHAVCASFLLE +MHRDERGRLDLATLPRVDYGLRDGLQRTVLRRAARGR-AAFDPPHHLVPSVQSYLRAVEL +GLGWGMLPSAQLPPGVLEGRHPDLEPVPSLGTVDLTLHWQRWSAGTAALDRLTDAVLRAA +PSVADAAD +>GCF_020097155_PROKKA_00508 +--------MNSDHLRALAAAVDEGTFDAAAAWLGISGSALSQRIKALEGQTGQVLLTRTV +PVRPTEAGERMLRLARQTLPLEEEALAALGRGTGRRAPLRVGVNADSLETWWTPVLREAA +TWDDVVLHLHAEDQGHTPELLRQGTVVAVVTDDPTPVTGCTVTRIGTMRYHAVAASFLLD +LHRDAHGRVDVATMPVVDYGPRDGLQRTMLERAARGRVSVPRPPHHLVPSVGAYASAVGM +GLGWGMLPTGQVPPELAAGSHPDLELVPELGTAEVPLYWQRWSAGTPALDRLTAAVTAAA +PAG----- +>GCF_023573625_PROKKA_02115 +MTTPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERLLRLARQTLALEDEALAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGR-PVADPPTHLVPSVHAYLRAVEL +GLGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAA +PSAGDTAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001698.fa new file mode 100644 index 0000000000000000000000000000000000000000..e561505be828954a6d13b149c21abdec83a2f164 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001698.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02175 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSS-----AGASSSDAAGGDAAFP +RSIEHVYGTTEIPQRPTRVATVSWVNQDVTLALGVVPVGMAAVEFGGNAEKSTDWFDAKL +AETEGAQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVP +AYGTSWQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHADLQGASFVYGTIDPAAAD +QISIYTDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQD +SVREAIESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKT +AQG +>GCF_003691675_PROKKA_01889 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSS-----AGASSSDAAGGDAAFP +RSIEHVYGTTEIPQRPARVATVSWVNQDVALALGVVPVGVAAVEFGGNAEKSTDWFDAKL +AETEGAQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVP +AYGTSWQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAAD +QISIYTDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQD +SVREAIESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKT +AQG +>GCF_005280335_PROKKA_00577 +------------------------------------------------------------ +------------------MATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAAL +EKVEGAERPVTWSEAAGIDAEAVASVRPDVILAAYSGLTREDYDRLSKIAPVVAYPKDVP +AFGTPWQQSTRMIGQALGKDAEAEALVEDVEGRIAAAAQKHPDLKDATFVYGTVDPTAAD +QISVYTLVDNRPRFLESLGMKQAPVVAENSPKDQAFFFTWSPERADELESDVLVSWALDA +SVADAIEADPLLSALPAVQKDGLVLQVDQQEVLSVSAISPLSIPFALERIVPPIAEAAAR +SRG +>GCF_020097155_PROKKA_00504 +-MPQSPSRRSVLAAGGSGLALLLAACSTGPAGSSVPSSSPASSAGSAAASSSASGSAAYP +LTVEHVYGTTEIPARPERVATVSWVNQDVALALGVVPVGVPAVEFGGNADKSTDWFDAKL +KEL-GGPTPVQWSEADGIDAEAIAAVKPDVILAVYSGLTREDYDRLSKIAPVVAYPKDVP +AFGTSWQQSTEVIGRVLGKEREAAALVADLERQIADAGAEEDGLAGASFIYGTLDPAAAD +QISIYTAADNRPKFLELLGMELAPVVAENAPEDGAFFFTWSPERADELESDVFVSWAASA +DVADAIEADPLLGAIPAVEKGGLVLQVDQQEVLSVSAISPLSIPYALEKVVPPIAEAARA +AKG +>GCF_023573625_PROKKA_02120 +MAPSPLSRRSLLASGGVGLTLLLAACSTGPAGGSASSSS-----AGASSSDAAGGDAAFP +RSIEHVYGTTEIPQRPARVATVSWVNQDVALALGVVPVGMAAVEFGGNAEKSTDWFDAKL +AETEGAQKPVQWSEASGIDAEAIAAVKPDVILAVYSGITQEDYDRLSKIAPTVAYPKDVP +AYGTSWQQSTEVIGRVLGKEQEAEELIADLEQQIKDAGEKHAGLQGASFVYGTIDPAAAD +QISIYTDVDNRPKFLELLGMEQAPVVTENSPEDQAFFFTWSPERADELESDVFVSWAAQD +SVREAIESDPLLGSIPAVKAGALVLQTDEQEVLSVSAISPLSIPFALEKVVPPIAEAAKT +AQG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001699.fa new file mode 100644 index 0000000000000000000000000000000000000000..49e3a78e0c04f7d622a9caefc860ad383a82bdca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001699.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02176 +MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTL-GAILTGHPV +PEGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAG +MALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGR-TPGAPSPMALVLAGAALTAG +ATAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALA +LGDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRAL +MVGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA +>GCF_003691675_PROKKA_01890 +MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTL-GAVLTGHPV +PEGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAG +MALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAG +ATAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALA +LGDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRAL +MAGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA +>GCF_005280335_PROKKA_00576 +MPR------------ALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAA +VTGMDGAAVLSRVPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALG +IALGVAGSLPAVMALAILGTLAAAALVTAVAAGAARVSG-VPGPPSPLSLVLAGAATTAG +ATAVTSALVVLHPAVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALA +LGTDLAHGLGARPERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTL +VLACALWGAVLVLVADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA +>GCF_020097155_PROKKA_00503 +MPSSP------TRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTL-QAMLAGEGV +PAGVDAAAVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIG +LALGVSGSTFWVLALAAAGTLAAALLVYAVAAAASRGAG-AGGAPTPIGLVLAGAAVTAG +AGAVTTALLVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALA +LGDDLAHGLGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTL +LIGSALWGAVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS +>GCF_023573625_PROKKA_02121 +MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTL-GAVLTGHPV +PEGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAG +MALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGR-TPGAPSPMALVLAGAAITAG +ATAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALA +LGDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRAL +MVGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001700.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c9d17346f0ee0ed9bfd52d840c841a3fdd50046 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001700.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02177 +MSL---------QCTAP-DDVVAR---LRRADRRRLGGACAGLAVAVLVLALLRVVWGTY +QVTVPDLVRILGGETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPD +ILGVTQGAAAAVVLGMLATAGQTGGGSDLMRAATALIGGLAAVVAVFATARSVGGERFVV +AGIAVAAAGQAVVAGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLVVALPLAGV +LHARLAPADVGPDLAHALGARPRPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARG +LTRGLPSLPAAALTGAALVLLADLVAGEAVPLLT-GAALPTGVLTGAAGAPLMLWLLLCQ +GRTPGGVRSA +>GCF_003691675_PROKKA_01891 +MNL---------QHTAP-DDVVAR---LRRSDRRRLGRACAGLAVAVLVLALLRVVWGTY +QVTVPDLVRILGGETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPD +ILGVTQGAAAAVVLGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVV +AGIAVAAAGQAVVAGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGA +LHTQLAPADVGPDLAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARG +LTRGLPSLPAAALTGAALVLLADLVAGEAVPLLT-GAALPTGVLTGAAGAPLMLWLLLRQ +GRTPGGVRPA +>GCF_005280335_PROKKA_00575 +MSG---------RGSATLEHAVARVRAARRRDARRVGTALAVLTAAVLALVLLRLTWGAY +MVAVPDLVRILTGTTIPGASFIVTEEKLPRAAAAVLAGAALGAAGALYRRGLGNPLASPD +VLGVTSGAAAGAVLWQAAATG-TGGTTDAARAAAALAGGLIAALAVLLAARGTGGERFVV +AGIAVAAGAQAVVAGTMVTLAEHDLQAAALWVSGSLTGVTWGRIGLLAAAVALALPLAAW +LHGRLEPADTGEDLAHALGARPRRTRPAALLLGAVLAAAATAAVGPLAFVALLATPLARG +LAGGRPSLAAAALAGAVLVLAADLLAAEAVALLADGTRLPTGVLTGAAGAPLMMTLLIRA +GRRGERTA-- +>GCF_020097155_PROKKA_00502 +MSARRETTTPGRRDAAPGGDAPETVRALRRADARRVAGVVLGLAVLTAGLMLLRVTWGTY +QVTVPDLVRILGGERIAGASFIVWEEKLPRAVAATLTGAALGAAGALYRRTLRNPLASPD +VLGTTAGAAAGVVLTLTASAGQAGGSSDLARAGAALLGALAAGAAVLLAARSVGGQRFVV +AGVGVAAAGQAIVSGAMLSLSEHDLASATRWIAGSLNGVTWGRIGLLAAVLALALPAAGW +LHRRLAPADVGDDLAHALGARPRTTAALALTVGAVLAAAATATVGPLSFVALLATPLALG +LTRGRPSLPAAALTGAGIVLLADVLGTEALGLIADGAALPTGVLTGAAGAPLMLALLLRA +GRSSEGTR-- +>GCF_023573625_PROKKA_02122 +MSV---------QRTAS-DDVVAR---LRRSDRRRLGGACTGLAVAVLVLALLRVVWGTY +QVTVPDLVRILAGETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPD +ILGVTQGAAATVVLGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVV +AGIAVAAAGQAVVAGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGA +LHTQLAPADVGPDLAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARG +LTRGLPSLPAAALTGAALVLLADLVAGEAVPLLT-GAALPTGVLTGAAGAPLMLWLLLRQ +GRTPGGVRPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001701.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2019ff4384b4833088b87c62570b8ac98e497f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001701.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02178 +MTAPPLTVPSPAA---------PRAGAADDVAIRLRGLTLGYGPASAPPIVADLDLDVPA +GRVTAIIGANGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVA +PEGMTVAQLVARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRA +WLALVLAQQTPVVLLDEPTSYLDLSHQVEVLDLVRALPDPR--------------GGG-- +-------RATVVAVLHELNLAARSADHIVAMAAGRVVAQGTPGEVIVPEVLAEVFGLDAD +VVADPLLGHPVVLPRGDGDRR------------ +>GCF_003691675_PROKKA_01892 +MTAPPLTVPSPAA---------PRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPA +GRVTAIIGANGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVA +PEGMTVAQLVARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRA +WLALVLAQQTPVVLLDEPTSYLDLSHQVEVLDLVRALPDPR--------------GGG-- +-------RATVVAVLHELNLAARSADHIVAMAAGRVVAQGTPGEVIVPEVLAEVFGLDAD +VVADPLLGHPVVLPRGDGDRR------------ +>GCF_005280335_PROKKA_00574 +M--TP---PHPAAAPAERPGADPATGPAQDPALRLRGVRLGYGRPDTPDTVGPVDLDVPA +GRVTALIGANGCGKSTLLRGLTRQLPLRGGSAEVLGRDLGAYSAREYARTVALLPQHPVA +PEGMTVAQLVQRGRHPHRGLFGTTGADDDAAVARALRHTDLEKLADREVAELSGGQRQRA +WLALVLAQRTPVLLLDEPTSYLDLAHQVEVLDLVRGLTRPD--------------GDE-- +------EPVTVVAVLHELSLAARVADRLVALRDGRVAAAGTPAEVLTPAVLAEVFDLDAD +VRPDPLLGHPVVLPRGAADRGAPLPSPTTQETR +>GCF_020097155_PROKKA_00501 +MTSSP---PTPAA---------PSTAPA--PALRLRGVELSYGPASAPPTVGPVDLDVPA +GQVTAVIGANGCGKSTLLRGLTRQLPLRAGTVDVLGRDAAGMSARDYARTVALLPQQPVT +PEGLTVAQLVERGRHPWRGLLGGRAAGDDAAVAAALARTGLVDLAARDAATLSGGQRQRA +WLALVLAQQTPVVLLDEPTSYLDLAHQVEVLDLVRTLPDPRAVGARTVEAAGGVVGGGAG +TEAGPPPRATVVAVLHELSLAARAADHVVAMAGGRVVATGTPAEVIVPEVLAEVFGLDAD +VVPDPLLGHPVVLPRGRGDRA------------ +>GCF_023573625_PROKKA_02123 +MTAPPLTVPSPAA---------PRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPA +GRVTAIIGANGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVA +PEGMTVAQLVARGRHPHRGLLGGRAAGDDAAIASALERTGLVELAEREAGTLSGGQRQRA +WLALVLAQQTPVVLLDEPTSYLDLSHQVEVLDLVRALPDPR--------------GGG-- +-------RATVVAVLHELNLAARSADHIVAMAAGRVVAQGTPGEVIAPEVLAEVFGLDAD +VVADPLLGHPVVLPRGDGDRR------------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001707.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2a9e6ec3238d85963dfe584c0d5291b9996d254 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001707.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02185 +MTQP------TTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALA +AWATTTASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRC +VLCDAVFVQVDPAAGRPVAVSDEERAAFERVLIPAED--- +>GCF_003691675_PROKKA_01899 +MTQP------TTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALA +AWATTTASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRC +VLCDAVFVQVDPAAGRPVAVSDEERAAFERVLIPAED--- +>GCF_005280335_PROKKA_00565 +MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR +AWSGVTPGRDVHRVVRAMEVQYEAPVVY-GPELTAKVWIARIGTSSYTLRHELWQDGRRC +VLCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT +>GCF_020097155_PROKKA_00490 +MSDS----------------QPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALK +AWDEGDVGRDVMRVVRAMTTEYERPVEY-GPELTAKVWVRALGRTSYTLHHELWQEGVRC +VTCDAVMVHLDPETGAPLPHDDARRARLQAVLVPAEG--- +>GCF_023573625_PROKKA_02130 +MTQP------TTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALA +AWATTTASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRC +VLCDAVFVQVDPAAGRPVAVSDEERAAFERVLIPAED--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001708.fa new file mode 100644 index 0000000000000000000000000000000000000000..131f69ec884982cc5575020dd176f310ea7e390e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001708.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02186 +M----EQDPSPDAPAP--------------SADVEALRGTPVSELTQLTPAASGALERLR +RDVERFDLEYRSALLQVEARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLS +LDLDALRTNVTDIAGARVIVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLH +CLVQVPIHLSTGTIPVTVEMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVA +ADLDTRMERLHDQVQETDRDDDAAAAWEDDGGPAFEDEPTVE-----PGEARPG-DAPGA +STA +>GCF_003691675_PROKKA_01900 +M----EQDPSPDAPAP--------------SADVEALRGTPVSELTQLTPAASGALERLR +RDVERFDLEYRSALLQVEARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLS +LDLDALRTNVTDIAGARVIVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLH +CLVQVPIHLSTGTIPVTVEMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVA +ADLDTRMERLHDQVQETDRDDDAAAAWEDDGGPVFEDEPAAG-----PGEARPGDDAPGA +STV +>GCF_005280335_PROKKA_00563 +M----EQDRDPEESSQ--------------STAIETLRGTPVSELTHLPPAMAGALDRLR +RDVERFDLEYRSALLQVEARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLS +MDLDALRSNVTDIAGARVIVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLH +CLVQVPVHLSTGSIPVTVEMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVA +ADLDTRMERLSDQVRQTDKDDDAAASWEDDGGPAFEDE---------GDDDGPDGDAPGT +STG +>GCF_020097155_PROKKA_00489 +MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR +TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS +LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH +CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA +HDLDARMERLHQAVH------DAGA------GPDEHDD---------ED------DWVGH +A-- +>GCF_023573625_PROKKA_02131 +M----EQDPSPDAPAP--------------SADVEALRGTPVSELTQLTPAASGALERLR +RDVERFDLEYRSALLQVEARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLS +LDLDALRTNVTDIAGARVIVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLH +CLVQVPIHLSTGTIQVTVEMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVA +ADLDTRMERLHDQVQETDRDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGA +STV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001709.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001709.fa new file mode 100644 index 0000000000000000000000000000000000000000..23c630cbb4d6f52cfc8d7a6475bee089fd8e77f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001709.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02189 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG +>GCF_003691675_PROKKA_01903 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG +>GCF_005280335_PROKKA_00557 +MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR +EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV +HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL +GRRA +>GCF_020097155_PROKKA_00484 +MST-QTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGR +EIPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLV +HRWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRL +GRRA +>GCF_023573625_PROKKA_02134 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001712.fa new file mode 100644 index 0000000000000000000000000000000000000000..33247bd19657ceccc68285627f5e944cdd9dff1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001712.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_02195 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQRGDTTLRTGADMTERLKDDRA +FDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGGGTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAI +EAYFEAVFSSLGELRSGMVDAADGAAQLADGTASAEDGASRLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQLQTGSAELTDGATQVADGTQQ +LYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTAEDGAGARIADAQTALAALAEEDPTLAESEQYAALQEALTG +ADERVTAVAGRAEEAAATSAAANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGAGQLESGATELDGGLAQLQDG +AGELRAGLGTLDDGAHELASGLSDGADRVPALTEDERDEAALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIA +AFNIMRPISGRLLAGRRNPVAIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRFWVPVVVLMGIGAAALALDVL +VVRRRRRFRMKDLHPALQA +>GCF_003691675_PROKKA_01908 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQRGDTTLRTGADMTERLKDDRA +FDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGGGTPRQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAI +EAYFEAVFSSLGELRSGMVDAADGAAQLADGTASAEDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQLQTGSAELTDGATQVADGTQQ +LYDTVIPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTAEDGAGARIADAQAALAELAEEDPTLAESEQYAALQEALTG +ADERVTAVAGRAEEAAATSAAANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGAGQLESGATELDGGLAQLQDG +AGELRAGLGTLDDGAHELASGLSDGVDRVPALTEDERDEAALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIA +AFNIMRPISGRLLAGRRNPVAIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRFWVPVVVLMGIGAAALALDVL +VVRRRRRFRMKDLHPALQA +>GCF_005280335_PROKKA_00549 +MLFRYELRRFRRGLPLLALLFILLVPAIYGALYLSANWDPYGAMNRLPVAIVNEDEPVQRGDTTLRTGADMTARLKEDHA +FDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGGGTPQQAQITLRRDDANGFVIGSVTASSQAKVEAAVNRSAI +EAYFEAVFSSLGELRSGMVDAADGAAQLADGSASAVDGASQLEDGIVQAHDGSGRLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGATSAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQLQTGSAELTDGATQVADGTQQ +LYDTVVPGLDRVIERQDAVAADVAAVDEDVQRVAEVAGTAGDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTG +ADERVTAVAGRAEEAAATSAAANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGAGQLESGATELDDGLAQLQDG +AGELHTGLRTLDDGAHELASGLSDGVDRVPALTEDQRDEAALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIA +AFNIMRPISGRLLAGHRNPVAIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLILQLASTGGTYPAEVLPGFFRALHPFMPMSYSIEAFRNAISGGLDQHFWVPVVVLMGVGAAALALDVL +VVRRRRRFRMKDLHPALQA +>GCF_020097155_PROKKA_00478 +MLFRYELRRFRGVLPTIALLFIVLVPTIYGALYLSANWDPYGNLSSLPVAIVNEDRPVESDGKTLTTGADITEELVDQHT +FDWHETTRDDAEAGLRDGRYYLVMEIPEGLSADLVSAN-TSDPQQAHITLRRNDANGFVIGSVTSSSQSKIENAVDKAAV +EAYFKAVFENLATIRQGMADARDGAGRLADGAGQADDGAAQLADGIVQAHDGSGQLAQGASDAQDGAGQLADGAGQLKDG +ADQLAAGATSAKDGAVQLQTGIGQAREGSQKLADGAGQIAAKVPDLRDGATALSNGLTQLDTGSADLADGAHQVADGTQQ +LYDTVIPGLDAVIERQDKVASDVATVNQDVQTLNDAVATAGSGAGGDIDTASEQLQALAESNPDIAVAPEYAALQQSLTD +AKEKAGSATSTAQDVADRSAAVNSRVQGFVSEDVAGNAKADITKLNDGAHAVAEGADTLHAGIGQANTGAQALADGVGRF +ADALDQLAAGATALDDGLAQLEDGSGRLVDGLGKLETGAGDLADGAGRLDQGAGELQTGLGKLSDGATSLDSGLAQLETG +SGDLKTGLDSLSDGATQLHDGLASGTDKIPALSEDAADEAALVMSRPVQVDMDVLNPAGVYGRGVAPLFFSIALWVFGIA +AFNVMRPVNGRLLAGRRNPLLLALSAWLPVGLLSVVGSLVMLAATVPLGIDPVHPWHLVGLVVFTALAFSLFAHLVMTAL +GTPGSAVLLVTLILQLGSAGGTYPADVLPPFFRWVSPLMPMTHSINAIRYALSGGQPAQFWGAVAFLAVFGAACLFLDMA +VVRRRQRFRMKDLHPALEK +>GCF_023573625_PROKKA_02139 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQRGDTTLRTGADMTERLKDDRA +FDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGGGTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAI +EAYFEAVFSSLGELRSGMVDAADGAAQLADGTASAKDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQLQTGSAELTDGATQVADGTQQ +LYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTAEDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTG +ADERVTAVAGRAEEAAATSAAANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGAGQLESGATELDDGLAQLQDG +AGELHTGLGTLDDGAHELASGLSDGVDRVPALTEDERDEAALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIA +AFNIMRPISGRLLAGRRNPVAIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLILQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGLDQRFWVPVVVLMGIGAAALALDVL +VVRRRRRFRMKDLHPALQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001713.fa new file mode 100644 index 0000000000000000000000000000000000000000..94b2e872fca05e2d02e1aef17f12f7e1862af940 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001713.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02196 +M----SSTPTDAD----HHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVL +PPQTHLAVLGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPI +DAARHPHALRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVR +LSVAPEAVVGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDH +GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN +>GCF_003691675_PROKKA_01909 +M----SSTPTDAD----HHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVL +PPQTHLAVLGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPI +DAARHPHALRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVR +LTVAPEAVVRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDH +GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN +>GCF_005280335_PROKKA_00548 +M----SSTPTDAD----HHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVL +PPQTHLAVLGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLI +DATRHPYALRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVR +LTVAPEAVVGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDH +GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN +>GCF_020097155_PROKKA_00479 +MTEDQTPAPIETDDVVAERAPEPAPGGSHQVG---RALTARGLTLRSIRGTVFGPVDVDL +PPGVPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGD---------------------M +DGIRHPHRLRRATTVARITDYVELEPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVG +FHPDHGDQVSSLPVEDRTILTCMLACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRL +GHRFVVSALTSAPVPRGAVVVELPTPGHDDLPAALPTRPSLED +>GCF_023573625_PROKKA_02140 +M----SSTPTDAD----HHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVL +PPQTHLAVLGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPI +DAARHPHALRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVR +LSVAPEAVVGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDH +GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001719.fa new file mode 100644 index 0000000000000000000000000000000000000000..a219046588bf9392dc191ff834ab086739ccd3f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001719.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_02206 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATP-SQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAE---PAQ +GEDD---------------------DGAP-SPILAADHLARVVLGAEPRVVTQLAERVLA +PLDEVSEAKRAVLEETLLAWLTHWGQRAPIAAELGVHPQTVGYRVGRLRELFGEALEDPD +ARFDLEIVLRARRDGVG- +>GCF_003691675_PROKKA_01919 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATP-SQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAE---PAQ +GEDD---------------------DGAP-SPILAADHLARVVLGAEPRVVTQLAERVLA +PLDEVSEAKRAVLEETLLAWLTHWGQRAPIAAELGVHPQTVGYRVGRLRELFGEALEDPD +ARFDLEIVLRARRDGVG- +>GCF_005280335_PROKKA_00539 +--MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKN +LTLGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVF +RDLSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAA +LVRGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVV +GAD--APARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAAR +PEGDGSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLA +PLAELTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPD +ARFDLELVLRARAGGMAA +>GCF_020097155_PROKKA_00469 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------MVL +SAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGV------- +---------------------------APGAAVLAEEHLADVVLGAEPEALRRLSERVLA +PLDGLSDAKRATLEATLAAWLAHRGARGPMAAELNVHPQTVGYRVGRLRELFGGALDDAD +ARFDLELALRSRR-GQG- +>GCF_023573625_PROKKA_02150 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATP-SQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAE---PAQ +GEDD---------------------DGAP-SPILAADHLARVVLGAEPRVVTQLAERVLA +PLDEVSEAKRAVLEETLLAWLTHWGQRAPIAAELGVHPQTVGYRVGRLRELFGEALEDPD +ARFDLEIVLRARRDGVG- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001721.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a535522927e0237faf9cb86f757dfc41d886997 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001721.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02216 +MPAQ---------PSPSGHTVHLSTSGVDARITPD-EFGGFVLEIGGAVQSHVDLADPAR +IRYEYLRRMAHVLDAASPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSF +VLAELPLPAGTDLVSVVADARLAAVDLA--LDGER----FDAVVLDIGTGEEGAEHLRGA +VFYGELLELLTAGGVLLVNIGDDAGLRFLGAELGALEEAAAE----AGVPGPWTLADQGM +LERLDWGNVVLAAGAPLGEAGCT----------------ERLAAAGPHPAAVLDPAESAA +LADRIRRA- +>GCF_003691675_PROKKA_01929 +MPAQ---------PSPSGHTVHLSTSGVDARIAPD-EFGGFVLEIGGAVQSHVDLADPAR +IRYEYLRRMAHVLDAASPTGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSF +VLAELPLPAGTDLVSVVADARLAAVDLA--LDGER----FDAVVLDIGTGEEGAEHLRGA +VFYGELLELLTAGGVLLVNIGDDAGLHFLGAELGALEEAAAE----AGVPGPWTLADQGM +LERLDWGNVVLAAGAPLGEAGCT----------------ERLAAAGPHPAAVLDPAESAA +LAARIRRA- +>GCF_005280335_PROKKA_00525 +MRAH---------PSPTGRTVHLSATGEDARILAD-ELGGSVLEIGGAVQSHVDPADPTA +LRYEYLRRMANVLDGVAPAGAPLRVLHLGAGALTLPRYVQATRPGSEQTAVDLDRELVSF +VLAELPLPAGTDLVSVVADARLAAVDLL--MDGER----FDAVVLDIGTGEDGAAHLTGA +EFYGELLGLLTAAGVLLVNIGDDDGLRFLGAQLRHMEAACAE----AGVPGPWTLASAAM +LERLELGNAVLAAGPALRGDGAAAGGDAGPEEDGGPLTPAALLARGPHPGAVLDEAASAD +LARRVAGR- +>GCF_020097155_PROKKA_00467 +MPTQPQDDASSPAPSPTARTVHLAASGVDARILPDPHAGGWMLEVGGAVQSHVDLADPTQ +VRYEYLRRIANVLDALAPAGEPLRVLHLGGGALTLPRYVAATRPGSVQTVVDLDRELMGL +VLEELPLPADADVYVVVADARAVVDDLLDPLEGESQAGAWDAVVLDIDTDAGAVAHLTGA +AFHAELLELLAPGGVLCVNIGDDDGLAYLATQLTALEAACADAAEGAGVPGPWTLGPNSV +LERRELGNAVLVAGPGLAGMDAA-----------------ALHAAGPHPAVVLDAHESAA +LAERITAAP +>GCF_023573625_PROKKA_02155 +MPAQ---------PSPSGRTVHLSTSGVDARIAPD-EFGGFVLEIGGAVQSHVDLADPAR +IRYEYLRRMAHVLDGVAPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSF +VLAELPLPAGTDLVSVVADARLAAVDLA--MDGER----FDAVVLDIGTGEEGAEHLRGA +VFYGELLELLTAGGVLLVNIGDDAGLRFLGAELGALEKAAAE----AGVPGPWTLADQGM +LERLDWGNVVLAAGAPLREAGCT----------------ERLAAAGPHPAAVLDPAESAA +LAARIRRA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001722.fa new file mode 100644 index 0000000000000000000000000000000000000000..8dc66807e668d31d595984dbfa7602b81478104e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001722.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02219 +MPPEPSAPSGERGPARPHPADVAARPDAP-SPRATALLFALAVAAGSVMPLQGRINSRLA +HLTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGL +LVLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAV +ALVVWPSLGEAG--GGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTA +GVLFLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLV +SGNLLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPA------------RRR +>GCF_003691675_PROKKA_01932 +MPPESSVPSAERGPSRPRPAAVAARPEAP-SPRATALLFALAVAAGSVMPLQGRINSRLA +HLTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGL +LVLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAV +ALVVWPSLGEAG--GGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTA +GVLFLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLV +SGNLLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPA------------RRR +>GCF_005280335_PROKKA_00527 +MSAR-AARAARAGEGR-QGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALA +ERSGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGA +MVFSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACV +VLVVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVA +GTGILALVHLGGRLGGGVG-GTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLV +SGKLLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPA---------RKG +>GCF_020097155_PROKKA_00465 +M-----------------PASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALS +LAVGSPALAACASFATGLAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAA +FVLTQAWTIPLIGVAVFTVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAV +TAVVWPRLQESG--SPGAWLALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAA +GTAVLAAA-TAVAAGTGAGMGPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMV +AGQLVGSLLLDVVAPAPGAQVTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG +>GCF_023573625_PROKKA_02158 +MPPEPSAPSGERGPARPHPADVAARPDAP-SPRATALLFALAVAAGSVMPLQGRINSRLA +HLTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGL +LVLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAV +ALVVWPSLGEVG--GGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTA +GVLFLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLV +SGNLLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPA------------RRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001723.fa new file mode 100644 index 0000000000000000000000000000000000000000..a85088902c8dfaf6dcb580a9772449ec74dcf4ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001723.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02220 +-----MKHEIVLTRGDLTLRPLTPDDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAEL +SEREGTFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHA +FEEWALERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWP +AVRGGLEARLAA----- +>GCF_003691675_PROKKA_01933 +-----MKHEIVLTRGDLTLRPLSPTDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAEL +IEREGAFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHA +FEEWALERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWP +AVRAGLEARLTA----- +>GCF_005280335_PROKKA_00515 +-----MSHDLHLTHGPIRLRPLTPDDAPRLRAIVDEASWAGMSTPLPETDAAMAEHLREL +MGRPGLQAFAVERDGEFVGRTALYDPVPTVRVDVGHTVYARPVWGTEVNPACKLLLLGHA +FEELGVARVGLRCDHRNTRSHRAILRLGATFEGTLRAFRRAADGTVADADHFSVTAPEWP +AVRAGLETRLGA----- +>GCF_020097155_PROKKA_00462 +MPAAQLPADLLLEHGAVRLRPLTLDDAPRLRALVDAGSWAGMSSPLPTSDEAMAAHLAQL +MAREDLTAFAVERDGEFVGRTAYYEHVPGVRVDVGHTIYAREVWGTEVNPACKLLLLRHA +FEALGVERVGLRCDHRNTRSHRAILRLGATFEGTLRAFRPAADGTVADVDYFSVLAAEWP +AVRAGLEARLAGSAPAD +>GCF_023573625_PROKKA_02159 +-----MKHEIVLTRGDLTLRPLSPTDGPALRELVDAVMWAGNSTPLPVDGAAMSAHLAEL +IEREGTFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHA +FEEWALERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWP +AVRAGLEARLAA----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001724.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f0f9baf779e77580ea86fe44a31786af3a42a35 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001724.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02239 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAARERLDARGRTVLAGFNDAHAHSVWFGQSRLDVDLEG +ARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPDRDGLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVL +QQPEGGRILTDAEGRPTGLLEETAMSLVTRLLQSESHEHIGACLARASQGYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALHSVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDGSMLGQTAAMTEDYCGHGHGR +GYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDVIAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMAT +QPNFISAFGGSVRERIGPERAALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRVVPSDQIAAIDVVATAVGGEFVHGGL +>GCF_003691675_PROKKA_01941 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLTARERLDARGRTVLAGFNDAHAHSVWFGQSRLDVDLEG +ARTAEEVHRRVRARAAELGPGAWVTCTGFDPGHLTGPQPDRDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVL +QQPEGGRILTDAAGRPTGLLEETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDGSMLGQTAAMTEDYCGHGHGR +GYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDVIAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMAT +QPNFISAFGGSVRERIGPERAALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVHGGL +>GCF_005280335_PROKKA_00506 +MQLDLIVENAHLLTGDPARPEATRLGVWRGAVVGVDEELDGLGARERLDARGRTVLAGFNDAHAHSVWFGQSRLDVDLEG +AHTAQEVYDRIRARAAELTPGAWVTCTGFDPGHLTGPQPDRDGLDAAAAGRPVLIRHNTGHAFTVSGAVLFLAGVGEQVM +QQPEGGRIITDAADRPTGLLEETAMNLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGIAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQAMVTLDALRPVDGHADDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDGSMLGQTAAMTADYCGHGHGR +GYLQQDAGEMRRECLGAAAAGWSLALHAIGDAALDFALDVIAEARARFGRPVMPHRVEHGGVVRDDQVARLAELEVVMAT +QPNFISAFGGSVRERIGPERAALSYPAGRLLRAGLVLPGSSDRPVAGGRPLDVIQDFVLRRTETGEQYGPDLERLTVAQA +LQAYTVGSAEATGWGGRKGRLVAGQLADFTVLSADPRAVPSEEIAAIDVVATAVGGEFVHGGL +>GCF_020097155_PROKKA_00442 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAAGERLDARGRTVLAGFNDAHAHSVWFGQSRLDVDLEG +ARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPDRDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVL +QQPEGGRILTDAAGRPTGLLEETAMSLATRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDGSMLGQTAAMTEDYCGHGHGR +GYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDVIAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMAT +QPNFISAFGGSVRERIGPERAALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLAAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVHGGL +>GCF_023573625_PROKKA_02171 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEQLDGLATRERLDARGRTVLAGFNDAHAHSVWFGQSRLDVDLEG +ARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPDRDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVL +QQPEGGRILTDAAGRPTGLLEETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALHPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDGSMLGQTAAMTEDYCGHGHGR +GYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDVIAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMAT +QPNFISAFGGSVRERIGPERAVLSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVHGGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001726.fa new file mode 100644 index 0000000000000000000000000000000000000000..a932be80b3eabd1f6cff36e3de341dd6511163eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001726.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_02241 +MTSGPP-SPAL--------PAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLLHVLTGRITPDV +GRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAAAALAEAPDDAGAGHRYSTALERAHLYDAWDA +GRRVDMDLEGLHACTDREHPLTSLSVGQRHRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDR +ALLRAVCTDIVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQM-QGSWRPPKGTGK +HQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDGADAAAGTAGGPGTAGDDVLLTADAVRVAGR +LEQPMGAALVPGGRVLVTGPNGAGKSTLLRVLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVG- +-ADEAGVDDLGRPLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVDEMTEALQ +VTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV +>GCF_003691675_PROKKA_01943 +MTSGPP-SPAL--------PAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLLHVLTGRITPDV +GRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAAAALAEAPDDAGAGHRYSTALERAHLYDAWDA +GRRVDMDLEGLHACTDRERPLTSLSVGQRHRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDR +ALLRAVCTDIVDLDPSQDGRPRRYSGGYAGWAKGRRRAQAAWEQEYAEQNAERERLELAVEDAREQM-QGSWRPPKGTGK +HQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDGADAAAGTAGGPGTAGDDVLLTADAVRVAGR +LEQPMGAALVPGGRVLVTGPNGAGKSTLLRVLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVG- +-ADEAGVDDLGRPLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVDEMTEALQ +VTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV +>GCF_005280335_PROKKA_00715 +MTLTPPHAPAL--------PAGASAHIRAECITLTLGDRTVLDQADVTVSAGSRLAIVGENGRGKTTLLHVLAGTLAPDA +GTVTRAGTLALVEQDLDADDD---RTVGDLIHDAVGESLAVLDRLEAATRALAEG--RPGADDDYARALETATALEAWDA +ERRIDVALEGLSACTDRTRPLNSLSVGQRYRVRLAVVLGSAVDLLLLDEPTNHLDAGALEHLTRALREHPGGVAVVTHDR +ALLKDVAETFLDLDPTSDGRPRQYAGGYAGWEKGRSAERAAWEQAHEQQVAEHAALAEAAEAARGRL-QDRWRPDKGTGK +HQRATRAAGVVQAFNRRVRDLEAHEVTVPEPPRALAWPASSTRAARP---------------------LLNAEGVDVAGR +LRGPVSADLTGGDRLLLTGPNGAGKSTLLHVLAGRLDPTAGRVLRHTGARIALLTQEAPAWNPRHTARQAFEVHLHRRGL +LADDDG--------GAPPLASLGLLEPRSMDAPVGRLSQGQQRRLHLALCLAERPDLLMLDEPSNHLSATLVDELTEALR +ATRSAVVVATHDRQMLRDLSDWPRLELTAEAVAR +>GCF_023573625_PROKKA_02173 +MTSGPP-SPAL--------PAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLLHVLTGRITPDV +GRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAAAALAEAPDDAGAGHRYSTALERAHLYDAWDA +GRRVDMDLEGLHACTDRERPLTSLSVGQRHRVRLAVTLGSRPD-LLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDR +ALLRAVCTDIVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQM-QGSWRPPKGTGK +HQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADRPDGDPRDGADAAAGTAGGPGTAGDDVLLTADAVRVAGR +LEQPMGAALVPGGRVLVTGPNGAGKSTLLRVLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVG- +-ADEAGVDDLGRPLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVDEMTEALQ +VTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV +>GCF_023573625_PROKKA_02213 +M----PTSRSLRSCVWNGTPQGHAAHIRAESIHITLGDRHVLNGVDVTVSVGSRLAIVGDNGRGKTTLLHLLAGILQPDS +GVVTQAGSLVLVKQDMATEGD---RTVGDLIAEATGPSKSALEALDATSAALAEGDDAADA---YSAALERATLLDAWDA +ERRVDIALEGLNACSDRDRVLSTLSVGQRYRVRLAVALGSTPDLLLLDEPTNHLDAAGLSFLTERLRDHAGGLALVSHDR +ALLRDVATTFLDLDPTRDGRPRTYAGGYQGWVEGRQRERVSWEQDHAAQVARHAQLTRAAAEARSRLSQGGWRPDKGTGK +HQRATRAAGVVQAFNRRVEDLERHEIDVPEPPLRLAWPKSSARRGMS---------------------IVNASMLTVERR +LDTPVSIGVNGGDRLVVTGPNGAGKSTLLAVLGQRLVPTTGYVQVNPSARIALLSQEVPDWDRTSPAHVAYETYLGKLGC +RSQ------------APSLGSLGLLEASATSTPVGRLSQGQQRRLHLALCLAQDPDLLLLDEPTNHLSSSLVDDITTELL +QTPCAVIVATHDRQMLDDLADWPHLDLDPKDMP- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001729.fa new file mode 100644 index 0000000000000000000000000000000000000000..582b6fe25d7eee398527de7670caa61af61e5860 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001729.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02247 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSFQSFAMALGGRIGVGNIAGVA +AAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVRGEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQ +IQANAVTAATTEAWGWDPLWVGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVDTLFVCTMTGLMILATNSFNV +LGPDGESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVAIAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIAR +LLLAGSMVFGSVQTSAFVWSLADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVV---PRR-EG +>GCF_003691675_PROKKA_01949 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLRDMVGQLVRGGSSSAGISSFQSFAMALGGRIGVGNIAGVA +AAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVRGEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQ +IQANAVTAATTEAWGWDPLWVGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVDTLFVCTMTGLMILATNSFNV +LGTGEGPPIVEHLPGVEEGPAWVQIGIDVVLPSFGPSFVAVAVFLFAFTTLLSFAFYAETNLAYLIPNKKAQRICIAAAR +LLLAASMVIGSVQTSAFVWSLADFGVGLYTWVNILALVLLSPVAIRLLKDYDRQRRAGQDPVLDPAAIGVRNAHLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVV---PRR-EG +>GCF_005280335_PROKKA_00499 +MEQFLAGANAIMWSLPMVFGLLALGLYFTIRMGAPQLRRIPDMIGQLVRGGSSSAGISSFQAFAMALGGRIGVGNIAGVA +TAISLGGPGALFWMWVTALLGAPVALAESSLAQLYKHKVRGEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVITGPQ +IQANAVTAATTQAWGWDPLWVGLAMAVLFCVIVFGGMHRLGRTVGLVVPFMAAAYIIVGVVVVALMWQQVPAMFGLIFTS +AFAADSLYAGMLGAAISWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAFVDTLFVCTVTGLMILSTNSFNV +LGPDEETVLVEHVPGIEAGPAWVQTAIDSVIPAFGPAFVAVAVFLFSFTTLLSFAFYAETNLAYLIPNKSVQRACIAVAR +LGLAASMVFGAVQTSTLVWSFADFGVGLYTWVNILALVLLSPVAIRLMKDYDRQRRAGQDPVLDPRAIGVRNATLWEQIH +DEYERTGDVTAALDHVADTAPDTRAISVVRSHGERGQG +>GCF_020097155_PROKKA_00437 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLKDMVGQLVRGGSSSAGISSFQSFAMALGGRIGVGNIAGVA +AAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVRGEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQ +IQANAVTAATTEAWGWDPLWVGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVDTLFVCTMTGLMILATNSFNV +LGPDGESLLAENVPGVEEGPAWVQIAIDAALPAFGPSFVAIAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIAR +LLLAGSMVFGSVQSSALVWAFADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVRGGPERGEG +>GCF_023573625_PROKKA_02179 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSFQSFAMALGGRIGVGNIAGVA +AAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVRGEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQ +IQANAVTAATTEAWGWDPLWVGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQIPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVDTLFVCTMTGLMILATNSFNV +LGPDEESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVAIAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIAR +LLLAGSMVFGSVQTSAFVWSLADFGVGLYTWVNIVALILLSPVAIRLLKDYDRQRRAGQEPVLDPHAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVV---PRR-EG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001730.fa new file mode 100644 index 0000000000000000000000000000000000000000..d1ba4a0852a4850e780fda8b36a0cf1a9854d084 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001730.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02254 +M----------------MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGA +AMISDWDHPRATVVHALPPLTEWLSRGIRHVAGGHRRGTHSLVGVAAFTAIATAAASIQV +PIAGHVYTPGQGVIAAFLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPA +SVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALV +SVVTAFTVVRAVRLVPLAARGVAALF------ +>GCF_003691675_PROKKA_01954 +M----------------MGPSHAATGAAAWLALTHWQSPIAALHLPAELQLLGAVTTAGA +AMISDWDHPRATVVHALPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAVATAAASIQV +PIAGHVYTPGQGVIAAFLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPA +SVAVGVSVHILGDALTNNGVALLWPLSPEPPTRLWWWQSSGRFRLPLLGRTGSWREWALV +SVVTAFTVVRAVRLIPLAARGVAALF------ +>GCF_005280335_PROKKA_00477 +-----------------MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGA +AMISDWDHPRATVVHALPPLTEWMSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQV +PIAGHVYTPGQGVIAAFLAAVAAKALRLLPNRGWRAAWALGILVAGAATVLSDGLWWIPA +SVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWAFV +SVVTAFTVVRAVRLVPLAARGVAGLLGAGAPS +>GCF_020097155_PROKKA_00432 +MSTPPAALALFLPRGPPAGPR--GCGDAAWLALTHGQSPVGVRHLPAELQLLGAVTTAGA +AMISDWDYPRA-------------------------------------TAIATAAASIHV +PIAGHVYTPGQGVIAAFVAAVAAKALRLLPNRGWRAAWPLGILVAVSATVFSDGLRWIPV +SVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALV +SVVTAFTVVRAVRLVPLAARG-AALF------ +>GCF_023573625_PROKKA_02185 +M----------------MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGA +AMISDWDHPRATVVHALPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQV +PIAGHVYTPGQGVIAAFLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPA +SVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALV +SVVTAFTVVRAVRLLPLAARGVAALF------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001731.fa new file mode 100644 index 0000000000000000000000000000000000000000..cc661ca1cace6d25bd20495e7e8de89751671c36 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001731.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02255 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>GCF_003691675_PROKKA_01955 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>GCF_005280335_PROKKA_00476 +MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM +VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>GCF_020097155_PROKKA_00431 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM +VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>GCF_023573625_PROKKA_02186 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001732.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab50cc445d0ce95bd6df2d8c3f80f36fd8c530de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001732.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02256 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ +HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTD-KEDA +Q +>GCF_003691675_PROKKA_01956 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ +HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTD-KEDA +Q +>GCF_005280335_PROKKA_00475 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ +HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA +Q +>GCF_020097155_PROKKA_00430 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ +HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA +Q +>GCF_023573625_PROKKA_02187 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ +HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTD-KEDA +Q + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001733.fa new file mode 100644 index 0000000000000000000000000000000000000000..91bcc3879083e0a2d5734f39bd441557701bd14e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001733.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02257 +MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSG-VVPGLPPVGPSEA +GEPR +>GCF_003691675_PROKKA_01957 +MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSG-VVPGLPPVGPSEA +GEPR +>GCF_005280335_PROKKA_00474 +MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVRLSTEAGISRT +PAREALLQLESWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGCAADAQRALQAHLDAAGTGVVVPGLPTVSQPEA +GEPR +>GCF_020097155_PROKKA_00429 +MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTDAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIAMCGNAAFDEIMGTFAPRLARLIH +AATGGSVDAARRLLDGHVQICAQLAAGRAADAQRALQAHLDAAGAGVVVPGLLPVGSSEA +GEPR +>GCF_023573625_PROKKA_02188 +MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSG-VVPGLPPVGPSEA +GEPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001734.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e38b394f7c44667789bf2e12b29e6f9f4fe4ac2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001734.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_02268 +MPTLRTVPLSAATREDHLARLRATSPEAPLDILVVGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR +YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAA +TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI +LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA +TTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED +VVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA +PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKNLVAARLRGETA +HDDVTAAAALAAADADA--APT-----------P------- +>GCF_003691675_PROKKA_01961 +MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR +YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAA +TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI +LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA +TTADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED +VVDFVVRETHPTRPSLTEHIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDGDPSLSVPLAEA +PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKNLVAARLRGETA +HDDVTAAAALAAADA----APVHGKEPVHGHDLPA------ +>GCF_005280335_PROKKA_00462 +----------------------------------MGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR +YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMSAHRHLSRRSMAA +TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI +LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA +ATADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED +VVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA +PRYLRAEIVHAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKSLVAARLRGETA +HDDVTAAAALAAADA----ASTH------------------ +>GCF_020097155_PROKKA_00493 +MPTLRTVELSPATRADHLARLRAADADHPLDVLVVGGGSAGVGAAFDAATRGLDVGIVDAGDWAGGTSSRSSRLMHGGLR +YLEMLDVKLVYEALRERDLLLTRTAPHVVRPLRFVFPLEH-ARDRGWIGAGVGVYDAMQSVGRRRAVGGHRHLGRKALAE +TFPGLDPEAAVGAVEYADAQFDDARLALLLVRSAVDLGAAALNHAPVVGYLKDGAGAVVGARVRESLTGEELQVHARAVI +LAGGVWTQEQQELAGVDGGLEVLASKGVHVTVPRERIAAEPGVGVITRTEKSVLFVIPSDEHWIIGTTDTPWRQDVDHPA +ATAADVDYVLEHANAVLSEDLTRADVVAVYAGLRPLLQPAAGADDASTKVSREHTVTELAPGLTAVAGGKWTTYRAMAED +TVDFAVRDLFPTRPSLTAHTPVLGGLGYAEIAARAAEIAAERGFDAARVDRLLRRYGTLLPHVLALVDADPALGEPLPGG +EAYLRAEVVYAARAEGAVHLDDVLERRLRLSTEVPDRGADAASEAAALVADVLGWDAARRDAEVAAYRALVAARRRAEGL +DDDAAAAAELAAAGERAGVVPVTSRETVT----PEEKGGAR +>GCF_023573625_PROKKA_02200 +MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR +YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAA +TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI +LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA +TTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED +VVDFVVRETHPTRPSLTEHIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA +PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIADEIRAYKNLVAARLRGETA +HDDVTAAAALAAADA----APT-----------P------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001737.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a72b43e887a960832a1eee694e075b1b88a3ed0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001737.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02285 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRRLPATPIL-ASVAEEAPAPEAPADDA +>GCF_003691675_PROKKA_01976 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPIL-ASVAEEAPAPEAPADDA +>GCF_005280335_PROKKA_00452 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPIL-ASVAEEAPAPEAPADDA +>GCF_020097155_PROKKA_00405 +MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM +GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR +LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD +RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES +>GCF_023573625_PROKKA_02224 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPIL-ASVAEEAPAPEAPADDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001741.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff2b3cc20692c25e65108764f7d0f0d9cda5c17a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001741.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02290 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>GCF_003691675_PROKKA_01982 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>GCF_005280335_PROKKA_00448 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>GCF_020097155_PROKKA_00400 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AIKNAREVALLPYAGAGRG +>GCF_023573625_PROKKA_02230 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001742.fa new file mode 100644 index 0000000000000000000000000000000000000000..5cbe7d09ff1fc18e76b85b1f83bd086d81858dbf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001742.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02291 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA +QR-GGGGGGGFGGGQQGGGFGGAPAGGGFGGNSDGGFGGAQQGGGWGGQQQGGGQAAP-Q +DPWS-GGGGGGWDTPSSNEPPF +>GCF_003691675_PROKKA_01983 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA +QR-GGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAP-Q +DPWS-GGGGGGWDTPSSNEPPF +>GCF_005280335_PROKKA_00447 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLKARSYDDRDGNRRTSWELDVDEVGPALKFATAKVTRA +QRSGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAPQGGGWGGQQQGGGQAAP-Q +DPWSGGGGGGGWDTPSSNEPPF +>GCF_020097155_PROKKA_00399 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDEEALFVRCSVW +REAAENVAESLTKGMRVIVQGRLKANSYQDREGNKRTSWELQVDEVGPALKFATAKVTRS +QR-GGGGGGGFGGGQQGGGFGGSPQGG-------GGFGGGQQQSGGWGQPSGGGQSAPAQ +DPWS-GSGGGGWDTPSNGEPPF +>GCF_023573625_PROKKA_02231 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA +QR-GGGGGGGFGGGQQGGGVGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAP-Q +DPWS-GGGGGGWDTPSSNEPPF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001743.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001743.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bc540c9bfee6c382c507018d1be15e2bd6726ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001743.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02292 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>GCF_003691675_PROKKA_01984 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>GCF_005280335_PROKKA_00446 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDKVDVWGRRKTAYEIQKKSEAIY +VVVDFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>GCF_020097155_PROKKA_00398 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVEKIDVWGRRKTAYEIQKKSEAIY +VVVDFTAEPAATQELDRVLNLNETILRTKIIRPEEQKISAE +>GCF_023573625_PROKKA_02232 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001745.fa new file mode 100644 index 0000000000000000000000000000000000000000..3b05784d858b84804c9026c3e5d611ec326aa158 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001745.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02294 +M--DIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGD----AA-RTP---AHDDGAARPAH +PG-AAADPATDPHVIWREQMKAATAASGAPCVCPP-----PPRE--GGAAEAGT------ +----------SAPPSSPDCPIHRWDYA +>GCF_003691675_PROKKA_01987 +M--DIMIAVAVGVFLLVAWTVGGWAIVRLGFTRDGD----AA-RAP---AHDDGAARPAH +RG-PAADPATDPHVIWREQMKAATAASGAQCVC-P-----PPRE--GGAAEAGT------ +----------SAPPSSPDCPIHRWDYA +>GCF_005280335_PROKKA_00442 +M--EIMIVVAVGVFLMVAWTVGGWVIVRMGFTRDSD----AASRAG---SQDDDGTRPVP +DGPVPVDPASDPNAIWREQMKAATAASGAACTC-PRRPVGTPSESPAGSGEQGAAVDSAV +DRALDPAADHAAVDPSPDCPIHRWDYA +>GCF_020097155_PROKKA_00395 +MPNEVLLVAGVGAALFVLWAVGGWLIVRMGFTRDRDRLPDGPGHAS---ALPDGDGAPSP +GR-LPADPAQDPHAAWREQMKAATVASGARCTC----------E--DGAV---------- +--------------PDPDCPVHRWDYA +>GCF_023573625_PROKKA_02235 +M--DIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGD----AA-RTPAHDAHDDGAARPAH +PG-AAADPATDPHVIWREQMKAATAASGAQCVC-P-----PPRE--GGAAEAGT------ +----------STPPSSPDCPIHRWDYA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001747.fa new file mode 100644 index 0000000000000000000000000000000000000000..2fe764d74f1e7ca2a0b9c6e5f7ca1877c723c32e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001747.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02296 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV +AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R +>GCF_003691675_PROKKA_01989 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV +AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R +>GCF_005280335_PROKKA_00440 +MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV +DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV +AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE +R +>GCF_020097155_PROKKA_00393 +MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV +VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE +R +>GCF_023573625_PROKKA_02237 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV +AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001748.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e7a78da1bf6bc87c49d4398902adb132e5f925c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001748.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_02299 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEITEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +Q--------QD +>GCF_003691675_PROKKA_01992 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRTSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEEAMAAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYNHLLEWRLDEGPHEQAEAEAELRRWWAEQPEA +Q--------QD +>GCF_005280335_PROKKA_00437 +MDLTTATLALPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRVSGDLDFT +TDAGPDAAEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEEDLLRRDFTVNAMALRLPGLELVDPYGGVQDLAAGVLRTPGAPEDSFSDDPLRMLR +AARFASQLGFTVADEVEAAMTAMAERIGIISAERVREELVKLVCGAHPRRGLDLLVRTGL +AEHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEAEYSPSAPDPVLRLAALLHDV +GKPATRRFEKGGAVSFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGEA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNKRKAERLAHAYDDLERRIAEIAEQEEL +AAVRPDLDGEQIMALLGIRPGPVVGRAYRHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +A--------EG +>GCF_020097155_PROKKA_00390 +MEPRTDTRPLPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLLLGRPVVDLDFT +TDADPDATERIGAGWAEAAWDVGRHFGTIGFQKGGWQLEVTTYRAEQYDPTSRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPAMELVDPHGGVRDLAAGVLRTPGAPEDSFSDDPLRMMR +AARFASQLGFGVADEVEAAMTDMAERIGIISAERVRDELVKLVRGDRPRAGLDLLVRTGL +AQIVLPELPALQLETDEHHRHKDVYAHSLQVLEQAMGEEERYSPERPDVVLRLAALLHDV +GKPATRRFEPSGAVSFRHHENVGAKLVRRRLKALRFDNDTIKAVARLVELHMRFYGYGEA +GWTDSAVRRYVHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIEEISAAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYAHLLEWRLDEGPHEQAAAEAELRRWWAEQPEA +AGASSGGGARD +>GCF_023573625_PROKKA_02240 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +Q--------QD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001749.fa new file mode 100644 index 0000000000000000000000000000000000000000..dd67d4d86955120e5087b461907b66c0a42de24f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001749.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_02301 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------DPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLS-ADMADIFEIAN +SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLMTALTRGWSPEKLEMATV +FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIGAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLG +VVLQAVILFLPLRGLGLGLRPRFGWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSA +EMAQAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFTVPLMFCLAGVVVLAGPL +GRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMAL +WVAVASSVSYVYQFVLTHVLTVRRFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAVA +AVAMGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG +>GCF_003691675_PROKKA_01994 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------DPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLS-ADMADIFEIAN +SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLMTALTRGWSPEKLEMATV +FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIGAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLG +VVLQAVILFLPLRGLGLGLRPRFGWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSA +EMAQAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFTVPLMFCLAGVVVLAGPL +GRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMAL +WVAVASSVSYVYQFVLTHVLTVRRFGDYGLASVLRAHVQTGLAALAAAAAGVVVVWLLGGYTGGFAWNSIGTALLTCAVA +AVAMGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG +>GCF_005280335_PROKKA_00436 +MASPDPSAHRGAPLPSALGAWHRRPQPPARPEPAPAPGPRPAASGLPTVEEVSAGGVVVREHDGGLEVAIIARYNRGGRL +EWCLPKGHPEGVEDHRQAAVREVEEETGIAGDILEPLGAIDYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDV +AWVRLEDVARRLSFANERRIVDLARQVVDRHFPRAPPGAPAPDPPPRTRGSSDHDWVTLEQQPLPAPRAGTPPAPAVADE +EPTTADPA----PATDPEAPAREDRPDETPEGERRAGRSTAIMASGTLISRVLGLVRAMLVTVAIGLS-TDMADIFEIAN +SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLGGTLVVMAVAAPLMTALTRGWSPEKLEMATV +FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIAAIGLYLAMFGAYRAGEDVAGWTSTQTLVLAGGHTLG +VILQAVILFLPLRGLGLGMRPRFGWKGIGLRETGRIAGYTLVTMMVTNVVLLLCQRYVTSATEARDRGELRIPGTEAWST +EMAQAAIPGVAAYNMAMLIAVLPHSVFVLSLATVLFNRLARAMTRQDMPAVRRTTAQGLRAFTVPLMFSLAGIVVLAGPL +GRVFGSTAETSMVAGIAVGAVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSSSLLMLLLSWAGAMLLPLWSMAL +WVAIASSVSYVYQFALTHVLTVRRFGDYGFASVLRAHGQTGLAALAAAAAGAVVVWLLGGYTGGFAWETIVTALITCAVA +AAVMAPVYVVTLKLLRFPELDDALRPVVSRVPALGRLLRVG +>GCF_020097155_PROKKA_00388 +MSS----------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------RT-----------------APRRALP-----ADD +APRPKEVEDVVLPASDPEAPAQAQ--EEVPEGERRAGRSTAIMAAGTMISRVLGFVRAALLTIAIGTTVGTVADIFEVAN +SLPNVIYLLLVGGVFNVVLVPQLIKHAKDADRGADYTSRLMTLAVLVMLAATVLVTAAAAPLMAALTRGWSPEMLQLGTV +FALWCLPQMFFYGMYALVGQILNANGRFGAYMWAPVLNNVVAIAAIGLYLVMFGRYSGGDLLGRWTPEQTLVLAGGHTLG +VILQALILFLPLRGLGLGLRPRFGWRGMGLRHTGRIAGYTLFTMAASNIVLLLSHRYINGASAAREDPSVRVPGTEGWDP +AMADALIPGLTAYNQAMLISVLPHSVFVLSLATVLFNKLARSMAAGDHAAVRETTARGLRTFAAPIMFSLAGVVVLAGPL +GRLFGSTAESAQVTGMAVGAVILLMSLSMPFRSGSFYLLRVFYAAESARIPMVVQVTTSLLTLAVTAAGAYLLPLWAITY +WAALASVVSHAFQFFFAHVLAVRRFGDYGFTHVLAAYATTGAAGVVAGAAGAVVAWLLGAYSGGWAWGSILSALVTCAVV +GLVMAPVYVVALRVLRFPELASAAAPLARRVPALGRLLGAR +>GCF_023573625_PROKKA_02242 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------DPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLS-ADMADIFEIAN +SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLMTALTRGWSPEKLEMATV +FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIGAIVLYLGMFGAYRAGDDLAGWTTAQTVVLAGGHTLG +VVLQAVILFLPLRGLGLGLRPRFGWKGIGLRDTGRIAGYTLVTMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSA +EMAQAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFTVPLMFCLAGVVVLAGPL +GRVFGSTAETAMVAGIAVGSVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMAL +WVAFASSVSYVYQFVLTHVLTVRRFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAAA +AVAMGPVYLVVLRAMRFPELDDALRPLVARVPALGRLLRVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001750.fa new file mode 100644 index 0000000000000000000000000000000000000000..4fe9b8275518e2ff6b671a17ef2de158a7fd05cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001750.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_02302 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSARELATGERTDDVQVLDLGLSE +GRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELFGESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLN +RLSERLAERVRPSDGTAAKAAAGASALAAADAATRKQQEERERAEREAAERAERERKEAAERAERERKEAAERAERERKE +AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAER +RELERRAEARRRAEEERAREAAEREAEKRAAQEREAA----------EREAQAGTAALPAVAAGAAAAQAPDADADGATP +---PTEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI--VAESA------PTAHEESRGTAAP--------VAAG +AGVATAAGA-AAAGS--------TAAAAAPDAQAAPATTGGGDGATVADPGDGHGRTRGGGPLALLLVLGLLAALVVGGV +----LLAQNLRG-GPAPQAASSE--------------------SESASSESASDTPSPSESTSPS----------PTPSS +ESAA----AAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTL +QSTGATGGAWFAYIADSPEG--ANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEI +AVR +>GCF_003691675_PROKKA_01995 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSARELATGERNDDVQVLDLGLSE +GRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELFGESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLN +RLSERLAERVRPSDGTAAKAAAGASALAAADAATRKQQEERERAER----------------------EAAERAERERKE +AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAER +RELERRAEARRRAEEERAREAERREAEKREAQEREAAEREAQEREAAEREAQAGTAALPAVAAGAAAAQATDADADGATP +PTEPVEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI--VAESA------PPVHEESRSTAAP--------VAAG +T--ATGATA-AAAGS--------TSAAAAPDALAAPATTGGDDGATVADPGDGNGRTRGGGPLALLLVLGLLAALVVGGV +----LLAQNLRG-GPAPQAAAAS--------------------SESASSESASDTPSPSESTSPS----------PTPTS +ESAA----AAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTL +QSTGATGGAWFAYIADSPEG--ANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEI +AVR +>GCF_005280335_PROKKA_00435 +MA------------------------------------------------------------------------------ +---------------------------------------------------------------------------PG--- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------------------AA----------ETDTVETRADEPAAAEPESTATAPAEDVDP--- +--EPTAPAPVVPAS-TAPDS--APDTEAIPVRRQRPVPRRAM--VVEPTTPDADRSPDAQRSRGAGAPLAAAGAGAVAAA +G--ATAASA-AAAGAAPSATSAPSTASAAPEATAAGTSPADGDGGAPVDPDQGGSR-RGGWPLALLLLAVLVGALVLGGV +----LLAQNLRG-APHRAGRPARLPHRDRRGARTRRQPPPTQSDEASPTEASPTESSPAASTSAS----------PT-ES +ETAA----AAPQPARALRMVPDLPAHESEHDGELPNLIDGDPSTAWRTFAYARPNFGGYVESMNLVVELEDRAEVNEVTL +QSTGATGGAWFAYIADSPEG--ENAREIGNGTFDQDSVTVPVPFDGAEAEAEYVIVSLTSLPRLDGTTPDLPFGLRLGEI +GVR +>GCF_020097155_PROKKA_00387 +MPQPLAVGSVLGGRYRITDHVVTSADQNMVFQGADQVLNRRVTVLVASPENATQVAASARELATGERQDDVQVLDLGLSE +GRTYLIAGGNPDPDVLLGLAYAQELYVEPFQTDSLGSEIFGESRTEQAHEYDDDDAYYADLDRRLRADQKQSQRRPGFLN +RISEKLNERVRPADGTAAKAAAGASALAAADAATKAQLAEQERAER----------------------EAREAQE----- +-----RAEREEAQEAERREREAQERAERERLE----------------RAAAAQAEKDRAARE--------AAEAEAAAR +RE----------------REAQR------------HA----------EAET--RRREEEAAAAAALAAAAPAADADPADA +------PTQAVPV--TEPAS--TPEAVPAPVRRPRPAPRRALPAVASAAAVAASVSAEEGASAAEAAPAESVAPEAVPTA +T--ATSSAAIAVAEAEPAVTEHRE------EAHAAPVAGGAGAGAPAAGATAAPARSTSGK--GWLMVLGLLALLALAGL +AGLFLLGQNTRSVEPAPSASASS--------------------AAPSTAQASSAPPAASSSAAPTASSSAAPSTEPAPST +SAAAPAPTAAPQAVAVTRQVPEMPELEAPNDATLANLIDGDPNTAWQSYTYARPNFGGYVGSMNLVVQLQERTTISEVQL +ENRGATGGKWIAYVANTAQGGEGDARVIGQGTFDEDSITIPVDI--AENQGQYVILSITGLPQLEG-AGQRPYGLQLTEI +GVR +>GCF_023573625_PROKKA_02243 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSARELATGERTDDVQVLDLGLSE +GRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELFGESRTQDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLN +RLSERLAERVRPSDGTAAKAAAGASALAAADAATRKQQEERERAER----------------------EAAERAERERKE +AEERARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEDRAAREREAEQARLAAEREEAER +RELERRTEARRRAEEERAREAERREAEKRAAQEREAAEREAE-----KREAQAGTAALPAVAAGAAAAQTTDADADGATP +PVEPVEPVEPVAAEKTDAPEPVAPDTEAIPVRRQRPVPRRAI--VAESA------PPVHEESRSTAAP--------VAAG +A--ATGATA-AAAGS--------TSAAAAPDALAAPATTEGDDGATVADPGDGNGRTRGGGPLALLLVLGLLAALVVGGV +----LLAQNLRG-GPAPQAAAAS------------------SESESASSESASDTPSPSESTSPS----------PTPTS +ESAA----AAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTL +QSTGATGGAWFAYIADSPEG--ANAQEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEI +AVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001751.fa new file mode 100644 index 0000000000000000000000000000000000000000..24a10aa5de307a3b8d67a46d8c30dbe7abf679d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001751.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02304 +MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD +ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG +>GCF_003691675_PROKKA_01997 +MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD +ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG +>GCF_005280335_PROKKA_00433 +MSTINVTDTDFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLDEMAVEHEGKAVIAKLNVD +ENPATAARFGVTSIPLVLGFQGGEKVAESVGAKPKAALEKEFSALLG +>GCF_020097155_PROKKA_00385 +MSTINVTDADFQAKVLDSELPVLVDFWAEWCGPCRMLGPVLDELAAEHEGEVLVAKLNVD +ENPASAARYGVTSIPLVLGFQGGEKVAESVGAKPKAQLEKEFAALLG +>GCF_023573625_PROKKA_02245 +MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD +ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001753.fa new file mode 100644 index 0000000000000000000000000000000000000000..e43efb99c73b234918f54eda81652c9705084af2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001753.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02307 +MTERGSAYERRPGLDPQDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVAARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSAR- +PR +>GCF_003691675_PROKKA_02000 +MTEQGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSAR- +PR +>GCF_005280335_PROKKA_00429 +MPEQASPYERRPGLDPKERGDRPAPVGQPAPPLIDALRPAAVELFGEDLPRAERYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELIPEGALVADVGSGAGLPGLCLALARPDCR +FLLIEPLERRVEWLDMVVEDLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGDGQLLAIKGRAAADEIAAARKVLRKYGGDEPEILTVGEGLLPETTTVVRVSAR- +AR +>GCF_020097155_PROKKA_00382 +---------------------------MSAPQLTAELRPAAEDLFGEALPLAERYVDHLA +TTGIEWGLLGPREVPRLWGRHVLNCAVVARLLPEGSLVADVGSGAGLPGLCLALARPDCR +FTLIEPLERRVAWLEMVIADLGLTNVEVVRGRSEQVADEIQVDIVTARAVSALKTLLPLT +MPLLRSSGHLLAIKGRSAAEEITAAQKPLRKYGGGDPEIVTVGEGLLPEPTTVVRVPARR +AR +>GCF_023573625_PROKKA_02248 +MTERGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSAR- +PR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001754.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f7812fd66e12bac98fefc748be37c5eb6d84b93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001754.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02308 +MSAENVTPAPEAEDAVVET------PAGQGSRVAEQDGAAV--------------SEAVR +RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVV--SEDHDERLDGLVGPDGRT +LEALQELVRLAVLAATGHRSRLILDVCGHRERRNVALRTAAQAAVERVRVGEGPVHLEPM +GAYERKIVHDVVADAGLTSESEGEGARRHVVISADD +>GCF_003691675_PROKKA_02001 +MSAENVTPASEAEDAVVET------PVGQGSRVAEQDGAAV--------------SEAVR +RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVV--SEDHDERLDGLVGPDGRT +LEALQELVRLAVLAATGHRSRLILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPM +GAYERKIVHDVVADAGLTSESEGEGARRHVVISADD +>GCF_005280335_PROKKA_00428 +MSAENVNPAAEAEDAVVETTPAPDAPQAPAAEERTGSDAAVAAGEGAESSAAESASDGVR +RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVV--SEDHDERLNALVGRDGKT +LEALQELVRLAVLAATGHRSRLILDICGHRERRDADLRETAQDAVERVRAGEGPVHLSPM +GAYERKIVHDVVADAGLASASEGEGARRHVVISADA +>GCF_020097155_PROKKA_00381 +MTAEHEGPLADA---------AEDSPAVEAPVEATAPDAAV-----------DEQAEAVR +RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVVPGEDDEDDRLADLVGPDGKA +LEALQELVRLAVLTATGHRSRLILDIAGHRRRRDAELRTLAGEAVERVRSGAGEVHLDPM +GAYERKIVHDVVAEAGLASESEGEGPRRHVVISG-- +>GCF_023573625_PROKKA_02249 +MSAENVTPAPEAEDAVVET------PAGQGSRVAEQDDAAV--------------SEAVR +RLEQEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVV--SEDHDERLDGLVGPDGRT +LEALQELVRLAVLAATGHRSRLILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPM +GAYERKIVHDVVADAGLTSESEGEGARRHVVISADD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001757.fa new file mode 100644 index 0000000000000000000000000000000000000000..3aa83da94c52896f9933515314609b934cd0d12d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001757.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02311 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTPPSAP-RPRAGFVVSKA +VGNAVTRNRVRRRLRAVVADQMRTAPLRELPVLVQVRALPAAAEADFALLRRETVGALGK +ALKPHLPAASE-HA +>GCF_003691675_PROKKA_02004 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAP-RPRAGFVVSKA +VGNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGK +ALKPHLPAASE-HA +>GCF_005280335_PROKKA_00425 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDHTRSTSPSVP-RPRAGFVVSKA +VGNAVTRNRVKRRLRAVVAEQMRAAPLRELPVLVQVRALPPAAEADHALLRRETVGALAK +ALRPHLPAVPRDEA +>GCF_020097155_PROKKA_00378 +MLPRDRRVRTPEEFRRIRRTGSRAGRSTVVVSVAADTDPARPGATSQPRRPRAGFVVSKA +VGNSVVRHRVTRRLRALLRAELDSPALRDRALLIQVKALPAAVDADHATLRRDVHGALGA +AVR-KLDQADR-SR +>GCF_023573625_PROKKA_02252 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAP-RPRAGFVVSKA +VGNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGK +ALKPHLPAASE-HA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001762.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001762.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e0ad02976a77324ed7092dad79736df29d805e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001762.fa @@ -0,0 +1,31 @@ +>GCF_003691675_PROKKA_01858 +----MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVS +VLLHSRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMI--R +PKKTQPAAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIIGAGGGFLVVPALVLLGGL +PMSAAVGTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGGLIGVPLVKRVPEKA +LKKGFGWFVLAMGLVILVREL----------IGLLV------------------------ +>GCF_005280335_PROKKA_00616 +M---AWLAVVLAVAVGLLLGLMGGGGSILMVPLLTYVAGLDPKEAIAGSLFVVGVTSLVS +VGLHARAGNVRWRTGLVFGLAGMVGAALGGVVGGFLPGTVLLIAFAVMMLVTAWAMI--R +PKR--PTAAPAEGGHA---PGR-ALGRIVLDGVVVGFVTGIVGAGGGFLVVPALVLLAGL +PMSAAVGTSLLVIALKSFAGLGGYLTSVTLDWPFLLAVTGVAVLGALIGAALVNRVPDKA +LEKGFGWFVLAMGVVMLVTEL----------VGLLA------------------------ +>GCF_005280335_PROKKA_02658 +MSGTLILTLVLAVGVGLALGTLGGGGSILTVPLLTYIAGMPPKEAIAASLLIVGVTSLSS +LVVHARHRRVRWRTGLIFGAAGMVGAFAGGLIGGQLPGAVLMVAFAIMMIATAIAMVTRK +PRR--DTDQPTADAGTE-RAHSLPMLRTMLEGIVVGLITGIVGAGGGFLVVPALVLLGGL +SMPVAVGTSLLVIAMKSFAGLAGYLTTVTLDWPLVAAVTAMAVLGALLGARLSGRIPADA +LQKVFGVFVLLTGTLVLVIELPPAWAIAAGGLGLITVVLVLVCRLTALNCPFGLARPTPG +>GCF_020097155_PROKKA_00540 +MV-PLALLVVLAAVVGLLLGLMGGGGSILTVPLLTLTAGMDPQEAIAGSLVMVGASSLVA +ALVHATRGAVAWRTGLTFGAASMVGALAGGFVGRDLPGPVLMVGFAVIMLISAVKMI--R +PRRK--------GAGHD-DAAPVPLGRVLLQGVGVGLITGVVGAGGGFLIVPALVLLARL +PMPVAVGTSLLVIAMNSAMGLVSQLGATALDWAVLGPMAAAAAAAGVVGVVLAHRVPAAA +LKRGFGWFVLAMGVLILAQQA----------LELLP------------------------ +>GCF_023573625_PROKKA_02088 +----MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVS +VLLHSRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMI--R +PKKTQPAAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIVGAGGGFLVVPALVLLGGL +PMSAAVGTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGALIGVPLMKRVPEKA +LKKGFGWFVLAMGLVILVREL----------IGLLV------------------------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001764.fa new file mode 100644 index 0000000000000000000000000000000000000000..55294af0cc87dda34f1594ecfef87cd0612bb88e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001764.fa @@ -0,0 +1,41 @@ +>GCF_003691675_PROKKA_02133 +M-------------------------------------LRLIGKRLLLLIPTLFGLSVLL +FVWVRSLPGGPATALLGDRA------TPEAVARVNAAYGFDKPLLEQYVTYMGRLLRGDF +GTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWAARHVGRWQDDVAVVLSL +IGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNFYVWDGIITAEWDAALNA +LTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKGLAPRLIRDRFIMRNALL +PVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFPVLQGFIIFIALLYSLIN +LVVDVSYGLIDPRVRVS--- +>GCF_005280335_PROKKA_00090 +MTALASRPGAASRASRSAPVSPASRSTRRTHRRRTLVGAGTVLRRLAGAVGVVWATATLT +FLMQFLLPGDRATLVFNLRAGQAQPRTAEELAPLNALFGFQDPVLVQYLHFLGGLLRGDL +GTSYVTFEPVTTVIGDQLAPTLLLTGASIAIAWAVALVL-LVATVRRARWVSGLASAVEA +LLAALPHYWLGVILLVVFALGLGLFPVVGG----------------------------TG +PAALVLPALTMGLPLAGYLAQTMRSEYASVLDQPFILTARTRGQSDAGIRVRHALRHALL +PGLSLTGWAVGAQFSAAVIAEGVFSRPGIGGVLVDAANGRDLPVVCGVVVLIAIVYVLAN +LAVDVLYTVVDPRLRSAR-- +>GCF_005280335_PROKKA_00267 +M-------------------------------------LRLIGKRLLLLIPTLFGLSVLL +FLWVRSLPGGPATALLGDRA------TPEAVARVNAAYGFDKPLLEQYTTYMGRLLRGDF +GTSTMTNRPVLEEFADRFPATLELSLFAIVFAVAIGIPLGYWAARHVGRWQDNIAVVLSL +IGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRLDATHYTNFYVWDGISTGEWDAALNA +LTHLVLPGIALGTIPLAIIARITRASVLDVQNADFVRTARAKGLAPRLIRDRFIMRNALL +PVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFPVLQGFIIFIALIYSLIN +LVVDVSYGLIDPRVRVS--- +>GCF_020097155_PROKKA_00135 +M-------------------------------------ARRILLRLALALAVLLGAYTAA +FLILYVMPGDPVTAMAAGGL-EAGAISDADLQALRAEHGLDRPLPVQYLSQLAAAVTGDL +GTSVQTGQPVTEAILDRLPTTLRLAWAALLVAVVAGPAIALVAAGTRRRWVRATASAIPA +LGAALPTFWTGLLLVQVFSFGLGWLPALGD----------------------------DG +LAGLVMPALTLGLPLSALIAQVMLRALDESGTQEYVETALASGQSRRRVLITHMLPNAAL +PTLAMLGVITGNVVAGAVVVETVFSRPGVGQLTVQAVTAQDLPVVLGVVLLSSLVFVLVT +LTVDLLSPLLDPRVGPAGAV +>GCF_023573625_PROKKA_00125 +M-------------------------------------LRLIGKRLLLLIPTLFGLSVLL +FVWVRSLPGGPATALLGDRA------TPEAVARVNAAYGFDKPLLEQYVTYMGRLLRGDF +GTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWAARHVGRWQDDVAVVLSL +IGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNFYVWDGIITAEWDAALNA +LTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKGLAPRLIRDRFIMRNALL +PVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFPVLQGFIIFIALLYSLIN +LVVDVSYGLIDPRVRVS--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001765.fa new file mode 100644 index 0000000000000000000000000000000000000000..cbbe5da8d5d5b6f6ab8728287afff8d7a6787565 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001765.fa @@ -0,0 +1,36 @@ +>GCF_003691675_PROKKA_02134 +M----SVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRN +PAAIAGAVIVLLFVLVAVLAP-VLA---PYAGTATPGMREIRPTHVPGPGEVAGYPLGLD +RFGGDVLSKLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSV +PNLLLAVSIAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRG +RITMSHVLPNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELG +INPWLAFLPGLCIAITALGFTLLGESLREALDPTSRRR +>GCF_005280335_PROKKA_00089 +MTAVLTSSQTPPP--------------PSDSSAAASPVSLV----------PATRRPRRA +DLGLAFALTGAAVLLVAALWPQLLATHDPRALDLAA------PLQAPSL----DHWFGTD +QNGRDLYSRIVHGTGPSLLIGLGAAAVGVGLGMLLGIVAAFGGRWADAAVSRTVEVLFAF +PSLLLALMLITVYGPSVSTLILAVGVGTAPGYARLVRGQVLAVRGSAYVQAAEVIGHPPM +TILLQHIVPNAVRPLVAVFMLGVGQAIVWASGLAFLGFGVAPP-SPEWGALLEAGRPYIT +AAWWLEIFPGLAVLATALTATALGRHLEARLQGET--R +>GCF_005280335_PROKKA_00266 +M----SVNLPPSPGSGPAEHAVDHALAPVEAGATQETTEAAADARGTSVWGAAFQRLRRN +PAAIAGAVIVALFVLVAVLAP-VLA---PYAGTDTPGMREIRPTHVPGPGEVDGYPLGLD +RFGGDVLSKLIWGAQASLIIGVVSTAFGLVGGMLLGLLAGTFGGWVDSVVMRTVDILLSV +PNLLLAVSIAAILGQTPFAVMIAIGVAQVPIFARLLRSSMLTQKGSDYVLAAQTLGLSRG +RITMSHVLPNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELG +INPWLAFLPGLCIAIAALGFTLLGESLREALDPTSRRR +>GCF_020097155_PROKKA_00136 +MTSAPAVAAEPTP------------------AASATPSDPA----------GARRRA-RP +RLGLLLSAGFLVVVLLAALFPSLLAPGDPFAGASGA------TLEPPGP----GHWLGTD +HLGRDLYTRVVHGTGLTVATAAAAVAGALVVGGTLGLASGYVGGVADTLLMRVVDVLLSI +PSLLLSLAVVAGLGFGPVQVAVAVGIGSVASFARIGRAQALRISQAPFVEAAPSFGTRRI +LVLLHHVVPNAVGPLVSLAVLEFGSALLAVSALSFLGYGEPRP-AAEWGGLISDGRSYLA +VAPWLTALPGLVIAATVLALQQVATSPAPADAP----R +>GCF_023573625_PROKKA_00126 +M----SVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRN +PAAIAGAVIVLLFVLVAVLAP-VLA---PYAGTATPGMREIRPTHVPGPGEVAGYPLGLD +RFGGDVLSKLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSV +PNLLLAVSIAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRG +RITMSHVLPNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELG +INPWLAFLPGLCIAITALGFTLLGESLREALDPTSRRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001766.fa new file mode 100644 index 0000000000000000000000000000000000000000..8404a7b696fdd418adf7e37f58296d7d0a0f3cc9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001766.fa @@ -0,0 +1,21 @@ +>GCF_003691675_PROKKA_02211 +MSLRLSHTTWDALDPHAIAEFWRALLGWEV-----DEPHLYRPGSDECSLVGPD-----G +QVVLFFRVPDAKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVD--DRRVDLGWAVLA +DPEGNEFCILDG--- +>GCF_005280335_PROKKA_00514 +MSLRLSHTTWDALDPHAVAEFWRELMGWEV-----TEPEAYELGSDECYLVTPH-----G +YTILFYRVPDAKRVKNRAHMDLAV-DDGTRDEEVERALGMGATMVD--DRRGDLGWAVLA +DPEGNEFCILDI--- +>GCF_005280335_PROKKA_00528 +MALKWYTLVVDCRDPQAQAHWWARALDWEVVHDTPEEAVAVPKGVGEEPVADPDEWRARG +QGLVFVPVPEGKTVKNRLHIDLAPHTSQDRDAEIARLEELGATRVDVGQDEEEVTWTVLA +DPEGNEFCVLSSRDS +>GCF_020097155_PROKKA_00455 +MSLRLSHTTWDALDPYAVAEFWRELMGWDV-----AEPDSYAPGSDECYLATAE-----G +YTVLFYRVPDAKRVKNRAHMDLMT-AGTTRDEEVERALGLGASMVD--DRRGDLGWAVLA +DPEGNEFCILDTGD- +>GCF_023573625_PROKKA_00218 +MSLRLSHTTWDALDPHAIAEFWRALLGWEV-----DEPHLYRPGSDECSLVGPD-----G +QVVLFFRVPDAKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVD--DRRVDLGWAVLA +DPEGNEFCILDG--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001772.fa new file mode 100644 index 0000000000000000000000000000000000000000..8d4f1f597a2c312cb8ae14fed16d4bd783dd618d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001772.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_00048 +MD-TSAPRTSPSTPPASAAHITPEGGSLRRTLKSRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALAAYVAIGFMVFLL +MQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELVAAALIMRYWLPDVPSWIWSATFLALLFGLN +ALSTRAYGESEFWFSLIKVATVVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGV +AAGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLVFENAGVLAAASVMNAVILT +AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVW +MGIAWSHYRFRRAYVAQGHDPKDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGH +KLVTGSKPVRYEDADLTRVLD +>GCF_003691675_PROKKA_02061 +MD-TSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALVAYVAIGFMVFLL +MQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLN +ALSTRAYGESEFWFSLIKVATVVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGV +AAGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLVFENAGVLAAASVMNAVILT +AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVW +MGIAWSHYRFRRAYVAQGHDPKDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGH +KLVTGSKPVRYEDADLTRVLD +>GCF_020097155_PROKKA_00296 +MNPTDSPRTAGPAGSTAAAASPEPHTGLKRTLAARHLMMIAMGGAIGTGLFVASGNSIATAGPGGALLAYVVIGFMVFLL +MQSLGEMATYLPVSGAFEEYATRFVSPSFGFAIGWNYWYNWAITVAAELVAAALVMRYWFPDVPSWAWSALFLALLFGLN +ALSTRAYGESEFWFSLIKVVTVVVFLVLGVLMIVGVLGDAAVGTDNWTTGEAPFVGGAPGILAIFLVAGFSFQGTELVGV +AAGEAEDPERTVPKAIRTVFWRILLFYVGAITVIGFLIPYTSPNLLGSDIEDIAISPFTLVFENAGVLAAAAVMNAVILT +AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALVVTTAVGALCFLTTFIGDGAAYVWLVSASGLAGFIVW +MGIAWSHYRFRKAYVAQGNDITDLPYRAALFPLGPIVALLLCTVVILGQNYEAFLNGVDLVAVASAYIGLPLFLALWIGH +KLVTGSKGVRPEEADLTRGRA +>GCF_023573625_PROKKA_00043 +MD-TSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALVAYVAIGFMVFLL +MQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLN +ALSTRAYGESEFWFSLIKVATVVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGV +AAGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLVFENAGVLAAASVMNAVILT +AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVW +MGIAWSHYRFRQAYVAQGHDPKDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGH +KLVTGSKPVRYEDADLTRVLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001779.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001779.fa new file mode 100644 index 0000000000000000000000000000000000000000..bfd0cd1aca58b6b1c1132e44b9417bc303da9cc1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001779.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00118 +-------MIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRT +SDGRGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAP-PAVYGGAGEQVLTLADLLAIA +AAADRPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRLGQVQVSLMSFHPDALRH +VAPLAGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGMAGP +SVAYVREHLADVKAWLAAGRRLRVWTVDEREDADSLLAQGVQELTTNRPEDVLRWVRERA +AARRERMPTGA-------- +>GCF_003691675_PROKKA_02131 +MPA---LVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRT +SDGRGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAP-PAAYGGAGEQVLTLADLLAIA +TAADRPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRH +VAPLAGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGP +SVAYVREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERA +AARRERVPTGA-------- +>GCF_020097155_PROKKA_00200 +MTGVLPLVIAHRGASAAFPEHTRAAMLHALAVGADGIECDVQLTRDRQVVLWHDPTVDRT +SDGRGPLADHTLAQLRALDVVSWHQGMGGDAPGDAAGRVPAVYGRRDEQVLTLADLLRMV +LAADRPLRLAVELKHPSPFGHELEERVLRELVAAGWDAETGLMGQVRVSLMSLHPGALQY +LAPLTGPDALCPLIDLVPDEIPSRLARGPLSRAAVRATVRQSLADAETMVWRGRAGLAGP +SVAYVRSHLADVKAWLASGRRLRVWTVDEREDALFLAAQGVQELTTNRPADVLRWVTQAA +TSASPGAISGRDMPSPAAR +>GCF_023573625_PROKKA_00123 +MPA---LVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRT +SDGRGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAP-PAAYGGAGEQVLTLADLLAIA +TAADRPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRH +VAPLAGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGP +SVAYVREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERA +AARRERVPTGA-------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001780.fa new file mode 100644 index 0000000000000000000000000000000000000000..3cf7f1b14b69b1e701b463c5e9f09b71dfcc567f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001780.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_00120 +----------------------MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVE +RIGVPGSGVPDHAAALEQVEAELAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAI +ERLAPLAPLHNPAAAQGLRAMAERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHG +IRRYGFHGTSDDLVTGLAAEHLGIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPL +AGLVMGTRSGDLDPSVVTHLMRNHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASG +DGRARNALDVASYRLAKYVGGYHVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAY +DAEANRARVA-----GPHTISAPESAIPVLVVPTDEEQAIARLTWELAR-------- +>GCF_005280335_PROKKA_00264 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------MLHLGNGASATAIRDGASVDTSMGFTPL +AGLVMGTRTGDLDPSVVTHLMRTQGHSAEEMDTLMNKESGLLGLAGHADMRQVVEAADAG +DRRARTAPDVASYRLAKYVGGYHVAVGGAQAIVFTAGIGENSAPFRARVVERLGALGVEL +DAAANEAGLSAAGDDGVAVISAPGSAIPVLVIPTDEEQAIARLTWELTR-------G +>GCF_020097155_PROKKA_00199 +MTASPATMTLPTVSARQLPEDALLVLVVNSGSSSLKYQVRELTPDGRDTDQPVVLKGLVE +RIGVAGSDVPDHAAALERVEAEITAVVGSRRLAAAGHRVVHGGERFQRPELVTNEVIRAI +ERLAPLAPLHNPAAAQGLRAVAQRWPDLPQVVVFDTSFHQSMPREAWQYAIPDELYTEHG +IRRYGFHGTSHDLVTGLAAEHLGLERSEFDGVVLHLGNGASATAIRGGRSIDTSMGYTPL +AGLVMGTRSGDLDPSIVTHLITAHGMSAEDVDAMLNKESGLLGLSGNADMRQVLEAAEAG +HRASRDALRIASYRLAKYVGGYHVAVGGAKAIVFTAGIGENSAPFRARVLDRLEPLGVRY +DHARNMVR-----GDEPRTISTDDSAIPVLVVPTDEEMAIAQLTHHVVEQAEAWTLG +>GCF_023573625_PROKKA_00128 +----------------------MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVE +RIGVPGSGVPDHAAALEQVEAELAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAI +ERLAPLAPLHNHAAAQGLRAMAERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHG +IRRYGFHGTSHDLVTGLAAEHLGIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPL +AGLVMGTRSGDLDPSVVTHLMRNHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASG +DGRARNALDVASYRLAKYVGGYHVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAY +EAEANRARVA-----GPHTISAPESAIPVLVVPTDEEQAIARLTWELAR-------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001784.fa new file mode 100644 index 0000000000000000000000000000000000000000..aab01c21c6f12be82e82ed9f416f7f45c73c2525 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001784.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00155 +--------MSGVGNEREWR------------------------WRIGVASPLVGSAGVFA +GLRQDLGLGWGLTLVAVTALGAMLALRGVHHRVEAEQARRNVFDAGAGSTAWVML-LMGA +AVIPGLVLNAIDDAGVRAVVAGLLGAVVEMQRRVHTTRGELFAYQAGSGRRENWVSRWAP +PRAPGIARNVGAVAALAGWLWRVMWRADRAGGSAHDAWRDPSPQTTDKGSGPSPSLAGAR +LSVWLAPLYGGVLSELSGGLQARGQEGAASEAHVPQADPSPGQRPTAGRRNRRRDRVHPA +QQNRCERSNTPTQQSGPPCAATGP +>GCF_003691675_PROKKA_02169 +--------MSRVGNEREWR------------------------WRIGVAPALVGSAGVFA +GLRQDLGLGWGLTLVAVTALGAMLALRGVHHRVEAEQARRNVFDAGAGSTAWVML-LMGA +AVIPGLVLNAIDDAGVRAVVAGLLGAVLAAAAHGILAA-------TTTLEEQ-------- +------------------------------------------------------------ +----------------------------------PRPEPVPLDR-------RRR------ +------------------------ +>GCF_020097155_PROKKA_01469 +MDAVAQNTGRRVGEPLTERSDAGTGHTAASQGRDGTLRGDAPAWRAAGVGAAFGLASVVC +SLQDHLAEWSAIGGAAAFMALGLLSMTGLRFVVDQEKARRTVFYAGERQGAWFLLNFLGI +FQIPRFLISGIADPTGLVLAAAGLGIVVAVANQALVSR-------YMTGRRQ-------- +------------------------------------------------------------ +----------------------------------PDPEPVPLG----------------- +------------------------ +>GCF_023573625_PROKKA_00168 +M--CQHGAVSRVGNEREWR------------------------WRIGVASALVGSAGVFA +GLRQDLGLGWGLTLVASTALGAMLALRGVHHRVEAERARRNVFYAGAGSTAWVML-LMGA +AVIPGLVLNVIDDAGVRAVGAGVLGATLAAAAHGILAA-------TTTLEEQ-------- +------------------------------------------------------------ +----------------------------------PRPEPVPLDR-------RRR------ +------------------------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001787.fa new file mode 100644 index 0000000000000000000000000000000000000000..b52714299176c4be217ef9b70cece6f202a0e707 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001787.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00200 +MKTPARLAVGM------LAASGLLLTGCASDPT-LDESWPEIRQKVVDAESLRLRVEGTA +A---------DKEEEKDDASASAAPSASL----------------------GTDASQSLN +VDLAGATDDSHLKGTMNMDMGAATMDIEVLRRDADVFFKL-KADGDDLPQEMGMFSTLVG +DRWI-----KTSADQAAQM-DISLQEIMSDLEEDMPAADAFDGKDLKAEEVELEGRTYLK +YALPEEHHEFGRTMLIDPESTTLYRLEDVNSEDEDVDANATFTEWNAVEAPEAPAKEDVF +DLAEL-QELA-----------------G +>GCF_005280335_PROKKA_00189 +MKSSLLTATGLPRAAAVLAAAGLLLTGCAADPT-LDENWPEIRQKVVDAQSLRLQMDGEA +AP--------DAEGSGQDSEITAAAA---------------------------------- +-DLSGATDDSHLKGTMDMDMGADSVDMEILRLGEEVFLKM-AADGDGVPAEMAMFEQLVG +DRWM-----LMPADEADSMAGISLKEIMDDLEADMPAAEAFDGKDLKAEKVELDGQEYLK +YALPEEFHDFARTMYVHPDDETLHRLEGTGGEDAEADTTATFSEWNAVQAPERPAEDQIV +DMAAL-QGLT-----------------G +>GCF_020097155_PROKKA_00125 +M-TPRLSRASL---TALLGAGALALSACGGDPAPAASSSAEAASSSAAGPTVSTSPNGSD +AAASSSSESAASESSASDVPAGQAPEAEVVWKDIQQGLDEAESVHILAEIDGGSGSEVQR +VDLAGDVAGTTVQGSVTGDSADFTGTMDFIHVGGQTYLKM-DGSGGGDASRMA---EALD +GRWLVDTQGMIPVD------EMNPQVFLDEMKQEFSTVTDAELAAMEGEVVQVDGEEMYR +YS-----DDSSWTMTVDKDN----HVREFRDTKSSGEGTVTMDRWNQVTPAAAPPAAEQV +TMDELSQEIASSGAGSSAGATASATVDG +>GCF_020097155_PROKKA_00145 +MKSPKIAAAAL------LATGGLLLSACATQPT-LEESWPEVRQKVVDAQSLHLKMDGTA +K---------------EDASGSASASSS-------------------------SDIQSGT +IDLAGATDDSHLKGTVAAKMGDGEVNMDILRLGQDVYMRINKAEGGQAPEGMDAFQQIVG +DRWM-----LMPADQASGMGELSLGTVMDDLEEDMPAADAFNGKDVKAEEVDLDGRKVLK +YALPEEHKDFGRTMYVDKETKELYRLEDVNSVESEADATATFTEWNAVQAPERPAEDEVF +DMQKLSEGLA-----------------G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001789.fa new file mode 100644 index 0000000000000000000000000000000000000000..76d15cc0f6d85fdcd8727b2a38ea69a06f79f6e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001789.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00217 +M--TANHSRHTAAADGQGAAAEHAGTGTATTDPRRDTRSRWGCSSRLGGGTGRLMGVSLA +VGVVGALGLGSAAWATTVAAGHADS-LAWIAAGAMALNGLLFGLLLTWLALVDRHSIRGA +DTNPEESIEGRWYEKATSGAFHDTLVVVGLGAAILSFGGYVISPAAVGAALFVLMGCAAA +IRYQIQKRRG +>GCF_003691675_PROKKA_02210 +M----------------------ATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLV +AGVVIALLIGAASYGLASSQGDAGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGA +VRDTEETIEGRWLEKAQSGAFGDLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVA +VRYALQKRRG +>GCF_005280335_PROKKA_00168 +MNTTADPRSRSASGPERA-----ASTSAAATPAGSAAPSAWGRSARLGGGTGRLVVVSLV +FGVLLAAMLGVIAYGLAGTADPADPRRPWVLGLVVASGALPVLAGTVWMLLVDRATIKGA +VRDPEESIESRWYDAAAGGAFHDLLVVLGLGTFVVSMTGWTAELSLVGAGLVLFMMADVA +IRYRVQKRRG +>GCF_023573625_PROKKA_00217 +M----------------------ATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLV +AGVVIALLIGAASYGLASSQGDAGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGA +VRDTEETIEGRWLEKAQSGAFGDLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVA +VRYALQKRRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001790.fa new file mode 100644 index 0000000000000000000000000000000000000000..1359d2651ff72fdcedad561f6d099de8e177a872 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001790.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00219 +MTRTVPARRRTTLAAAV-AAVSLAVTAAAPALSAPGNGNGNGNGNG----SASQGQARSNDLSATRGNKVNDAAALAPHL +VGQTLDWEACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGHTITLRVAKTETSKGNPERQGIALVNPGGPGGSGLP +WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVL +GEEKTSYIGYSYGTWLGSWYQRVFPQHTHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVARHDEIFGLGDNP +MQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAAYIRIMESEAAATDPAGQRTQIERILAEARASLPAE +ERDSFDRFAARGLETVGEREQLVAATQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMY +WPAQTSMPAQPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAPIRDYFLTGAQP +AEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDAIERQLIDSRAVTPDVEAFLED +>GCF_003691675_PROKKA_02213 +MTRTVPARRRTTLAAAV-AAVSLAVAAAAPALSAP----GNGNGNG----SASQGQARSNDLSATRGNKVNDAAALAPHL +VGQTLDWDACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGHTITLRVAKTETSKGNPERQGIALVNPGGPGGSGLP +WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVL +GEEKTSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVARHDEIFGLGDDP +MQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAAYIRIMESEAAATDPAGQRTQIERILAEARASLPAE +ERDSFDRFAARGLETVGEREQLVAATQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMY +WPAQTSMPSQPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAPIRDYFLTGAQP +AEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDAIERQLIDSRAVTPDVEAFLED +>GCF_005280335_PROKKA_00161 +MTRTAPTRRRTTLAAAVAAAAALTISAAAPALSAP----GNGNGNGNGQSSASQGQARSNDLSTTRGNQVNDAAALAPHL +LDQELAWEACDFGSPALNTRFGAIPGTACADVTVPRDWKDPQDGHTITVRVAKTETSKGNPDRQGIALVNPGGPGGSGLP +WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVM +GEEKTSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDVSRDGLQTTWNLQPRSRDRQFQDMMLPYVARQDAVYGLGTDP +MEIRQRWEDAGGTRTILGQIVAGSYLLPAMYSTSQYPMAASMIAAFISIMETETAATDEAGMQAQLERITAEARATVPAA +DRAAFDRFIEQGSEVVAERDELAAAVRTGQPVTFSGTFSAIRCQDGQWNTSEGYWTSWVNDLGRKAPWIAAFMGPSECMY +WPAQTSMPSQPGGKDTPSAVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAPIRDYFLTGEMP +AEKSLCEAHPLPGETQTHQVAGTPTHKGDIKISMRTDAVREANRITLDAIERQLLDSRAVTPDVEAFLER +>GCF_023573625_PROKKA_00220 +MTRTVPARRRTTLAAAV-AAVSLAITAAAPALSAP----GNGKGNG----SASQGQARSNDLSATRGNKVNDAAALAPHL +VGQTLDWEACDFGSESLNARFNAIPGTACADVTVPRDWKNPEDGHTITLRVAKTETSKGNPERQGIALVNPGGPGGSGLP +WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVL +GEEKTSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVARHDEIFGLGDDP +MQIRQRWEDGGGTRTQLGMIVAGSFLLPAMYDTSQYMSAGAVIAAYIRIMESEAAATDPAGQRAQIERILAEARASLPTE +ERDSFDRFADRGLETVGEREQLIAATQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMY +WPAQTSMPSQPGGKGAPSTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYGTECVDAPIRDYFLTGAQP +AEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDAIERQLIDSRAVTPDVEAFLED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001794.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3f15acbc5e9523cb4c0618ca2865a4a83b46f10 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001794.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00252 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG +LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLVQDLQDA--- +------ +>GCF_003691675_PROKKA_02264 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG +LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT +RRPRRP +>GCF_005280335_PROKKA_00118 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADATVLHAPG +LVSTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLAFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDLGVELGKILYRNAPGTAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLRDAWLT +RRPRRR +>GCF_023573625_PROKKA_00252 +MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG +LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH +RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV +GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT +RKPRRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001797.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001797.fa new file mode 100644 index 0000000000000000000000000000000000000000..9653054de0183d8fa80c3cc6f35ece00d6eaf8fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001797.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_00273 +MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQLDGVRPDFAALIDGRPCGWV +ELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIALYVSGSPVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRP +ITRVSQLADRLAPLARFLRERLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG +VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTDSRGEPWLWFYEDFLQRYDPA +ARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPSVVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKN +LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARRIKRDRR +ITVAIGNPPYDRVTSGTGGWVEHGDGE-DALFDDVIGPAQEQGVIFSAQASLYNLYVYFWRWAIWKAFQQDPGDQAIISF +ITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQEENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEK +FAALDEVARLDPDDGTWECLPGGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADP +SADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFFVS +PKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAEAAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDA +YVQRFDEALEGSPVRVPLTVDPALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYD +PATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET +VSLGGDQADLLDEILARDLIPANELPEPTPAERKVPKTIKRDFSTAQEEMF +>GCF_003691675_PROKKA_02288 +MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQLDGVRPDFAALIDGRPCGWV +ELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIALYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRP +ITRVSQLADRLAPLARFLRERLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG +VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTDSRGEPWLWFYEDFLQRYDPA +ARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPSVVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKN +LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR +ITVAIGNPPYDRVTSGTGGWVEHGDGE-DALFDDVIGPAQEQGVIFSAQASLYNLYVYFWRWAIWKAFQQDPGDQAIISF +ITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQEENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEK +FAALDEVARLDPDDGTWECLPGGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADP +SADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFFVS +PKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAEAAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDA +YVQRFDEALEGSPVRVPLTVDPALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYD +PATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET +VSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKRDFSTAQEEMF +>GCF_005280335_PROKKA_00083 +MDRDAVNALAEEYSRGIGQALSMGVAAEPEAQLTVPFAAFLSRFAQEVELGRLDLLREAQLDGVRPDFAAALDGRPCGWI +ELKAPGHTVVGERWRGREKSQWALLSQLDALLVSNGELLALYVAGAPVETCALPVDGAAGWDPDRLRRVLEQFTLAQPRP +ITRVSQLADRLAPLARFLRERLAEGLEHSYDSVVEAKAAWDHTMQHTTSPEEFSGDVAQVVAYSMAIAGLSGQADRNADG +VVSLEEAKHALETAHRNVLAASLGPILGIPALMQHIAPEVGAITRLVAGMDVAAIERSTDSRGEPWLWFYEDFLQRYDPE +ARSRAGVYYTPISVVECQVRVVDALLRERFGQNLGFGAPSVVTLDPATGSGTYPLAIIDRAESVAREERGDAGAKQVAMN +LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMPTGLFGDARVLAEAAESARRVKRDQQ +ITVAIGNPPYDRVTSGTGGWVEQGSGSGDALFDDVIKPAQDSGVIFSAQASLYNLYVYFWRWAIWKAFQQDPKDHAVISF +ITASSWLTGPAFVGLRRLAQATASEIWVMDLGGEGRGARKEENVFDIQSPVAIVTLVRTGKASREAKVFYRRFRGSRAEK +FTALDRIQRLDAADG-WEQIAAPGGAPFMPASGGEDWTAMPQLADLFPWQQPGIMYNRAWPVASDQNTLRRRWQELLSDD +DADARAGKYVTGNSGRTIHTAVAGLPTLASLPADAEPRPIVRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFLVS +PKTARINGGPAVTVSTAVPDKHHYVGSFGGKDVIPLYRDAAAAEPNVTVGLLELLADRLGHDVTPEDLAAYVMAVAAHDG +YAQTFDEALETSPVRIPFTADASLWDAAVALGERLLWLQTYGERFTSADRPRGRVPRVPGLGWSEAVTHIPADTASLSYD +AASRELRVGDGVVTGVSPEVRAFSVSGMNIVDKWLGARTAKGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET +VALGDQQAELLAAILAGELITAADLPVPTAAERKVPKTIKRGVSPHQEGLL +>GCF_023573625_PROKKA_00271 +MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQLDGVRPDFAALIDGRPCGWV +ELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIALYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRP +ITRVSQLADRLAPLARFLRERLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG +VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTDSRGEPWLWFYEDFLQRYDPA +ARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPSVVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKN +LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR +ITVAIGNPPYDRVTSGTGGWVEHGDGE-DALFDDVIGPAQEQGVIFSAQASLYNLYVYFWRWAIWKAFQQDPGDQAIISF +ITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQEENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEK +FAALDEVARLDPDDGTWECLPGGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADP +SADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFFVS +PKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAEAAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDA +YVQRFDEALEGSPVRVPLTVDPALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYD +PATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET +VSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKRDFSTAQEEMF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001798.fa new file mode 100644 index 0000000000000000000000000000000000000000..e74046f5a2148840704a4514b3793c908d7bf998 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001798.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00276 +MTGSAPAQLRPLRATDAPAVLAAFHAGTVGMADPAEVTDDASARAYVDGLVQAEGTDAVA +VVERGTDTLIGLVAVVRDEAHGTGALTAWLHQGWRGDAIMSRAATTVADAELAEGGLERI +ELAHRADSPTAGAVARAAGLRHEGTQRGRLRTGGRRLDVHLYGRLAADPLPEERVRPLPW +ASDARPWADR +>GCF_003691675_PROKKA_02291 +MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA +VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI +ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHLYGRLAADPLPEERVRPLPW +ASDARPWADR +>GCF_005280335_PROKKA_00079 +MTGTARAQLRPLHSDDADAVFEGFRSDPVGMARQGDVSDEASARFYVDRMLESEATDAVA +VVDPATDRLIGLVSVVRDEENRSGWFSYWLNSAWRGDAIMARAAATVADAELAEGGLERL +ELGHRANNPTSGSVARAAGFLHEGTQRGHFLIDGRRQDVHLYGRLPSDPQPAEKVRPLPW +ASDERPWSGR +>GCF_023573625_PROKKA_00275 +MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA +VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI +ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHRYGRLAADPLPEERVRPLPW +AADARPWADR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001799.fa new file mode 100644 index 0000000000000000000000000000000000000000..1cdd72962e8494eaafef540782fc6cb50a6a87c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001799.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00285 +MPEGDSLVRVAHRLRPVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP +AARPGARPLTLISHLKMEGRWLVSALDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP +TADETTVLGHLGPDLLDPAWDTPDDGAALLAEGMRRLTARPERPVGLALLDQRLVSGIGN +IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPATGARRRTTGVRPNPG +RPFGVEVLV---------PAGPPLGTAPGRTPGARGGG----------APSYWVYGHDRA +PCLRCRGPVRQEDYGSAEDDARRLWWCPHCQG +>GCF_003691675_PROKKA_02307 +MPEGDSLVRVAHRLRLVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP +AARPGARPLTLISHLKMEGRWLVSAVDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP +TADEATVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN +IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA +RPFGVEVLV---------PAGPSPGTAPGRTPGARGGG----------APSYWVYGHDRA +PCLRCRGPVRQEDYGSPEDDARRLWWCPHCQR +>GCF_020097155_PROKKA_00048 +MPEGDSLVRAAHRLRPVLAGRVLTHADLRVPQLATARLTGWTVSEVEPRGKWLLMRLTPP +ADRPDAAPHTLVSHLKMEGRWMVTGRDARWPAPAWQVRAVLETAEHRAVGAQLGRLELAP +TAEEDRLLGHLGPDLLDPAWDDPARGAELLAEGVRRLTARPERPVGLALLDQRTTCGIGN +IYRCESLLLAGLDPHRPVAAVPDVSGLLTLARDLLRANVPPAAPFIGWPRTTTRVRPDPS +GPYGLRVVVEDRGFPGGLPGGPVPDDAPHASATSTSGAGLGRRGDLPRGPHYWVYGHRTT +PCGRCGGPVTFEEYGSPEDDERQLWWCRTCQR +>GCF_023573625_PROKKA_00291 +MPEGDSLVRVAHRLRPVLEGRVLTHTDLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP +TARPGARPLTLISHLKMEGRWLVSAIDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP +TADEAAVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN +IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA +RPFGVEVLV---------PAGPSPDTAPGRTPGARGGG----------TPSYWVYGHDRT +PCLRCRGPVRQEDYGSPEDDARRLWWCPHCQR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001800.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee0e7ea90deb6e19ccdafc2fffeb8d285757c689 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001800.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_00286 +---MSIDAAPPEDG----GTAPTGTSPAPEALEDALPHPSDPSVTPFLLFEGDAGAAMDA +YLTAFVEYLPVTEVRRDLFDDSSPRGAEWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTP +AISLFVELPDATAVDAIHDTLLAGGGRDYMPPDDYGFSRRFAWVGDRFGVTWQLNAA +>GCF_003691675_PROKKA_02308 +---MSIDAAPPEDV----GTAPTGTSPAPEALEDSLPHPSDPSVTPFLMFEGDAGAAMDA +YLTAFVEHLPVTEVRRDLFDDSSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTP +AISLFVELPDATAVDAVHDALLAGGGRDYMPPDDDGFSRRFAWVGDRFGVTWQLNAA +>GCF_005280335_PROKKA_00068 +MSETTTDPGLPDDVGVDAGADPTGTAPAPAALEESMPHPSDPSVTPFLMFEGDAGAAMDA +YLSVFVEHLPVTEVRRDLFDGSSPRGAEWAGKVLHGELEVAGQRLRFFDSFTSHGFTFTP +AISLFVELPDPTAVDAVHDALIAGGGQDYMPPGDYGFSRRFAWVGDRFGVTWQLNAA +>GCF_023573625_PROKKA_00292 +---MSIDAAPPEDV----GTAPTGTSPAPEALEDSLPHPSDPSVTPFLLFEGDAGAAMDA +YLTAFVEHLPVTEVRRDLFDESSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTP +AISLFVELPDATAVDAIHDALLAGGGRDCMPPDDDGFSRRFAWVGDRFGVTWQLNAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001804.fa new file mode 100644 index 0000000000000000000000000000000000000000..18e6f5d58137a7e89705097ee8731fee01c93ddc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001804.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00329 +MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT +GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS +RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD +PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT +PADLLAEFAKIKGAVVDDKTMLS +>GCF_003691675_PROKKA_00045 +MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT +GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS +RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD +PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT +PADLLAEFGKIKGAVVDDKTMLS +>GCF_005280335_PROKKA_00006 +MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT +GTVKVSGKDVTRMADHRRAAWIGRVFQDPTAGTAPNLTIEENMALAWRRGHTRGLARGVS +RSRRGLFREELTKLELGLEDRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD +PSRAELVTRLTQQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEAQKAGRT +PADLLAEFAKIKGAVVDDKTMLS +>GCF_023573625_PROKKA_00336 +MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT +GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS +RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD +PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT +PADLLAEFGKIKGAVVDDKTMLS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001806.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001806.fa new file mode 100644 index 0000000000000000000000000000000000000000..119c367ae5bed9fa19d0f6b1fe865c9fb187de7e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001806.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_00369 +MSTTPTPPVSHGSAPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF +QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGKPGSLLSVE +FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWV-RPLYWGV +YFFLGAASARLL--------PRIRTAPAALGVIAVILMVLTVTATRTGALV-----VAER +QPWSVFAALPGILVVLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFR----DL +AAVRPVDFYVAIASFTFLVPLALALGYRRV---RWLFELPTAGRVRARPRTRATVPGAAD +AVPAQTAEPASTTAPLPVVEPASPPQPAAGPTPAAEPAAGAPARVRAPRPRPRHAD +>GCF_003691675_PROKKA_00085 +MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF +QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE +FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWV-RPLYWGV +YFFLGAASARLL--------PRIRTAPAALGVIAVILMVLTVTATRTGALV-----VAER +QPWSVFAALPGILVVLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFR----DL +AAVRPVDFYVAIASFTFLVPLALALGYRRV---RWLFEFPTAGRGRERPRTRAAVPEAAD +AVPAQTAEPAPTTAPLPVVEPASEPQSTAGPAPATEPASDAPAQV--PRPRPRHAD +>GCF_005280335_PROKKA_02394 +--------------------MDAIRGTAILLMLLLHATMIPAVVGGMEPVPWLVAITDAT +APFRMPVLMFLSGMLLDRALAKPAKRYLSGKFRVLLWSYVVWAVVYFMVMGRPGELFRPW +TWV-QTLYLWFLAFLLAYYVLALVLRRIPAIVVAVAALVPHVVLVGAERGFLARFFLYMT +VFFAGAAFTRFLAARPGILEPRRRDGHLLVG---LPLLVVGVVAIRSGGALPHPAGAVVG +AVAAVAVAMGLVLVVQALVPR-PRGPLVR-VGQQSLVYYCVHYPVMVLVVRLGERLSWDV +VVVSLVSLVAAV-----VVCAVIAEGRDRVPVLDALFRAPAPPR-RRRPVTH-------- +-------------------------------------------------------- +>GCF_023573625_PROKKA_00376 +MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF +QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE +FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWV-RPLYWGV +YFFLGAASARLL--------PRIRTAPAALGVIAVILMVLTVTATRTGALV-----VAER +QPWSVFAALPGILVVLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFR----DL +AAVRPVDFYVAIASFTFLVPLALALGYRRV---RWLFEFPTAGRGRERPRTRAAVPEAAD +AVPAQTAEPAPTTAPLPVVEPASEPQSTAGPAPATEPASDAPAQV--PRPRPRHAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001807.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001807.fa new file mode 100644 index 0000000000000000000000000000000000000000..e78369669d7bbaf9e286a1bc578e6f8df0e2a111 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001807.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00387 +MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRASHPPAEDVEDQGAAFDVGTLVSRRNAL +GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSSAASASPSATLTEMVTET +AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA +VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP +DKASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLP +QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP +>GCF_003691675_PROKKA_00111 +MAPWPPTRSRRPFPQVTEGGGAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL +GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPEASSSSAASASPSATLTEMVTET +AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA +VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYAGRWPHLHFEVFP +DKASITDATNNVLTSQIAMPAEQSAQVYATSAYDGSTENFAQVSLETDNVLSDGYETQLP +QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPA---------RP +>GCF_020097155_PROKKA_02441 +MAPWLPTRSRRPFPQVTEGGEAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL +GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAA-SSSAASASPSATLTEMVTET +AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA +VYLWHADALGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP +DKASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLP +QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPARP +>GCF_023573625_PROKKA_00393 +MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRAFHHPAEDVEDQGAALDVGTLVSRRNAL +GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPAASSSSAASASPSATLTEMVTET +AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTAAEGVPLTVTMNVIDMANGDAAMTGAA +VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP +DKASITDATNNVPTSQIAMPEEQSAQVYATSAYDGSTENFADVSLETDNVFSDGNETQLP +QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001808.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001808.fa new file mode 100644 index 0000000000000000000000000000000000000000..b70ef3ecbb544da4cf3a1c007861a46840636d76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001808.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_00390 +MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG +VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA +DGHVAAAIENGKVGRMLDRLTALVPEIR +>GCF_003691675_PROKKA_00114 +MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG +VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA +DGHVAAAIENGKVGRMLDRLTALVPEIR +>GCF_005280335_PROKKA_02566 +-------------------------MAAVRALRTLLAEGYATPEAPVAVTGAG------- +-WPDYDARVLPGLAAAQELAGVDVDYLRHVDRVSDAGIDAASLADLGTLFTYVLRGERFS +EGHIGAALANGKVGRMLDRLAELVPQVR +>GCF_023573625_PROKKA_00396 +MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARQIASYGAPAPGTLGG +VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA +DGHVAAAIENGKVGRMLDRLTALVPEIR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001809.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001809.fa new file mode 100644 index 0000000000000000000000000000000000000000..1fbe70aa45e3241595ea54c6592425bb787977a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001809.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00395 +MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL +EDGTDHLDTATLYGGGRSEELVGRALARAGSGVRERVLLASKGGLVRDGQRRIDGRPETL +RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT +RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA +GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW +EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR- +>GCF_003691675_PROKKA_00119 +MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL +EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL +RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT +RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA +GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW +EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR- +>GCF_020097155_PROKKA_02433 +MDTA-----ANPALTTDLRSPRRVAGKDVRPVGLGCMNLVHGYSGFLSEREAVDLVVGVL +ADGTDHLDTATLYGGGLSEEYVGKALTRVGADVRDRVLLASKCGLSRDADRPIDGRPETL +RAQVDASLRRLGQDRIDLYYLHRLDPRVPVEESVGALAEAVAAGKIGAIGLSEVSGATLD +RAATEHPVAAVQNEYSLATRNPEWGLLEACRRHGAALVAFSPVCRGLLTDAPPVVADLPD +GDMRHAMPRFQGPAWEANLRLREEFASEAARLGVPAASLAVAWVLAQGADVVAIPGTTDP +AHWREDRGAEEVSLTLEDLARLDALVNHATVQGRRYSDAQQASVDTEDAPQQG +>GCF_023573625_PROKKA_00401 +MDATPHPRPAEPGPLPDPAAPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL +EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL +RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT +RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA +GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW +EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001810.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001810.fa new file mode 100644 index 0000000000000000000000000000000000000000..605b7fbc40e8bd2824c815e6a3662df9e31b5954 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001810.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00431 +MASDHRPPHPVSPHPDDLD----GGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGV +FRALLGLTVASAVLYAASTLRNLLPGAAQDIADSLPEGSAQSPAMTAEAIEGALTGSVWF +ATLLGLAVYAIVLVGLTRRSNAARIMGALFASIAIFVTLLGTIRLFVFPAGDVVLPLVLG +GLFALVNAAWLVCAFNPGLATTFLRRRA------ +>GCF_003691675_PROKKA_00152 +MASDHRPPHPVSPHPDDLD----GGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGV +FRALLGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWF +ATLLGLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLG +GLFALVNAAWLVCAFNPGLATTFLRRRA------ +>GCF_005280335_PROKKA_02526 +MASDPRPPNPASPDPASPDGFRPGDGRPVVGPEDARRRIAGHSGPHARPLIRPNERTPGV +FRALVGLTVASAAVYVVSLLLGLRPGAAEEIAATLPADASRSPAMTAESIQAALTGSVWV +AVLLGLGVYALVLVGLLRRSNTARIVGAIVAALAVFVTLLGAIRLFVFPAESVVAPLLLG +LLFALVNAAWLVCAFNPGLATTFVRRDAGPRRPA +>GCF_023573625_PROKKA_00434 +MASDHRPPHPVSPDSDDLD----GGGRPVVGPDEARRRIAGHSGPDARPLIRPDARTPGV +FRALLGLTVASAVLYAASILRNLLPGAAQDIADSLPEGGAQSPAMTAEAIEGALTGSVWF +ATLLGLAVYAIVLVGLTRHSNTARIMGALFASIAIFVTLLGAIRLFVFPAGDVVLPLVLG +GLFALVNAAWLVCAFNPGLATTFLRRRA------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001812.fa new file mode 100644 index 0000000000000000000000000000000000000000..e2468800325b60313aaa81ab4e0e7fba99303bee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001812.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00476 +----MTATPQTPA---QPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSA +HRMPHEMVEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSL +LSIVQMPAGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAK +GARLRERMAADR +>GCF_003691675_PROKKA_00194 +----MTATPQTPA---QPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSA +HRMPHEMVEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSL +LSIVQMPAGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAK +GARLRERMAADR +>GCF_020097155_PROKKA_02355 +MTAEQTTQPTSDAPCTRPLQEEAPVVSVVMGSDSDWPVMGQAVEALRELGVPVEVGVVSA +HRMPHEMVDFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLRSLDGLDSL +LSIVQMPAGVPVATVSVDGARNAGLLAARILAAGTDDGAAHLRAALQDVAAGLNAQARAK +GARLHERAADGA +>GCF_023573625_PROKKA_00476 +----MTATPQTPA---QPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSA +HRMPHEMVEFGARAHERGIRVIVAGAGGAAHLPGMLAAVTPLPVIGVPVKLKSLDGMDSL +LSIVQMPAGVPVATVSIDGARNAGLLAARILASADTAEGDRLRAALAEHADELNAQARAK +GARLRERMAADR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001815.fa new file mode 100644 index 0000000000000000000000000000000000000000..26d16e26b4f12843c3ad73cd6c44ad810e39254a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001815.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_00536 +MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF +MIPKAFLGRSDTVDTTAIHTRPV-VEHAAS-------GAAHR- +>GCF_003691675_PROKKA_00260 +MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF +MIPKAFLGRSDTVDTTAIHTRPV-VEHAASGAHAVETGAAHR- +>GCF_005280335_PROKKA_02413 +MIRNGKAIDHSNVGGVWGSLIAFLVAYVAFLGSLYAMGFWTLENAWVPGLIALALAMVTF +MIPQVFLGRSDTVDTAAIHTRPVAVEHPVSGAHAVETGAARRH +>GCF_023573625_PROKKA_00539 +MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF +MIPKAFLGRSDTVDTTAIHTRPV-VEHAASGAHAVETGAAHR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001816.fa new file mode 100644 index 0000000000000000000000000000000000000000..948063f9ce3bfe2a7caedb9fe25ac8f97b460b2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001816.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00569 +MDSRVNSGGVVGKVDNLTCLAGLVTTEDPARVRALRGTVLAVALLNGAYLVVEIILALGI +GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG +DPDPPAAGVLLGAAVGSLLVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGAVLIALS +GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD +>GCF_003691675_PROKKA_00293 +MNR--------------------AAVADRRRTRTLRGTVLAVALLNGAYLVVEIILAVGI +GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG +DPEPPAAGVLLGAAVGSLLVNIVCVVLLARVRVDGGSLTRAAWLAARNDLVAGVVLIALS +GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD +>GCF_020097155_PROKKA_02259 +MDAMTETS---------------HPRPDPARVRALRGTVLAVSLLNLAYMLVEIGVALGI +GSVSLVADSVDFFEDFAVNMLIVIALGWPLARRARVGKVMAGIIVLPAIAALAMAAVKVG +DPEPPATGPLFWTGVGSLLVNLVCVGLLARFRADGGSLTRAAWLAARNDLIAGIVLIALA +GATALTASGWADIIVGVLLVVLNGGAAKEVWQAATEERLAAQALAGEFDDD +>GCF_023573625_PROKKA_00571 +MNE--------------------VPEADRRRTRALRGTVLAVALLNGAYLVVEIILALGI +GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKVG +DPDPPAAGVLLGVAVGSILVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGVLLIALS +GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001822.fa new file mode 100644 index 0000000000000000000000000000000000000000..47cb82f39d805bd89cd4b59563b919fa99dd8907 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001822.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00625 +MASKDWARKISDVPEGTRRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA +SLTVGVSWPVGARWFRHAGGMTPLSLAEPTGRYLSFAEREEIAILHAQGQGVRQIARTLG +RDPGTISRELRRNCATRSGKQEYRATVAQWKAQEAARRPKPAKLATNQRLHDYVQARLNG +VVLGPDGVAVPGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE +AIYQSLFIQGRGALKRELVACLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA +VPGHWEGDLIIGTERSAIGTLAERKSRATILVHLPRLEGWGERPPVKNGPSLGGYGAEAM +TAALIKAMATVPEQLRQSLTWDRGKELAGHVQFTMATGTKVFFADPHSPWQRPTNENTNG +VLRQYFPKGTDLSRWSAEDLAAVAYTLNNRPRKVLDWKTPAEVFAEQLRSLSTHGVATTG +>GCF_005280335_PROKKA_00734 +MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA +SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG +RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG +VVLGPDGVAVQGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE +AIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA +VPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGGYGAAAM +SAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPTNENMNG +LLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETSGVATTT +>GCF_005280335_PROKKA_00746 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------MRISHE +AIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA +VPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGGYGAAAM +SAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPTNENMNG +LLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETSGVATTT +>GCF_005280335_PROKKA_00749 +MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA +SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG +RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG +VVLGPDGVAVQGPVGPGFKGRKMKPRRAEVK----------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-------------------------------------------------SLE------VV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001824.fa new file mode 100644 index 0000000000000000000000000000000000000000..82d1e574e0a960ab6fdf37b2a23dbcd091adbde9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001824.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00629 +MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG +EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST +DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPK +TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT +WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL +>GCF_005280335_PROKKA_00401 +MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG +EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPNTDLPEPLGLAEST +DRGQSWTVLSRGGQSDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ +TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT +WTASDRPVGTATALGAGITDDGQTEALLVVGSTVLSTTDGGNTTESLL +>GCF_020097155_PROKKA_02200 +MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPEYG +EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST +DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ +TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT +WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL +>GCF_023573625_PROKKA_00602 +MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG +EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST +DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ +TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT +WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001825.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001825.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ee0e8a97584e25c86a7d1454afab1f80dc663d6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001825.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_00632 +MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV +AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI +>GCF_005280335_PROKKA_00404 +MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV +AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI +>GCF_020097155_PROKKA_02197 +MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV +AEAVSALDGVDDVRIELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI +>GCF_023573625_PROKKA_00599 +MTESARTPLPGATNGCSCCAPAADATAPAGHQSADPTGTSAGDATYQVEGMTCGHCVGSV +AEAVSALDGVDDVRVELVAGGASPVTVTGPASADSVRTAIEAAGYRVRI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001826.fa new file mode 100644 index 0000000000000000000000000000000000000000..00c59dc87be86a76e824b5063e89bc929a1fcc98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001826.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00635 +MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA +LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG +HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH +SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV +LETFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY +TVDNQAIVIPENIDAIRALTGTVDDGGESIRCTDRALGVRQDFVRSSVAAR +>GCF_005280335_PROKKA_00407 +MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA +LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG +HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH +SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV +LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY +TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR +>GCF_020097155_PROKKA_02194 +MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA +LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG +HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH +SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHNWTIELTRPAEKQEV +LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVVLWEDILTVDGNELYYTY +TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR +>GCF_023573625_PROKKA_00596 +MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA +LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG +HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH +SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELIRPAEKQEV +LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY +TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001828.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001828.fa new file mode 100644 index 0000000000000000000000000000000000000000..92367d105c2da574b7c0d0e0de5f8540e8561e8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001828.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00640 +M------------ARPGDPGRECRRGLDVRIGTSGWIYKHGRGTFYPQGLRIADQLDHCT +ERDRVSRLRALPQRGP-------------------------------------------- +---------GPAL----------------------------------------------- +------------RRIVLRRRAR-------------------------PWVGRLRELTGA- +------DAAGARPAHVSFYNDNHGHAAFNALTLRRMAEAEA +>GCF_003691675_PROKKA_00377 +MISGTLRLPRRVKARPGDPGRGYRRGMDVRIGTSGWTYRHWRGTFYPQGLRIADQLDHYT +ERFRTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVH +TLDLLGDHAGPLLLQLPAHLHRDDGRLAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDR +HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGAD +DGGPAGDAAGARPAYVYFNNDNHGHAAFNALTLRRMAETEA +>GCF_020097155_PROKKA_02185 +--------------------------MDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYT +ERFRTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVH +TLDLLGDHAGPLLLQLPANLHRDDDRLAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDR +HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRVLTGAD +NGGPAGDAAGARPAYVYFNNDNHGHAGFNALTLRRMAETGA +>GCF_023573625_PROKKA_00609 +MISGTLRLPRRIKARPGDPGRGYRRGMDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYT +ERFGTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLDEPQDWVQRIVH +TLDLLGDHAGPLLLQLPAHLHRDDDRLAGFLGLLPERVRVAVEVQHESWLDKDVFDLLDR +HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGA- +------DAAGVRPTYVYFNNDNHGHAAFNALTLRRMAEAEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001830.fa new file mode 100644 index 0000000000000000000000000000000000000000..19d4e91d9d407bfb0bd89408f97fb972ca73f2f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001830.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_00663 +MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRDRIDALLDEGSPFLEVGALAA +HGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFP +DREHFGRIFRNQALLSSQRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTRVVPVDVNTPYDVREVIDRLVDGGSVHE +FKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV +TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF +QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM +>GCF_003691675_PROKKA_00400 +MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRDRIDALLDEGSPFLEVGALAA +HGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFP +DREHFGRIFRNQALLSSQRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVNTPYDVREVIDRLVDGGSVHE +FKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV +TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF +QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM +>GCF_005280335_PROKKA_02300 +MTASTTAPDSESAPTAAERNAAGHARLEQEVAELVARTALGGPERSRERHTARGKLLVRDRIDALLDEGSPFLEVGALAA +HGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPLTVKKHLRAQEIALENHLPCLYLVDSGGAFLPRQDEVFP +DREHFGRIFRNQALLSSRRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPPPAPAWEVAPAQEPAKDPAELTSVVPVDVNTPYDVREVIDRIVDGGSVHE +FKPLYGTTLVTAFARIDGHPVGILANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV +TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMDAAEVEAF +QAPVRQQYEDQGSPLYSTARLWDDGIITPGQTRRVLSLALDVISRPPLPDTRFGLFRM +>GCF_023573625_PROKKA_00633 +MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRDRIDALLDEGSPFLEVGALAA +HGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFP +DREHFGRIFRNQALLSSQRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH +AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVNTPYDVREVIDRLVDGGSVHE +FKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV +TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF +QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001832.fa new file mode 100644 index 0000000000000000000000000000000000000000..61832548836394793c1d5118b80d85879cedb0ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001832.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00666 +M--------TERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLD +HAYAADQPFGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGR +SEVTAIRESSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGT +GERA +>GCF_003691675_PROKKA_00403 +M--------TERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLD +HAYAADQPFGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGR +SEVTAIRESSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGT +GERA +>GCF_005280335_PROKKA_02296 +MGRAEPGAAPERVEIVQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLD +HAFAQTQSFGRPLVNSMLTLSTLVGLAVAQTTQGTLVAQLGLGEIAFPAPVFHGDTLYGR +SEVRAVRESSSRPGQRIVTFAMTGENQHGDVVVRAERTCLMWTEAAHADARAQAA-ADAA +EERA +>GCF_023573625_PROKKA_00636 +M--------TERVEIEQRGRYADELAVGQVYLHRPGRTLTEADNVLFTTLTMNPQALHLD +HAYAAAQPFGRPLVNSMLTLSTLVGLAVGQTTQGTLVAQLGLGEIAFPKPVFHGDTLYGR +SEVTAIRESSSRPGQRIVTFAMTGENQHGDVVVRAQRTCLMWTAQAHAEAKAKAADAAGT +GERA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001833.fa new file mode 100644 index 0000000000000000000000000000000000000000..e280895b862426837d2cbcb52b45c14cc6b53ee7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001833.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00667 +MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVIPEARPAARDAVAAAWAGRAT +GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP +QTRVVALCETAAGILAAAELAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR +ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAAALGCTATVCLHPRQVPVVRSAYTP +APEAVERARRVLAAAEGRHGAFELDGTMVDEVVLAQARAVLRRADAARPAGA +>GCF_003691675_PROKKA_00404 +MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRAT +GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP +QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR +ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTL +APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAPRPASA +>GCF_005280335_PROKKA_02295 +MSALALGPAVMFTPADRPERYAKALERADAVILDLEDAVTPDARPAARDAVRAAWEGRAA +GGADGGPLDVARVVVRVNPAGGADYTADLAMLAETGWRTLMLAKAESAAQVDGLVAAMGE +DVRVVALCETAAGVLAAAELAAHPNVGALMWGAEDLVASMGGSSSRTADGAYRSVVTHAR +AAVLLAAAAHGAAAWDAVHLDLADEAGLAAEAEDAVALGCAATVCLHPRQVPVVRSAYTP +AAEAVERAHRVLSEAEGRRGAFELDGAMVDEVVLAQARAVLRRAEAAGAAAG +>GCF_023573625_PROKKA_00637 +MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRVT +GGVDGGPLDEGRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP +QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR +ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTP +APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAARPASP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001836.fa new file mode 100644 index 0000000000000000000000000000000000000000..a358b2ce7cb0c41d278f992ea7dbff28d60d4e92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001836.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00739 +MIRFLHGIGGRPAHFEPLADALGA-----VADLAASPALPGH----PGTDA--GGQGRPR +AARPATDADPVLDAARTWAAQA--GPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDS +NVPVTDTALAARAAKARLAARPDWRSVLRASLARDLLVPEPWRERILTDLDATPDHPMRE +LWAAVLAADTRALWAGITVPTLYVRSTRDVHQRDLDAVTQHATVVDVST---GHWPHVTE +PEAVAAAIRRWHTT-GVHPT-R +>GCF_003691675_PROKKA_00470 +MIRFLHGIGGRPAHFQPLADALDA-----AADLAASPALPGH----PGTDA--GGQDRPR +SARPAIEADPVLDAARTWAAQA--GPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDS +NVPVTDIALAARAAKARLAARPDWRSVLRASLARDLLVPEPWHERILADVDATPDHPMRE +LWAAVLAADTRTLWAGITVPTLYVRSTRDVHQRDLDAVTQHTTVVDVGP---GHWPHVAE +PGAVAAAIRRWHTT-GVHPT-R +>GCF_005280335_PROKKA_02191 +MIRVLHGIGGRPGHLAPLLDALGHGSTEDAAD--ASPALLGHGDAVPAAPAPTGGAADPA +A---GADHDWILAAARDWAARAREGAGPDLLIGHSTGGVIALRALAEGLVRPRGLVVIDS +NVPVDAAALAARADKARLAAAPDWRDRLRASLARDLVAPKPWPARILADLDATADHPMRA +LWSAVLTADPRPLWAAASVPVLYVRSTRQVHQADLDKLTDRARVVDVSAHAGGHWPHLAD +PAGVARAIRDWRAETGA----- +>GCF_023573625_PROKKA_00703 +MIRFLHGIGGRPAHFQPLADALGA-----AADLAASPALPGH----PGTDA--GGQDRPR +AARPAIEADPVLDAAHTWAAQA--GPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDS +NVPVTDPALAARAAKARLAARPDWRSVLRASLARDLLVPEPWHERILADLDATPDHSMRE +LWAAVLAADTRALWSSLTVPTLYVRSTRDVHQRDLDAVTQHATVVDVGP---GHWPHVAE +PEAVAAAIRRWHATVAAQPSHH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001844.fa new file mode 100644 index 0000000000000000000000000000000000000000..49bd40ae7a5f7b51af4395f874b382186ce4cd7b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001844.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01013 +MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY +NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL +IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV +AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD +>GCF_003691675_PROKKA_00727 +--------------------------------------------MAAVGRRLGVAPSALY +NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL +IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV +AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD +>GCF_005280335_PROKKA_01875 +MDETPEPPRTRRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY +NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEAPVVAALRAWARSYRDVFAAHPPLIPL +IATLPIEGAPSTQRVYETVCAVLARTGLAPGQVLARVIALESFIYGSAYDVDAPADIFEV +AGAQERLPAFGAAAEAFREGGGTRATGARNPYADAPFEEGLDLLLAGLDD +>GCF_023573625_PROKKA_00956 +MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY +NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL +IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV +AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001845.fa new file mode 100644 index 0000000000000000000000000000000000000000..380c47c42c94dfd8dfd7a4b7f4230a8a8439557a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001845.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_01016 +MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAKAERIARQLEVGMANVN +TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQTYFVQD +>GCF_003691675_PROKKA_00730 +MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVTADIHDAFVAELVSLAEAMKPGEAA +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN +TPAGEGAEIPFGGIKRSGFGRELGPLGMDEFVNKQMYFVQD +>GCF_005280335_PROKKA_01872 +MSTPTGYRVQDPSTDQVVETFPTLADGEVDQLLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETFEGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERVARQLEVGMANVN +TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD +>GCF_023573625_PROKKA_00960 +MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD +LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM +IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV +PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY +IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAT +DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD +AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN +TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001848.fa new file mode 100644 index 0000000000000000000000000000000000000000..785af72dbb6f09d39baefeb9b979615f13f7a42a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001848.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_01076 +-MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLM +LAAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVI +GEMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVG +GYDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEA +VQNAAACSGHLRILVQPDHTPES-VPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLH +EALASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA +>GCF_003691675_PROKKA_00795 +-MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLM +LAAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVI +GEMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVG +GYDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEA +VQNAAACSGHLRILVQPDHTPES-VPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLH +EALASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA +>GCF_005280335_PROKKA_02322 +MTQSPVFVILATIALIALSALFVIMEFSLLAARRHRLEAEAGTSRAARAALRSVDELTIM +LAGAQLGITLATFALGAITKPAVDAWLGPVLTGWGLPAAVAGTASFFLSLLLVTFLHLVV +GEMAPKSWAIAHPEFAAKAVAGPARAYVWAVRPLLAFANAVANRLVAASGVTPTDRAAVG +GHDADSIRQLVEHSASSGALDEQAHGQISGALDLQDATVGDLVSPPRDLVTVPADATAED +VQAASVASGHLRILVRPADGPDDGVPGVVHVRDTMVLGPREPVAPLVQEALTLPVDTALH +EASSAMRAAGRQLAVVTSEGRTVGVVTLTDLFRRVLPVSG +>GCF_023573625_PROKKA_01025 +-MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLM +LAAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVI +GEMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVG +GYDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEA +VQNAAACSGHLRILVQPDHTPES-VPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLH +EALASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001854.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca6d6eaaf68364fc2877ea34e5a151d77df5db2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001854.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01160 +MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR +YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV +APSPAA-AEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAA +ETWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADAVRARPHSRT--GASS +>GCF_003691675_PROKKA_00879 +MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR +YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV +APSPAA-AEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAA +ETWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRT--GASS +>GCF_020097155_PROKKA_01627 +M-------------------------LVRAARAAVHELGPTASMDEIAAHAGTSKSVFYR +YFGDRAGLRQAVAERVTASMERRLREAAVDAPDGVSALHRMVAECLSVAASSPAVYAFAV +TQGGAADGTGPDLGPFFERIAALLAEGLARTLPAADAGPGTT--LVLWPRVAVGTVRAAV +EAWLATEESVRPDPVRTAHDVAGWLLAGLRSADPSAS--PAA------DTHTPTQQGEPS +>GCF_023573625_PROKKA_01110 +MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR +YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV +APSPAA-AEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAA +ETWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRT--GASS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001855.fa new file mode 100644 index 0000000000000000000000000000000000000000..a9d770d1cf7a1cb39fd5015235d6e99adade984c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001855.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_01212 +MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT +SSRLGSVVEPFMHSTLQLARGRGELHIVSQAQLLHPYATMLAADYDAYTVAGALAEAVER +VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP +GPHTALHVGLGGAVCPACRPPGAAHPAPETFDLLSALAAGGWATADASGAPARREAAGIV +AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP +>GCF_003691675_PROKKA_00931 +MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAMAKGVRKT +SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER +VPAVDDDGRRAQYRLFHGALAALARGAHNPRLILHSFLLRALAQAGWAPTFDRCARCGAP +GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADTSGAPARREAAGIV +AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP +>GCF_020097155_PROKKA_01573 +MS-------GARHGGYSANSFRTEAIVLRTHRLGEADRIVEAITPEHGVLRCVAKGVRKS +SSRFGSVVEPFMHSTLQVARGRGELHTITQAQLLHPYATAVAADYEAFAVAAALAEGVER +IPALDADGRRAQYLLFHGALAALARRAHDPRMILHSFLLRTLTQAGWAPTFDRCARCGAP +GPHTAVNVALGGAVCAEHRPPGSASPAPETFALLTALTAGDWAVVDTAGPLARREAAGIV +SAYLQFHAERRLVALSVLDQEIAPPAPRAERSA +>GCF_023573625_PROKKA_01169 +MSASGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT +SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER +VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP +GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADASGAPARREAAGIV +AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001858.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ecfe80867f8db61654a5c86f3a67935728c5d1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001858.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_01290 +MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS +ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS +>GCF_003691675_PROKKA_01009 +MTTETAADETGTDAGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS +ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS +>GCF_020097155_PROKKA_00710 +---------MSVDNDSHQHGYISDKERYLGRMKRIEGQARGIAKMIDEEKYCIDILTQVS +ALTRALQGVATGLLDDHLKHCVLDAAKLSDE-AAVEKIQEATDAINRLVRS +>GCF_023573625_PROKKA_01248 +MTTETAADETGADTGAHRHGYISDKDRYRNRMKRIEGQARGITKMIDDEKYCIDILTQVS +ALTRALQGVATGLLDDHLKHCVLDAAKKGDEDAAIAKIQEATDAINRLVRS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001861.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e5ec221ee0e8fec33052a2dda5d8f17a853719f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001861.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_01357 +MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS +MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG +KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN +LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCAL-EGTRGCYEVRDPMD +LALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMV +AITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIF +YGDWLIRQGGLAGVTP +>GCF_003691675_PROKKA_01077 +MIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS +LVLAYLITHGLLAVLGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG +KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPASGVILFVIWSN +LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCAL-EGTRGCYEVRDPMD +LALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMV +AITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIF +YGDWLIRQGGLAGVTP +>GCF_020097155_PROKKA_01431 +MIGLLIGGVLGLILSGLGTPLFIRYLVKRGYGQQVRDDGPQTHKSKRGTPTMGGFVIISA +LVLGYLLTHGILALLGSELAGPTASGWIVLLLTVGMAFVGWIDDYTKIAKQRSLGLTPKG +KIILQGLIGTAFAVLALLFPNADGVTPASTAVSFVRDIPWLELAFAGPVVGVVLFVIWSN +IITTATTNAVNLTDGLDGLAAGATAMVTGAYVLVSLFQASQSCGLTEGAEACYVVRDPMD +LGLLAAVLTGALLGFLWWNTSPAKIFMGDTGSLGLGGALAGLAILSRTEILVVILAGLMV +AITLSVIIQVGWFKISGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLISLVCVIIGLALF +YGEWLLQHGALQAVAR +>GCF_023573625_PROKKA_01312 +MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS +MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG +KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN +LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCAL-EGTRGCYEVRDPMD +LALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMV +AITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIF +YGDWLIRQGGLAGVTP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001862.fa new file mode 100644 index 0000000000000000000000000000000000000000..5da24db1b8bf0c5ab51d13425c692ef14e0540c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001862.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01382 +MSVTS------------EIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALV +APFEGRFDLVAGLEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIE +VSEDLRA-GSRVLLLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDT +HVLFAA +>GCF_003691675_PROKKA_01102 +MSVTS------------EIARARSLIRVVPDHPSPGVAFQDITPLLADARALRACVEALV +APFEGRFDLVAGLEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGNASIE +VSEDLRA-GSRVLLLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELTALGGRAVVPDT +HVLFAS +>GCF_020097155_PROKKA_01893 +MSGVALSAAGRQAADVPGLERAATLFRSVPDFPTDGVVFQDITPVLADPAALRAVVEAMI +APFEGAYDAVAGLDARGFLLAGFAAALTGTGVIPLRKAGKLPVSVAHVDYALEYGAASLE +APPELAVPGVRVLILDDVLATGGTLAAARDLAERCGAEVAGSAVVLEVEGLGGRERCPDA +LTLFSA +>GCF_023573625_PROKKA_01337 +MSVTS------------EIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALV +APFEGRFDLVAGLEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIE +VSEDLRA-GSRVLLLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDT +HVLFAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001863.fa new file mode 100644 index 0000000000000000000000000000000000000000..8cfa6ee1a0cccf9fdf0cc5c8b117fa5a6289bde1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001863.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_01405 +MTEHTR-DDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEG +VDLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVRE +ELHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGV +DAGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVK +GGRR +>GCF_003691675_PROKKA_01135 +MTEHTR-DDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEG +VDLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVRE +ELHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGV +DAGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVK +GGRR +>GCF_020097155_PROKKA_01402 +MTEHTQHDDAARPALVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHVLDSG +VDLADPDAIAGAARAMDLRQSTDPDVESVVVGGTDVTDAIREDRVTDVVSTVAVVIPVRE +ELQRRQRAAIAGAGRIVAEGRDITTVVAPDAHARVLLTASAEARMARRSGQLQRAGAGER +DAATLERQVSGRDARDSAVSTFDRPAEGVALVDSTELDFEQTVAAVLAAVQDQAGVDAVP +G--R +>GCF_023573625_PROKKA_01355 +MTEHTR-DDVAPAPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLHEG +VDLADAEAVAAAAVAMDLDQSTDPDVEAVRVGGTDVTEAIRGPEVTDTVSTVAVVIPVRE +ELHRRQRAAIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGETGV +DAGTLHRQVAGRDARDATVSTFDRPADGVALVDSTELDFEQTVAAVLAAVEDQAGIPAVK +GGRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001865.fa new file mode 100644 index 0000000000000000000000000000000000000000..8bbe4f8cd752667ed9f0f790beb3ec3eb9f33a05 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001865.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_01410 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------MVQQRVVRAPGRSDPGGSVPPTALAAAAREGV +TTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHTALALVESGRLEAARAVLSRRAADEEASDDVLA +ALLDAKAAQARERGVALTWSAELTAPAPLRPLDLLTVLGNLVDNDLDAAAAPDLSAVDRWVDVEVVSDATGLVVQVADGG +PGPSDADRRRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVATDSGTVFTVEVPREPTPQEET-- +>GCF_003691675_PROKKA_01140 +MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALVSALRA-GDAPALQAGIDGWI +AEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGDTVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQI +SDVAIMAQAQIPGILLGSAAVAAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRARLHND +AAARLLGWEGAGE-------PRLPTELSAALPGAVSGEASLAAGGRVLVVQQRVVRSPGRSDPGGSVPPTALAAAAREGV +TTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHTALALVESGRLEAARAVLSRRAADEEASDDVLA +ALLDAKAAQARERGVALTWSAELTAPAPLRPLDLLTVLGNLVDNALDAAAAPDLSAADRWVDVEVVSDAAGLVVQVADGG +PGPSDADRGRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVATDSGTVFTVEVPREPTPQEET-- +>GCF_020097155_PROKKA_01396 +MRHPWSIARRVAASLVLLLSVIAVFSGWAGWRQARDATFVVEERHVLGVARLAAREEVVVDALGSPAGAAALQARIPSVV +DDAGVSWLTLLDARGTRVASWRPEQVGTAYPAPVDRALAGESWTEVSATGPAGISVRALVPVRDAE-GAVVGVLTMGVRV +SELEVAASAQLPRLAVTFALTLAAGLGAALLVARYLHRVTLGRGPEDLAESFLLSAAAMDSLEASLVVLAPDGSIRQHNA +AAVHALGLPARTEDGTVPAAARLPEELARALEEHADADFPARVGDRLFVVRQRVLGA-ARPRRGGAVDD-----AAREGI +SPAPAGTRVLMLHDRTDLQRLTDDLALSRTLTAALRSQTHEHANQLHTALALLDSGRTDAARDVLTRHRRPDQDAEDVVS +ALLEAKAAQAAERGVELTYAVRLSAPAPLAALDLVSVVGNLVDNALDAAADAAEPA-GRWVDADVTCDADGLLVQVADGG +PG-LDPDGDRVFEPGWSTKPAGIAGRGMGLALVRSIASQAGGVVEVATDSGTVFTVEVPPAGPEQDGEAA +>GCF_023573625_PROKKA_01360 +MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALVSALRA-GDAPALQAGIDGWI +AEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGDTVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQI +SDVAIMAQAQIPGILLGSAAVAAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRVRLHND +AAARLLGWEGAGE-------PRLPTELSAALPGAVGGEASLAVGGRVLVVQERVVRAPGRSDPGGSVPPTALAAAAREGV +TTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHTALALVESGRLETARAVLSRRAADEEASDDVLA +ALLDAKAAQARERGVALTWSAELTAPAPLRPLDLLTVLATW-------WTTPSTPPPHRTCPRQT-------------GG +ST-----------SKWSRTPRA--------WWCRWPTAAPDPPTRTAAGSSTGAGRRSPSAPPDAAWGCG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001867.fa new file mode 100644 index 0000000000000000000000000000000000000000..653d6378b6838bbeda93451ce098faf142888597 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001867.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_01417 +MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD +GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ +VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA +DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH +RAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRGLEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE +DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE +AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR +>GCF_003691675_PROKKA_01148 +MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD +GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ +VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA +DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH +RAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRGLEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE +DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE +AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR +>GCF_005280335_PROKKA_01482 +MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD +GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ +VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA +DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH +RAKVGIRWVAADECATPEGAAAALADVDAVCVPGGFGVRGLEGKLDALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE +DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE +AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR +>GCF_023573625_PROKKA_01367 +MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD +GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ +VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA +DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH +RAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRGLEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE +DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE +AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001873.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6a743d277eaa1fbc37169b67f79270369d2e56d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001873.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_01506 +--------------------------------------------------MLATTLEQIS +VAGARGRPRIRPDRLIADKGYPSKANRAWLRRHGIAATIPERADQITHRRRRPGRPIDFG +EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARNYHAGLSLAATLHWLTTLL +>GCF_020097155_PROKKA_00640 +---------------------MTTKIHLVCDGKGRTLAFVLTGGQVADTSMFPDTIDEIR +VVGVKGRPRTRPERVIADKGYPSKKNRAWLRQRGIATTIPERDDQIAHRRKKPGRPIDFG +RDQKRRYKGRNAVERCFNKLKQWRGIAARSDKTPRNFHAGLSLAATLQWV---- +>GCF_020097155_PROKKA_01746 +MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS +VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG +EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL +>GCF_020097155_PROKKA_02236 +MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS +VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG +EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001875.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001875.fa new file mode 100644 index 0000000000000000000000000000000000000000..b928a67c66116134632b86aa4c822cb163f943ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001875.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_01583 +MTTPRATLPSRRRGRTPARAALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE +GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT +GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLPPAELDNTYTLSVRQDRAEELGLE +TLADIKDLPTEEQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG +SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL +DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD +>GCF_003691675_PROKKA_01294 +MTTPRATIPSRRRGRTPARAVLAVLGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE +GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVADVVDVEWDYT +GTAWITYLGHTDPIPDPQAQWAAVRDEDAQQGLVWLPPAELDNTYTLSVRQDRAEELGVE +TLADIKDLPTEDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG +TCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL +DNATTARLNARVDVDGEEPTQVAWDWLREEGLITD +>GCF_005280335_PROKKA_01339 +MTTPRATLPSRRRGRTPARVALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE +GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT +GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLPPAELDNTYTFSVRQDRAEELGLE +TLADIKDLPTQDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG +SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYSAAPIVREEVLAQHPEIADLLAPVTARL +DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD +>GCF_023573625_PROKKA_01510 +MTTPRATLPSRRRGRTPARAALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE +GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT +GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLSPAELDNTYTFSVRQDRAEELGLE +TLADIKDLPTEDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG +SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL +DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001876.fa new file mode 100644 index 0000000000000000000000000000000000000000..33677e7f61b52a2bfb4fbd50edb2ae0d8849e847 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001876.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01586 +MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT +LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV +ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY +ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA +>GCF_003691675_PROKKA_01297 +MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT +LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV +ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY +ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA +>GCF_005280335_PROKKA_01336 +MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANALTAVGLT +LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPDVLEAARGMGMGPV +ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY +ALVGTLGIVVVALLLDGLLVLLGRLTISKGLRA +>GCF_023573625_PROKKA_01513 +MSEFLASRWPDILFRAWQHGWLVLQALAIATVLAIALAVIATRIKALTPIANAFTAVGLT +LPSFALIGVLIPLVGIGTVPAVVVVVFYALLPILRNALVGLRGVDPEVLEAARGMGMGPV +ALFTRVRLPLAWPVILTGIRVAGQLGMGVAAVAAYVLGPGLGSYIFTGLVSLGGANALNY +ALVGTLGIVVVALVLDGLLVLLGRLTISKGLRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001877.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001877.fa new file mode 100644 index 0000000000000000000000000000000000000000..65aa86404b3f6daf1f51d49da4477d243537a036 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001877.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01588 +MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA +VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL +GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL +GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE +DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG +ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG +AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA +NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR +RAVRAEAERDLRG +>GCF_003691675_PROKKA_01299 +MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA +VSSALIGCALGAWFAGPVANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL +GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL +GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE +DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG +ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG +AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA +NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR +RAVRAEAERDLRG +>GCF_005280335_PROKKA_01334 +MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGPGLTGFT +VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL +GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLSDALFATMAGGAAQPFWL +GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE +DIRRSLDSEHRESLADLRGPAAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG +ESDALTVTVITSVTNIAVTFIAIALVDRVGRRPMLIAGSAGMAVSLGLMALAFSFAETGG +AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA +NFTVSTTFPWLADIGLTLAYGLYALMAALSLAFVAAFVPETKGKTLEQMSDIVVRSPGQR +RAGRAEAERDLRG +>GCF_023573625_PROKKA_01515 +MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA +VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL +GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL +GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE +DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG +ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG +AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA +NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR +RAVRAEAERDLRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001880.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001880.fa new file mode 100644 index 0000000000000000000000000000000000000000..dc44cb2ad4e956a2f742f390636db93ddf00949e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001880.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_01625 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------------------------------------MRLR +FNDYRDKPAVDPRYFTDPEGHDMAVAVAGIRLAREIVSQPAMA-AWAGRELAPGEQ-AQTDEEIADYVRRTHNTVYHPVG +SVRMGADDDAMSPLDARLRVKGVTGLRVADASVMPEHVTVNPNITCVMIGEKAAQLILA-DRA +>GCF_003691675_PROKKA_01331 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------------------------------------MRLR +SNDYRDEPVVDPRYFTDPEGHDMAVAVASIRLAREIVSQPAMA-AWAGRELAPGEQ-AQTDEEIADYVKRTHNTVYHPGG +SVRMGADDDAMSPLDARLRVKGVTGLRVADASVMPEHVTVNPNITCFMIGEKAAQLILA-DRA +>GCF_005280335_PROKKA_00817 +MTAEPLTTDAPDDGTPAHES---DVLVIGAGSAGCVLARRLL-DAGRTVTLVEAGDQDVNPD-IDDVSRLGFLWESEVDW +NYRTTPQPGLAGRSLHLPRGKVMGGSHALNATIWVRGDAWDYDTWAAEHGCTGWSWQDVLPYFKAIENTALGEDAVRGRD +GLLDISTDYPHHPIQQAMYDATVQEGVPENPDYNSGD--VEGVGWMQLNVR-DGKRFNTWRAYLKPVADHEGLTLVTGAQ +ARRLLLDGT-RVTGAEF--DRDGETLTITAD-EVVLCAGALGSPEILLRSGVGPADHLREVGVDVAHDLPGVGRNLHDHL +LVPVVGVTEKEAPAPEVAVAQVHYFAKSDPALPVADTQPIFFSVPMYTNTAGDPMVGPETGFSLLAGIVRPLSRGSLTLS +GPAPEDPVQVDLGAYTAPE--DLQAMLFSLRQCRRIAAQPALAEGWGATEIHPGPNVGDTDEELIAYIRNTTTTYHHQVG +TCAMGSGEDAVVD-PATLRVYGLEGLRVADASIMPQVTSGNTNAPSVMIGERAAAMITGVEPF +>GCF_023573625_PROKKA_01554 +M-----TTTTPDASTPQPDTPVYDYIVVGGGSSGAALAARLSEDPQISVALLEAGPTDVDLDEVLELRRWPELLESGLDW +DYPIEPQENGNSFMRH-SRAKVLGGCSSHNSCIAFWPPREDLDQWEA-MGATGWGAEHTLPLVKKLENNR-AEGDHRGHD +GPVELMDVPADDPAGVALLEAAAQAGIPTT-TFNTGETVVKGANWFQINRKQDGTRASSSVSYLHPILDRENLDILTDHW +VSEVLFDDDRRAYGVRHVADRHGRQAEIHARAEVILSAGAINTPKLLMLSGIGPAEHLAEHGLDVRVDAPGVGSNLQDHP +EAVISWESKQPMYRDATQYWEIGIFSPTKEGLDRPDLMMHYGSVPFDMHTYRQGYPTADETFCLTPNVTHAKSRGTVRLR +SNDYRDKPAVDPRYFTDPEGHDMAVAVAGIRLAREIVSQPAMA-AWAGRELAPGEQ-AQTDEEIADYVRRTHNTVYHPVG +SVRMGAEDDAMSPLDARLRVKGVTGLRVADASVMPEHVTVNPNITCFMIGEKAAQLILA-DRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001884.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc3d708c0b6ea5f2a600aa0d6ab396ff984f0199 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001884.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_01683 +-MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSS---- +GTHADPATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHR +LTTLSAYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLE +ACFGDTAAGRWVAAHAAEYGFVIRYPVGAEDVTGFAHEPWHLRYVGSAEAARVEAAGGVL +ETAWGLPPAPDYAD +>GCF_003691675_PROKKA_01387 +-MRRTLPLAALAALALLAAGCGTPAAGPSSTPTTPTSGSASAAASSRAASSTAPSS---- +GTHADPATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAADLLDAAAAAGHR +LTTLSAYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLE +ACFGDTAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVL +ETAWGLPPAPDYAD +>GCF_005280335_PROKKA_01195 +MARRALPAAGLAVLAALAAGCSLSDGQPAPSETT-SAPAASSASPSGTATGPAPSSAAPA +GAHSDPAALDVVVNKARPLSPVDWAPQDLVPVPGSDLPLRAEAARAAGGLIEAAARSGHA +LSTLSAYRSHAYQAQTYGHWVDELGRQEADRVSARPGHSEHQTGLAWDVGDPESPQCHLE +ACFGDTAAGRWVAEHAAEHGFVVRYPAGAEHVTGYAPEPWHLRFVGREAAAAVEAAGGVL +ETAWGLPAAPDYPG +>GCF_023573625_PROKKA_01612 +-MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSS---- +GTHADPAALDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHR +LTTLSAYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLE +ACFGDTAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVL +ETAWGLPPARDYAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001886.fa new file mode 100644 index 0000000000000000000000000000000000000000..82ed863c45955179811af2cc81d731d2c50a87db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001886.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01780 +MTR-VPPAHGHRPALRDSTGSAHGPG-VEPGARPRLSAEDLLAARDALAPFGRLSRQEPI +EWAAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVD +WNDDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGT +AWARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLGAV +>GCF_003691675_PROKKA_01487 +MTR-VPPAHGHRPALRDSTGSAHGPG-VEPGARPRLSAEDLLAARDALAPFGRLSRQEPI +EWAAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVD +WNDDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGT +AWARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLRAV +>GCF_020097155_PROKKA_01021 +MDRHLLPA---------------GPGEVTPRPRIALDPARLHAARAALSVFGPVHRQEPI +EWAAEEPLAPDLAEFYREVGPDWVEIDTLGLPLLMFPLERLWDEQAGYRWNHRTGAMLAD +WNEDWTVVAKQGAEPFIHEAATGHVLMAHGEEGWEDRLGEPVPVFRDVAEMTLALCAAGA +AWAGSDDPFTADWHVRPEVTSAVVDGLEQVLGDRARAVDVARRLGHLRAA +>GCF_023573625_PROKKA_01709 +MTR-VPPAHGHRPALRDSTGSAPGPG-VEPGARPQLSAEDLLAARDALAPFGRLSRQEPI +EWAAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNHRTGALLVD +WNEDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPEPVFRDLAEMTRALAAVGT +AWARFDDPFTVDWHLTEEVTTAVVAGLEAVLGAHDRAVDLARALGYLRAV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001889.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1d8852db2c85c78266892aedf81dd049c06a7b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001889.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_01846 +MSGERV-------------GFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVV +ASDRISAYDHVLEPPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVA +GRAMVVKRLDMFPVECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSA +KAEVGEHDENITFEQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVD +PATGQVVLGDEVLTPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPP +ELPADVVAKTRDRYVEAYERLTGRPFDA +>GCF_003691675_PROKKA_01542 +MSGERV-------------GFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVV +ASDRISAYDHVLEPPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVA +GRAMVVKRLDMFPVECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSA +KAEVGEHDENITFEQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVD +PATGQVVLGDEVLTPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPP +ALPADVVAKTRDRYVEAYERLTGRPFDA +>GCF_005280335_PROKKA_01022 +MSHETPASDTTPHSGAAPRGFAGAEALELPGWRHVYSGKVRDLYEPADAAPGESETLLVV +ASDRISAYDHVLSPPIPDKGAVLTQLTLWWFERLSEGYNGAAGAPVEHHVVSTDVPEAVA +GRAMVVKRLRMFPVECIARGYLTGSGLAEYRESGTVTGLPLPTGLVDGSRLDPAIFTPSA +KAEVGEHDENITFEQMSERVGAEAAERLRYLTLDLYSRAEAIARDAGIILADTKVEFGVD +PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTSDASGWDRASGAEPP +ELPADVVEKTRARYVEAYERLTGRPFEA +>GCF_023573625_PROKKA_01766 +MSGERV-------------GFTGAEALELPGWRHVYSGKVRDLYEPADAEPGRSATLLVV +ASDRISAYDHVLEPPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVA +GRAMVVKRLDMFPVECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSA +KAEVGEHDENITFEQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVD +PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTGPDSGWDKAGGEAPP +ALPADVVAKTRDRYVEAYERLTGRPFDG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001891.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b74a9eaf586f8e8913356276fe542b9e88a1deb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001891.fa @@ -0,0 +1,48 @@ +>GCF_002008305_PROKKA_01878 +MPTPPDLSAFRTPAA-------------------------------------------TGRPPRGLRLGLAAALAVVWFA +VLGLGGPVFGRIGDVSSNDQATFLPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVT +DVAGPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHVGGPAGLVAELGGAFAGI +DGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVAVYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVA +RHREELLVRADVGEALRAAVRGSFGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGR +AAFWPTIPSPERARRRAQRRAARGRAFTPPLDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVWVATTVVLLALCGGLLQL +RADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAGDAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGVTD +------AEGGAG---AASAPEPQPRVVDGRVLVSATLADPGESLAAQQTVARLRDRLADLPATGEILVGGPAAQALDTNV +TTQRDLRVVIPLILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFVFLVALGID +YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMVQLAFIVAFGVLLDTLIVRSLLIPA +LVRDIGPKVWWPAKVD +>GCF_003691675_PROKKA_01574 +MPTPPDLSAFRTPAA-------------------------------------------TGRPPRGLRLGLAAALTVVWFA +VLGLGGPVFGRIGDVSSNDQATFLPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVT +DVAGPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHVGGPAGLVAELGGAFAGI +DGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVAVYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVA +RHREELLVRADVGEALRAAVRGSFGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGR +AAFWPTIPSPERARRRAERRAARGRAFTPPRDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVWVATTVVLLALCGGLLQL +RADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAEDAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGALD +------AEGGAG---AASAPEPQPRVVDGRVLVSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNV +TTQRDLRVVIPLILAMLLVVLAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFVFLVALGID +YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMVQLAFIVAFGVLLDTLVVRTLLIPA +LVRDIGPKVWWPAKVD +>GCF_005280335_PROKKA_00981 +MRTPPDLSALRSPDARRAAGSADPDSAAGRPEGLGASAAGRDGERTDGRTGDRTGERTAGRPSAWLRFGLAAALFVVWFA +VMGLGGPTFGKIGDVSSNDQSTFLPASAESTRAGEEAAAFRDGEAVPAVIVAEADLSDPAQAFPALGGLAETLRGVDGVT +DVAGPIPAEDGEAVQFLAFVDSSDGAEREVADVVEDLKGILADPAAADADLADTVAADADWHLGGPAGLATELGGAFAGI +DGLLLLVALVVVFVILVIVYRSVLLPILVLLTAVGALCAAILAVYGMAVAGWIQLNGQAQGILSILVIGAATDYCLLLVA +RHREELLVREEVTASLLAAVRGSFGAITASASTVALALLILLVSDLNSNSSLGPIAATGILFAWLAALTLLPALLQLAGR +AAFWPTVPSPENARRRATRRAERGRAFVQPEDAAGRPLAGLEEDHGVWTKVGAAVARRPRPVWLATLAVLLVMSAGLLQL +QASGVAQEDVLLGESDSRQAQALLTEHFDAGSGAPAQIVAPAEDADAVLAAVEADPGVAEASVTTDEAPAPAGPPPGVTG +GGEGTPAEGGAGRPEAAPQPDPEPKVVDGTVLISATLADPGESLAAQATVERLRAELADVGSGGEVLVGGPAAQALDTNT +TSQRDLVVVIPLILAMLLVILSMLLRSILAPVLLVAATVISFGAAMGVSALVFRHVFGFENADPTVPLYGFVFLVALGID +YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMLQLAFIVAFGVLLDTLVVRTLLIPA +LVRDIGPKVWWPARAE +>GCF_023573625_PROKKA_01798 +MPTAPDLSAFRTPAA-------------------------------------------PGRPSRGLRLGLAAALAVVWFA +VLGLGGPVFGAIGDVSSNDQATFLPASAESTRAGEEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGLLGEVPGVV +DVAGPIPSEDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAAAPALAGTVAADTEWHVGGPAGLVAELGGAFAGI +DGLLLLVALVVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVAVYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVA +RHREELLVRAEVGEALRAAVRGSFGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGR +AAFWPTIPSPERARRRTERRAARGRAFTPPRDGAGRPIAGLEEDHGVWTRVGTVVARRPRPVWVATTVGLLALCGGLLQL +RADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAGDAEAVLAAVAEDPGVAEAEVTADAPEAAAGPPPGVTD +------AEGGAG---AASAPEPQPRVVDGRVLVSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNV +TTQRDLRVVIPLILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFVFLVALGID +YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMVQLAFIVAFGVLLDTLVVRTLLIPA +LVWDIGPKVWWPAKAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001893.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e300dceab700266165911dd3122ec93cf0cbb95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001893.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_01892 +MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPPAPAATPSPVADLESVRAAIRAHGGPLASTAHVCGRPA +PTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVPVEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPAR +PAGDDAAAGLLLALREPVREVFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP +ATAVDEAPTAPAPVKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGEIEDFFRDLPADAMPQDAPWH +FSVSEKIVAITQGRSYYTWEVRPSVAARVLSRLVTRTPAGIGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVF +YNVVGGNVRAIDGPTTYSTFPANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS +AAVLEAAFADNPLGQGRERTPLAVVVRMD +>GCF_003691675_PROKKA_01588 +MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRAAIRAHGGPLASTAHVCGRPA +PTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVPVEALLNSAFVDAHADERPADRGVPRWRLAGLVDAVLPPAR +PADDDAAAGLLLALREPVREVFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDPDAAPASP +AAAVDEAAGAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGEIEDFFRDLPAEAMPQDAPWH +FSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAGIGLGDPTTMQLAIQEAGLPRIVLAAAAGAAGKVAGKRGVF +YNVVGGNVRAIDGPTTYSTFPANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS +AAVLEAAFADNPLGQGRERTPLAVVVRMD +>GCF_005280335_PROKKA_00966 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------------------------MF +YNVVGGNVRAIDGPTTYSAFPANVSAKLPPADPDGVAREVSAMIRAADIPEWARRSFAGTVVMDANDIGRNALGRDTAAS +AAVLEAAFADNPLGQGRERTPLAVVVRMD +>GCF_023573625_PROKKA_01812 +MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRAAIRAHGGPLASTAHVCGRPA +PTPSAADAPRGLRGAARTLTATRRDVAARLADSRERADVPVEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPAR +HADDDAAAGLLLALREPVREVFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP +ATAVDEAPTAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGEIEDFFRDLPADAMPQDAPWH +FSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAGIGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVF +YNVVGGNVRAIDGPTTYSTFPANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS +AAVLEAAFADNPLGQGRERTPLAVVVRMD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001901.fa new file mode 100644 index 0000000000000000000000000000000000000000..f9074e212fed38d246eeb4a75f8e8a06b8c534c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001901.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_01917 +MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG +VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN +TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL +VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV +RRALEGAGVSIKAFA +>GCF_003691675_PROKKA_01613 +MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG +VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGQVRYVKPHGALYN +TIVRHEAHAQAVVDGVKAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL +VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV +RRALEGAGVAIKAFA +>GCF_020097155_PROKKA_00878 +MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAATCRAAVAAG +VTIGAHVGYRDLAGFGRRFLDCSPTELADDVLYQIGALEALAGAAGATVRYVKPHGALYN +TIVHHEEHAQAVVDGVAAFGADLPLLLLPGSVALEKAEKAGLRGVAEAFADRGYTPQGTL +VSRREPGAVLHDEDEVAARMVRLATEGVVTAVDGSDVRVAAESICVHGDTPGAVSMAAAV +RRALEDAGVTIASFA +>GCF_023573625_PROKKA_01837 +MSHAPQIDLNSDVGESFGSWTMGDDAAIMPSVSSANVACGFHAGDPSGIAQTCRDAVAAG +VTIGAHVGYRDLAGFGRRFLDCTPTELADDVLYQIGALDALARAAGGRVRYVKPHGALYN +TIVRHEAHAQAVVDGVRAFGSDLPLLLLPGSVALDKAAAAGLRGVAEAFADRGYNPDGTL +VSRREPGAVLHDEDDVAARMVRLATEGVVAAVDGTDVRVDAESICLHGDTPGAVAMAAAV +RRALEGAGVSIKAFA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001905.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c43722bfecf7abed514ca0c3d4241db3a02c515 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001905.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_01967 +MSELDE------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------LDFAALSAFLAWWFGKTGV +DWIRREDG +>GCF_003691675_PROKKA_01661 +MSELDE------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------LDFAALSAFLAWWFGKTGV +DWIRREDG +>GCF_005280335_PROKKA_00892 +MSELDELDFVAVEIHTAGTDPASVCAVDMALVRGGEIVAAERWPVRPPTGPTSFSRLHTQ +LHGVDEAAVADAPEWPEVAAQLDLLGEHLPFVASGADRDRGAYEAATRATGGTPQAHEWR +DALALVGRLRPDVDPPRIATAAQALGVPDGARPAGAGSEAVRTAEVVLALARQSGRGTVR +RLWSEAAPPTPDEPIIPESLRRRHATEPSVPPAGAHRWAPPAPAPAPASAAPAGRGGGVG +WKLAGTAMVGIALGAALFFVASVAVIMEYLEDGRGSDATVGMGIAALSAFLAWWFGKTGV +DWIRRQDG +>GCF_023573625_PROKKA_01893 +MSELDE------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------LDFAALSAFLAWWFGKTGV +DWIRREDG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001908.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6938fa234c2d9aff4a263abcd2139c63d1bc9ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001908.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_01996 +MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP +LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA +ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV +DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA +AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY +>GCF_003691675_PROKKA_01690 +MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP +LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA +ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV +DGIDGVFIGPSDLSASLGLLGQQSHPDVVAAVEEVITKVKAAGKIVGVNAFVPAQADAYA +AAGADYVNVGADVALLARAAEALADRWCPAPSNAAADGQSAPRASY +>GCF_020097155_PROKKA_00797 +MPVRLNAQPLVRDLFTPEARAARGGRPAAGMFLSSGDVTAAEICAGAGMDYLLIDGEHAP +LSLESVLAQLRAVAGYGVPVMTRVPSLDAVLVKQFLDLGAQTLLVPMVDTAEQAAEAVRA +VRYP----PHGVRGVGSALARSGRWNRIDGYLTHDADHVGLFVQIETAAGVENARSIAET +SGVDGIFVGPSDLSASMGLIGQQTHPDVVAAVQSVIAAANAAGTVVGVNAFAEPQARAYA +EAGADFVNVGADVALLARAAEALADTWCPTP-EAAADDDAGSRASY +>GCF_023573625_PROKKA_01922 +MPVRHNPQPLFRDLFTPEAVAARGGRPAAGMFLSSGDPTTAEICAGAGLDYLLIDAEHAP +LTLQDVLAQLRTIAGYRVPTLVRVPALDTVAIKQFLDLGAQSLLVPMVDDAAMARRAVAA +ARYPDGSAEGGVRGVGSALARSGRWNRIPGYLPGAADHVSVIVQIETAAGVRNADEIAAV +DGIDGVFIGPSDLSASLGLLGQQSHPEVVAAVEEVIAKVKAAGKFVGVNAFVPAQADAYA +AAGADYVNVGADVALLARAAEALADRWCPAPSDAAGDGEGAPRASY + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001910.fa new file mode 100644 index 0000000000000000000000000000000000000000..e00d583b013cc8f26e83de36c9458c4acd172300 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001910.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02001 +MKILPPRSAASPRPLAPAVAVAALSILVGGLLPQSPSATTEGAPDARPRDDAARATT---VGAAATPASAAPVEGAGVAT +VPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDAVKRVEIRVRQDGAWGPWQVLDRPVLPEDAAPARTGTD +PFVAFGADGAQLRVTTVDGAAPAGLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGEEPAEARTV +ATVSDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIYAYYTKTLGWGDFPYHLI +TDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGVSTMGNYDVVAPSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGST +KYAAGTPVTVDTIFPHRATSATACPGQHLMARFDDLRDRAEAIATAAGQP---------PAAVT-----PAPTPAPTTER +STAGTYTVQPNDGWWTIARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIARRT +GVSAAELQRLNGMTASTVLHPGMVLITAATAPASPPAPAPAPG----TYTVREGDGWWIIAHRTGVTMETLQRLNGMTAT +TVLHPGMVLRTGQ--TASAPAPSPATYVVQANDGWWLIAQRTGVSMERLQRLNGMTVSTMLHPGMVLRTA +>GCF_003691675_PROKKA_01695 +MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATT---AGTATTPASAAPVEGAGVAT +VPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDAVERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTD +PFVAFGADGAQLRVTTVDGAAPAGLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTV +ATASDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIYAYYTKTLGWGDFPYHLI +TDRFGNIYEGRRGALNSNPLGTHAGGFNRGTMGISTMGDYDVVAPSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGST +KYAAGTPVTVDTIFPHRATSATACPGQHLMARFDDLRDRAEAIATAAGQP---------PTPAT-----PAPTPAPTTEP +STAGTYTVQPNDGWWIIARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIARRT +GVSAAELQRLNGMTASTVLHPGMVLITAATAPTSPPAPAPAPAPAPDTYTVREGDGWWIIAHRTGVTMETLQRLNGMTAT +TVLHPGMVLRTGQ--TASAPAPSPATYVVQANDGWWLIAQRTGVSMERLQRLNGMTVSTLLHPGMVLRTA +>GCF_005280335_PROKKA_00856 +MKLSAPRSAAPARS-PPAVVVAALSVLVGGLLPQQPVPTTAVPPPPPRLADAAALRTLAPAGSGRAPAAASEVRGAAVAA +VPQEGEALA---DAPAGVVLGEPVVDRPFTVAAAVWDAAADHAVERVEIRVRQDGAWGPWQVLERAVLPEGAAVTRTGTD +PFVAFGADGAQLRLTTADGAAPAGLELSLIDPGTAATDEAVASAHPAVSADQAAQDAALPRGVKSSAVVGGAEPAPARTV +STASEARARILPDVITRAQWGADESWAQASPQFEQVRALTIHHSAGTNDYTRAQAVEQMRAIYAYYTKTLDWGDFPYHLI +TDRFGNIYEGRRGALDANPLGTHAGGFNTGTMGISTMGNYDVVAPSEEVVDAMARATAYYLYRDGLDPYGRVTLTSGGST +KYAAGTPVTVDTIFPHRTTSNTACPGRHLMARFDDVRDRAATIAAAAGQEAPAPEPEPIPTPEPEPTPRPEPEPIPMPEP +TTPTTYTVQDGDGWWVIARRTGVPAATIQELNGMTESTVLHPGMVLRLVADVSAPAPTPVTTGTYTVQPNDGWWVIARRT +GVPAEELQRLNGMTADSLLHPGMVLITAATAPAPAPAPAPAPAPAPGTYTVRDGDGWWVIAHRTGVTMETLQRLNGMTAD +TLLHPGMVLVTGQNATAAAPAPAPATYTVRPNDGWWIIADRTGISMAELQRLNRMTASTLLHPGMVLRIA +>GCF_023573625_PROKKA_01927 +MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATT---AGTATTPASAAPVEGAGVAT +VPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDAVERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTD +PFVAFGADGAQLRVTTVDGAAPAGLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTV +ATASDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIYAYYTKTLGWGDFPYHLI +TDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGISTMGDYDVVAPSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGST +KYAAGTPVTVDTIFPHRATSATACPGQHLMARFDDLRDRAEAIATAAGQP---------PTPAT-----PAPTPAPTTEP +STAGTYTVQPNDGWWIIARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPDDGWWVIARRT +GVCAAELQRLNGMTASTVLHPGMVLITAATAPASTPAPAPAPAPG--TYTVREGDGWWIIAHRTGVTMETLQRLNGMTAT +TVLHPGMVLRTGQ--TASAPAPSPATYVVQANDGWWLIAQRTGVSMERLQRLNGMTVSTLLHPGMVLRTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001911.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ec9323046946ddbb1471392309adb0a2cd92bfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001911.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_02032 +MTELTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLTFGELADRSRRLATGLAARGV +TRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAGAARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWD +ALADSAPLAEDVAVGGDGPIALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT +LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVSTAGEPLPPSVLEWGRAALGTE +IRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAAEIRDGQIAIDAASPMFWFPGYLGEPEKTAERFTPDGRWYL +TGDTARQDDDGWFFFSSRDDDVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL +AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGATD +>GCF_003691675_PROKKA_01739 +MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLTFGELADRSRRLATGLAARGV +TRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAGAARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWD +ALADSAPLAEDVAVGGDGPIALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT +LVLGATSVQYRGAFSPATMVEVISSQDVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVSTAGEPLPPSVLEWGRAALGTE +IRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAAEIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYL +TGDTARQDDDGWFFFSSRDDDVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVADPDAL +AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAG +>GCF_005280335_PROKKA_00788 +MTERTGQASEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLTFGELADRSRRLATGLAARGV +TRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAEGAARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWD +ALADSAPLAEDVAVGGDGPIALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPDDLFWNAADHGWAYGLYYGIVGT +LVLGATSVQYRGAFSPATMVEVIRSQGVTNLAGAPTMFRALAKAGEVTEDAPLRLRRVSTAGEPLPPSVLEWGRSALGTE +IRDHYGQTELGMVICTLAHPELAAPPRPGSMGVPLPGIAAQIRDGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYL +TGDTARQDDDGWFFFSSRDDDVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVVAFVVPAGAVVDPDAL +AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD +>GCF_023573625_PROKKA_01967 +MTERTGQAHEAGTIDRLMAGWVADVETPDACAAHLLCDRWPADAVAFRFVAEDMSAVDLTFGELADRSRRLAAGLAARGV +TRGDRVPVMMSKREELVITLLALWRLGAVHVPLFTAFAAGAARMRIEGAAARLVVAEPRQAEKLTDIPGIEIIRTGPEWD +ALADSAPLAEDVAVGGDGPIALLFTSGTTGRPKGVPVPLRAAAAFAVYLTCAVDLRPEDLFWNAADHGWAYGLYYGIVGT +LVLGATSVQYRGAFSPATMVEVIRSQDVTNLAGAPTMFRALAKAGEVAEDAPLRLRRVSTAGEPLPPSVLEWGRAALGTE +IRDHYGQTELGMVICTPAHPELAAPPRPGSMGVPLPGIAAEIRGGQIAIDAASPLFWFPGYLGEPEKTAERFTPDGRWYL +TGDTARQDDDGWFFFSSRDDDVILAAGYRIGPFDVESVLIDHPRVQEVAVVGLPDPEGVRGEEVAAFVVPAGAVADPDAL +AAELQAKVRDEYSKHAYPRRVHFVDRLPKTPSGKLQRFLLRQGAAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001915.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001915.fa new file mode 100644 index 0000000000000000000000000000000000000000..03969b6f72538a7280bf14b4d178a5c44e7e75aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001915.fa @@ -0,0 +1,44 @@ +>GCF_002008305_PROKKA_02048 +MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSAKKTFFAGGDLDSLAQAGPED +VESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEIALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMV +GVERALMEWLLQGTARDARAAMEKGIIDEVVTDPADLVPAAKRWILEHRDDA------------------DAAAKPWDVK +GFRIPGGTPAQASFASRLPAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQAFH +SDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAAERGRERVGALLEGRVAKGRMSR +EDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDSVFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHF +FSPVDRMKLVEIIRGEQTSQRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARHAG +FPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQGAGFYEYPEEGPKHLWPGLAEH +FATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPSANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADR +YGERFRPGDTLRQRAERGEGPGR +>GCF_003691675_PROKKA_01754 +MSEHMITWDQDTDGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSAKKTFFAGGDLDSLAQAGPED +VESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEIALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMV +GVERALMDWLLQGTARDARAAMEKGILDEVVTDPADLVPAAKRWILEHRDDA------------------DAAAKPWDVK +GFRIPGGTPAQASFASRLPAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQAFH +SDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAAERGRERVGALLEGRVAKGRMSR +EDADAVLARVQPTEDYQDLAHVDAVIEAVFEDVELKDSVFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHF +FSPVDRMKLVEIIRGEQTSPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARHAG +FPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQGAGFYEYPEQGPKHLWPGLAEH +FATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPSANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADR +YGERFRPGGTLRQLAERGEGPGR +>GCF_020097155_PROKKA_00732 +MTENTITWDQDAEGVVTLTMDDPTAKVNTMNGHWQESMRAAVERLEQERESITGVILTSAKKTFFAGGDLDQLGPSGPED +AEDVFAMTEHVKSLLRRLEKLGRPVVAAINGAALGGGLEIALACHRRVAVDDPRIKVGLPEVTLGLLPGGGGITRLVRML +GLEKALMDWLLQGTQYRPAQAKEKGVIDELVSSPEELLPAARRWILEQGAAAAKAREGGPEETDEALGAPSYAVKPWDRK +GFRLPGGTPQQPQLASRLPAFAATLVKTLHGADLPAPRAILSAAVEGAQVDFDTASRIETRYFTSLVTGRVSTAMVQAFH +TEMGAIRAGAGLGERVSERHTIATAAVLGAGMMGAGIAHALATSGIDVVLKDVSKENAERGKAHCADLVGKAVARGRMDQ +SAADEVLGRIRTTDDYADIAGVDAVIEAVFEDFDLKSEVFAEVEKVVGRQTLLCSNTSTLPITQLQGPRERAADFVGLHF +FSPVDRMKLVEIIRGEQTSQETVERAYDLVQQIRKVPILVNDGRGFYTSRVFGTLVLEAAAMVEEGVDPQRVERTARQAG +FPGAPLAMLDEVSLTLTQHVRREAEKAAEAAGTERAEQPGERVVDRMVEEFDRPGRARGAGFYEYPAEGPKHLWPGLREH +FAAEVDVSDEDLKDRFLYRMALETAACFEAGVLTDTASADIGGILGIGYPPHTGGPATFATNRPGGLADFVSRADALADA +YGERFRPSDWLRERAAAGQGLA- +>GCF_023573625_PROKKA_01982 +MSEHMITWDQDADGVVTLTMDDPQARVNTMNERYQDAMDAVVDRLEAERDTVTGVVLTSAKKTFFAGGDLDSLAQAGPED +VESVFALTQRVKGQLRRLETLGRPVVAAINGTALGGGLEIALACHRRIAVDDPGLKVGLPEVTLGLLPGGGGITRLVRMV +GVERALMEWLLQGTARDARAAMEKGIIDEVVTDPADLVPAAKRWILEHRADA------------------DAAVKPWDVK +GFRIPGGTPAQASFASRLPAFAATLRRQLHGADLPAPKAILSAAVEGSQVDFDTASRIETRYFVSLVTGHTSSAMIQAFH +SDMQALRSGAALGGPSRERSTITTAAVLGAGMMGVGIAHALALNGVDVMLKDVSLEAAERGRERVGALLEGRVAKGRMSR +EDADAVLARVQPTEDYQDLAHVDAVIEAVFEDLELKDSVFAEVEKVVGPDTLLCSNTSTLPITLLQGPRERSQDFIGLHF +FSPVDRMRLVEIIRGEQTSPRTVERAYDLVQQIRKLPILVNDGRGFYTSRVYGTLVLEAAALVEEGVDAQRIERAARHAG +FPASPLAMMDEVSLTLIQHIRREEEKAVAEAGGERPVRPGERVVERMVDEFGRPGRAQGAGFYEYPEQGPKHLWPGLAEH +FATGADVPEQDLQDRLLYRMAIETARCFDDGVLTDAPSANLGGVFGIGFPPHTGGPVTFMTHREGGPAAFVARADELADR +YGERFRPGDTLRQRAERGEGPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001916.fa new file mode 100644 index 0000000000000000000000000000000000000000..94abe759beb62ad5d21242c11f2e46fc04b0b217 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001916.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_02049 +MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV +SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAMNQAAARIRSGWESLLVAGGV +ESMSRVPMGSDGGAWAMDPATSLATDFVPQGVSADLIATREGFSRAELDRFAAQSHRRAA +AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSSVETLATLKPSFEALGREAGFDAVAL +EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM +LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH +PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV +>GCF_003691675_PROKKA_01755 +MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV +SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV +ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDSFAAQSHRRAA +AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLAKLKPSFEALGREAGFDAVAL +EKYSSLAEIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM +LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH +PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV +>GCF_020097155_PROKKA_00731 +MTRDAYLFDAVRTPRGLGKPTGSLHEVKPVGLLGGLFDALRERHPEWDPAGVDDVVLGVV +TPVGDQGGDIARVAALKAGMPESVAGVQLNRFCGSGLEAVNQVAARIRSGWEDMLIAGGV +EAMSRVPMGSDGSAWAMDPATALDLHFVPQGISADLIATRQGFSREDLDRFAVQSHHRAA +QAWSEGRFEGSVIPVTDMNGLTVLDRDETIRPDASLETLAGLRPSFAAMGEQAGFDAVAL +NRYTDVDEIHHVHHAGNSSGIVDGAALTLIGGEEAGRRAGLTPRARIVSAAVVGSEPTIM +LTGPTPACRKALDVAGMTASDIDLVEINEAFAAVPLQLMRDLGWNEEQTNVNGGAIAMGH +PLGATGAMILGTLVDELERRDLQTGIATLCIGAGMGVATIVERV +>GCF_023573625_PROKKA_01983 +MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV +SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV +ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDRFAAQSHRRAA +AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLATLKPSFEALGREAGFDAVAL +EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM +LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH +PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001918.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f22875ac97ef69b289a21db430bb5638e703f89 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001918.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02062 +MS---------------------EHFDVAVLGLGPGGEVAADRLLKAGK-NVVVFEREL---IGGECAYWACIPSKTVLR +PPEARTEVQRAAGVSGAELDWAATAKYR---DYMIRNLDDQAQVDGYIKEGA----------------VVIKDEARITGP +GRIQ------AGDREITAEH-IIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGV----------- +------ETATFLARFGVAITLIHCGERLLDREG------PRVGELAHQYLQEAGIDIRLATSAVQARREGADSIIELQTR +DGDP-------AGE-VAADVVIFGTG-----------------RTPRTEGLGFEHAGVTLGD----HGEIQIDDHCRAGE +NTW------------AIGDVTGIMPFTHVAKYQGRIAADAI----LGRPHPAT----------------------YDGIP +RVVFTDPEIAGAGLTQEQATKQG----IRTIATELDLADAIARPWTYEQDSRGHLGLLADADRKILIGAW--------AV +GPMAGEWIHHASLAIRTQLPIDTLLDQVAQFPTYHEAYQVALEQ--------------LDLT------------------ +--P +>GCF_020097155_PROKKA_02222 +MS---------------------EHFDVAVLGLGPGGEVAADRLLKAGK-NVVVFEREL---IGGECAYWACIPSKTVLR +PPEARTEVQRAAGVSGAELDWAATAKYR---DYMIRNLDDQAQVDGYIKEGA----------------VVIKDEARITGP +GRIQ------AGDREITAEN-IIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGV----------- +------ETATFLARFGVAITLIHCGERLLDREG------PRVGELAHQYLQEAGIDIRLATSAVQARREGADSIIKLQTR +DGDP-------AGE-VAADVVIFGTG-----------------RTPRTEGLGFEHAGVTLGD----HGEIQIDDHCRAGE +NTW------------AIGDVTGIMPFTHVAKYQGRIAADAI----LGRPHPAT----------------------YDGIP +RVVFTDPEIAGAGLTQEQATKQG----IRTIATELDLADAIARPWTYEQDPRGHLGLLADADRKILIGAW--------AV +GPMAGEWIHHASLAIRTQLPIDTLLDQVAQFPTYHEAYQVALEQ--------------LDLT------------------ +--P +>GCF_020097155_PROKKA_02426 +MTEDLAPTTGPDDATP--GAPDEEAVDVVVIGAGPVGENAAQYAHTAGGLEVALVEADL---LGGECSYWACMPSKALLR +PLEVAGAAAHLGGLTDPDIDLPGLLARR---DEWRSHLDDAGQVEWAEDAGL----------------RVVRGHGRLAGP +RRVEVLGDDGAPARVLRARHAVVVATGSTAVVP--GELRGVSPWTSRDATGVREVPGRLAIVGGGVVAV----------- +------EAATWMAALGSDVQLLVRGDRLLSGQE------PVASRLVLEGLVDAGVRVRFGTSVERAERADVHAESDVGVP +HGGPVRLTLAGSGETLEVDELLVAAG-----------------RRPALDGLGLEALGLSAEDLQDESGTAVVPASDGAAP +WLY------------AVGDVTGGPALTHWGKHRARLLGERIAALATGRPAPSG---------------EEAGEGVPEAVP +QVVFTSPQVARVGVTEAQAREEGGEGELRVVDVPLTSAAGAA---LLRDDAAGRAVLVLRGDR--VVGAT--------FV +GFEVAELLHAATVAIVGEVPLDRLRHAVAAYPTASEVWLRLVEEALGRG------------------------------- +--- +>GCF_020097155_PROKKA_02440 +MSSVI-----PDTARPSSGHAGVHRADVVVLGHGLAGLVAACELLEAGR-SVVLVDQERAADLGGQ-AWWSFGGLFLVDS +PEQRRLRVRDSVDLAWS--DWRETAGFTGGDDALPR-----AWAEAYVHFAAGEKRAWLRERGHRLFPVVGWAERKVPAP +G---------VGGNSVPRFH-ITWGTGP-GIVEPFAAVVEQAAFDGRLTYLPRHRVTELVTQNGAVCGVRGDRLADDDGA +RGTSSSRTVTGAFEVRAQAVLIASGGIGADHDAVRAAWPDRLGTPPERML--SGVPAYVDGSGVAAARAVGAHMLHPDRM +WHYT-------EGV-ANWDPVWPGHGIRILPGPSSLWLDAAGRRLPHPRWPGFDTLG-ALGEICRPGGARRAEG----AD +HTWFVLNERIIGREFALSGSEQNPDLT--GRSLGHVLGRAT----QGVPAPVRAFLDHGEDFVQAATVEELVDQMNELQD +RTGGGGPRVELHAVRQAVAEHEDG------------AARAGVDP---QLDAVRRARQYL-GDR--LIRTAAPHRLTDPAA +GPLIAVRLRTLTRKTLGGLHTD-LRGRVLDELGGPVPGLYAAGEAAGFGGGGMHGFRALEGTFLGGCLFSGRTAGRALAE +DVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001919.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001919.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b7c53f50dbec2da6057744e3b3c052981026e37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001919.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_02090 +MVTRPVLQQPVVDAVDIRSVAEFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV +LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRESLDAAHDHALRLGGRLVLDRSDDEDEP +LYVFADPAGHPFCVFVG +>GCF_003691675_PROKKA_01798 +MVTRPVLQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV +LTFQRTDELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP +LYVFADPAGHPFCVFVG +>GCF_005280335_PROKKA_00688 +MITHPALQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV +LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP +LYVFADPAGHPFCVFVG +>GCF_020097155_PROKKA_00604 +MVSRPVLQQPVIDAVDIRSVADFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV +LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVLDRSDDEEEP +LYVFADPAGHPFCVFVG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001920.fa new file mode 100644 index 0000000000000000000000000000000000000000..adc9fc31823065af8579204ced32beb9e08c3ac1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001920.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_02091 +MTDADLDDMFRLLGDAEVMRYYPRAKSRNEVRRWINWSKDNYATHGFGLWVIEHRTTGDF +IGDCGLTWQNVDGQEVLEVGYHVLPEHQGQGLATEGASACLRHGFETLDATMVTAIINPD +NMASRRVAERIGMTVWKSTRDPRGAPIVVYSSHGHEA +>GCF_003691675_PROKKA_01799 +MTDADLDDMCRLRGDAEVMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF +IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD +NMASRRVAERIGMTVWKRTRDPSRAPIVVYSSHGQEA +>GCF_005280335_PROKKA_00687 +MTDADLDDMCRLLGDAEAMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF +IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD +NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA +>GCF_020097155_PROKKA_00603 +MTDADLDDMCRLLGDAEVMRYYPRAKSRNEVQRWINWSKDNYAEHGFGLWVIEHRATGDF +IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRYGFETLCATMVTAIINPD +NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001923.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001923.fa new file mode 100644 index 0000000000000000000000000000000000000000..1baca4711aed2c6352251e389d947f651aaa04f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001923.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02101 +MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW +LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW +LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD +LAADLVGAGIGAALAVRRG-----RTR +>GCF_003691675_PROKKA_01808 +MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW +LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW +LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD +LAADLVGAGIGAALAVRRG-----RTR +>GCF_005280335_PROKKA_00678 +-------------------MLPLIPADLLRALGLVLIPAAWAVAGWPSAAVMLLVFGAQW +LTRWLVPGSALDWGAQAVLLAAGWFSVTGLYHRVEALDLVMHAAASAAVVGLVAVAARAR +LRRRGEDPGALVRRLGPVLSAAALTGAGVGLGVLWELAEWWGHTVVTAEIGVGYDDTIGD +LAADLLGAGAGAALAVRGQLRAAGSAR +>GCF_023573625_PROKKA_02041 +MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW +LTRWLAPGGALDWAAQAVLLLAGWLSVIGLYPRVPWLDLLVHAAASAVVACLTALVVGAW +LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD +LAADLVGAGIGAALAVRRE-----RTR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001926.fa new file mode 100644 index 0000000000000000000000000000000000000000..279d15b03a19e217a62c365afeb690dbfd636d56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001926.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02124 +---MSTEPTPSSATPETES-AAPSSSGLPQAAPQAAWPERVETGEHQVSYRATVAAPAHE +LWAMLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDE +LVEWAHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSL +TRLAGRHL +>GCF_003691675_PROKKA_01832 +---MSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHE +LWAMLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDE +LVEWAHPGGHRWRWAFRDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSL +TRLAGRHL +>GCF_020097155_PROKKA_00573 +---MSTEPTPSPATPETEP-AAPSSSGLPQSAPQAAWPERVETGEHQVSYRATVAAPAQE +LWAMLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDE +LVEWAHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSL +TRLAGRHL +>GCF_023573625_PROKKA_02062 +MGDMSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHE +LWAMLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDE +LVEWAHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSL +TRLAGRHL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001927.fa new file mode 100644 index 0000000000000000000000000000000000000000..7cd6434ee7a6ef028c082b1bd501fb17a842e00d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001927.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_02135 +MSEHTPAH---TPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA +EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL +LPQVQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV +HASSVHAAILGEHGDTEFPAWSSARIGPTPLLEWPTPADPLFTRADLDEVADTVVNAAYE +VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT +RVIQPELDAAEMRALHASADALRREARSLGF +>GCF_003691675_PROKKA_01843 +MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA +EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL +LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV +HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE +VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT +RVIQPELDDAEMRALHASADALRREARSLGF +>GCF_005280335_PROKKA_00637 +MSEHTPA----APASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA +EVLDLAHGTPFTSASAMTGGADPDVLADCEVVVITAGAKQRPGQTRLDLGAHNVEILRGL +LPQVQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV +HASSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPAAPLFTRADLDEVADTVVHAAYE +VIRGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT +RVIQPELDAAEMRALHSSADALRREARSLGF +>GCF_023573625_PROKKA_02073 +MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA +EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL +LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV +HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE +VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT +RVIQPELDDAEMRALHASADALRREARSLGF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001929.fa new file mode 100644 index 0000000000000000000000000000000000000000..933328f2e9f205fd5a5fe88a4345118222b3a2ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001929.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02156 +MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM +DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA +GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG +APFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG- +>GCF_003691675_PROKKA_01869 +MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM +DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA +GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG +ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG- +>GCF_005280335_PROKKA_00604 +---MLVADDQQLMRTALAHFVSTAEDLEVVGTAADGVEAVEMAKDLRPDVVLMDMQMPRM +DGIEATTAIMAEAPEVRVLAITTFSSEAYLVPALRAGASGYLVKDAPPEEVVEAVRQVHR +GDAVFSPRVARELIETVTQQSERRESAAAHALTELEELTPRELEVVTELAKGSSNAEIAQ +ALFLAEATVKSHLGKIMDKWQARDRVQVLIRASRAGLVSFDD +>GCF_023573625_PROKKA_02099 +MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM +DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA +GDAVFSARVAADLVEAVTAAPEHAAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG +ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001930.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001930.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a188f1688c067f406527cb9d64db9ae1d05954c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001930.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_02171 +MTDIRRTATALTLGAAVVTGLGAPAAVA--QTTAPATETATTAPA-SESPAP-QEEEKDD +NGNWGLWGLAGLLGLAGLAGR-RKRE-VHAEPVRRDHHVAGAHRDH---DVHRVDDRAGD +V--RTEGADARRREADGTLGDATRRPGTGDAR +>GCF_003691675_PROKKA_01885 +MTDIRRTATALTLAAAVVTGLGAPAAVA--QTTAPATEAATTAPA-SESPAP-QEEEKDD +NGNWGLWGLAGLLGLAGLAGR-RKRE-VHAEPVRRDHHVGGAHRDH---DVHRVDDRAGD +V--RAEGAD-------------TRRPGTGDAR +>GCF_020097155_PROKKA_00507 +MADIRKTATALTLSAAVLVGAGAPAATAAESSTAPATETATTAPASSQSPEPEQTEEKDD +NGNWGLWGLAGLLGLAGLAGRGKKREVVHAQPVREAPRVQPTHTENHHVDTTRVQDGVRD +AGHRAGGTD-------GT-------PGNG--R +>GCF_023573625_PROKKA_02116 +MTDIRRTATALTLGAAVVTGLGAPAAVA--QTTAPATETATTAPA-SESPAP-QEEEKDD +NGNWGLWGLAGLLGLAGLAGR-RKRE-VHAEPVRRDHHVAGAHRDH---DVHRVDDRAGD +V--RTEGADARRREADGTLGDATRRPGTGDSR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001932.fa new file mode 100644 index 0000000000000000000000000000000000000000..da0b1167c7ae0b21406021bf6249ab12215a4efd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001932.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_02187 +MPSTAVPPRDSGAASTLPARTGHRGV--SILRTAALVLVVAAFVWLALTVRLPGVDELRA +QLDGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYG +IARAVGREVVLRWLGRHAETVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGI +FAGSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLTVGGLTLWAVRHWRRAARSA- +-----EEPENPQSGHDTPSPRRRRGVS +>GCF_003691675_PROKKA_01901 +MPSTAVPPRDSGAASTLPARTGHRGV--SILRTAALVLVVAAFVWLALTVRLPGVDELRA +QLDGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYG +IARAVGREVVLRGLGRHAETVERRLEDTGFLALLALRVAPGLPYWPVNYGAGALAVPLGI +FAGSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAE +GPAGSEGPESPRSGQDTPSPRARRGVS +>GCF_005280335_PROKKA_00562 +MPSSAAPPSD--AASSRPDRRGSSGSVGTASRTLLLVVVMALFIWLATSVRLPDIDTLRD +RLASFGFWSWLVFVLAYAGVALTPVPVTLMALTGGVLFGAVQGSVLSVAGALLGSIGAYW +IARALGRDVILRGLGRHADTVEEHLEDAGFLALLTLRVAPGLPYWPVNYGAGALGVPSGM +FVGSTAVGVIPGQVSLVALGAFAVHPGVLNGVILGAGWLAVGVLTVWAARHWRRAANHDD +GEGGED--------------------- +>GCF_023573625_PROKKA_02132 +MPSTAVPPRDSGAASTLPARTGHRGV--SILRTAALVLVVAAFVWLALTVRLPGVDELRA +QLDGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYG +IARAVGREVVLRWLGRHAATVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGI +FAGSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAE +GPAGSEGPESPRSGQDTPSPRARRGVS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001937.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001937.fa new file mode 100644 index 0000000000000000000000000000000000000000..76a8e3aa9ccd7019d01617092f17c89dae6ce6d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001937.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_02207 +MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG +WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRHTKPGDVLF +LDIPEGDFTLPDEPRPLLMLTAGSGLTPVMSMIRTLVPTRRDADVVLIHSSRTPEDALFR +EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA +LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADVEVDAPGDVPLLVVAEEAGVAAPA +GCRMGICHACLTPLRSGRVTDLRTGQVHGEPGELVQTCVSAAAGPLSLSL +>GCF_003691675_PROKKA_01920 +MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG +WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF +LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR +EELAELADQFPGLRVVHRHTADEGRLDLSSPAELEDLCPDWRDRAAYACGPAEFLDDAED +LWRREAGEDLRIERFRADFAAGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS +GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL +>GCF_005280335_PROKKA_00538 +MAGPSLLSRLASTLLHPLTPQDVLGLLDPVHSSRQLRGVVTSVRRETPGTATIAFRPGPG +WRLHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTVPGDVLF +LDVPEGDFTLPEEPRPLLMLTAGSGLTPVMSMIRTLVPARRDADVVLVHSSRTPETALFR +EELAELADQFPCLRVVHRHTADEGRLDLSSPAELEALCPDWRERAAYACGPAPFLDDAED +LWRREAGGELRIERFRADFAPGVAGAGGRVVFEHSDAEADAPGDVPLLIVAEEAGVAAPA +GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGDLVQTCVSAAAGPVSLDL +>GCF_023573625_PROKKA_02151 +MVGPSLFSRLASTLLHPLAPQDVLSLLDPVHSSRQLRGVVTSVTRETPGTATIAFRPGPG +WRAHDAGQWARIGVDVDGVRQWRSYSLSAPAGADPEITVSDIGLVSGTLVRRTKPGDVLF +LDVPEGDFTLPDEPRALLMLTAGSGLTPVMSMIRTLVPARADADVVLIHSSRTPEDALFR +EELAELADQFPGLRVVHHHTAETGRLDLSSPAQLEGLCPDWRERAGYACGPAGFLDDAEA +LWRREAAADLTIERFQADFAPGVAGAGGRVVFEHADAEADAPGDVPLLIVAEEAGVAAPS +GCRMGICHACLTPLRSGQVTDLRSGEVHGEPGELIQTCVSAAAGPLSLDL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001938.fa new file mode 100644 index 0000000000000000000000000000000000000000..bbcf44def97843594cf3d31246b21eab18abe06f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001938.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_02209 +MSIPQDSGRPRPD-----APTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGW +RHAVGVLA--SAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGR +WFLNTMVIGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLL +LTYIGNLVPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARI +FFSIILRLVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWG +VFAAGAVLAALPVMALFLFLQRYIVSGLTAGGVKG +>GCF_003691675_PROKKA_01922 +MSIPQDSGRPRPD-----APTSPLAAALAQQETDPLRWEEDPAPPRRRRSFGRWMRELGW +RHAVGVLA--SAFALFPLLYVLSASLDPTGTMASSNRLFSSFSGQNYVDLFSDPNRPFGR +WFLNTMVIGVITSVMTVFLGALAAYAFSRMRFTGRRVGLLTLLLVQMFPQLLAVVAIFLL +LTYIGNLVPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTIPPSLDEAAKLDGASHARI +FFSIILRLVTPILAVVALLSFITTVSEFVIASVVLTDPSAQTLAVGLYGYVSETRSENWG +VFAAGAVLAALPVMALFLFLQRYIVSGLTAGGVKG +>GCF_005280335_PROKKA_00535 +MSIPQDPSARAPQGQAAPAAASPLAAALAQQEIDPLRWEDGAPPPRRRRSFGRWLRELGW +RHVVGVLA--SAFALFPLLYVLSASLDPTGTMASSNSLFSSFSGQNYVDLFSDPSRPYGR +WFVNTMVIGLVTSFSTVFLGALAAYAFSRMRFAGRRVGLLTLLLVQMFPQLLAVVAIFLL +LTYIGDLVPVLGIGSQLGLILVYLGGALGVNTYLMYGFFNTVPASLDEAAKLDGASHVQI +FFSIILRLVTPILAVVGLLSFISTVSEFVIASVVLTDPAAQTLAVGLYGYVSETRSENWG +VFAAGAVLAAVPVMALFLFLQRYIVSGLTAGGVKG +>GCF_005280335_PROKKA_02645 +M-------------------TFTLLAPHQSAAISEAGIEQAARDLTRARTLGR----IGL +VPAFAILTVLAVISIFPIYWMFVTAFRPAEQMLSTNPLPGPFSLENFQYVWD--TIPILS +MLGNTFVMALVIAIGQLFVAILASYGFSRWTFRGQKILFLLFVGSWLVPFQVTMIPNYVR +IAEMGLL------NNMVGVILPQLAAAFAV--MMLKQHLDSFPRELLDASDMDGRSPWRT +LWEVVVPNLRPALAALAIMLFISAWNEYLWPSLIMQG-SNDLIQVGVRSFLG-SEGNNWG +AVMAASALACLPIFLIYIFLQRYVVDAFVRSGLK- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001939.fa new file mode 100644 index 0000000000000000000000000000000000000000..06438e17b6268292a33f36376f07a1faee00a241 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001939.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_02213 +MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG +SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA +KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN +LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA +MNIF---------RMPATHEGVHWGETVIPVPREDLADAGTAVDLGVRPENL-------- +-VVSDDAAGLPVEVDTVEELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPD +PERVHLFHAETGERLN-------------------------------------------- +-------------------R +>GCF_003691675_PROKKA_01926 +MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG +SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA +KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN +LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA +MNIF---------RMPATHEGVHWGETVIPVPREDLADAGTTVDLGVRPENL-------- +-VISDDAAGLPVEVDTVEELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPD +PERVHLFHADTGERLN-------------------------------------------- +-------------------R +>GCF_005280335_PROKKA_00531 +MASVSFRSATRQYPNAPRPAVNRLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSSG +SIHIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA +KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRAQIAQ +LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKDGTLQQVDTPRSLYEKPVNVFVAGFIGSPA +MNIF---------RMPVAADGVHWGESVIPVDRATLADAGQSVDLGVRPENL-------- +-EIT-DRGGLAVEVDTVEELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPD +PERVHLFHAETGERLN-------------------------------------------- +-------------------R +>GCF_005280335_PROKKA_02650 +MARLVLNQITREF--GDFVATDRVSLEVDDGDFLVLLGPSGCGKTTLLRMIAGLLEPSSG +SIEVDGDDITALPARKRDLAMVFQSYALYPHLTVEKNLAFPLRVRKLPKAEIAARVRAAA +EAVEIDHLLSRKPKELSGGQRQRVALARALVREPKAFLMDEPLSNLDAKLRTATRRELAA +LHRRLGATFVYVTHDQVEAMTMATKIALLNGGRIEQYGTPEQLYDTPSSVFAAGFLGSPA +MNLLDATLTTTDGRITAFAPGV---EAVL----WEGATPERDVVLGVRPEHLSVFAGGAP +EAVPTAGAALRGTVELVENLGREQLV--HCRVGDER--VTVSCAREEAWQAGELVVIAAP +LTRLHLFDRRSGRRLEWRPAAQSEAPLRAAMAPSAGRPQENASRFRAARGGATAPASRSA +DVRSTEEAAQSEASLRTATR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001940.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001940.fa new file mode 100644 index 0000000000000000000000000000000000000000..29c02105d10c0ef517f3d493670b4688fd814cef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001940.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_02214 +MEHIDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA +VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEG-DDEGGCRVT +HTYDWTALTDPKRVQKALRTGEGQLRASIDRLAELAERQ--G +>GCF_003691675_PROKKA_01927 +MEHIDETALPAPEDRVVSATHHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA +VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEG-DDEGGCRVT +HTYDWTALTDPKRIQKALRTGEEQLRASIDRLAELAERQ--D +>GCF_005280335_PROKKA_00530 +MEHIDETALPAPQDRVATASREVDAPAGVVFELIADPARQPEWDGNDNLAGAEPGQRVTA +AGDVFVMTLRKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGIRDEPRCRVT +HTYDWTELTDPGRIRRALRTGPEQLRASIDRLAELARTQPQA +>GCF_023573625_PROKKA_02153 +MEHFDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA +VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEG-DDEGGCRVT +HTYDWTALTDPKRIQKALRTGEEQLRASIDRLADLAERQ--G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001941.fa new file mode 100644 index 0000000000000000000000000000000000000000..1c38ff556943580b054baccdc8cf2fa4d8d063d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001941.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_02218 +MQ---IAEQE---RIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLAS +SAFVIGATLSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGAS +YAFASTAVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATL +GITVVSLVLGLLVR--EAPAAAGVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGF +MLLVGLSYAGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVY +PALLCFTAALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTL +MLFADVGLGLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA +>GCF_003691675_PROKKA_01931 +MQ---IAEQE---RIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLAS +SAFVIGATLSRVVTGHVVDRFGKRRVLVAALVAVALSCTLYLVASSLPALVAVRMLHGAS +YAFASTAVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYVWLFRATL +GITVVSLVLGLLVR--EAPAAADVDGERAAGEVPLEHPAPAVGFRLRSVLHPAVLPISGF +MLLVGLSYAGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVY +PALLCFTAALLVLAFATRDWQVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTL +MLFADVGLGLGPVLLGGLVASAGYGAMYAALAGVLVVAAGYYFVMHGRRHGRRETVARA +>GCF_020097155_PROKKA_00473 +MHHPVTAPAEAAPRIVTPVFAVAWLVNFAQYLTFYLLATTMALYAVKQFGAGDAAAGFAS +SAFVVGATVARIFAGHVVDSLGRRRMLLVSLSVVTLACAAYLPASSLGLLVAVRLVHGAM +YAVASTAVMTLAQSVIPASRRAEGTGYFALGTTLATALGPAAGLMLVSAAGYPGMFWATT +AVAAVGLAFGLALRVPDEPASA--------------RPHLVRGFRLGGILHPAVVPIGVF +MLLVGVAYAGVITYLNGYAEQRGLGAGAGLFFLAYALVTLVMRFVLGRVQDRRGDNAVVG +LGLVCFAASLVLLAVARQDAVVVLAGALCGLGYGTLMPAAQAIAVRLVPPHQMGTGISTL +YLGVDVGIGLAPLPLGALLAAGGYLWMYLVLAGFVVLAGVYYVLVHGRTPAAR-AVAR- +>GCF_023573625_PROKKA_02157 +MQ---IAEQE---RIASPTFVLAWVVSFLQFLAFYALVTTMAVYAVRQFAASDAGAGLAS +SAFVIGATVSRVVTGHVVDRFGKRRVLVVALVAVALSCTLYLVASSLPALVAVRMLHGAS +YAFASTAVMALAQAAIPDGRRAEATGHLALGTTLATAIGPALGLFLAGSIGYAWLFRATL +GITVVSLVLGLLVR--EAPAAADVDGERAAGEAPLEHPAPAVGFRLRSVLHPAVLPISGF +MLLVGLSYAGILTYLNAYSVERGLTAGAGLFFLAYAAAMLVMRLTLGTLQDRRGDDAVVY +PALLCFTAALLVLAFATRDGHVVLAGALSGLGYGTLMPAAQAIAVNAVPSHQLGAGISTL +MLFADVGLGLGPVLLGGLVASAGYGTMYAALAGVLVIAAGYYFVMHGRRHGRRETVARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001945.fa new file mode 100644 index 0000000000000000000000000000000000000000..1429c661074b9653d36d89abcc237e2d37b8656b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001945.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_02259 +M--------------------------------NVSAEQL-------------------- +------------------------------------------------------------ +--------IGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR----- +>GCF_005280335_PROKKA_00463 +MTRLLPGDSLTLDLAPEDPADLLARLRAAGVAMNESAERLITDARVCAVVPER--VTVVE +RTLAELGLPDGGTLPELRRAVEAAGLRECPPTVAPLLRLVTLDQANAPDSLLRHGRAPDD +SAHVFSPSLSDEPGVHRGLYLRVVDHVPWLRGFVCDDLHVFGPEDRWILAL----- +>GCF_020097155_PROKKA_00700 +MADLIDRAGIELTLA-GDPHELLTQLQAAGVRFNDSARTLLFRPALARDLQTSRPVRVVE +RSLTDLGLPNGGTLPQLRRAALAAGLAPCPPAVAPLLRLRTLDQVNAPDSVLRHGRAPEG +SVHVLSPSLGEDPRVHRGFYLRVVDEAPWLRGFMCDDLHVMGADDRWVLSAPTSAP +>GCF_023573625_PROKKA_02190 +M--------------------------------NVSAEQL-------------------- +------------------------------------------------------------ +--------IGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001947.fa new file mode 100644 index 0000000000000000000000000000000000000000..77ece01a978f344ab9121e0c17d04f36e5b05029 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001947.fa @@ -0,0 +1,60 @@ +>GCF_002008305_PROKKA_02272 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------MGVNGLPGTGKTTTLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEVAGFE +MVVASANNAAGESISEEIPQVESRIVV----------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------------------------------- +>GCF_003691675_PROKKA_01964 +M------------------------------------------------------------PAPS--------------- +-----------------------------------LGEEDKRAI------------------------------------ +-------------------------------------------------------------------------------- +--------------PALQPSLSSSNVTAHEHTGHPQAARIDVVARADVVEAG---------------------------- +--------GPGLMGVNGLPGTGKTTTLGDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRVRELRPEVVGFE +MVVASANNAAVENLSEEIPQ---RSAIKDSRNVDADYFAELA-AALG---GSRGEEDALGEDSLTSEQPGTSGLATAPMA +TAPTPPRS------------------------------------------------------------------------ +-------------------------------------------------------------------------------- +------------------------------------------------------ARRR---------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------PTR-------------------------------------------------------------------- +----------------------------------------------------------------------G +>GCF_005280335_PROKKA_00460 +M------------------------------------------------------------PAPS--------------- +-----------------------------------LGEEDKRAI------------------------------------ +-------------------------------------------------------------------------------- +--------------PALQPSLSSSNVTAHEHTGHLQAACIDVVARSEVVEVG---------------------------- +--------GPGLMGVNGLPGTGKTTMLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEVVGFE +MVVASANNAAVENLSEEIPQ---RSAIKDGRHVDADYFACLATAAVG---GSGGGRGRPG-------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------------------------------- +>GCF_020097155_PROKKA_00410 +MGDTRGRTQQDIVRFWQLQELFDPQPLPKLTPRTSPPFGKRVITWRAEDGDVALPWNRLAPPPPTTKGAAREWRHTLYLR +IYALEDAYQTLHSAFPADADAYDERPGGRSAAAGALVDADGRLIGGTGVLSSALWGIGRLCRGEGFDDSLVDGFEAAGEA +FVDAADRAAGVPDDDAFGEQPVLTAGMLVALIRLAQHSAGVEGMPALAGHEVRIASQVVSASSGDETPDIDFLNSFYLSD +LHRVGEAIARGDVGPALDAYLTPDGDVDTQR-------RVDVVARPDIVDAGVEPARVPAGRWPAKTSYALARSQQFAVN +RALNELGAEPGLMGVNGPPGTGKTTMLRDILAANVVERARKLAGFADPSGAFTGRTLAWTGEGRRHRTVHELRPELTGFE +MVVASANNAAVENISEEIPH---RDAIKDSGRADADYFADLATAALGLGVENADEDGAPG-------------ACDGPAA +EQPAAASSGAWGLVAARLGNKVNRARFRDAVLFGGASGGRGARGRGLDTLLKDWAASPSAPAQWTAAREAFHRALHEVDR +GLTERRDAAQRTVRTAAAREAVRAAERRLAELSRQRTAKWAGAEAIRRELSAAQAEAGRIRDALDLHRDAKPGFWETITS +FGVAGQQWRETYQPLLEAWSTADAGRAALAADTEAAERRLSELEAQIVHLDGECARRRGDLADLEAAVRADEERFGGRHP +SAVVDAQTRETTTPWLDEEMEKARTELFLAALELHRAFIAAAARDLRPSFQAAMEVMAGAAPRDLEAEKRRAAWQVFFLL +VPLVSTTFASFDRMFTGMGRESLGWLFVDEAGQASPQYAAGAIWRANRAVVVGDPLQLEPVVTIPVTVSRSLAKAHGVSS +TWIAPEASVQRLADRVSRYGTTLPQGEDDVWVSSPLRVHRRCDDPMFALSNDLAYGGLMVSGVQRKGPEEDPFERTGDGE +IFASSWMDTPARTPGTHLQPNQIERVRRGIEACRRWGIPCTEIIAISPFREVADALRVLSDEFPGLTAGTIHTAQGREAD +VVFFVLGGAPDKPGARNWASSRVNLANVAVSRAKRRLYVIGDREAWSRHNYFRQIAEALPRAAEPDAGRER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001949.fa new file mode 100644 index 0000000000000000000000000000000000000000..60beee4f44fe6129c9eb5419bdee74b7a091ba86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001949.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_02283 +MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP +PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD +DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPD-APMKAGVALVDVL +TAKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPS +IAPYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALE +DALSAQTAAHWRDVLQAERLPAGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRH +PVQWDPPVAHPRHAPPALGADTAAVNTWLD---------AR +>GCF_003691675_PROKKA_01974 +MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPERGDDTRGWAP +PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD +EVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPD-APMKAGVALVDVL +TAKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPS +IAPYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALE +DALSAETAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRH +PVQWDPPVAHPHHAPPALGADTAAVNTWLD---------TR +>GCF_005280335_PROKKA_00808 +M-EHTDEPRGGG-PLEGIVIADFTRVLAGPYATMLLADMGATVIKVESP-GGDDTRTWRP +PEHEGVSTYYLSVNRNKRAVALDLSDREDLDTAYALLDRADVFLENFKPGGLAKFGLDPD +SVAERWPHLVHASITGFGTASGTALPGYDLLAQAVSGMMTVTGEPDGAPQRSGVAIFDVI +TGLHAAIGVLGALQERTRSGRGQHLELNLLSSALSGLVNQTSAAIAGGVTPHRMGNEHPS +LYPYGPFRAADRELIIAVGNDRQFARLVEQLGRPELAEDPRFLTMKDRNAHRGELGPLLE +EALAAQSAGEWFEQLRDAGIPCSPILTLPEGVEFAAGLGLDPVVEV----GEQRIPTVRH +PIRFSRTPARHELAPPALDADRDWVRAWIDQTPPSTAADAD +>GCF_023573625_PROKKA_02222 +MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP +PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD +DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPD-APMKAGVALVDVL +TAKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGADVVPRRMGNDHPS +IAPYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALE +DALSAQTAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRH +PVQWDPPVAHPHHAPPALGADTAAVNTWLD---------AH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001951.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a503ac3b849c7f93924c0eff94e24ad5e75b189 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001951.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_02298 +MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE +AGSYEDWTKDELAKRARELDIEGRSTMTKDELIEALRNH +>GCF_003691675_PROKKA_01991 +MAEKKAEKNGAPMGPGTSSIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE +AGSYEDWTKDELEKRARELDIEGRSTMTKDELIEALRDH +>GCF_005280335_PROKKA_00945 +MATQKKSESDTP------QIKDPEMYEALRRDGASKEKAARISNAAARDGREEVAERGGE +SESYEEWTVDELEDRAKELDLTGYSDKRKDELIAMLREH +>GCF_023573625_PROKKA_02239 +MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVA----- +-------------KRARELDIEGRSTMTKDELIEALRDH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001952.fa new file mode 100644 index 0000000000000000000000000000000000000000..4d5d3a71231d5e409cae55695441f4804dac36d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001952.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02300 +MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV +REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA +IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR +IVDLARQVVDQHFPPGGARGPRP +>GCF_003691675_PROKKA_01993 +MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV +REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA +IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR +IVDLARQVVDQHFPPGGARGPRP +>GCF_020097155_PROKKA_00389 +MSSPDPTAHRGAPLPSALGAWRRRPPQPPRPLAPGAPAARPQSGAGLPTVEEVSAGGIVI +REHAGDLEVAVIARYNRGGRLEWCLPKGHPEGAEDHRQAAVREVEEETGIAGCILEPLGS +IDYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVSIDDVARRLSFANERR +IVDLARQVIPQHFPTGRPPG-RP +>GCF_023573625_PROKKA_02241 +MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV +REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA +IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR +IVDLARQVVDQHFPPGGARGPRP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001956.fa new file mode 100644 index 0000000000000000000000000000000000000000..82d01009f29dbb5228d337ee3343ef0477f063f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001956.fa @@ -0,0 +1,37 @@ +>GCF_003691675_PROKKA_00257 +MTVGHGAHGPRHSDPRYVALQTEREKHARAAARGTSVWSADQDAAVPREPLRIPELLLGA +LLAMEAFSVPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAIVS +VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP +YGSFLTGILADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA +CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV +RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR +LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR +RRVL-AAARRGQHAPSSGGHAVP-DL +>GCF_005280335_PROKKA_02416 +MAVRHQTRGPVDTDPRYRALLEARAAQERQAARGTAAWSRDDATGLPREPLRIPELILGA +LLAMEAFGVRLGPLGVPLNEAAMLLLLFLALCRRSRRDTSALGLSAVLAGAVMVFLAVVS +VNQGIPDMEWLRRWVRIAALVGLVGCIAGGRLDLRSVLTGLLAAMAANVPLFYAGVVPTP +YGSFLTGFLADKNVAGLYYAAMPVLALAVVRSRRWKLAILLAAAVCLFLTGSRTSMAGFG +VALVWLAVTPRLAAGLRVVLLVVLGWAVGFAEENLSRLEVFGDRTGTDWLRGTIQAATEA +KAATTPWHGRGLTEAYVTIGRDTWLYHDSYAGLFTEGGVVLLVAVLGAYAFFGLRLFSTR +LRTPSRVAVEAAAAVVFVTATQLGEVFITIPGMLIVAAGVSLWLRERDAPLESEVRERRR +RQVL-AAARRGSTPESSADLAAPGSA +>GCF_020097155_PROKKA_02298 +MP-PHLPSGPALQDPRYQAVLAERGRREAATARGVSVLTAEDAAG-PRTSLRVPELLLGF +LLAMEAYTLPAGGVPVPLNEAAMMVLLGLALCRRAKRRASALGVAALLAVLVGVYLAAVS +LAMGVPDAVWLRRLVRMAALTALVGCFAARRVDLRSVLTGLLAAMAVNVPLFYAGLVPAP +YQGFLTGFLADKNVAGLYYAAVPVLALTFVRRPGVRLLLLSASGLCVFLTGSRTSLAGFA +CALVWVVLTPRMGPVLRVALLALLAWAVGFAEENLARVGVYSDREGTDWFRSVIQTATGV +KVEATPWTGQGLAQSFVELDAGRFLFHNSYAALYVEGGVVLTAAMLTAYAVYGLRLGATR +LRTPSRVAVEAAAVVVLVTATQLGEVFVSIPSMLILAAGATLAITEADAPLDAQARARRE +ERTLRQAAARGH-------------- +>GCF_023573625_PROKKA_00536 +MTVGHGAHGPRHSDPRYVALQAEREKHARAAARGTSVWSAGQDAAAPREPLRIPELLLGA +LLAMEAFSLPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAVVS +VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP +YGSFLTGVLADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA +CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV +RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR +LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR +RRVL-AAARRGQHAPSSGGHAVP-DL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001958.fa new file mode 100644 index 0000000000000000000000000000000000000000..41bf253255d8075f35a730f98706be5c97f67c29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001958.fa @@ -0,0 +1,40 @@ +>GCF_003691675_PROKKA_01643 +MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLADVRRARLRSEKPDTQGASSDYYLGSLVVNRATTPEG +VPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVLDYEGRPEAGEDLATLRRRGAPAGTSFQVDAIGVAVETIAA +ACRRALERQTPADDQEVMFDGDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV +FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGGSWSALLTRDFASLRAALAPSQTAMASGARTIIGVLLAAGQTA +VESGPSSDQCQDDADTGAYGTIVDFPNLLLHVLRVMQEKGEGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQGDAAWS +QRFLVTLLRMRLLLDTYVIRTLATTGTQADEENWVLSRAQKLETESGE-RSPRRRLGVKNTFQDPQVQDAVRNLQAMFQV +TDTRRTSKYFLYRILRWLDAQPEDGVDGVAFQHMLEDLARERLRAYEADKTWDAGVNVPNFVFNALDYILWDAGRTSPME +REHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGEEQEALTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQY +SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNSMRRVIQEWQGKRP +>GCF_005280335_PROKKA_00905 +MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLRSEKPDTQGALSDYYLGSLVVNRATTPED +VPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVLDYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAA +ACRRAMDRQTPADDQEVMFDGDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV +FAHVWDACAVLDRHIQLQFSTERPKDGVEAARDAVFGASWSALLTRDFASLRAALAPSLTATVSGARTIIGALRAAGQTA +VESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKGEGAEPGLPRWSQDSTGAVRLEDGSLLEQFAQHGQDDAAWS +QRFLVALLRMRLLLDTYVIRTLATTGTQADEENWVLSRAQKLETESGE-RSPRRRLGVKNTFQDPQVQDAVRNLQAMFQV +TDTRRTSKYFLYRILRWLDAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNFVFNALDYILWDAGRTSPME +REHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGEEQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQY +SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNRMRRVIQEWQGKRP +>GCF_020097155_PROKKA_00844 +MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLGSEKPDTQGALSDYYLGSLVVNRATTPED +VPIDEVVDGQQRLTTLTVLAAVAEHVIRAGVLDPRALAVLDYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAA +ACRRAMDRQTPADDQEVMFDGDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV +FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGASWSALLTRDFASLRAALAPSLTATVSGARTIIGALRAAGQTA +VESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKGEGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQDDAAWS +QRFLVALLRMRLLLDTYVIRTLATTGTQADEENWVLSRAQKLETESGE-RSPRRRLGVKNTFQDPQVQDAVRNLQAMFQV +TDTRRTSKYFLYRILRWLHAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNFVFNALDYILWDAGRTSPME +REHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGEEQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQY +SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNRMRRVIQEWQGKRP +>GCF_023573625_PROKKA_01873 +-MSERNAPETLTIGEVFAAGRHYRVPVYQRSYAWTEVEVSTLLADVRRARLRSKALESRGNVSDYYLGAMVVNRTQTPAG +DQIDEVVDGQQRLTTLTVLAAVAEQITQAGVLDPVALAVLDYEGRAEAGEDLATLRRRGGHRHGAFQVEAIGIAAQTVRG +ACERATDRQATADGQTVVFDADDLAYLWNHVRLLRTELPEGTDLNHYFEVMNTRGEQLAKHEVLKAMLMRPLRDESERQV +FAQVWDACAVLDRPVQLQFASEQLDPDISPARDAVFGDTWSTLVTTDFESLRAALEPSLAETELGGRTSLDSLLSSRGAG +EGTSASAEKRSD--ETGSYGTIIDFPNLLLHVLRVMEESGMASGSGRPAWGQEPKNAVRLEDNSLLEQCAERRQDDARWS +KRFLVMLLRIRFLLDTYVIRTLSTTGTRADEENWVLVGALKVESGAEEGSSRRRRLGVKNTFEDPAVQEAVRNLQAMFQV +TDTRRASKYFLYRILRWLAERPVDRVDGEAFQRMLEDLARERLRAYDADEGLDLGVKVPNFVFNVLDYILWDLGRNPSAE +AGALGAALGDVERSVLSQRAGSFRFRYRTSVEHFYPVVPGEGQKVLTSTEVNRFGNLCIMGRRENSQRNNLMPVSKVKQY +SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNSMRRVIQEWQGKRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001961.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d270a4bc0fb4c553fb8f01f07da9c25dd6d303b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001961.fa @@ -0,0 +1,60 @@ +>GCF_003691675_PROKKA_01646 +MAIHNESELETYICEYLEQHDWLYSPNDAGYDRKNAIFPEDVHAWLAENQPEDYGRIVKADAPASAQQAQRDQITTRLID +VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYERMRLRVMRQVHFNPA-TNQSVDLVLFVNGLP +VATIELKTDSTQSIGHAKKQYRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN +-GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTMLAAVREEGAGASYLIEHSAG +SGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLL +QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLDDGGEADTESILAAEVAA +TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQQGE +FRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVKIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMD +QYIQDMGYTDVGTLVAFSGEITDDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL +SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLEAVTDPNLIHDLGTKLDAAGVYDWDEVDAFAEV +WVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH +LVQLVGDQPGGEELIDLSDVQLVSIRQKKTSSGDIGLTGGAALKGTTAVGGGQVREEQRGPLEEVIEKINEIFAGEGVDA +SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIVGRGGDPSKMIVAAIGEYL +YWKVRSEGTGPVDVAHGRSAVFADETAPSQGTSVDERARATPSRVRKGS +>GCF_005280335_PROKKA_00902 +MAIHNESELETYICEYLQSHGWLYSANDEGYDRKNAIFPEDVHAWLVENQPEDYGRIVKADAPASAQQAQRDQITTRLVD +VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYERMRLRVMRQVHFTGAHESESVDLVLFVNGLP +VATIELKTDSTQSIGHAKKQYRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN +GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTKMLAAVREEGVGKSYLIEHSAG +SGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEPTSKSALVKQTLL +QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA +TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQQGE +FRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVRIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMD +QYIQDMGYTDVGTLVAFSGEITDDDFGLEKVTERSMNPPVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL +SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLGTKLDAAGVYDWAEVDAFAEV +WVVWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH +LVQLVGDQPGGEELIDLSDVQLVSIRQNKTSSGDIGLTGGTALKGTTAVGGGQVHEKQRGPLEDVIEKINEIFAGEGVDA +SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIVGRGGDPSKMIVAAIGEYL +YLTVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASATPSRVRKGN +>GCF_020097155_PROKKA_00841 +MAIHNESELETYICEYLERHGWLYSANDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKADAPASAQQAQRDQITTRLID +VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYEHMRLRVMRQVHFNPA-TNQSVDLVLFVNGLP +VATIELKTDSTQSIGHAKKQYRERNSKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN +GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTTMLAAVREEGAGKSYLIEHSAG +SGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLL +QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA +TGRPENISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQQGE +FRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVKIIVEHFRANVAHLLDGQAKAMVVTDSRAAAVRYKRQMD +QYIHDMGYTDVGTLVAFSGEITDDDFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL +SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSENDIQAAFEPYYAGAKLETVTDPNLIHDLGTKLDAAGVYDWDEVDAFADV +WVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNHDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH +LVQLVGDQPGGEELIDLSDVQLVSIRQKKTSSGDIGLTGGAALKGTTAVGGGQAREKQRGPLEEVIEKINEIFAGEGVDA +SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIVGRGGDPSKMIVAAIGEYL +YWKVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASATPSRVRKGN +>GCF_023573625_PROKKA_01876 +MAIHNESELETYICEYLEQHGWLYSPNDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKADAPASAQQAQREQITTRLVD +VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYERMRLRVMRQVHFNPA-TNQSVDLVLFVNGLP +VATIELKTDSTQSIGHAKKQYRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPY +GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTMLAAVREEGAGKSYLIEHSAG +SGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLL +QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA +TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQKGE +FRPEGDRAAVGKQTTEVDQTEASKKLMRWVKLHPTNIAQKVKIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMD +QYIQDMGYTDVDTLVAFSGEITDDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL +SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLGTKLDAAGVYNGDEVDVFADV +WVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH +LVQLVGDQPGGEELIDLSDVQLVSIRQKKTSSGEIGLTGGAALKGTTAVGGGQVREKQRGPLEEVIEKINEIFAGEGVDA +SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFVKMTDIVGRGGDPSKMIVAAIGEYL +YWKVRSEGAGPVDVAHGRSAVFVDETAPSQGTSVDERASATPSRVRKGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001962.fa new file mode 100644 index 0000000000000000000000000000000000000000..a648eb65642a1201e7ced9f70ca0bbdf90db31fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001962.fa @@ -0,0 +1,29 @@ +>GCF_003691675_PROKKA_01647 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------MA---------- +-----------RIVEVMTRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED +---- +>GCF_005280335_PROKKA_00901 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------MAGLNQRIISVL +ALPKPSLKEQREIAEHLDRETAKIDALISKAERFIELAQERRAALITAAVTGQIEIPTED +---- +>GCF_020097155_PROKKA_00840 +MCSRYLGYLVLSSFFLEQVNASTYGTKMPRANWDFIKTIEVWAPDFDTQRCIADYLDRET +ATIDALIAKQVELMNRLRERRQAVIDRAFVSTSEIVILRRHLVLNDSGAWGEDPTGADDV +AVLRSTEQTVDGYWAISDPALRTLSQTERQNTRLREGDLIVTKTSGSFKHVGKTTLVDNE +VAEGGYGFGNFMQRLRLKSTMIPKFLWWFMRTDQARSWINLVATTSTGLMNLNGSTLGRM +EVPLPSLVEQREIADHLDRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED +---- +>GCF_023573625_PROKKA_01878 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------MAGLNQRIISVL +ALPKPSLKEQREIAEHLDRETAKIDALIAKAERFIELAQERRAALITAAVTGQIETTSEL +HRRW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001965.fa new file mode 100644 index 0000000000000000000000000000000000000000..46940b4bc16d30ecad6ecfade835f6e710a55925 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001965.fa @@ -0,0 +1,21 @@ +>GCF_003691675_PROKKA_01700 +MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF +GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY +ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED-- +>GCF_005280335_PROKKA_00851 +MSFTQTDTPLTQDELAKVIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF +GPQAEGEQVDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHIDVSVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAACTFPLTGVGCVSRIY +ADRGVFLLDASGVVRVRELHGITWEELEEAHPGVRFEKLEA-- +>GCF_020097155_PROKKA_00788 +MGFTHTENPLSHEELAQVIAADIAPGSYVNLGIGQPTTVSDYLDADQHVTLHTENGMLGF +GPQAHGEQVDEDLINAGKIPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDRKLMPECTFPLTGVGCVSRIY +ADKGVFLLDSSGVVKVRELHGITFEELQATHEGVTFEEVDASA +>GCF_023573625_PROKKA_01928 +MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF +GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL +ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY +ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001968.fa new file mode 100644 index 0000000000000000000000000000000000000000..706ad63483a28862340369cc837676ae0b9500f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001968.fa @@ -0,0 +1,25 @@ +>GCF_003691675_PROKKA_01703 +MTDDVDAPGAR---PASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARR +MLLTLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGV +LHGAHLMYIARVHTERILRVNLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPA +TEHTLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGP +DHRDPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR +>GCF_005280335_PROKKA_00848 +------------------------------MLRSFTPGRPSLTVSDAAAAAGTTRATARR +VLHTLVHEGYAVQEGRDFRLTPRVLELGHGYWTGTSLAEILSPVLTRASQELEQSCSAAV +LDGPFLLYIARVHTERIIRVNLDVGTRMPAFLTSMGRVLLADLPPATVRRVLEAAPRTPR +TPRTVTDVEALLEEIAQVRRQDHAVVTAELDDHLSSVAVPVRGPDGAVVAAINTALP--- +-HRTPGA--------AEPSADEQTRAAVA--QALPVLRAAARDAEDALVALRR +>GCF_020097155_PROKKA_00785 +MS----LPSTEITSPAPGDGYVRALATGLAVLRAFTPDVPRLTLTEAADAAGVSRATARR +SLLTLVELGYAVQDGRAFELTPKVLELGHGYWSGRSTSEVLRPVLTRASQRLHQSCSAGV +LHGAHLMYIARVHTERILRVNLDVGTLLPAFSTSMGRVLLAGLDDAEVRRVLEGAPRTPA +TAQTLTDVDALLEEVRRVRERGHALVHGELDPNLSSVAVPVRDRDGRVVLAVNTALS--- +------TRRGRL---GEALSPAAAEAAAA--EALPVLREAADDAEAALELLGR +>GCF_023573625_PROKKA_01931 +MTDDVDAPGAR---PASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARR +MLLTLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGV +LHGAHLMYIARVHTERILRVSLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPA +TEHTLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGP +DHRDPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001969.fa new file mode 100644 index 0000000000000000000000000000000000000000..7593bb193c53596f8379f8e460e4e0d28a865df4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001969.fa @@ -0,0 +1,17 @@ +>GCF_003691675_PROKKA_01706 +M------------SAEQPIGHDMDRTSQEVLDAGMAVRREVLGDAHVDRAEARKDATTED +FQNLITRYAWGTIWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQE +ILLQTAVYASVPAANIAFKLAQE-----DADLAEGRPL +>GCF_005280335_PROKKA_00846 +MSGGRTEHAGGADAGQTPLGHQMERTSQEILDAGMAVRREVLGDAHVDRAEATKDATTDD +FQNLISRYAWGTIWTRPGLDRRMRSAVTITAMVSGGYWEECAMHLRAALRNGLSRDEIKE +ILLQAAIYSSVPAANVAFKLAQEVFAQVDEDLAAGRPL +>GCF_020097155_PROKKA_00779 +M-------------GEQPIGHDMDRTSREVHDAGMAVRREALEDAHVDRAEANKDAATED +FQNLITRYAWGTVWTRPGLDRRMRSAVTITAMVAGGYWDECAMHLRAALRNGLSREEVQE +ILLQTAVYCSVPAANIAFTLAQRVFAEVDADLAAGRPL +>GCF_023573625_PROKKA_01934 +M------------SAEQPIGHDMDRTSQEVLDAGRAVRREVLGDAHVDRAEARKDATTED +FQNLITRYAWGTIWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQE +ILLQTAVYASVPAANIAFKLAQE-----DADLAEGRPL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001971.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c558b7f6386ecb5c6e5455269fe8552e5bcbe6d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001971.fa @@ -0,0 +1,41 @@ +>GCF_003691675_PROKKA_01708 +MTSA-AADLAAVADVGLLDPAWAGSRAEAATADRTFLGHLLDVEAAWVRVLARHGLATEA +EAAAAAAAGDPDAYDLAALARAAQGGGTPLIPALKALRAQLPAGSRAVHLGATSQDVVDS +ALMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLPSTFGLRAANWLDG +LGQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVTAFTLVEDLAAELG +L--AAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGELGEPLAAGRGGS +SPMPHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEWPALRRLLRVAG +GTAALTRELVSGLRVHEDRMRRNLELTGPLLVSEPIMAELAPELDEASGEPGSGKRLIQD +VVDRSLACEGNFRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRLLAARRGTTTPP +RT +>GCF_005280335_PROKKA_00844 +MTDLDALDLS--ADAGLLNPAWAGRPVARATADRAFLQRMLEVEAAWVAVLAAHGLATDE +QARQAEEACDPAGYDLVALARAAQGGGNPLIPALKALRERLPAGSTAVHMGATSQDVIDT +ALMAMAAEVGRGLGEDLRGLAAALAGLAREHRGTPMVARSLAQHSLPSTFGLRAANWLDA +VGQAAQRLERATAALPVQWGGAAGTMASLAGHVDRAHRAGRLDESVTVFTLVEDLAARLG +L--SAPAGPWDTNRMAVTGVAAALADVTAACGKIANDVLLSSRIENGELGEPLAAGRGGS +SAMPHKQNPVLSVLVHSAALSAPGMLAQVYTAAGAANDERPDGAWHAEWPALRQLLRVAG +GAASLTRELAEGLRVNADRMAENLAQTGPVLVSERLMAELAPAIDEACGEPGAGKAAIQG +AVDDSLAGRGEFRALLREAVPDTVSDDRLDELLDPAGYTGEAGALVDRILAAHAELIDT- +-- +>GCF_020097155_PROKKA_00777 +MT----------------------RP---------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------RVG +IVGAAPAGPWDTNRMAVTGVAAALADVVAACGKVANDVLTSARIENGELGEPLAAGRGGS +SAMPHKQNPVLSVLIHSAALSTPGLLAQVYTAAGAANDERPDGSWHAEWPALRQLLCVAG +GAAALTRELVSGLRVHTGRMAANLALTGPLLVSERIMAELAPELDALFGGPGSGKAVIQG +AVDASLAGEGDFAELLRAAVPAEVSDARLADLLDPVAYTGEAETLVDRILAAHAPRLRAS +A- +>GCF_023573625_PROKKA_01936 +------------------------------------------------------------ +-----------------------------------------------MHLGATSQDVVDS +ALMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLPSTFGLRAANWLDG +LGQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVTAFTLVEDLAAELG +L--AAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGELGEPLAAGRGGS +SAMPHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEWPALRRLLRVAG +GTAALTRELVSGLRVHEDRMRRNLELTGPLLVSERIMAELAPELDEASGEPGSGKRLIQD +VVDRSLACEGNSRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRLLAARRGTTTPP +RT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001972.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcf7f60136b7c14d9c0cc853bd7aa1fceaff5820 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001972.fa @@ -0,0 +1,21 @@ +>GCF_003691675_PROKKA_01786 +MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA +RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV +VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA +EAARAQLWRVDVERP +>GCF_005280335_PROKKA_00702 +MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLEAMHPDMRASGAA +RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV +VGSFDIEVQSPDEFFMNQLDLDPARVMTALAAQASATRNPPLTVRDVLERLVPCGAPLFA +EAARAQLWRVDVERP +>GCF_020097155_PROKKA_00612 +MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLETMHPDMRASGAA +RHRAEVMDAAFDDARVEGWEQLVLGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV +VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVSDVLERLVPCGAPLFA +EAARAQLWRVDAERP +>GCF_023573625_PROKKA_02020 +MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA +RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV +VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA +EAARAQLWRVDVERP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001973.fa new file mode 100644 index 0000000000000000000000000000000000000000..571c90157935f245b5779dd9b1db0f28efe535df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001973.fa @@ -0,0 +1,13 @@ +>GCF_003691675_PROKKA_01857 +-------------MRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVS +TALDRAGFAIVSAAMQYCLADPEKAEDEEKLTVAELEKLFMTLA +>GCF_005280335_PROKKA_00617 +-------------MRSADPETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVS +TALDRAGFAIVSSAMKNCVADPERAREDESLTVEELEKLFLSLA +>GCF_020097155_PROKKA_00541 +-------------MRTADAETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVS +TALDRAGFAIVSSAMKNCVADPEKAREDEGLTVEELEKLFLSLA +>GCF_023573625_PROKKA_02087 +MIPLPATVTKEVAVRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVS +TALDRAGFAVVSSAMQYCLADPEKAEDEEKLTVAELEKLFMTLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001975.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d485347c4652c4114cfa62a1c13f13211737d61 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001975.fa @@ -0,0 +1,25 @@ +>GCF_003691675_PROKKA_01950 +MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRCYAPGQIRTAAQIRVLRA +AGLTVDDVRSVLADPASLPARLETHAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPA +RPGPVAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFVTLFQALAEAGSAPAGPLWT +ALRPVPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLL +DDAPGGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG +>GCF_005280335_PROKKA_01324 +MA---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +----------VEEQRLALPVDGELPEGFAVQGLRIASGVLPRREEAAVTVRV-------L +D--------------------------------------------------------- +>GCF_020097155_PROKKA_00436 +MSPLMTVGEFALATGLSAKALRFYDERGLLAPADVDAHSGYRRYEPGQIRTAAQIRVLRA +AGLTVDDVRSVLADPASLPARLEAHAAEVRRRRDLEDRALALAAAGVYAAPDPDDDGGPA +RPGPVAERTVGPTPWAGVVQRVALDEAGEEATTERANAAFATLFQALAEAGSAPAGPPWT +ALRPVPSAADVVETVLAVPLSGPAPAGLRVDGHEVVTGTLPRRVERYVDVRADAGEVDLL +DDAPGGALPHPGLLGLMDAFDVEDAGTAPEIRQILADPEAGHVELAVTVREEAGAGQG +>GCF_023573625_PROKKA_02180 +MSPLMTVGEFALATGLSAKA---------------------------------------- +------------------------HAAELRRRRDLEDRALALAVAGVYAAPDPDDDGGPA +RPGPVAERTVGPTPWAGVVQRVALDEAGEESTTERANAAFATLFQALAEAGSAPAGPLWT +ALRPVPGAADVVETVLAVPLSGPAPAGLRVDGHEVVAGTLPRRVERYVDVRADTGEVDLL +DDAPGGALPHPDLLGLMDAFDMEDAGAAPEIRQILADPEAGHIELAVTVREEAGAGQG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001976.fa new file mode 100644 index 0000000000000000000000000000000000000000..ef2936db898e9a803d8f77ae6939a0a2758377b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001976.fa @@ -0,0 +1,41 @@ +>GCF_005280335_PROKKA_00196 +M---------------TASR-LIPPAVDPASLPRDLPGLRAHFRPVVEEIARGALERDRA +RLLPFEAVRALGCAGFSVLRVPREAGGPDVDVRTVTALLVDLAAADSNVAHLYRSHLGFL +DAL-RFQPQPVRDRWHALVLAGATVGNASTERGGNALGTLNTRLTAPAGGDDDGAPGAAW +TLTGTKYYATGSIFSSHTRVSAAVVRADGSLAPGRGFAVVPVDAPGVCLEDDWDGFGQRL +TGTGTAVFEDVAVDPRDVLERIPGSPEAVHEAAWFQLILLAVLAGIARAARDDAAARVAA +RVRTFNTGLGVPFREDPLIQEAVGRIAAKASAAEAVVLAAADALDASLAAGA-------- +-ATGADRWGFTGPVPPAFAEAELAVEHAQITVPELALGAAQELFLTGGASDTSVAKGLDR +HWRNAQTVATHNPIAFRARAVGDYWINGT-LPEGLNAIGDAPAAPSSSAVDAAQPAPEPA +EAGA-R +>GCF_020097155_PROKKA_00148 +MPLTDPTDA-------PTPLGTVPPLVRPADLPRDLAGLRRHFAPVFARVAEGSRERDRR +RILPFAEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL +DSL-RFQPAAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPPAAGD------GPW +TLTGTKFYATGSIFSSHTRVSAAQTDADGHPAPGRRFAVVPVEAPGVRLDDDWDGFGQRL +TGTGTAVFDGVAVPPQDVLDRVPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAA +RVRTFNTGLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHD-------- +-A-GRTGSGAPEEVPASFTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDR +HWRNAQTVATHNPIAFRARAIGDYWINGT-VPEGLNAIGDAPAASAPLG-D----APAPG +EAA--R +>GCF_020097155_PROKKA_00597 +M---------------TTPV-LDRPAPTSAADAPDTAELRARFAPVFARIAANEARRRDA +AVPPHAAVRLLAETGFTALRLPRERGGSDATLTQLLDLLVDLAAADANLPQALHGHFMFT +EQVARDVHPRLTDWWLDEVAAGKVFANALVDPPA------ATGLPGVTARRDPRDP-EAF +LLTGTKQYSTGTLLADWTLVAAH--DDAGALQP----LVVEVAGPGVEARDDWDGIGQRG +TASGTTVYTDAPAPAWRRVDLERPAAAPGYPFLW--LILAATQAGIAQRALDDFAEILRR +RSRSYQHAASASPAHDPVLQHQLGAAAAQVRALRSVVLGAVPALEAAYTAAAGAAPAIGA +AATESPDDGAAEAFEAAHTEAWVAAASASSVAADLTLRLTSDLFETAGASAVVAGPGLDR +HWRNARVLASHTPLPHRRRQIGECLLHGTPAPHSADAVETASSTDADPSRDSVSPSPSTP +AATKEQ +>GCF_023573625_PROKKA_00199 +MPLTDPTDASAPPAATPVPLGAVPPLERPADLPRDLAGLRRHFAPVFARIAEGSRERDRR +RILPFEEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL +DSL-RFQPEAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPAPAGD------GPW +TLTGTKFYATGSIFSSHTRVSAAQTDADGRPAPGRRFAVVPVEAPGVRLDDDWDGFGQRL +TGTGTAVFDGVAVPPQDVLDRAPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAV +RVRTFNTGLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHE-------- +-A-GRTGSGAPEEVPASFTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDR +HWRNAQTVATHNPIAFRARAIGDFWINGT-VPEGLNAIGDAPAASAPLGAD----APASG +EAA--R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001979.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001979.fa new file mode 100644 index 0000000000000000000000000000000000000000..0183cc5ff1926cdb8876040d3ff47db59035a391 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001979.fa @@ -0,0 +1,25 @@ +>GCF_005280335_PROKKA_02190 +M--STHQHDHGHPRPEASEQTGREHGAPAPQVDPDEDPRAFWEGRYG-GERVWSGKVNAT +TAALVAGLGVT--PGRALDLGCGEGGDVLHLAEAGWDVTGIDLSEAAVARARDAARERGV +TQRTRFLAADLSDPAADWGAHEAGAAGYD---LVTASFLQSPVALDRRRILRRAADSLAP +GGHLVLVSHGAPPPWAPPQLAERGDFPSPAAELAALGVPADGDARWEVLTAELRERDTTG +PDGRSTRLKDT---------------------------------------VVVVRRR- +>GCF_005280335_PROKKA_02581 +MHSTTDQH-------AASGRYGDEHA-------------ELYDLMYG-SLPDWK-----Q +LPALCRRVRPA--ARTVLEFGIGNGRLALPLAEEGFEVTGLEASGVLAG---------QL +AARARDLPVDVVVGDFRERLTQDR---FDLCLLMTNTLFMTEGVADQRRVLRRAAEALAP +DGMLIVETYDPQVYLEKPAVS---NFSMPLGDDALLTDTVIVDR----LNCSVHIHHTVV +RRGEVTVLRERSSWLTPRELDLVCEEVGLKRTLRFADLAGSPITDSTRNVVSCYERR- +>GCF_005280335_PROKKA_02669 +M------------------------TGATRHDSPSQNPQEFWEGRYRYAERVWSGRPNPS +LVNAVQHLA----PGKALDLGCGEGADAIWLATQGWLVTGVDISATAIARARREAQRQQA +SAATRFVTADL----ARWEP-DDGP--YD---LMTASFLHSPVPLPRIAILQRAATTVRA +GGHLVVLSHAALPPWVDAADHPAHSFPSPARQFVELNL---NEHDWLVLSIQTHTRHATA +PSGEAAELTDG---------------------------------------VLLLQRR- +>GCF_020097155_PROKKA_02089 +M---SDQHSPGHE---------HRHGGAAPQIDPGMDPREFWENRYG-GEQVWSGKVNAT +TAALVAGLDLPDGPGRALDLGCGEGGDVVHLAEAGWHATGVDISEAAVARGREAAAARGV +AERTRFLAADLTDTSADWGARDDGAAGYD---LVTGSFFQSPVALDRARILRHAASLVAP +GGHVVLVSHAAPPSWAPPEVAARGDFPTPAGDLEALGIMTEGDEDWEVLVAEVRGRESTG +PNGEAGHLDDG---------------------------------------VVVVRRQR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001981.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba906064b0c3064c898983f3d145aad75b13a25c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001981.fa @@ -0,0 +1,25 @@ +>GCF_005280335_PROKKA_02337 +MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK +RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK +ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI +LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT +EAMGMLNHHFAAAA +>GCF_005280335_PROKKA_02342 +MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK +RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK +ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI +LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT +EAMGMLNHHFAAAA +>GCF_005280335_PROKKA_02640 +MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK +RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK +ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI +LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT +EAMGMLNHHFAAAA +>GCF_005280335_PROKKA_02651 +MTDFKWRHFQGDVILWAVRWYCRYPISYRDLEEMLAERGISVDHTTIYRWVQCYAPEMEK +RLRWFWRRGFDPSWRLDETYVKVRGKWTYLYRAVDKRGDTIDFYLSPTRSAKAAKRFLGK +ALRGLKHWEKPATLNTDKAPSYGAAITELKREGKLDRETAHRQVKYLNNVIEADHGKLKI +LIKPVRGFKSIPTAYATIKGFEVMRALRKGQARPWCLQPGIRGEVRLVERAFGIGPSALT +EAMGMLNHHFAAAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001982.fa new file mode 100644 index 0000000000000000000000000000000000000000..df240616e01a3875fb90665a47acb7ef72f7b322 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001982.fa @@ -0,0 +1,33 @@ +>GCF_020097155_PROKKA_00310 +M-DRCNRARAMGSRAAQSGRRRCHDDDGAMGALVRVHAAQSCSRSRVHPAS--GSRRRNP +HHPPSRTSAAVPDTATPVPCPAPPRL------------HRPRPRAGPD----PRAHHLTR +VTTDRT------GVADTPRHDRCRTPEGHARRGMGGLVQDHRFSTACTPCADAAGEVEQA +PSMTIAARH----------------QACRY-----------TSTARSATEH--------- +-------RSGETSTELAARLLAEAPQRDWRLRDLAALVHLSASQLGRAFTQRFGMPPMRY +LAHIRAHRLAELLVETDLPIGVAMTKVGWRSRGHAARQFTDVVGISPSEYRRTAIGRTLT +ETSPWPSATQGSPVAPGRESLEKSPP +>GCF_020097155_PROKKA_00409 +MPTTFSDQRKLSVVLFEGF------------ELLDVFG----------PVQLFGSL---- +--PDVAIEYVGPH-TGPVISSKGARVVADLAYED---------LARPDILMVPGGQG-TR +TLVDDAGFLAWLGQAGSRADLVASVCTGSALLAAAGLL-EGYSATSNKRAFTWASGFGDD +VDWRPRARWVHDRDRWTSSGVAAGMDMATGMIADLYDADTARAVTLRAEYEPHTDSTRDP +FADV-------------------------------------------------------- +-------------------------------------------------YRLG------- +-------------------------- +>GCF_020097155_PROKKA_00655 +M-------RHVVTIACPGT------------ALFDVGI----------PSRVFGAARTAN +DEPAYDVTIASPTGAGPLLTKDGVSV--DLPGVDQIKETDTVVVASSDALLDPLVR---R +DMASALAPFLLQGQAVRPGVRVAAVCSGAFLLGELGLL-DHRTATTHWRLADQLAKLFPS +THLQTESLYIEDDGVLTSGGVAAGIDLCLHMIRQDYGVRIANDVARSCVVAPFREGGQAQ +YVQTPVPRSADPSMNDLVHWLLETLDQRHTLEDIAHRGHMSTRTFERRFRREHGTSPGQW +LTAARIQRAKELLESTDLPVERIAELVGLGTASNLRTHFTRCVGRTPQAYRRSFTAGS-- +----------------NSTNVSGQYS +>GCF_020097155_PROKKA_01773 +M-DRCHRARAMGSCAAQSRRRRCHDDDRAMGALVHLHVAQSCSRSRVHPTS--GRRRRNH +HHPPPRTPATAPGAATPVPRPGPPRL------------HRSRTWARPD----PRTHHHTR +LSTGGT------GVADTPGRERCRTAERLARRGMGGLVQDHGLLATAPPHAVV---LRKA +AAMSTEPSW----------------RVCPD-----------ETTPSHAC----------- +--------PTETAAHHAARLLAQDPGRDWRLRDLADLVHLSTSQLGRAFSQRFGMPPIQY +LAHVRAHRLAELLIETDLPIGVAMAQVGWRSRGHAARQFTAIVGVSPSAYRRTATQRA-- +--------SLRCPCCGQRNEL---PR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001986.fa new file mode 100644 index 0000000000000000000000000000000000000000..2055067cafb561b3a47069c08783d8fb2c052464 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001986.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00013 +MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV +AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP +VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG +ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEPWTF +>GCF_003691675_PROKKA_02031 +MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAL +AGTEAHVWAPRDLTGPLAEAGLAAGRVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP +VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG +ILSEDGKGVVDRVLSGLAEGVTDYRRLAPGELWTF +>GCF_023573625_PROKKA_00013 +MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV +AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP +VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG +ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEAWTF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001988.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001988.fa new file mode 100644 index 0000000000000000000000000000000000000000..49c24d67296d34f932ae3c0d1ee92823a2b24d97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001988.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_00028 +MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG +GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGTIALGQLTTLEDANNLMVGGTGQIAAHA +ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL +VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV +VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA +VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEIK +>GCF_003691675_PROKKA_02046 +MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG +GWDSFQRELQQAMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA +ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQTMDDLVTAWRVDPAHVAWTGGGSFDQL +VMADIARTAGVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV +VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA +VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEVK +>GCF_023573625_PROKKA_00028 +MPSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG +GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA +ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL +VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV +VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFVPPGVSAEERTELEALIAEAVDTPEWKEA +VQRNYWNPVPLSGAELEEFIAAEKERIGTLTEEIK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001990.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001990.fa new file mode 100644 index 0000000000000000000000000000000000000000..849c01d32aa662b25a79581c17276881c592f6b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001990.fa @@ -0,0 +1,24 @@ +>GCF_002008305_PROKKA_00031 +METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAAFIMFSGVYFGGLFGDSTMAI +LMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIGGMAASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSS +VVADSVLRGLASLVLGLGIAVVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR +PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSVKRRLDRRRAHPQFGRGAIRGLAAPEAAGNSTTGMAMG +ALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVWALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGIT +LFCGLGIYATTGAVFDLLMLLGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI +LAIVLAFSVRAAVVRRTRQDV +>GCF_003691675_PROKKA_02048 +METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAAFIMFSGVYFGGLFGDSTMAI +LMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIGGMVASVCVVFLAPVLAEFSTRFGPAEYFALALFAFVATSS +VVADSVLRGLASLVLGLGIAVVGIDAVTGAERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR +PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGAIRGLAAPEAAGNSTTGMAMG +ALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVWALLASFFIAMVVLLAINLPFAQLWAKLLLIPKHYLYAGIT +LFCGLGIYATTGAVFDLLMLLGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI +LAIVLAFSVRAAVVRRTRQDV +>GCF_023573625_PROKKA_00030 +METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAAFIMFSGVYFGGLFGDSTMAI +LMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIGGMVASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSS +VVADSVLRGLASLVLGLGIAVVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR +PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGAIRGLAAPEAAGNSTTGMAMG +ALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVWALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGIT +LFCGLGIYATTGAVFDLLMLLGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI +LAIVLAFSVRAAVVRRTRQDV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001992.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001992.fa new file mode 100644 index 0000000000000000000000000000000000000000..a36fa64909ede00c5fd3df9aed721a18d981b647 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001992.fa @@ -0,0 +1,30 @@ +>GCF_002008305_PROKKA_00121 +MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYGLSPEQARGGLTAAEARTLMA +EGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAADLDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTL +DDAGVELLAVMVNRADPRDLDAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM +EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYLGAAFPVFVTHDDTFTTAAKV +SRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRTDVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEIL +QRRDVCDLVVLGPAAAVRELASREGVDLSGIELVDPADSPDLERYAQEYARLRAHKGVDAERAREVMQEGAYFGTMMVHL +GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDAQQLADIAVASAATAAQFGVD +PRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEGPLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNT +YKAVQQSSGAVAVGPVLQGLNKPVNDLSRGTTVEDIVNTVAITAIQAQAQG--------- +>GCF_020097155_PROKKA_00198 +MPQGILVTTTTAGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVEADPMVLLMREQFGLTAEQARGGITAAEARSLMA +EGRGDELQERCVEVYDRMARECGVVVVEGTDLTGADAAADLELNAGLALNLSTPVVAVVSGAGLGAQEAADAVDLTRHAL +AEAGADLLAVMVNRADAGRLDEIAEAIRPGRRSWPVYVLPELPELAHPSVAEVAAALDLEQVAGRPTQDRDVTEVKAVSM +EGGNFLEVLREGALVIVSGDRSDAILATLASSLTPDFPTPSGMILTNGILPNAQLQRLYQDAAFPVLATDDDTFGTAADV +SRVRSELSSAQPRKTAAALGTWHQRVDGDELLQRIDLPRTDVVTPLRFLHDLIERARADRRTVVLPEGEDARVLRAAEIL +QRRDVCDLVVLGGEAEVRELASREGVDLTGITLVDPATSEDRERYAAEYRRLRSHKGVDLERAREVMLEGAYYGTMMVHL +GDADGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDARQLADIAAASAETAAQFGVD +PRVAMLSYSTGASGSGDAVDKVRAATELVRAAHPELKVEGPLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNT +YKAVQQSSGAVAVGPVLQGLNRPVNDLSRGTTVEDIVNTVAITVIQAQTGSPQPTPKDAP +>GCF_023573625_PROKKA_00129 +MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYGLSPEQARGGLTAAEARTLMA +EGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAADLDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTL +DDAGVELLAVMVNRADPRDLDAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM +EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYLGAAFPVFVTHDDTFTTAAKV +SRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRTDVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEIL +QRRDVCDLVVLGPAAAVRELASREGVDLTGIELVDPADSPDLERYAQEYARLRVHKGVDAERAREVMQEGAYFGTMMVHL +GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDAQQLADIAVASAATAAQFGVD +PRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEGPLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNT +YKAVQQSSGAVAVGPVLQGLNKPVNDLSRGTTVEDIVNTVAITAIQAQAQG--------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001993.fa new file mode 100644 index 0000000000000000000000000000000000000000..9246fff0f9e2dc95ea018e6cd7573f1b42f62812 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001993.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_00166 +MEYTKKWLPLEAQVERLVQRGLEVDDLTRALRLLESVGYYRVTGYLYPFLESEKQVDDQG +HTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEGVERIEVAVRMRIGYVLGRTSPFAH +ENPTCFDDSFTRANTDSRDPRPSKQVLWL-ERVKQRRDGSDEQFVAHFRQKYDDHMPVWA +LTELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMMGSWLASLNYVRNVAAHHARLFNR +KLQNAPSRPAAGMV-PLLDHLREPAAPKGDFGTYNALAIIAYMLRPIEAERSWAPRLAEL +FRTFPTSHALSV-QSMGVPEDWHTLDLWR-G +>GCF_003691675_PROKKA_00353 +------------------------------------MGYYRVTGYLYPFLESEKQVDDQG +HTKIRVLNRYQPGTALHHAEEIIDFDRQLRMLVMEGVERIEVAVRMRIGYVLGRTSPFAH +ENPTCFDDSFTRANTDSRDPRPSKQVLWL-ERVKQRRDGSDEQFVAHFRQKYDDHMPVWA +LTELLELGHLSNLYQGMLQKDAEEVATAFGIPQKKMMGSWLASLNYVRNVAAHHARLFNR +KLQNAPSRPAAGMV-PLLDHLREPAAPKGDFGTYNALAIIAYMLRPIEAERSWAPRLAEL +FRTFPTSHALSV-QSMGVPEDWHTLDLWR-G +>GCF_003691675_PROKKA_02025 +MRYSKPHLPYDQQVRLLASRGLNVGREGDAVRALKRIGYYRLSAYTYPM--RAFTTDDAG +--TVHRSDDFVEGACLSDAVALHDFDHRLRRTLLPAIQSLEIALRTKVGYHLGKHGPLAH +LDRSGLDPQRCDAVSRGPDHTGTKYDTWRSEYDSLQRKAGREDYMVHFATKYDGDVPVWA +ATEFMTMGCLIGLYRMMQPKDARRIAEEVGVKNPQVLFGWLKALNVLRNHCAHNARIWNR +STVYPPDKINRRMVEEELHHLVSADTNK----VYFLTAVLAYLLRHVDPDSRFASDLRTT +MGKFPSVLGWTPGHTMGFVDGWSTEALWSIH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001998.fa new file mode 100644 index 0000000000000000000000000000000000000000..0eb5edaf923945889db2e443a11cd2865c42a75d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001998.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_00271 +MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS +AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF +GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP +>GCF_003691675_PROKKA_02286 +MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS +AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF +GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP +>GCF_023573625_PROKKA_00269 +MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS +AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF +GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002003.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d7a0d65823d16be1ad3acfd0517f21fc2cb6142 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002003.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00453 +MTAITVVGGTGYAGAAIVAEAARRGHTVTAISRTAPGTQAES-VRYVTGDLTRSVPDIAG +AEVVVAALSPRGDNAGKLRDAYRS-LAQAAATNGARFVGIGGFSSLRPAQGAPRFVEGDD +LPPEFAAEAREMNDILTDLATGSVDVDWLFVSPAAEFGSHAPGEALGRYRVSGEVALFDQ +DGKSAISGADFARAVLDEIETPTRHRAQIHFAY +>GCF_005280335_PROKKA_02503 +MTAITVVGGTGYAGAAIVTEAARRGHTVTAISRTAPGTQAEG-VDYVTGDLTQSVPDIAG +AEVVVAALSPRGDNAGRLRDAYRS-LAQAAATNGARFVAIGGFSSLRPAEGAPRFVEGDG +LPPEFAAEAREMNDILADLATGSVDVDWLFVSPAAEFGSHVPGEALGRYRVSGEVALFDQ +DGKSAISGADFARAVLDEIETPTHHRAQIHFAY +>GCF_020097155_PROKKA_02490 +M-KIAVIGATGMVGSRVVAEARARGHEVAAGSRS--GSRQDGWFDVDVADTAAVARVIED +NDITVLAVPPVRTGDGDVTAIRRSHQALIAAAPQGRFIVVGGAGALQLPDGS-LLKDSAE +FPAEYKAESDVFGDILEDY-RASQGLAWTMLAPAPMI---APGERTGAYKTETDIP---- +-AGETVSAEDFAVALVDEAESGAHRGTRFTVAN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002004.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b643edbf20721cbcba1737bf0e458d6d08c093a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002004.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_00455 +MVTMRQAGAKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQK +MLTQTLRALEEDGLVTRTVYAEVPARVEYRLTEAGHSLRAPLQALEEWSITHLADVLHAR +NHYQT-- +>GCF_005280335_PROKKA_02502 +--------MKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQK +MLTQTLRALEEDGLVMRTVYAEVPARVEYRLTEAGHSLRAPLEALEKWSITHLADVLHAR +THYQT-- +>GCF_020097155_PROKKA_00141 +M-------NRSWNPLLASCPSRTSLARIANKWTALIVIALAEGPLRFGGLHDGVDGISRK +VLTDTLRDLERDGIVARTDHGGVPRRVEYELTALGRTLETPLAALVDWAAEHHDAVEAAR +VDYDERR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002007.fa new file mode 100644 index 0000000000000000000000000000000000000000..64c0a4841aa8686cee454efcccf880299d734bc1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002007.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_00515 +MASFDILYIRPAGSGWGPVHELVQLTRRLFDARLIEVDDTGDVNRLQRASALLPRGPRVR +DRHLLVMGPQPAAIAHVAHPRLWLPGYRSVAVWIIDSFWTDRTPRLLRDRPHVDRLFITD +PQLVSEWSGQTGLPVGVLPWGSDTTRFTSAQEGTDRPVDVLRVGRQPRAWSDDARTSRDA +AAHGLHFAGRPPFSDDPARNQMLVREAMGRARVVLAFSNLVSPAPYTHPTRDYLTGRWTD +ALAAGCLVAGTAPASAASLLWPGATVEISPTSRDDAWPVLAQLASEWTPQAAADRQSEAR +RRLDWRYRLRDLCMAMDWAVPDRLTAELATL------- +>GCF_003691675_PROKKA_00240 +-MSVDVLYVRPGGSGWGPVDVLARLAARLLEGRLVEVEDRGAASWAQRASVLLPRGRRAR +GRRLLVLAGNPAALALAARRDLWWPGHESTAAWIVDSFWTDRIAGIARHRPHFDRLFVTD +PDLVDEWSALTGRPVDALPWGSDT--LAVAADDGPRPVDLLRLGRQPEAWDDDARTAREA +QDHGLVFRGRPPSSPDPLQNQEAVRAALAQARLVLAFSNLVSPAPYTHPTRDYLTGRWTD +ALAAGCRVAGVAPRSAATLLWPEATLEVSPNSRAEAWPVLAEAAAAWTPERAAEQRRRAR +RELDWRLRLQRLCTAMGWPLPPTLDAELAAL------G +>GCF_005280335_PROKKA_02436 +-MTLDILYVRPRGSGWGPVAELVALAARLFDARVAVVDDHGEVSLFRKTAASLPRGRRRP +GHHLLVVAPHAGMAAYAARPRLWFPGYDSTAVWVIDSFWTDRTPRLLRGTAHVDRVFITD +PQLVEEWEQITGTPVSVLPWGADTALYPSAAH--HRDIDLLRLGRQPKAWADDDATAADA +RRRGLRFAGRPPMNDDPGQNQHNVREALMGAKLVLAFSNLVSPAPYTHPTRDYLTGRWMD +ALAAGCLVAGTAPAAATSTLWDGATLEISPTSREDAWPVLTAAAEGWSPERAAEQQERAR +RTLDWRWRLRQMSSVMGWPEPPRLTQELERLISSPQQG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002008.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a4a1d0694998b4c3bbd14ebecfa3b217fe417bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002008.fa @@ -0,0 +1,28 @@ +>GCF_002008305_PROKKA_00525 +--------------MGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFE +AVLAIGLVMEAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSQYGVLALVALALVAYLV +AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDT +YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGFALTFLTGSRTSMAGLL +CAVVWILVSPYLGRVLRIALGVVLGWFVSWAEVNLADLGIFGDRTGTDWFREQIQEASAE +KVADTSFFGQGLSTAFVELDNVTMFFHNSYLGLLVEGGWPFLIVVVGAYLWLCLRPFART +HRSPSRVAVEAAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQENEESQGAPAKDRAH +RRKLDRIIERSRRAGV +>GCF_003691675_PROKKA_00246 +MRPSTPRDRTAARAMGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFE +AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV +AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDT +YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGSVLTFLTGSRTSMAGLL +CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE +KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART +HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH +RRKLDRIVERSRRAGR +>GCF_023573625_PROKKA_00525 +MRPSTPRDRTAARAMGAVAPPEARPARRHPSLGLFPDGQAAWTRSPWNPLVTPASPRLFE +AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV +AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGILYGMTVGALINVPLFYAGLAPDT +YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGAALTFLTGSRTSMAALL +CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE +KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART +HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH +RRKLDRIVERSRRANR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002009.fa new file mode 100644 index 0000000000000000000000000000000000000000..d82b8e3a5a1c72d88bf4ff1a82b256162753ed2b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002009.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00528 +MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVA +GLADHRPAALQPFMVAEADLVLAAAQEHMRFALREVPQAVARVFTVLELAALVRILDARN +GRDWIPAGRGVRAFAAEAAHHRALARSSAQPLDVVDPFRGPVEGYAEMIRIMDPALETIA +DALARAVTPTP +>GCF_003691675_PROKKA_00249 +MLIVCTGNVCRSAYASRALQGRLAALVPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT +GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD +GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA +DALARAVTPTP +>GCF_023573625_PROKKA_00528 +MLIVCTGNVCRSAYASRALQGRLAVLAPGRVEVGSAGSQPNQALTVPPPLVRLGAEAGVT +GLEGHRPAALQPFMVAEADLVLAAAQEHMRFALQEVPQAVARVFTVLELAALVRAMDQRD +GRDWIPAGRGVRAFAAEAARHRALARSTAQPLDVVDPFRGPVEGYAEMIQIMDPALETIA +DALARAVSLAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002010.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4366d821a5b7c3ede2fcf5154665f48bb24eb98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002010.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_00582 +MVGDMSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGAGAARTEAP +RTAGTGPAQAAAEAEPSTEAGSARG +>GCF_003691675_PROKKA_00315 +----MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEAS +RAAGTGPAQAAAETEPSTQAGSARG +>GCF_023573625_PROKKA_00583 +----MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEAS +RAAGTGPAQAAAETEPSTQGGSARG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002014.fa new file mode 100644 index 0000000000000000000000000000000000000000..25403356dc80158362cf0ced37b14909c2ae42f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002014.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_00613 +MTMIKEPGVS-PTAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVS +AHLACLTGCGLVSSRPVGRASLYSLAAEPELLEVLAAAERLLTVTGHAVELCPHS----- +-GPAATGALPHDAGH +>GCF_003691675_PROKKA_01773 +--------MS-PAAGLGPAAALFHGFSDPTRLAILRHLATGEHKVRELTEHLGLAQSTVS +AHLACLAGCGLVASRPVGRASLYALAAEPELLQVLAAAERLLTVTGHAVELCPHSGTPGP +DGPAAA--------- +>GCF_020097155_PROKKA_00703 +--MIQEKGATLDEVATVAYAHLFQAFAEPTRLAIVQHLASGEHRVRDLVEHMGLAQSTVS +KHVGFLVECGLATMRPEGRSTWYSLAQSELLRTLIAAAERLLDATGTQALLCTHLRLPHT +HHASDT-----DKK- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002015.fa new file mode 100644 index 0000000000000000000000000000000000000000..460338821e09582acdec770395d2390bc46d0694 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002015.fa @@ -0,0 +1,42 @@ +>GCF_002008305_PROKKA_00702 +MHRLGPELQGILAWCRSRGVPTAFWNKEDPVHFNTFLTAAGEFDAVFTT---DLDCVPRYKRELGHENVHFLPFAAQTAQ +SNPVEVFDRVEGCAFAGAYYAKYPERLADLRELSAELSADGRRFDIYDRNHGRATSGYTFPEDYQRYIVGGALTPGLLDV +PYKGYTVNLNLNSVKQSQSMFARRVFELLASNTLTVSNFSRGLRLMFGDLVVSTDSGRQMRRRLEAIEAQPNGNERLRAV +ALRKVLREHTYTERLEFVASRSGVTLPDAAVERPLMVVPSTLGRDAAAVVELVRRWAGQTWNDWVLAVQGKVEEFAPMPL +ELQDPRVVLFDELADLDGLARTRGCTLAGMLDPNDWYGPHYLEDMVLTLRWADVKTCGHVEHYAVDSVDGSLERRELGTA +WRLQDKILPCRSLSRLDWAQVADCNGVARQLDAAQLSGLAVSPLEYCAGGATSEEPALAPASSLDVYEGLTLTEIRQHAD +DLVFAESSDDMPVMDLGTIFEGMKSFDEMTLTWEDGVPRVTSSLGAGRHQYWINSLARPVEFHQNGNDQPVYFDVSVGLD +IMLVAYWLDADGQRFGHAMIPARQYTTVKIPEQARAMRWGLRVSGSGSAVVHRVVNGPYVAPSVPMLAGSS--DVLITNI +YPAYDNLYRNGFVHSRLRRYREMGHRLETILVGEGDGPRFREFEDVDVAVLRVQDLIATLATGEVKTLVVHCLLPETWNV +LKATSDLPPTTVWVHGFEIQPWWRRRFNYATEEELDAAKMLTEQRLAMWREVFDSSPDNMHFIFVSRWFAETVFEDVGIR +LPDHRYSVIHNPIDDTVFPYQEKTAQHRLRVLSIRPYHSHVYANDLAVAAVLELSNEPWFNELDFTFIGDGPLFEETLAP +LWDFENVLIRKGFLTHAEIASEHARHGVLLVPTRSDTQGVSRDEAMSSGLVPITSAVAAIPEFVDEEVAFLAPPEDHRAL +ADAVRTLRAEPARYLRMSAAAARRVRRQSGADHVLDAELRLAFRTDGDHSAPSVRPHPEREAHRP +>GCF_002008305_PROKKA_00891 +MLR-----------------------------------------AVFDTLPQDSDAVRRLRAAAAP------PRRRRTSP +PRPA---------APAGA--------------------------------HGD--------------------TPG---- +-YRGY---LHLADV---------------------------------GD------------------------------- +---------TYTAQ----EASTLLQLENAALKRRLFAEPA---------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------PPLPPTG---------------HED +E-------------DL---------------------------------------------------------------- +-----------------------------------------------AAAPRRVADHLARADAADQLGDDAPRHLVVVGV +YPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVHVLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEP +IQDALAGHRFFVFMHGFESRRWIRTVRNHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELV +FPGQRTAIVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTVIGDGKHFGLFEAA +FADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMASGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGL +ADGLRRLMEDPDLFLRMSQAAAARVRAQTSPEHTVDHEMALM----GLAAGPGGR--GEENA--- +>GCF_003691675_PROKKA_00613 +MLR-----------------------------------------AVFDTLPQDSDAVRRLRAAAAP------PRRRRTSP +PRPA---------APAGA--------------------------------HGD--------------------TPG---- +-YRGY---LHLADV---------------------------------GD------------------------------- +---------TYTAQ----EASTLLQLENAALKRRLFAEPA---------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------PPLPPTG---------------HED +E-------------DL---------------------------------------------------------------- +-----------------------------------------------AAAPRRVADHLARADAADQLGDDAPRHLVVVGV +YPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVHVLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEP +IQDALAGHRFFVFMHGFESRRWIRTVRNHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELV +FPGQRTAIVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTVIGDGKHFGLFEAA +FADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMASGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGL +ADGLRRLMEDPDLFLRMSQAAAARVRAQTSPEHTVDHEMALM----GLAAGPGGR--GEENA--- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002019.fa new file mode 100644 index 0000000000000000000000000000000000000000..340cc2cc92d3998d4281a9ef17957457271568ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002019.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00888 +MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVE------ +-------LGDDCKVQNLALVYEP--ARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDD +WEAVG--VDIGDGAAIGARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIG- +-------WVGRTGR-----RLEEKDGVWVCPDTGETFIERDGALRPAEPAQEEENHG +>GCF_003691675_PROKKA_00610 +MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVE------ +-------LGDDCKVQNLALVYEP--ARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDD +WEAVG--VDIGDGAAIGARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIG- +-------WVGRTGR-----RLEEKDGVWVCPDTGETFIERDGALRPAEPAQEEENHG +>GCF_005280335_PROKKA_01215 +M---------------------------SKLRMLSRMPKK---GRFMFIISGGDRARYMS +RKGLVRGMGENVWFQPRALPNDPNLIRFHNNIVVASGVTFVAHD---VINLMIGRKNGVR +LPVNEDCIEVMDDVFIGSGSVILPGVGIGPRAIIAAGTVVTKDVPPDSIVRGVPAKRLGD +FSVLEAQRLADAGRFDGMTRAQIDDVLW----------------------------E + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002020.fa new file mode 100644 index 0000000000000000000000000000000000000000..124969a7f0915b498e132a60a55ca60a90b7f598 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002020.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_00889 +MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQ-GPEVAAFEEEFGAAMVDGRA-CVAVNSG +TAGLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAK +VT------ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTF +GAWGMFSLYPTKNMTSGEGGMVSVGEADVARRLRLLRNQGME--VQYRNELVGFNNRMTD +IHAAIGRVQLTKVGAWTRRRQEIAARFD---AELRGVTV---PTVLEGA---EHVYHQYT +VRLPEELAGTRADVLARLKDEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIP +VHPSLTDADVTRVVEAVNTVVAEAAA +>GCF_003691675_PROKKA_00611 +MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQ-GPEVAAFEEEFGAAMVDGRA-CVAVNSG +TAGLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAK +VT------ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTF +GAWGMFSLYPTKNMTSGEGGMVSVGEADVARRLRLLRNQGME--VQYRNELVGFNNRMTD +IHAAIGRVQLTKVGAWTRRRQEIAARFD---AELRGVTV---PTVLEGA---EHVYHQYT +VRLPEELAGTRADVLARLKDEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIP +VHPSLTDADVTRVVEAVNTVVAEAAA +>GCF_005280335_PROKKA_01223 +MTDRIFLSSPDVTQAEEDALVRAFRSNWIAPLGPEVDAFEAEL--AEYTGRAHAVVLSSG +TAALHLGLLNLGVGPGDLVPTSSLTFAATANAIAYTGAEPVFVDAD-ESGNMNPALLEQA +LATLRGEGHEVKAIVPVDLLGKTADHAAIGRIAAEHGAVVLSDAAESLGATRDGKQSAAY +GVAAAVSFNGNKIMTTSGGGALLTDDEEMATRTRYLATQARQPVVHYEHTDIGYNYRLSN +ILAALGRAQLNRLEEMIERRRALRIRYRELFAAVPGVEMFGEPSGADGGPTRDNFWLSSV +LVDPDAAGFTAEDLRAHLAGQDIEARPLWKPMHLQPVFAGRRAFTDGTGERLFTTGLSLP +SGSVLDESRISRVLDSITAFLESRA- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002022.fa new file mode 100644 index 0000000000000000000000000000000000000000..225066a3b0d65e0913b47cbd1053bddae1f44508 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002022.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_00945 +MTATTHILLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV +EAVAKVGYTARPSAF +>GCF_003691675_PROKKA_00664 +MTPTTRTLLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV +EAVAKVGYTARPSAF +>GCF_005280335_PROKKA_01992 +MTATTHTLLRAEGFSCPSCVRKIEKAVDALPGVTGSKVHFETQRIEVDHDAERTSVQDLV +DAVDRVGYRARPSVF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002024.fa new file mode 100644 index 0000000000000000000000000000000000000000..dae9dc1e04e6f57a4454660a361acdd091f73894 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002024.fa @@ -0,0 +1,27 @@ +>GCF_002008305_PROKKA_00970 +MTTAMTT-----TTDVRPAPRD----ESAEILIIGSGFAGLGMGAQLRRHGREDFLILDRAQQVGGTWRDNTYPGAACDV +PSHLYSFSF----APNPQWSGFYTPGPEIQDYLVRFSEDEGLTPHLRLGADMLEAHWDPETERWTVRTPRG-TYTGRWLI +MGTGHLADPRLPDVPGLDAFEGEVIHSARWDHTVDLKGKRVAVVGTGASAIQVIPELAATAAELVVFQRTPAWVTP---- +--------RVVKPY--------SAAVRRMFER----APHTMQRERDDI----------FWFAESNYAQRRGVPAALDQVR +AQALGHLAAAVSDPELRERLTPRYLPGCKRVLVSNDYYPAMAR---DNVTLEDSALDRVEGSRLFGVSGHG-------YE +VDVVVLCTGFEAAQPPFAERVHDGEGR---SLADHWSSGMAAFDSTAVAGFPNLFAINGPNTSLGHNSIVYIIESQIAYI +LEALDRVEHEGIRTMVPETLAQEEYVDRLQERAATSVWL-VDGGCHSWYVDPRSGKLTLIWPDYAYDFRARNGHFTGE-- +----GFL------SSASGEPEPMPVREPERSVALI +>GCF_003691675_PROKKA_00683 +-MTTTTT-----TTDVRPALRD----ESAEILIIGSGFAGLGMGAQLRRHGREDFLILDRAQQVGGTWRDNTYPGAACDV +PSHLYSFSF----APNPQWSGFYTPGPEIQDYLVRFSEDEGLTPHLRLGADMLEAHWDPETERWTVRTPRG-TYTARWLI +MGTGHLADPRLPDVPGLDAFEGEVIHSARWDHTVHLKGKRVAVVGTGASAIQIIPELAATAAELVVFQRTPAWVTP---- +--------RVVKPY--------SAAARRMFER----APHTMQRERDDI----------FWFAESSYAQRRGVPAALDQVR +AQALGHLAAAVSDPELRERLTPRYLPGCKRVLVSNDYYPAMAR---DNVTLEDSALDRVEGSRLFGVSGHG-------YE +VDVVVLCTGFEAAQPPFADRVHDGEGR---SLADHWSSGMAAFDSTAVAGFPNLFAINGPNTSLGHNSIVYIIESQIAYI +VEALDRADHEGIRTMVPEALAQEDYVDRLQERAATSVWL-VDGGCHSWYVDPRSGKLTLIWPDYAYDFRARNGHFTGE-- +----GFL------SSASEDPEPMPVREPKRSVALI +>GCF_005280335_PROKKA_00813 +-MTTQTTETTAPTTDAAPGAAAGGDVQTVDAVVIGAGFGGCYLVHRFADEMGMSVIGLEKGDDIGGTWYWNRYPGALSDT +QSHLYRYSFHKGLLEKGDWSHTYVNQKDILEYFELVDRELDVRRHFRFGEEVASATWLEDEQRWELVTKSGLTLRATYVV +NAVGLLSAVNMPTIKGIDSFQGEILHTGAYPEGKDLSGKRVGVIGSGSTGTQVVTALGPQVKQLTHFVRSPQYSVPVGRR +EVTDEEKARIKANYDEIWEQVKNSSVAFGFEESSTPAMSVSAEERERVYEKAWNEGGGFKFMFGTFSDIATDEEANETAA +AFIRNKIGEIIEDPEKARKLTPHDLYA-RRPLCDDGFYATFNLPHVDVVALKETPIKEITAEGIVTAPESGVEGGEQLHE +LDVIIFATGFDAVDGNY--RRMDIRGRDGVEINEHWEGQPTSYLGVATDNFPNWFMILGPNGPF--TNLPPSIETQVEWI +TDFIDYARQNGIATVEPKAQTIEEWTQTCTEIANATVFTKVDSWIFGANVEGKKPSVLF----YLGGLGNYRGVLDGERD +AGYPGFELTRADGTQAAASPQPADVSA-------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002027.fa new file mode 100644 index 0000000000000000000000000000000000000000..d87955e0dd63c0f882cd3e9091ec8addb74e3199 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002027.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01291 +MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGFADAGPSADAGSDHSLVVEHNLDGL +NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYVSIAPYRSQT +HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV +SAEGRTAKKAISTRPDDPTCLTGLQLA +>GCF_003691675_PROKKA_01010 +---------------------------------------------------MVEHNLDGL +NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYVSIAPYRSQT +HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV +SAEGRTAKKAISTRPDDPTCLTGLQLA +>GCF_023573625_PROKKA_01249 +MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGCADAGPSADAGSDHSLVVEHNLDGL +NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTLPMPEDEFYVSIAPYRSQT +HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV +SAEGRTAKKAISTRPDDPTCLTGLQLV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002028.fa new file mode 100644 index 0000000000000000000000000000000000000000..bbb7f000bfc4aac51c8abe6bfb68d966126b3dab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002028.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_01294 +MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR +AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR +SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK +THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT +GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR +SSAREARRGSAPAGMSVRTWTERIPRNAHRETE +>GCF_003691675_PROKKA_01017 +MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR +AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR +SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK +THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT +GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR +SSAREARRGSAPAGMSVRTWTERIPRNAHRETE +>GCF_023573625_PROKKA_01252 +---------------------------------MKPGEGRHPRRHGPGSRCSPTPPQAGR +AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR +SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK +THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT +GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR +SSAREARRGSAPAGMSVRTWTERIPRNAHRETE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002030.fa new file mode 100644 index 0000000000000000000000000000000000000000..65fe5de18a7903ba2460a5a2c02cd351d6b5aec6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002030.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_01385 +MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG +LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL +LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA +VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR +WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR +RDLDQTTTST +>GCF_003691675_PROKKA_01113 +MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG +LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL +LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA +VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR +WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR +RDLDQTTTST +>GCF_023573625_PROKKA_01340 +MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG +LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL +LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA +VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR +WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR +RDLDQTTTST + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002033.fa new file mode 100644 index 0000000000000000000000000000000000000000..503427845c9809d3363dce9bcd90800bfd59568e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002033.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_01395 +MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR +LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG +>GCF_003691675_PROKKA_01128 +MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR +LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG +>GCF_023573625_PROKKA_01345 +MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR +LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002034.fa new file mode 100644 index 0000000000000000000000000000000000000000..dfa0b4b26144efedae9fbf317368f3b5f2073091 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002034.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_01396 +MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV +LLLPS +>GCF_003691675_PROKKA_01129 +MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV +LLLPS +>GCF_023573625_PROKKA_01346 +MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV +LLLPS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002038.fa new file mode 100644 index 0000000000000000000000000000000000000000..963bea63120504b8131b6644858817dae513cf99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002038.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_01615 +MRLVWDRSAWEDYTHWQTTDRKVLNRINTLIDAALRDPFEGIGKP------EQLKYGAAG +AWSRRITEEHRLVYLVDGEDLIILQARYHY +>GCF_003691675_PROKKA_01325 +MRLVWDRSAWEDYTHWQTTDRKVLTRVNTLIDAALRDPFEGIGKP------EQLKYGAAG +AWSRRITEEHRLVYLVDGEDLIILQARYHY +>GCF_020097155_PROKKA_01188 +MT---------------------------------RKPSGPFGPPLAPASAAAIARRAAG +AWSRRITAEHRLVYLVDGEDLIILQARYHY + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002043.fa new file mode 100644 index 0000000000000000000000000000000000000000..ddc5fd0595c52999803286ecc51f05e842f2ac84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002043.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01623 +MSTFNENVVELAALEHFAELGYRRVHAPEIAPGEPDAERDSYEDVVLWGRLRDALRRINTSADAALIAEAVKTVQRAGSQ +SAVDENARLHKLITEGVPVEHRGDDGLLRTTRLWLVDFDEPANNDWVAVNQFTIVENGKNRRPDVLVMVNGLPLALLELK +NPAAGHATLKSAWNQVQTYRHDIPSVFVPNAVTVISDGTSAAMSSYSGAFEHYAPWKTIEGREVVSNRPALEVLIKGVFE +PKRFLDLLKNFVVFSDETVTDKSTGQPTRALLKRVAKYHQYWAVNAAVESTVQASSPDGDRRGGVVWHTQGSGKSFEMVF +YAAKIMRDPRMANPTLVFITDRNDLDDQLFGETFAPARILPETPVQAATRSDLRAKLKRASGGIVFTTLQKF----APGE +DGDANPVLTDRRNVIVIADEAHRSQYGFSETLDRHGRLKSGLAKHMRDALPGATYLGFTGTPIESNDKSTRAVFGDYVDV +YDLTRAVEDGATVRIFYESRLAKI-ELSEADLAALDDLADEITESVEKDTATAAKSRWSRLEAVVGAEARLDLVARDIVE +HWEKRRESLF------GKGMIVTMSRRIAVRLYEKIIALRPDWHSDDPAQGKIKVVMTGSASDPAEFQPHIHSKDVRKDL +KLRAKNADDPLELVIVRDMWLTGFDAPSMHTMYVDKTMQGAGLMQAIARVNRTFRDKPGGLIVDYIGVFANLQNALSEYS +PSDRDQAGVPIDEMVQVMLEKHDIVRGLLHGV-------QFDSSPE-------LTAAQRLNEYAKVLDFVMADPD---RT +SRFNDQVLALAKAFALAGARDEAAAIRNDVRLFTDVRAAILKIQNPDS-GRGGSGAVEVDTALSQLLNEAVTANQVVDVY +MLAGIETPEISILSEEFLDSFAEKDRPNLQMGLLRRLLNDQIRTVQRTNVVQGRKYSEMLEETVNRYTNRSLTTAEIIAE +LVKLAKQMRDAQKRHEELG--LREDEVAFYDAVVQNDSAVMELGDETLKAIAQELVTSVRQSATIDWNLKESVLAAMRSK +VRRILAKYDYPPDAEAKAIELVIEQAELFARGVS--A +>GCF_023573625_PROKKA_02203 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +--------------------------------THANAPLTPTGRLRMVHRHLRDLLTQSNSGGIYFTTLQKFGLTQAERD +AGADHPVLSDRRNIIVMADEAHRSHY---DTLD-------GYAAHLKNALPNASLIAFTGTPIAEGERDTRRVFGDDIDV +YDLHRAVEDGATVPVSFEPRLITLSRVDGVDDESLDAAADELTAGLDEADRDRIQRGVATLEAVYGAPHRLQTLAEDFVR +HWEDRRDAMQPTMGVPGKAMIVCATRSIAARLYERIVALRPEWHDDADDKGRIKVVYDANPSDTGEIKKHMRRPSALAAV +KKRLKNPADELEIVIVKDMLLTGFDAPALHTLYVDRPLKGALLMQTLARVNRTFRGKEDGLLVAYAPLAENLQQALAEFT +RDTRTAGTKTLAQNTEEAAEIIETMVGMLADTVGVDWKATYQSDPKNGWRKALLEVTSRLRSPGTPGNTDPEDPTVRPVA +DTFRSQASRLHRAWALAGRVAAVERFRLDVKFYEEVRTWLAKLDAQDRIARGEPIPEEIARLLGEMVVDSTEATGVMDIY +AAAV---------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------G +>GCF_023573625_PROKKA_02206 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------EEAA--------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------APSKAELAIE-----GLRTDLLKEATRVTGGNE----IRRAQFSERINAVMAKYT +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +--------------------------------------------------------------------NQQLTAAEVIAE +LVEMAKEVVAEADRGRRFTPPLHDDELMFYDVVAQNEAALDVMGDDVLAQIARDLVATMRRDIKTDWTVREDVKAKLRAS +IKRLLRKYGYPPDQQPEAIVEVMRQMEAVAPRMAEGQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002044.fa new file mode 100644 index 0000000000000000000000000000000000000000..1517a0830a503e2d77b08996646cdbbaae53ebf7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002044.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_01897 +MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV +LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP +GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA +GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG +MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE +VAPYLLSPTGLDELIRRDV +>GCF_003691675_PROKKA_01593 +MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV +LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRSEMDAAAREGGHVAMISTGWDP +GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA +GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG +MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE +VAPYLLSPTGLDELIRRDV +>GCF_023573625_PROKKA_01817 +MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV +LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP +GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA +GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG +MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE +VAPYLLSPTGLDELIRRDV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002047.fa new file mode 100644 index 0000000000000000000000000000000000000000..2330a8475c87a1573834c48710d2409b960a91d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002047.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_01962 +MTTAVRTCAASACAFNAETSCSALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH +RLECTYNADLACTAEGIEVTDVATCATYTID +>GCF_003691675_PROKKA_01655 +MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH +RLECTYNVDLACTAEGIEVTDVATCATYTID +>GCF_023573625_PROKKA_01888 +MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH +RLECTYNADLACTAEGIEVTDVATCATYTID + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002051.fa new file mode 100644 index 0000000000000000000000000000000000000000..32768cc19c90275fee1db8efc5f4535035a4dfb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002051.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02042 +MTPTTSTPATFHDTRVDQQFIAGQWRDGASGDRASDINPYTDDVVAEFALATAEDLDEAY +RAAAAAQEEWAAMPPKDRAAVLRRAAEILEERRDEVIDWLVKEAGSTRIKADSEVSLAIA +ITQEAASFPTRVHGKIFDSNTPNRETRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG +NAVVLKPASDTAVTGGTLIARVFEEAGLPAGVLSVVVGSGSEIGDAFVTHPVPRLISFTG +STVVGKQVAANAVTGDTIKKVALELGGNAPLVVLDDADLDAAVDQAVLGGYLHSGQICMS +VQRVIVDESVYDEFLPKYEGAVKALKVGDPAEEGVLVGPIINDSQVESLRKKIASAEADG +ARALVGGEIQGRVVPPFVWVDATADMDIAREEIFGPMTVVLKAHDEAHALELANDHEYGL +SSAVFTQDLDRGLRFANGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWALEEFT +TDHTIGVTRVG +>GCF_005280335_PROKKA_00776 +MSPTTHAAATFHSNDVSKQFIAGQWRDGAAGSTKQDLNPYDDAVVAEFALASEADLDEAY +RAAADAQKEWAAVAPAKRAAVLRRAAELLEERRAEIVDWLVKESGSTVIKANIEVSLAVG +ITQEAASFPTRVHGTIHPSNTPDREMRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG +NAVVIKPASDTPVTGGTLIARLFEEAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG +STPVGKQVGANAVSGDHIKKVTLELGGNAPVVVLDDADLDAAVEQSVTGGYLHSGQICMS +VQRVIVDEKVYDEFLPKYEGAVKSLKFGDPREEGVLVGPVVNDQQLETLKKKIASAEADG +ARALVSGEIEGRVVPPFLWVGAEPDMEIARDEIFGPMTVVLKARDEAHALELANDHEFGL +SSAVFTQDLDRGLRFADGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWAIEEFT +TAHTIGVKRLG +>GCF_020097155_PROKKA_00744 +MTPTTHASGTFLGNDVGKQFIAGQWRDGAAGSTKQDVNPYDDSVVAEFALASEADLDEAY +RSAAEAQKGWAETGPKERAAVMRRAAELLEEHRDEVVDWLVQEAGSTVIKANIEVSLAIA +ITEEAATFPTRVHGKIFDSNTSNRESRVYRSPIGVVGVISPWNFPLHLSQRSVAPALALG +NAVVIKPASDTPVTGGTLIARLFEQAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG +STPVGKQVAANAVLGENIKKVALELGGNAPLVVLDDADLDTAVEQAVTGGYLHSGQICMS +TQRVIVDAKVYDEFLPKYEQAVKALKVGDPRGEGVLVGPIINDSQVEGLQKKIASAEADG +ARALVGGEVEGRVVPPFVWVDVDPDMEIAKEEIFGPMTVVLKARDEEHALELANHHEFGL +SSSVFTQDTGRGVRFAQRVAAGMTFVNEMTVQDEAHVAFGGARNSGLGRFNGEWAVEEFT +TDHTIGVTTVG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002052.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ce4bc7ebfb8f117c8bc579e5baa47634c0f283b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002052.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_02043 +MSEPIGLRDAAIEWLKMRSLDGQVPLTREDIGDFRWNGEPFPLISTQNGIRKPAGFDAAL +SFYTVYRPKGHARPYEDEIGDDGLMRYKWQGTNPRLPANQGLFRAYERGLPLIWFVGVGM +SPARFQVVAPVYVVGREDERHQIVFAPMEPEDYSPELMHESVLEASLKRYLRREVKIRVH +QPHFRSTVLAAYDNHCAVCNFAHPELLDAAHIVPDREVHGLPTVVNGLAMCRIHHGAFDN +HFLGITPDF---TVEIRQDLLDEVDGPMLRHGLQDLHGRKLMKLPTRRADRPCRENLAWA +YERFREATVADVA +>GCF_005280335_PROKKA_00774 +MVEPAGLRNDAIRWLAERTLDGQLSVTREDLADYRWDGEKFPLISTMQGIRRPAGWSATL +SIRTAFRRSGETRPYEDEIGDDGLIRYKWRGDNPQQPENVGLRNAMHQRLPIIWFIGISM +NPAQYQVISPVYILGEEPERQQFVMAPFAEEDYVPDLMTGSVMESSLKRYLKRETTVRLH +QPLFRSTVLAAYGNHCSVCNFAHPELLDAAHIVPDREVHGLPTVTNGIALCKIHHAAFDR +RFLGLRPTQGRPVVEIQQDLLDEVDGPMLRHGLQDLHGKPVMTMPKRRVDYPSNENLAWA +YAEFTRAGRA--A +>GCF_020097155_PROKKA_00742 +MVEPDGLRETAIQWLIERTLDRQVSLTREDIADFRFQGEPFRLIPSYQGIWKPARFEATL +SIVTTYRAPGQERPYNDALGEDGLHRYKWRGDNPNHPENVGLRRAMERQLPIMWFTGVGG +KPPQYQVTAPVYIVNEERDRQQFVLAPLEDASEIPERGEGSEMVTALRRYMKRETVVRLH +QPVFRSTVLVAYEDHCAVCNFAHSELLDAAHIVPDSEEEGVPDVTNGMALCKIHHAAFDR +RFLGIRPTKDVPVVEIRQDLLDEVDGPMLRHGLQELHGKPLMKVPSRRADRPGTDKLVWA +YERFLNATAADVA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002053.fa new file mode 100644 index 0000000000000000000000000000000000000000..d348ea9bb079198040fadd4fc9e1f563af41448a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002053.fa @@ -0,0 +1,28 @@ +>GCF_002008305_PROKKA_02073 +MLTTSTTSHPVAIIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ +YNLDAAAQRLLEAAGWTAPDADVLPTGHELREHYLEPLAQLPQLAESIRYGARVTAVSRA +GIDKTRTARREETPFLVRIQTTDGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA +RAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTT---IIWAART +ADLTRVYGGGDQDELAARGALGSRLRQLVDSGRIAVLTSFTITRFRADDT-LTVHAVTPD +GEREVSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLEPLIDPEFHSCGSVEPHGER +VLAHPETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCT +TDLGGGCDAPATAGDA------CCS-SPQLIELPLGR------------- +>GCF_005280335_PROKKA_00737 +M----------------------------------------------------------- +------------------------------------------------------------ +--------------------------EDVHARAVIDASGTWTTPNPLGQAGLPAPGEAEA +LAAGQITAPLPDVLGADQARFAGQHVLVVGAGHSAANTLLELGTLAQDTPGTRISWAVRS +ADVARVYGGEDRDELAARGALGTRLRHLVETGTIQVHPSFTITAFTTTGLGMMVQASTPA +GEEHLVVDVVVPATGFRPALGMLSELRLELDPAVEAPRQLGPLIDPEFHSCGSVTPHGEK +MLAHPEPGFYIAGMKSYGRAPTFLMATGYEQVRSIAAALAGDRTAADNVELQLPETGVCS +TDLGGSCDAPAPATAADTADQGCCAPAPQTLPAPASRLPVLLPVQAATCC +>GCF_023573625_PROKKA_02001 +MLTTATNPHPIVVIGAGPIGLAAAAHLAERGLPFLILEAGTAAGAAIAEWGHTRLFSPWQ +YNLDAAAQRLLEADGWTAPDADALPTGHELREQYLEPLAQLPQLAESIRYDARVTAVSRA +GIDRTRTTRREETPFLVRIETADGHSEDVLASAVIDASGTWSTPNPLGQAGLLAPGEQQA +HAAGHITAPLPDVQGRDRDRFAGKRVMVTGAGHSAANTLLDLADLEADTT---IIWAART +ADLTRVYGGGDQDELAARGALGSRLRQLVDSGRIEVLTSFTITRFRADDT-LTVHAVTPD +GEREVSVDVLVPATGFRPDLGMLSELRLALDPAVEAPSQLGPLIDPEFHSCGSVEPHGER +VLAHPETNFYIVGMKSYGRAPTFLMATGYEQVRSIAAALAGDRKAADAVHLELPETGVCT +TDLGGSCDAPAPAGDA------CCS-SPQLIELSVGR------------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002054.fa new file mode 100644 index 0000000000000000000000000000000000000000..a58b33d2990b70259585dee677674cf65a452d87 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002054.fa @@ -0,0 +1,28 @@ +>GCF_002008305_PROKKA_02096 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------MGGASATLRTRGLGRHGRNARVLASHNPLIYRARLLGDRAVN +GTPLERHYRLGG +>GCF_020097155_PROKKA_00596 +MTTTTDRTDTISRPADVGTADSGVPTTAHPADRPQFLAARARLAPVFAWLAETAAERDRE +RVTDREATDRLAAAGFPGLRVPEDAGGAGLTFPEAARLYVELAEADSNVLQALRVHVVNV +ETVLGSPDGPRRERWLHRFATGETVANATTEIGNRTGHYETRLTTRPDGSAVVNGRKAYS +TGTLYADWTIVVVEDEDGAERAATVRSDAPGVTLHDDWDGFGQRLSASGTTEFTDVVVDP +EELTPVGQSLDDGSSIFASQAIFQFVHLVGLTGIARAVVRDAAAYVAGRTRGFSHGAAPR +PGDDPQVLQVVGELEAAAFGAQAALDAVVGPLDRALRAEAAGAPLAEAEVDAVYTAVYAA +QQVIARAALD-AATRLFEVGGASATLRTRGLDRHWRNARVLASHNPLIYRARLLGDRAVN +GTPLERHYRLGG +>GCF_023573625_PROKKA_02036 +MRLIHNK----------------------------------------------------- +-----------------------DCCG--------------------------------- +--------------WF----------------------------------AIRRGASARH +TG---------------GA-------------------DG-------------------- +---------------------------------------------------------AP- +PSREP------------------------------------------------------- +----ARDALERAATRLFEVGGASATLRTRGLDRHGRNARVLASHNPLIYRARLLGDRAVN +DTPLERHYRLGG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002057.fa new file mode 100644 index 0000000000000000000000000000000000000000..9ddc8ad4cdd574f3619015e2b090524a4a696a52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002057.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_02166 +MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL +ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT +RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT +RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP +DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW +RGFVETAGLVRAAIAERGGLDAGGAEDRLRN +>GCF_003691675_PROKKA_01880 +MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL +ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT +RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT +RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP +DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW +RGFVETAGLVRAAIAERGGLDAGGAEDRLRN +>GCF_023573625_PROKKA_02111 +MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL +ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT +RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT +RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP +DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW +RGFVETAGLVRAAIAERGGLDAGGAEDRLRN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002058.fa new file mode 100644 index 0000000000000000000000000000000000000000..2fa026279f632c5efac2eddeb98c2280e9ba1201 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002058.fa @@ -0,0 +1,19 @@ +>GCF_002008305_PROKKA_02191 +M----------------------------------------------------------- +------------------------------------------------------------ +------------G----------------------------------------------- +------------------------------------------------------------ +-----------GRPAAGLDPPQTAQSGHADDPSSARTVFDRFVFGNHIRSFSVD +>GCF_005280335_PROKKA_00551 +MTTTIQDPWAQPTPAGAYDDLLVRALPVTRAQRRWEPADGPMPSLFVSHGAPPTLDDPQW +LADLFDWAQSMPKPRAIVIVSAHWEDAPVAISSAAAGTPLVYDFGGFHPRYYELQYATPD +ATDLAARVAGVLG-QGRPGSVHQ-TGRGLDHGAYIPLMAMYPDADVPVVQVSMPSMDPSA +LLDLGVKLRSLREEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDKWAAEMTHAGDVDSLI +GYLDKAPGARIAHPTADHYVPLLLTMGAANDPSSARTVFDRFVFSNHIRSFSVD +>GCF_020097155_PROKKA_00474 +M--TLADPWAQPTPAGAYDDLLARALPLTRRQKLWEPSDGRMPALFISHGAPPTLDEPQW +LNDLFEWAQTMPKPRAIVIVSAHWENAPAAISASAAGTPLVYDFGGFHPRYYTLRYDTPD +ATDLARRLAGVLGAQGQ--EVHQHTDRGLDHGAYIPLMAMYPDADVPVLQVSMPSQDPAD +LLRLGERLRELRDEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDTWAAEMAHAGDVDALM +GYLDRAPGARIAHPTADHYVPLLLTMGAAHDPSTTRTVFNRFVFSNHIRSFTVD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002062.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c1e34ca6dc525da05df8e2cb2f1925efd406066 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002062.fa @@ -0,0 +1,24 @@ +>GCF_002008305_PROKKA_02210 +MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTEGLGGTLAKIVLLGLVDAFAAFLLFQLAAAGDWVVFALTLAV +TIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYVAFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLE +EGGDLYLLTLRDGEPVLGGADQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR +GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFTDPELRDPLLRVTVWTFAFAF +LSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPAFLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLS +VLVVNLWLGFPYMFLVTTGALQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG +PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEIDK +>GCF_003691675_PROKKA_01923 +MSPSSTASDRSDAATAALDDAARRTGPGRRRRADARGTDGLGGTLAKIVLLGLVDAFAAFLLFQLAAAGDWVVFALTLAV +TIGINWIYLRRGGLPAKYLAPGLFFLMLFQVFVVVYSSYVAFTNYGAGHNSDKAAAIEIIQRSSSIRVPDSPVYDITVLE +EGGDLYLLTLRDGEPVLGGADQALEPVEAQMQDGEPVGVEGYTTLRFGDLLQRQDQVARLKVPLSDDAADGTLETRDGSR +GYVYAPRLEYDEARDTFTDLESGVEYRDNGEGQFQADDGSTLQTGWRVFVGLDNFTRAFTDPELRDPLLRVTVWTFAFAF +LSVATTFAVGLLLAIAFNRSDMRGKKVYRVMMILPYAFPAFLSGLVWAGLLNPEFGFVNTVFFGGADIPWLTDPWLARLS +VLVVNLWLGFPYMFLVTTGALQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG +PRFPDAGSNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEIDK +>GCF_005280335_PROKKA_00534 +MSTSSTTSARPDAPHEDPADAGRR---GLRGRRADRGPDGTAGTLVKIALLGLVDAFAAFVLFQLAAAGDWVVFAVTLAV +TLLINWIYLRRGGLPAKYLAPGVFFLVLFQVFVVVYSSYIAFTNYGAGHNSDKPAAIEIIQRSSSIRVPDSPVYPVSVLE +QGGDLHLLTVRDGQAVLGGADEPLAPVEAQMDGAEAVAVDGYTTLKFGDLLSRQDQVTQLKVPLSDDPADGTLETRDGSR +AYVYSPRLEYDEAQDTFTDLESGVVYRDNGEGRFQADDGSTLQTGWRVFVGVDNFAKAFTDPSLRDPLLRVLVWTFAFAF +LSVVTTFALGLLLAIAFNRADMRGKNVYRVLMILPYAFPAFLSGLVWAGLLNPEFGFVNNVFFGGADIPWLTDPWLARFS +VIVVNLWLGFPYMFLVTTGALQSLPEDVDEAARMDGAGPWRIFRSIKLPLLLVSVAPLLISSFAFNFNNFNIIYMLTGGG +PRFADAATNIGATDLLITVVYKTAFSGVGRDYGLASALSIVIFLIVATISAISFRQTKALEEIDS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002063.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4b30bcf7013eb796a0a39eca4321e752a6d7e78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002063.fa @@ -0,0 +1,28 @@ +>GCF_002008305_PROKKA_02211 +MQSTTTGGLFRRPLSLTLTAAFSALALTACGGGSSAPASSSP----------AGATEQGT +ATASPS-QDLSEAGASTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFI +TQNPTGEGPDVIVGAHDWIGSLVQNGTIEPLELGERAGDFVESSVQAVTYEGQTWGVPYS +VENIAILRNTELAESTPASFDEMIAEGRKAVDAGEAEYPFVVGLDAVNGDPYHLYPFQTS +MGAPVFKQAEDGSYDTGSLAMGGPEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNA +AYFITGPWNIEEAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVN +YLSTEAAQDALFAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFW +GGAEMSIIKGEGDPVQTWQKMISDIEGRIGQ +>GCF_003691675_PROKKA_01924 +MQSTTTGGLLRRPLSLTLTAAFSALALTACGGGSSAPASSSP----------AGATEQGT +AAASPS-QDLSEAGATTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFI +TQNPTGEGPDVIVGAHDWIGSLVQNGTIEPLELGDRAGDFVESSVQAVTYEGQTWGVPYS +VENIAVLRNTELAESTPASFDEMIAEGQKAVDAGEAEYPFVVGLDPVNGDPYHLYPFQTS +MGAPVFKQAEDGSYDTGSLAMGGAEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNA +AYFITGPWNVEEAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVN +YLSTEAAQDALYAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFW +GGAEMSIIKGEGDPVQTWQKMISDIEGRIGQ +>GCF_005280335_PROKKA_00533 +MTSTTPRAALRRPLGLTLTAAFSALALTACGGGGGTAASSSPAAGGSASSSAAGGSDQGA +ASSSSAGQDLTEAGAATITMWVDQNRQKPLQAVAEDFKEDTGITVELVVKDNSKMKDDFI +TQTPTGEGPDVIVGAHDWIGSLVQNGTIAPLELGDTADAFSETSVQAVTYDGQTWGVPYS +VENLAILRNTALAEETPASFDEMIAEGQKAVDAGDADYPFVVGLDPVNGDPYHLYPFQTS +MGAPVFEQQEDGSYDVSSLAMGGAEGQAFAEKLAEYGESGVLNPNMTADIAKEQFNAGKA +AYFITGPWNVDEAEEAGVDFAVEEIPSMGDQPAQPFVGVNAFFVSAESENQLAANEFVVN +YLSSEEAQDALYAEGKRPPALTASFEKAAVDETVKAFGEIGEDGVPMPAAPEMGAVFEFW +GGAEMSIIKGEGDPAQTWDKMISDIEGRIGQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002064.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ec6a8791c24af4fcf863c23f404a8cff9eec6ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002064.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_02212 +MVGIKDVARMAGVSTATASRALTGSGPVAAATRTRVQEAVATLGYVADSAASSLASGRTR +NIGLVTPSVHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL +ITLSFRLSVFEFAGLERLGRPVIAIGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL +GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL +LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP +LEQGRRAVRLALGALDGAA---------------HPHRIMHHLALRPRASTAP------- +---------------P +>GCF_003691675_PROKKA_01925 +MVGIKDVARMAGVSTATASRALTGSGPVAVATRTRVQEAVATLGYVADSAASSLASGRTR +NIGLVTPSAHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL +ITLSFRLSMFELAGLERLGLPVIAVGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL +GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL +LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP +LEQGRRAVRLALGALDGAA---------------HPHRIMHHLALRPRASTAP------- +---------------P +>GCF_005280335_PROKKA_00532 +MVGIKDVARMAGVSAATASRALTGSGPVASSTRTRVQEAVAALGYVPDAAASSLASGRTR +NIGLVTPSVHRWFFAAVLEGAADELVRRRYDLTLYDVGQDHDRRSAVLTDLLPRRRLDAL +VTLSFRLSPFELDGLARLGRPVVAVGGRLPSGEALPEWFTAVQVDDARAARMATGHLIEL +GHREIAYMGRVADDIEFQVSTERTRSFLDALAAAGLRTPADWMLPADFTIGDAYHRARAL +LADPEHRPTAVLCISDEMAMGTLMAAQSLGLRVPEDVSVMGLDGHPDAARLGISTVDQTP +VDQGRRAVRLALGALDGTPTRPASSTTWPCNPGRAPRRRERRAGSRPRRRRPPSTPPSPR +IVGHVPARERTPPWPP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002065.fa new file mode 100644 index 0000000000000000000000000000000000000000..98bd4879d3ec8a8c72970aaae38b42c36a18ac1e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002065.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_02217 +MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA +ELAEAFDLDVSTVHRQVAAAMKAGLVERVVDPDGGSARLHRPTEEGRARLAAELSSRADN +VAQIVSSWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRL +>GCF_003691675_PROKKA_01930 +MMQTSEGAWADPVRGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSVA +ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN +VAQIVASWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRP +>GCF_023573625_PROKKA_02156 +MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA +ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN +VAQIVSSWPAEDVVEFSRLLRRFNEGAEARRGHPWPRPQTGPGAEDPRL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002066.fa new file mode 100644 index 0000000000000000000000000000000000000000..cdc819feed709e6546c67c577cbced0f47e5b1eb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002066.fa @@ -0,0 +1,13 @@ +>GCF_002008305_PROKKA_02242 +MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR +RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG +LTVHGPAVVALAYRLPARVALRRLCRAHL +>GCF_003691675_PROKKA_01944 +MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR +RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG +LTVHGPAVVALAYRLPARVALRRLCRAHL +>GCF_023573625_PROKKA_02174 +MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR +RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG +LTVHGPAVVALAYRLPARVALRRLCRAHL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002067.fa new file mode 100644 index 0000000000000000000000000000000000000000..50af6ccbc765ba16a9993a08a4bc578f8385cf3a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002067.fa @@ -0,0 +1,19 @@ +>GCF_002008305_PROKKA_02243 +MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM +LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP +MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD +WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE +ARPSP +>GCF_003691675_PROKKA_01945 +MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM +LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP +MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD +WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE +ARPSP +>GCF_023573625_PROKKA_02175 +MTLPTPSGRWTTTARPAFAVAAALSLGGNLLSLWIGSWKSSDLPADAGYAGVLEGGWEHM +LNQPTYFTFLSNFLVGLTSLLLALRLHRPGTLFRVLRVTGVVCIVITGVVFNVLLRDADP +MTAVERFNDTLQHIVTPILTPVLWAVFGPRRQITWRVVWLSTLIPLAWLAFTLLRGPWLD +WYPYTILDVPRLGYDGVAVYVVAILVFFVAVAALLRVADGLLARAGVGVGAGAEAEARVE +ARPSP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002069.fa new file mode 100644 index 0000000000000000000000000000000000000000..aff36f5681247371ec9288c6f5351ccf97ccf5ae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002069.fa @@ -0,0 +1,19 @@ +>GCF_002008305_PROKKA_02262 +M----------------------------------------------------------- +------------------------------------------------------------ +------RNGQSGAGPPATA---------PSPRSTRD---------------------VDV +GWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPDVR +HVQVPGAGRDVHLDAPERVAELVRGFAA +>GCF_020097155_PROKKA_00417 +MSGLGRRSAGPVTREDGTRLHVLDSGGSGPALLLLHGLAGYAREWAQVAERLAAACRVVA +FDQRGHGSSTRRPADLSRTAHVGDVVAVADALGLQRFTLVGQSMGAHTALLAAAAHPARV +GRLVLIEGGVGGEGPEATAGVIDWFRAWPIPFATVDDAVAHLGGGPAARVWAEGLEETDA +GGVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPDVR +HVQMPGAGHDVHLDAPERVAELVRGFAA +>GCF_023573625_PROKKA_02193 +M----------------------------------------------------------- +------------------------------------------------------------ +------RNGQSGARPPAIA---------PSPRSTRD---------------------VDA +GWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPEVR +HVQVPGAGHDVHLDAPDRVAELVRGFAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002072.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ebd6358ec679cc3de20af6f8aabb5776307e71e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002072.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02269 +MGTIFLYEIAGTAILLLLGVGVVANVVLSKTKGNGGGWLLISFGWGLGVFAGVYVAAATG +AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQTET +DQGAILGTFATGPEIRNPLWNMVTELIATFVLVFVVLLFGSTPSGLGPLAVALLVVAIGA +SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV +>GCF_003691675_PROKKA_01962 +MGTIFLHEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG +AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET +DQGAILGTFATGPEIRNPLWNMITEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA +SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV +>GCF_023573625_PROKKA_02201 +MGTIFLYEIAGTAILLLLGVGVVANVVLTKTKGNGGGWLLISFGWGLGVFAGVYVAAATG +AHLNPAVTVGLLVSGAEEYAPGIAVTLGTTLAYFAAQLIGAFLGAALAWLAYRDHYQAET +DQGAILGTFATGPEIRNPLWNMVTEVIATFVLVFVILLFGSTPSGLGPLAVALLVVAIGA +SLGGPTGYAINPARDLGPRLFHAVAPIRHKGGSDWGYAWVPIVGPLVGAVLAGLAAPLFV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002076.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7ff6ecfdfa0c7d5216c9ce0ee97379779e792c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002076.fa @@ -0,0 +1,19 @@ +>GCF_003691675_PROKKA_00242 +MRAVGAVKASILRTVRRGAPVSWAPEWMGLGNLLYQGLWAYEGASLGEPRFVLLPENRVG +VIELFPRLREKRFLRRSHVPFTAQRVRPWE----NEERSTGRFAPPLLEDFIRDDLLPGS +AVSPATDSY-DDAIVVNVRRGDYYSVERHRAQFGMDQEKYLRSALAEAVRTQGPVGRIVV +ISDGLDWCRDHVNDLLSEFAPVEYEDGDIAHDLKAIIHAKRLIITNSTFSYWGGYIGDVL +NPGRQVIAPWFFSRTENGGRSHLLAPSWTVIEGDF----- +>GCF_005280335_PROKKA_02430 +MKFLDKSKSRALKAIRRGDPVSWVPDWMGLGNILYQGLWAFEGDDRQEGRRVLLHPKREA +AVALFPTLRGRYFVTRDRVPFTARRVMPWR----EESPEPIPYQPAELPGFIREVLLPGS +PVAAVPDGLSEDDVVINVRRGDYYSVPQHEAEFGMDQVAYVRAAISRAAAVSGPIGRILV +ISDGLDWCRENLGPVLEPHGPVIYEDGDLFHDLRTIVHARRLVITNSTFSYWGGYIGDEL +HPGRLVIAPALFSHNLNGGRAHQLKPSWTVLEDGCWDRAR +>GCF_023573625_PROKKA_00514 +MNRLLDMKSNALSAIRRGRPIAWVPEWMGLGNLLYLGHWAYEGSAEDEDRRVLLHADRGA +AVGIFPRLRERLFVRREDVRFTDRRVMPWSGAATRQRPDHIPAQAH--EAFIRDLLLPDS +PVATPPHCL-KGMLVVNVRRGDYYSVKDHQDDFGMDQVEYIKAALKTSVAAHGSPDGIAV +VSDGLDWCKEALGGVLEAVAPTTYVDGDLTHDLGTIVHAERLIITNSTFSYWGGYIGDVL +SPGREVIAPWFFSRSQDGGRATQLRPHWTALEGDFY---- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002077.fa new file mode 100644 index 0000000000000000000000000000000000000000..35005a9618a11d3365ff435b63ed98a899cf0697 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002077.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_00324 +------------MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW +VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR +>GCF_005280335_PROKKA_02272 +------------MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW +VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR +>GCF_020097155_PROKKA_01826 +MPLPFEFERMLFMPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW +VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002079.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a3c58c90f49eb249791482f2ff6d819927838e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002079.fa @@ -0,0 +1,16 @@ +>GCF_003691675_PROKKA_00358 +MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTKSLAARMGTTAPNVTETVKRLAAQGLV +EYQPYKPVTLTGKGCEHAIAMVRRHRLLESFLAASLGYSWDEVHAEAERLEHAASDELIE +RIDQMLGHPTHDPHGDPIPTPVGQRERPAHAVRLDAAEPGFYRVLRISDADPQRLIRFQQ +AGIVPDSVVEVAEAGHFRLRVVAVGPVELIETDAAAIWLVPSSTRG +>GCF_020097155_PROKKA_00672 +MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV +EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE +RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ +AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG +>GCF_023573625_PROKKA_02012 +MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV +EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE +RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ +AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002082.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002082.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c56d0a7c6488ceac8161b766fa2b54f5f0df271 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002082.fa @@ -0,0 +1,30 @@ +>GCF_003691675_PROKKA_00539 +MPVSAPSPSSSRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAAWTSVGMVRDLMRGHWGVDIL +AVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARRDLSALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRP +AEVLPVDGTVASAEDGGEVAVDLDESSLTGESLPVTHRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAES +RAPMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGMSRAATSGVIVKSGGTIEALG +SVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAASAEQYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVA +VLEGR-------------------RVVVGKRAYVTQAAPDTVTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQ +ALHRLGARQVLMLTGDAEATGRHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGARG +STAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPALVGALFQELVDVVAIVNALRA +MKPGPHEAERLGDLAAAPARGERQAVSA +>GCF_005280335_PROKKA_00799 +MTRL------SR-----FARSYPLVAVTLAVLALVLGLHAAGLDAAAAVIATVYVAGHIAWAAVGMVREVLRGHFGLDIL +AVVAMTASLLVGEHLAALIIVLMLTGGEALEDFAAARARRELTALLEKAPQTAHLLGADGEAREVPAAQVRPGDELLVKP +NEVVPVDAELLSAEAA------FDESSLTGESLPSAKAAGDAVLSGSVNGTAAVRVRATAAAADSQYQRIVELVEQAHEQ +KAPVVRLADRFALPFTAVSLAIAGVAWWASGDPVRFAEVLVLATPCPLLIAAPVAFLGGMSQASRRGVIVKGGGVLESLA +HARAVAFDKTGTLTHGRPRLQRVEPAEGFTADAVLAAAAAAEAYSTHVMAEAVVRAADDAGLARLSARGGTEEGTRGVRA +LVRGTDGGAGAGTGTDTHEPGAAVEVRVGKLAFVREVAPDAPEARFAPGETAAYVSVDGRHAGTLVLADALRENAGETVA +ALRAEGFERAVMLTGDNEHTARSLAAEAGLDDVAHSLLPEDKVRLLAELQPRPVIMVGDGVNDAPVLAAADVGIAMGARG +SSAAGESADVVITRDDIGRTVEAVRIGRHTYRIALQAVLLGVALSVGLMLVAAFGHIPAVAGALTQELVDLACILYALRA +-RTSPRGTPQ-GAAARARGRAPQEAARA +>GCF_023573625_PROKKA_00776 +MPVSAPSP--SRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAAWTSVGMVRDLMRGHWGVDIL +AVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARRDLSALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRP +AEVLPVDGTVASAEDGGEVAVDLDESSLTGESLPVTRRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAES +RAPMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGMSRAATSGVIVKSGGTIEALG +SVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAASAEQYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVA +VLEGR-------------------RVVVGKRAYVTQAAPDTVTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQ +ALHRLGARQVLMLTGDAEATGRHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGARG +STAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPALVGALFQELVDVVAIVNALRA +MKPGPHEAERLGDLAAAPARGERQAVSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002084.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ed8cd176c346740e09b270c1576e307e59f9154 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002084.fa @@ -0,0 +1,48 @@ +>GCF_003691675_PROKKA_01105 +---MTVSMRVMSAGDGYKYLLRSVAAADGDRSLSTPLTRYYAEEGTPPGRWLGSGLTGLGDGQLAVGDQVSEAQLQLLIG +MGRDPITGEPLGRAFPQYAPVADRIERRVDELPDELGPAGRAEAVAQIEAEEASRGTRRAVAGFDYTFSVPKSVSVLWAV +ADAGTQALIAEAHHDAVAEVVD---------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------------------------------- +>GCF_005280335_PROKKA_02653 +---MTVSMRVMSAGDGYKYLLKSIAAGDGDRSLSTPLTRYYAEAGTPPGFWMGSGLGRLGHGDLVEGGQVSEAQLALLVG +MGHDPITGEPLGRAYQQFASITERIKQRVDALDPELGPATRAQEVAAIEAEEAERGTRRAVAGYDFTFSVPKSVSTIWAV +ADAGTQALIADAHHAAVAELVAFLEREVAATRVGATGPDGAVAHVDVAGVVAAAFDHYDSRAGDPQLHTHVVVSNKVLTV +QDGRWRTLAGRPMHSVVVAVSELYNAALADQLTRVLGVEWEARERGRDRNPAWEIEGVPDELVTEFSTRSRHIEAEKDRL +IAGYVAKHGRQPSARTVLKLRAQATLATRPEKQVRSLADLTAEWRQRAGRVLRRDANGWARTFTASTADAPRRVLRADDV +PLDVVREVGQTVMETVGEKRSTWTRWNLHAEASRQLMGWRFASIQDREAITGLVVDAAEHASLRLTPPELASSPLQFRRV +DGTSRFRPHASTLFSSEVLLAAEDRLLARAATTAGPVVPLETVERIARKPDARGRVLGEDQAAALAAIAVSGRVVDVLVG +PAGAGETTAMNGLRRAWEKEHGTGSVIGLAPSAVAAQVLADDLGIATENTAKWWQNHLMYGTTFTAGQLVIIDEASLAGT +MSLDRLTHEAEKAGAKVLLVGDWGQLQSPGAGGSFAMLVHARDDAPELTDLHRFTNEWEKTTSLQLRHGRAEAIDALIEH +GRITGGDEEAMIDAAYTEWRADLAAGRASILVTETHATVTELNARARADRIIDGTVNPTRELPLRDGTAVSEGDLVITRE +NDRRLRNGRTWVRNGSRWTVTGVREDGSVIIRPAGRRFGGGIVLPADYVAEHLDLGYAITAHRAQGVTTDTAHAVVTATT +TRENFYVSMTRGAHSNHAYVTVDREDAEHAVPHPGDNPNVTARSILYGVLQHIGAELSAHETVAAEQDRWGSIAQLAAEY +DTIAQAAQHDRWATLLAASGITAEQIEDVLGSDAYGALSAELRHAEANHHDLDALLPRLVAARSLDDADDIASVLHARVA +RATARPAGSGRTRKAPRLIVGLIPHAGGQMADDMRRALDERRELIEGRADAVLRGYLTDEEPWTADLGAAPRGDKQKAAW +WRAARTVAAYRDRYGITDDRTPLGPTPESTSQKIDAIRARAALNRAQAIAHEGTTADAVRPATTSRPAPSL +>GCF_020097155_PROKKA_01772 +MVWVTVSMRVMSAGDGYKYLLRTVAAGDGDRSLSTPLTRYYAEAGTPPGRWLGSGVTALGNGEIAPGAQVSEAQLQLLVG +MGRDPITGVPLGRAYPVYSSTADRVADRVNQLDPALGAVERGRRVAQIEAEEAARGSRRAVAGFDFTFSVPKSASVLWAV +ADAGTQALIAQAHHEAVAAVVAFMEREVAATRTGATAGDGAVAQVDVTGLIATAFDHFDSRAGDPHLHTHVVISNKARTV +LDGKWRSLDGRPMHAAVVALSELHEAVFADHMTRTLGVSWEPREMGRDRNPSWAITDVPEELAAEFSTRARQIEVEKDRL +VAEYVATHGRQPSDATVIRLRAQATLGTRPDKQLRSLAELTAEWRTRASQQLGVDATVWARTITVGER---QMLLRADDV +PLDLIGQVGRSVVEVVGEKRSTWRRWNLMAEAARQTMGWRFATVEDREAITAMVADAAEHASLRLTPPELTTSPVEFRRL +DGTSVFRPKHSTVFSSDTLLAAEDRLLQRTRATTGQSVDLATVEAITGRPDAEGRVLGRDQAAALASVAVSGRVVDVLVG +PAGAGKTTAMNALRRAWETEHGAGSVVGLAPSAVAAQVLADDLRIATENTAKWWTTHQHTGATFHAGQLVIIDEASLAGT +LSLDRITQAAEEAGAKVLLVGDYAQLQSVDAGGAFSLLIHDRDDAPELVDVHRFTHDWEKTASLELRHGRAPVIDTYLAH +DRIHDGDAEAMTDAAYTAWRHDRQAGLVSVLIAETRENVTALNVRARADLILDGTLKPGPEITLSDGSAAGVGDTIITRR +NDRRLRNRHGWVRNGQTWTITAVHDDGSITIRPPGTRFGNSIVLPADYVAEHVDLGYAVTAHRAQGITTDTAHVLVEPTT +TRENLYVAMTRGRESNKAYVILDRPD-DHATAHPGDSPDATARTVLYGVLQHSGAELSAHETITAEQDRWGSIAQLAAEY +ETIAAAAQHDRWTTLVRGSGLTGDQAQAVIDSDAFSALTAELRRAEANHHNVDTLLPRLIRARGFADADDIASVIHHRLA +NATTRPAGSGRTRQAPRLIAGLIPEATGPMTPDMQQALTERRHLIETRAEAVLDTALHTHEPWVTALGPIPTSGRERQQW +RRRAVVVAAYRDRYQITDP-TPLGAQPEDTAQRIDRARAETAV---RTLTRPTMEDERGRPAAQATRHLDL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002089.fa new file mode 100644 index 0000000000000000000000000000000000000000..38b9143349f7e71a6f6b9cb327e175436ae33bbf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002089.fa @@ -0,0 +1,28 @@ +>GCF_003691675_PROKKA_01704 +MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE +PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP +QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF +PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA +GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW +KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM +TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST +VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA +>GCF_020097155_PROKKA_00783 +MTERVALIGAGPSGMALLRALALAEDEGAVVPEVVAFERQADWGGQWNLDWRTAADRFGE +PVHSAMYRDLWINGPKECMEYPDYSFDAHFGRPVSSYLPQEAMKDYILGRVAHVAERIRP +LIRFGTVVRWVQPLDDGTFEVTSVDLTTGAARTEAFDRIVVATGHFHAAHTPSWPGVEDF +PGLVQHAHDYRTPEPFAGRRVLVIGSSYSGQDLALQLHRGGAAHVTTAYRKAPQELDWPA +GMDERPEVQGFAGSRVAFADGSSAEYDAVLLCTGYRHHYPFLPAELALSGPNLPFVPSLW +KSVVWQADPRVLYLGATQQWFTLTLLDAQAFFARDVLLGRAPVPSAQERQADIDAWTARM +AAIDSTPVALAFQADQIRDLTAGTGYPEMDLDGVIATFLQMGEDKRESLTRYRDRTHRSL +VTGTRAAAHPVPWMHHPDGSLEGYLAHFPG +>GCF_023573625_PROKKA_01932 +MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE +PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP +QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF +PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA +GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW +KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM +TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST +VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002091.fa new file mode 100644 index 0000000000000000000000000000000000000000..d20dc552a83509364f5818490e0dac7311a37497 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002091.fa @@ -0,0 +1,19 @@ +>GCF_003691675_PROKKA_01710 +MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF +RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP +VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN +HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS +VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH +>GCF_005280335_PROKKA_00842 +MSDPVQKQDDDTFDNARVLDPAATQDSQEQISEEMAAVHGQASGETQPRLDFPPYRSSVF +RHPTKSMAHADPESIELWSPAFGHRDVHQLESDLTVGQNGEPIGERIKVRGRVLDGQGRP +VRGQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGVGRTITDDRGFYEFTTIKPAPYPWKN +HHNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFSLDPIYQGITDQKARDRLVATYDHS +VSEHEWNTGYYWDIVLTGSHRTWTEDEEGDH +>GCF_023573625_PROKKA_01938 +MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF +RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP +VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN +HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS +VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002096.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4b82f43c3e58ecd914f3a7878bc9a03992e4fec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002096.fa @@ -0,0 +1,25 @@ +>GCF_003691675_PROKKA_01777 +MVNANEYEPLELSHLHPAAQPVA-----RLPAAERVQRIRA-DRW-----IGYPKAVEAV +ERL--ETMLGWPAKQRMPNLL-LVGPTNNGKSMIIERFRRQ--------HPPSSEPDR-- +------EQVPVVCVQMPSEPSPLRFYTAILSVLGAPLRPRPRLVELERLALSLLREVGAR +MLVVDELHNVLAGRGDTRREFLNLLRFLGNEL-----RIPLVGVGTREAYLAVRSDDQLE +NRFEPFVLPLWE----ADDQAR--SLLASFAASFPLRKPSVID---TEDMARYLLARSEG +TIGELAHLLTAAAVAAVESGLEAIDHRTLT-----------------MANYTGPTERRRV +FERE----------------------------LL +>GCF_020097155_PROKKA_00635 +M-DALLWHTQALTPAPAPPEPVLLREFSTLSTQDQDEYWTRMHRWMCASTLDCDRTAAIR +RGMDRVLQRNEYARSGAKTIIGLSAPNGVGKSTFIKSYAQDRYQRMMHDQPVDKLPSRTD +SGGSPSHWIPQVYITLRAASEVPDVNAAILSYLGYPIMGRTT--KDTTLLVHAVARHGVK +LLILDDAHMLRAKQARA-RDVLDYVKFLNTMMGERDGTLVLVGANMEGG--PVYQDPQVA +ARLHAFALQPYTVQQDTTERVAWQQLLAGAEKKFMPYLDSATEGTLTRELAGQIWARTQG +HLGDTHQLITTALLDAFDQGDTTLVSEHLQGVRLSARAEAAEADLAREATLTSRREQNRK +AKR------------------------------- +>GCF_023573625_PROKKA_02217 +M-NSHDWHHQAVTSQPSGLKPITVRKFERLNQQEQNEHWTALNRWMAAQPIDCPRVRQTS +TRMQAEVLRNEYAPRGAKTIIGLSAANGVGKSTLIKRLAHQLYRETVPTTDPGILPTRTV +GTGATVDWIPQVYITLRAASRIQEVNTALLSFLGYPTIGQTR--ATTTRVVEAIRTHGVQ +LLILDDAHMLKTSQADA-RDVLDYLKFLNTELGELGGTMILVGANLEDS--DVYADAQIA +TRLAPLQLQPHAIFP-VSERARFQAMLRGVEEKFMCHLDTATTGTLTNELAGEIWQRTQG +YLGDIHRLITTVILETFDAGEDVITRERLRAVPLSARATAAEASLREAATQRSRRTENRR +KKKAGSTPPAQTPSQDAAGSSSDSPTAAVPETKE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002098.fa new file mode 100644 index 0000000000000000000000000000000000000000..263d22a118453908a92e0cfc6faf68a1ea9842f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002098.fa @@ -0,0 +1,24 @@ +>GCF_003691675_PROKKA_01797 +MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADIDAAVAAARAAFDEGSWVRMR +PNVREDLLWRISNLITERLEDFALLESLDQGKGV--GIASAFDVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFH +SYTRREPVGVCGQIIPWNFPLLMAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAAL +TAHPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADANIDAAVDGALMGFTLNSGQACESGTRVFVHAD +VYDRFNEALAAKMRQMSIGPGTEDAAIT-PLVSQEQLDRVMGFVEEGKRDGAVALTGGQRHGD-AGFYVEPTLFTETTPE +MSIVREEIFGPVAVSVKFTDEDEVIRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSG +WGRELGAESLELYTQVKSVTIAL +>GCF_005280335_PROKKA_00689 +MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADIDAAVAAARAAFDEGSWVRMR +PNVREDLLWRISNLITERLEDFALLESLDQGKGV--GIASAFDVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFH +SYTRREPVGVCGQIIPWNFPLLMAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAAL +TAHPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADADIDAAVDGSLMGFTLNSGQACESGTRVFVHAD +VYDRFNEALAAKMRQMSIGPGTEDAAIT-PLVSQEQLDRVMGFVEEGKRDGAVALTGGQRYGD-AGFYVEPTLFTETTPE +MSIVREEIFGPVAVSVKFTDEDEVIRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSG +WGRELGAESLELYTQVKSVTIAL +>GCF_005280335_PROKKA_00823 +MTET---------LTYAD----LLAA---VVAPEGAGTEIKDPATGDLIGYAPQSTTADLDAAVELARTA--QRDWAKLS +HAERSAALNRAADAIEANSAALAELLSREQGKPVKNGPNAAFEVGGCVAWTRATAGFEVQPETIVDDET-----GRAELH +WM----PIGVVGGIGPWNWPMMISVWQIAPALRMGNTVVLKPSEYTPLSVLGLVHVMNQA-LPEGVLQVLAGDGELGRAF +TSHDGIDKITFTGSTATGKAIMKGAADDLKRLTLELGGNDAGIVLDDADPKAIAEGLFWGAFINTGQTCAALKRLYVPDS +LYDAVCEELVAVARRMPMGPGLEEENVLGPLQNRAQYEIVERLVQAAKDGGGRVLLGGDPDPERPGLFYPTTIVADIDND +NPLVAEEQFGPALPIVRYTDLEQAIEWANGLDVGLGASVWSADPERAKEVAMRLEAGSVWINKHGTIDPRVPFGGVKHSG +MGREFGVLGLKEMAEAKSISV-- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002099.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bd6cb4881e609f115827cfd1cbb86abefd626e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002099.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_01854 +MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAG------------------ +----------------------------------LLLSGTYGYCYYPY +>GCF_020097155_PROKKA_00549 +MGMKQRISKVGADVAVAGLLAVSGAVPGQALTDSGRQDCSAGGGYVGARGEQQRYGDRMS +FDVGGRTTKVVNRYTYGFDSGLRMSQNWRVSSESLLLSGTYGYCYYPY +>GCF_023573625_PROKKA_02084 +MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAG------------------ +----------------------------------LLLSGTYGYCYYPY + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002103.fa new file mode 100644 index 0000000000000000000000000000000000000000..a4bf77b567c6cfbf61ca2efcc5f251bbc802a63d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002103.fa @@ -0,0 +1,16 @@ +>GCF_003691675_PROKKA_02186 +MKYRPQHEANPLPFSP-----------FKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNL +TFDPPMVMFSANQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPGESEWD +RIAEHGVTKVYADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDD +DVITADGR----LDIPRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRS +>GCF_005280335_PROKKA_00824 +MSARTE-------FDPAALGDRETTLLVKSLLIPRPIAWVGTLSADGVPNLAPHSFFTVA +SSEPPIVLIGS-----AGRKDTLRNAEATGEFTVSLVTRALAEAANRTSAPFAP---EVD +EFAAASLTPEPSVVVGPPRVAASPAALECRLHEVHPV-GDSFLLMGRVVHVSVDT----- +DVLTTDARGRTLPDPAALGPVSRLGRMEWGGLGEVFELERPSA-----------G +>GCF_020097155_PROKKA_00157 +MKYRPQHEANPLPFSP-----------FKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNL +TFDPPMVMFSANQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPSESEWD +RIAEHGVTKVYADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDD +DVITADGR----IDIPRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002104.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa4c63d5f2e2d9b95cc031d6fd7aedcde8238e66 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002104.fa @@ -0,0 +1,25 @@ +>GCF_003691675_PROKKA_02304 +MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK +LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE +QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV +IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD +RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ +LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL +LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA------ +>GCF_005280335_PROKKA_00809 +MAD-RPAVIDHPDYFLLDSDLTDAQRALRDRVRDFGREQVLPIINEWWEKAEFPEPLLPG +LADLGIIGTYIEGYGCPGMSRIEAGLVAREMGRIDGSVNTFLGVHSNLCMGSIYILGSDE +QRQRWLPAMAKLEKTGAFALTEPKHGSDSVSLETSARRDGDEWVITGHKRWIGNGHAADV +VVLYARDEADGEVKAFVVEKQEDGSFPAGYNPTVITGKVGKRAILQADIVIENLRVKEEN +RLVNCESFAGVNRVLKATRGGASWEAVGHGMAAFEIAAAYALEREQFGAQIGGYQLVQER +LATMLTDLTTMQLMCVRMAELQERDELTLAMASMVKMHTSRKALDMTRTARDIVAGNGLL +LERHIGRHLTDMEVVSTYEGTDSMQALIVGRDITGISAFTRSRRKS +>GCF_023573625_PROKKA_00288 +MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK +LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE +QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV +IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD +RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ +LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL +LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002108.fa new file mode 100644 index 0000000000000000000000000000000000000000..00685c8b1d85ac7b9b1134020d501e75e97b9269 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002108.fa @@ -0,0 +1,28 @@ +>GCF_005280335_PROKKA_00761 +MTLAHPASRPMPATSPATPGATPPDPAARLVPLRGADHAAVLAEAVRVRASGGIPVVGDE +RWPAALMAAQVEHAAATLRDLAVRDPRAAAEIAWAAFTSGSTSRPRVVLRTEASWRAGHR +VAADWLGLRPGEELLVAVHPVSSMAVHAASLCGALGARLRVTARARLSAADLA-GPVVLD +ATPSQLVDALDLL----DDGAPSTLRVALIGGDRLPAGARDRAAAHGIRVAHFYGSAEAS +FVAVDLDGAGLRPLPDVRLRIADGADDAGPAGPNTPDPNTPRARTGLLELRSDQLAAPDD +SRLSSGAPRWREDGWLTTGDRATWDPDAGVLEVHGRADDVILTAGATVAAADVEAELAAA +------------RDGSGRPVASGVLVVGVPDRRLGERVCAVVEPARGQDPEAALQMLKTA +ARAGLSPAARPRRWVLVDRLERTGSGKIRRALPAATRHAAGRQDHA +>GCF_020097155_PROKKA_00724 +M----------------SPLAPVPDPAARLAFLADADHAAVLAEAVAVRARGGVPVVGDE +RWPADLRAAQREHAVVQLRRLAARDPDLAARVGWAAFTSGSTSRPRVVLRTDDSWRAGHP +HVAAWLGLAPGEAMLTAVHPVSSMALHAAAWCAATGHRLAVSPHARLTAADLT-GPAALT +ATPSQLTDALDLL----DDGAPSTLRVALVGGDRLPAGARERAAAHGLRTVHYYGAAEAS +FVAVDLDGSGLRPLPGVELEVAEPDVLADADGP----------RTGVLRVASPQLAVPDD +SRLASGAPRWDAEGRLTTGDRVTWDPAAGILTVHGRADEVVLTAGATVSAADVEAELAAV +------------AGPDGRPVAAGVLVLGVPDPRLGQRVAAAVEPAPGVAPEDALAALQGV +ARARLSPAARPRRWVAVGRLERTGSGKIRRVTPPELR--------P +>GCF_023573625_PROKKA_01993 +MI---PPVRLPPSDDDVAPAVS------RLAPLRGADHEAVLRRALEARTAGLVPLVGDE +RWSVAQWQAGVGHAEALLAELTARAPDRAARIGWAAFTSGTTGRPRVILRTADSWRTGHR +LVEDWLGLEPGESLLVPVHPVSSMAVNAADLCAHVGARLLVPSRARLRAADVTGGAAAVH +CTPAQLADLCDLLAAVRAASAPAGPRVVLVGGDRLPGQLRERAAALGLRVVHYYGSAEAS +FVAVDPDGSGLRALPGVRLEI----------------------REGVLHVRSDQLAEPDG +TRLTDGTPRWGADGWLCTGDRAQIDDD-GVLHLRGRADDAILTGGATVIPAEVEAELLRA +TVRRESTASGGDSAPHAVPVCTAVLVQGEPAPRLGSLVVAHVEPAPGLPADVVLAALKEH +ARTHLPPAARPRRWQVVDRLERTGSGKIRRMAPDVAAIPDPPGGSA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002109.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c58813430a5fc0b949b50ef6bd16fc13c1f7e5e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002109.fa @@ -0,0 +1,25 @@ +>GCF_005280335_PROKKA_00762 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------MVASALTGGDPALPGIGPVAAVREVLDAAGIA +LAEVAVVEVVEAYAAQVWAVLDELGLSAEAG---------AARADDWGVDPRVNAEGGAL +AFGHPWGASGAVAATHAVRRLQSCPPGSSALVTCAVGGGMGVALVLDVA +>GCF_020097155_PROKKA_00725 +MSAVGLDAAPVWITAVSRTPVTARSRAQAHLGAGELAAGPVGEVA--AGTHPAAVVLGNG +AGPGGNVARIAALAAGLGVATPGWTVDAQCGAGLVAVAQAAGHAVATGRACVGGGVESPS +TAPERSIDGVSYAQAPMVPAGWDDPGMTAAADALAAARGIGRARQESFAARSHVLAL-AG +GLR-------LPDDDGPRRLDAAALARFRAVTPGADPATAVTGATAARIADGAAAVLVTP +--HSAVVRETDGVSTASVRGVDVLRPCRVLSWSLTGVDPALPGLGPVSAVRDALDAAGRT +LEGVAVVELVEAYAAQVLAALDDLGLTGASGTSAPGASGPATAHDPWGVDPRVNAAGGAL +ALGHPWGASGAVAVVHAVRRLQAEPPGAVGLAACAVGGGMGAAMVLEVA +>GCF_023573625_PROKKA_01992 +MTT----TPGLWITAAARTAFTARSRGQAGLDAGALSAQAVAAVTGPAAADVAAVVLGNC +TGPGGNLGRIAALAAGLGEHTPGWSVDAQCGAGLAGVLQAAQHAAFTGRPCVGGGVESPS +TAPQRSRDGVPYTQAPMVPSGWPDPGMTAAADALAAADAMPRARQEAFAARSHALALAAA +GLRRIERVPGAPDDDGPRRLDARALARFTPVHPDADPAAAVTGGTAARIADGAAAVLVVP +CERSPVGRDEPAGG---------LRPVRIVGAEIRGGDPALPGIAPVAAVERALAAADWR +LGEVAVVEVVEAYAVQALATLDRLGLTDHARPGPASLGSDRQGLDDWGVDRRVNAAGGAL +ALGHPWGASGAAAVVRAVHRLQGQPPGARAVVACAVAGGLGITMLLEVA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002112.fa new file mode 100644 index 0000000000000000000000000000000000000000..51213afc99c5cbcba3905344320286a356c32b5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002112.fa @@ -0,0 +1,27 @@ +>GCF_005280335_PROKKA_01077 +MTTAT-PRQPLIEDHAYLSNQHSGALLTREGDVTWLCLPRFDAPSVFTSLLGEPEHGRWSLRIADGEVRERAYLPGTLVL +RTRWRGPDGEAEVLDFMPLTSHRGSGRAHDDDAGALADEGEAA--RADLVRLVRCTSGSVSVDQCLQFRMDYGEVVPWVS +RQTDPADESFLAVVAGGDALAVHGPDLRPDSTAHRGRTRLEAGQSAAWTLAWYPSWSMAPAAPDPERALEATVTDWVEWL +GE-----PLATGPRADRVARSLLVLKGLTHRDTGGIVAAPTASLPEDFGGVRNWDYRYVWLRDTALTLEALMAHNHTDDA +CAWRDWLLRAIAGDPRD-VQIMYTLSGERRMPERDLEHLPGYEGSRPVHVGNGAADQWQADVIGTVMLALGRLRDAGVDE +DRWSWTLQKRLVERVLEHRDTKEHGLWEMRGEPAYFTHGRVMMWAALDQALHAARDHGLPAEDEELAAWEQARDELREEI +LTEGVGPSGGFRQTYGSEETDASLLQIPHTGFLPHDDPRMLATVADVERDLVTETGLVMRYRASGMDGLPGEEAPFMMCG +FWLVEQYARSGRLADAERLMARLDECSNDLFLMAEEYDDGRDRMAGNFPQAFSHLGLIRAVDALEE-ARGAAGGEG-- +>GCF_020097155_PROKKA_01012 +MTAQTAPASPLIEDHAYLSNQHSGALVTRAGDVTWLCLPRFDGPSVFTSLLGAPEHGQWSLGIADGEVVERAYLPGTLVL +RTRWRGPEGEADVLDFMPLADHAGSGVVDADDVGILMGEGEGPLRRADLVRLVRCTSGTVEVDQWIRARLDYGEVTPWVS +RQEDPAGEEFLAVVAGGDALAVHGPDLRPDGMRHRGSTRLEEGRSQAWTLAWYPAWTTAPAAPDAEHALEKTVTGWVEWL +GD-----PRARGPRAERVARSLLVLKGLTHENTGGIVAAPTASLPEDIGGVRNWDYRYVWLRDTSLTLEALMAHNHTDDA +AQWRDWLLRAIAGEPKDNIQIMYTLSGERRMPERELGHLPGYEGSTPVNVGNGAADQWQADVIGTVMLALDRLRDAGVDE +DQWSWPLQKRLVERVLAHRDTKEHGLWEMRGEPAYFTHGRVMMWAALDRALHGVREHGLDATEEETAEWERVRDELREEI +LTEGVQEDGAFRQTYGSDETDASLLQIPHTGFLPHDDPHMLATVAQVERDLTTETGLVRRYRATGMDGLPGEEAPFMMCA +FWLVEQYARSGRVEDAERLMARLDDCANDLFLMAEEYDDDRGRMAGNFPQAFSHLGLIRAVDALEECAEDARAAE--- +>GCF_023573625_PROKKA_01718 +M-----SAQPRIDDHAFLSHQLSGALVSREGAITWLCLPRFDSASVFTSLLGTREHGEWSLGIEDGEVAERAYLPGTLVL +RTLWRSPSGVAEVLDFMPLLDADGVGDAQGDDGGPDGTGASEAAPRADVMRLVRCLAGRVRVTQSVFARLDYGEVEPWVS +RQEDADGESFLAVVAGGDALAVHGPDLEPVDGHHEGTTELVAGESAQWCLTWYPAWGMAPSAPRAEDVLEATVRRWRGWL +EESTRQAPRADDPLADRVQRSLLVLKGLTHRATGGIVAAPTTSLPEDIGGVRNWDYRYVWLRDTALALEALLAYGHVEVA +TAWRDWLLRAIAGEPHE-VQVMYTLSGERYMPERELEHLPGHADSRPVVVGNGAADQWQADVIGTVMMALCALRDAGVPE +DEWSWPLQKRLVERVVAHREDPDHGLWEMRGEPAFFTHSRVKMWAALDRALHAVATHGVPATEAETAAWERHRDELREEI +LTRGVHADGHFTQAYGSDAVDASLLQIPHTGFLPPDDPRMLATVRRIEEELVTDTGLVLRYRPDGSDGLPGEEAPFLACA +FWLVEQYARTGRLDDADALMERLDACANDLDLMAEEYDDGQDRMAGNFPQAFSHLALLRAADALALVRAGDGAGEAGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002113.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d9fc3350a9b7b7d80f979c38ec900c006ccfa86 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002113.fa @@ -0,0 +1,24 @@ +>GCF_005280335_PROKKA_01297 +MSSPTGGSTAADASPRNRAPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAGLSGWSAVHPGTGETLVATNL +LSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSGWFEVGLTQ---SMTSAPKGLIIPAIALIGLLGNIAGDAAP +IVLPPLAALIFLKLGWHPIAGIALAYAAATGGFAANLMIGMSDALVQGFTQEAAVIIDPDIETTVPMNWWFIAASVVVLL +PVLWLVTSKIAIPRLGSYQATDDVEAGDMEVTDVQRRANRWALVALALFAALVVAACIPQGSFLRNAETGSLTTDAPLMN +GIGLILAVAFFLPGLVYGVRAKTITGSSDVARMMVESMATMASFIVVVFFASQLLSYVSASNMGAILAIRGAELLQGQDG +IVLILGIIAISAVVNLFVGSASAKWAILAPIFIPMMMLLGYHPAFTQMVYRIGDAVTNPITPMFPYFALVLTYAQRYDKK +LGIGTFISTLVPYSLAMGLVWTVMMVVWYLLGWPMGPDGPIHLPTP +>GCF_020097155_PROKKA_01206 +MTSPTGGSTAADASPRKHTPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAGLSGWSAVHPGTGETLVATDL +LSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSGWTICAATTWCGTTRPAPR---------------------- +-------------------------------------------------------------------------------- +----------------------------------------WS------------RSC---------ARTCS--------- +-------------------RAR---------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------------------------- +>GCF_023573625_PROKKA_00610 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-GIGSLIATMLPSSIAFLLAWTGMVIGWMWLALPLGPNAPVQ---- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002116.fa new file mode 100644 index 0000000000000000000000000000000000000000..aeb8d91dcb48766497778cfc4103c43ae19082e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002116.fa @@ -0,0 +1,19 @@ +>GCF_005280335_PROKKA_02431 +---------------------MSQPTAAGFRFYDAFNGSAADPSPHFNVARYRAHYPGPP +TPGQAGCAISHFRVLESFASSLGHEDGVALVSEDDVLMPPETEAVLEGILKDDS-FEIAV +LADR--GPT-NPSLAFQRL----LMTEAELSLLSRPI--VCGGRIRRLGRFEGNPYMAAL +YLVTRSGARKLASGLVDDAGGPWTIADDWPLFRDRYGLDIRVLRPGLVTYMGGS----TT +R---DAESLARDALSAAGDGRPLTRLKTAVGLRSRSRAARLVVRATLRDIATR +>GCF_020097155_PROKKA_02276 +MPDIVDYRVIALADSTRLEGFLAQPLGRRFRPFEAVDARKGYGPEDFDAEGFEVRFGRPP +LNGEVGCTLSHMSVLREFAVEDGAVTDVLVVAEDDARFSRFTSEVLNRLLETSAVRGLVV +LA----DPY-GPVDMRGRLGAPTLEDKLQQSLLRRRLRPLAGAPRFAVGRWSRGLVGTGF +YLVSRDAAKY---------DIAW------------------------------------- +---------------------RLRH------RRGGAR---------------- +>GCF_020097155_PROKKA_02312 +MGQITDRYVISLEGSPRREAFFSQPGVADFVVWDAFDGRTGAGRDRFDVVAFERRAGRPP +EGGEIGCTLSHAGLLADFAAGLGRPDDLMLVAEDDVVFTPDFEAVLGRVARTRG-WGWTL +LAQGLEDPFRDPFWAKSRDRAP-------QSLLAKPVGPPSSPWRYRLGNWDGELWGTGL +YLVTREAARALTDHATRE-GLSWA-ADDYVTWHAAAGVKVWILLPTIAGWVGESEINATT +RPHLQIQSYAAHPMGRQAWSRRVSR------FRAGARIAWKEMRGDTRPWAS- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002117.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9b282ddd8db7566eb7a17dc2cf2e5e870b58f38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002117.fa @@ -0,0 +1,10 @@ +>GCF_020097155_PROKKA_00329 +MPQKYTPEFKAKALKLIEERVRAEQCSAWVACTAVGEALGGISPHTLRNWWKQDRVDHGE +APGLSTAEAEEIKKLRRENLELRRANEILRKASAFFAAELDRPTTR +>GCF_020097155_PROKKA_00416 +-------------MQLIEERIRAKQCSGWAACAAVGEALGGISPHTLRNWWKQSHVDRGE +TPGVSTDEFEEMRRLRRENLELRRANEILRKASAFFAAEHDRPTTR +>GCF_020097155_PROKKA_00665 +MPQKYTPEFKARALELIEERIRAEQCSGWGACVAVGEALGGISPHTMRNWWRQGRIDRGG +APGVSTDESEEMRRLRRENLELRRANEILRKASAFFAAELDRPTTR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002120.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5935bb10f2e84114e6cb847309103c1a48a4e9d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002120.fa @@ -0,0 +1,8 @@ +>GCF_002008305_PROKKA_00171 +--------------MDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLM +LGILAAFAEFERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIEMGIPKAEVA +RTFEVSRQTLYTSLRRVVSS +>GCF_005280335_PROKKA_02330 +MKYVREGDLVKVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLM +LGILAAFAEFERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIQMGIPKAEVA +RTFGVSRQTLYTSLRRQASD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002122.fa new file mode 100644 index 0000000000000000000000000000000000000000..b6756a453073173507f3b67cce5749c9c5aab1a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002122.fa @@ -0,0 +1,14 @@ +>GCF_002008305_PROKKA_00189 +MSQQDLATAVGLERTMVNRIEGGQRKVTALELASIADALGTRMQSFFTEPAPALVSHRSA +QGLDTTESAVDHLLAELLADVEFLHGLHPIEGFGVRDPWEQPKSVHEADDMAARAREHVG +YTATEPVKDLQAHLATAGLLLFSRNFGVDAADAGTVLLAEGGISLVNSTPKVGRRRLSAV +HELGHYLLADEYTVDWRTAHTGPDIEGRLDRFARAFLLPAAVLLQEWPAAAHSGDVRTAA +VKIAGTYLVDMSTLARRLHDLELVDASTANDIRAVQTTQTDIITHDLYPSDEMAGTTQPR +VYQKHVIALFEAEKLSRERTLDLLDGTFDDDDLPDLPPRQEQEIWEYVS +>GCF_005280335_PROKKA_00212 +---------------MVNRIEGGQRKVTALELAAIADALQARMQSFFTDPAPSIVSHRSA +QGLDATESAVDHLLTELAAAVEFLHGLRPIQGLATREPWEPPTSTEAVEDMAARARAEAG +YGPDEPAKNLQDHLATAGLLLFSQDFGADAADAGSVLLEEGGVAIVNSAPKVGRRRLSAV +HEFGHYLLADEYTVDWRTAHTGPDIEGRIDRFARAFLLPATAMASVWPRAVTANGTRTAA +VTIAGSYLVDMSTLARRLRDLDLVDASTANDIRAVQTTQTDIVTHDLYPSHELEGLTQPR +TYQKHVLALFEAEKISRDRALGLLGGTFTDADLPELPPRQEQEIWEYVS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002123.fa new file mode 100644 index 0000000000000000000000000000000000000000..3549718b99b81940b305a1db6d02e2e340607870 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002123.fa @@ -0,0 +1,6 @@ +>GCF_002008305_PROKKA_00191 +MAPHSSTPLFAVGYGKIEKVRTNFPDAFRDQKVTSQLKHFIDSTTSLTFHWGSLSIGTLR +PWGR +>GCF_023573625_PROKKA_00191 +MAPRSSTPLFVIGYGKIKKVRTDFPNAFRDQKVTSQLKHFIDSTTALTFH---------- +---- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002124.fa new file mode 100644 index 0000000000000000000000000000000000000000..749ed4666b7c6b9a01bbee62c86168070ac3ac0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002124.fa @@ -0,0 +1,18 @@ +>GCF_002008305_PROKKA_00254 +MATQARDGRFSNEVLPQDERPSRFGPGLIIAASFIGPGTITTSIVTGAEQGFVLAWAVVF +SILATIVLQEMSGRLGLATRMSLGHALREVFSSVPARLVMAILVVAAIGIGGASYAGGDT +VGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIERVLTVMVGLLGLLFIVTAVLV +QPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFLHASLVQEKWGPGLDSRESLRA +ARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRDLASALEPLLGDAAGWVFAAGM +FAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWGAVLAIGAVIALTGTNPTEVIV +IAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANALGGLVCLVVIGLAVYQLGGLAG +LWD +>GCF_003691675_PROKKA_02268 +------------------------------------------------------------ +---------------------------------------MAILVVAAIGIGGASYAGGDT +VGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIERVLTVMVGLLGLLFIVTAVLV +QPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFLHASLVQEKWGPGLDSRESLRA +ARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRDLASALEPLLGDAAGWVFAAGM +FAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWGAVLAIGALIALTGTNPTEVIV +IAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANALGGLVCLVVIGLAVYQLGGLAG +LWD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002128.fa new file mode 100644 index 0000000000000000000000000000000000000000..87e26c34d9fa89b181dedc499cb67616ac9007a7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002128.fa @@ -0,0 +1,6 @@ +>GCF_002008305_PROKKA_00502 +MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW +RHRALRKARSTKFDLHWRLRMSQQR +>GCF_023573625_PROKKA_00501 +MADYHGFYRDELGIDVLAVRPNLAGWEGESSIQDDEHVGWRAANDAEIPPVGVADFLREW +RHRALRKARSTKFDLHWRLRMSQQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002132.fa new file mode 100644 index 0000000000000000000000000000000000000000..e416d4f301f6c1ff4a12dc4e3be8c4c06b5dfb7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002132.fa @@ -0,0 +1,20 @@ +>GCF_002008305_PROKKA_00596 +MATMIQ------ESMDSEYDDVRFPQERTQGLILGLTLEQVIVV-LAGVLIGMAFILRGG +PAMFVGIGLMAVIGAFGATRFRGRSLPGWVWVAAQYLRRGATDQLEYRQGMAPAHVLELV +DGEPQAPVSEAGPQAQRDAKGRIKPGEPARFRLPGVAGELMVYAMP-NGAGFVWDPRARE +AVVCAKVMTTRGFDLESFDAQEERSLSWGSSLAALSRLPGVVRIQASDQTTLISGAAVED +FYESKQEGAGRTGASIDPFLDQAFRELMKEA-QSMPVHEQWLTLVVSPSKITSQVKALGG +GTPALMEHMLKLMTTVESTLPRSGTQVTAWHSPRTLAGLSRSAFDPDASVMVSTMKADGK +TAGTAPSSAGPMAVEVHAGHMVTDGNYHRTYKVSELPQNLARLGFLDELVFAGDFRHTVS +VFLAPVERGAAVRSVQRRKTDWHTNSRLMNKLGRIGSLEHDQSLEDVEREEAELRRRHTG +VEVVVLVTVTGASRSELESAAAEVVASGITAECELRPVWMEQDAAFVAGALPFGRMKL +>GCF_020097155_PROKKA_01792 +MSSRKKNNSHEPEATGSELVPVKFSRLTRRGILLGLSAAQLVTVGIAIATIITALYAGGG +MWLAYTAPVWATAVLLTWVPVAGRPVIEWVPVAGWWVYRTTIGQLLYRRRI--------- +----------------------VTPRPAGTLALPGDQARLREYEDPTTGAGMIHDPHQNT +LTVVCEI-THPAFVLLDPAEQERRVTAWGRVLATVCRSGRIATLQILERTLPDSGTGLAE +WWTTHGQPDDTSWAA------TTYAELINRAGPAGERHATTLSLSLDMRNAARQIRTAGG +GIRGAAAVLRQEMNTLTAALRSADLTPSGWLTPGQIAVILRSAYDP---AIAATLERHGE +I-GHDLATAGPVAVNETWSRIRTDSAHHAVLWISEWPRSMVYPGFLSPILLSSGIQRSFS +LICTPMRSDQAARDIRKKKVEHISDQAQRAKIGQIEDASQTAEYHDVLQQEADLTAGHGI +LRYTGLITVTATTIEDLDAHVAALEQAAIQANCETRLLAGQQAKAFTAAALPLCR-QV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002133.fa new file mode 100644 index 0000000000000000000000000000000000000000..f25213d0462addd6472b871b49b9785425425920 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002133.fa @@ -0,0 +1,20 @@ +>GCF_002008305_PROKKA_00597 +MREEPKVDLFQIIEPGKMSLREARVAQRKMKMAQAQAQRLRNREAREERFPQPQWGKAGP +RGARQLRGLRTLAPRPVRTTTHTAATAYPFVAGPGLGARGLMIGKDMHGGGAFCFDPWAL +YEAGIISGMSMMLFGQVGTGKSSLAKSLAVRQVLAGRKLSVASDKKGEWTRVVKGLGGSV +IQVGPGLDTRLNPLDPGTRPSTDVQGEPMTDRAWASMVRTRRMSILVALVKILTDREMTS +PEHHVLSAGLDAAVAVADAEGRPPIIPDVIRALDAARTDPDAMKAEAASVTMMTLGRVSS +GDLAGMFDGETTVVLDEQACATSIDTSALLGASPEAVRVVNACAGAWTEAMVTTRDGGQR +IVIYEEGWDNISSEADLRRMVEQWKLSRAYGIFNVLVLHKIADLDMAGDQSSKMAAMARS +LLADADVKVIYRQDRSALKITTSEMELSDRERSLVRSLPKGTGLWRLGDSSFEVQNVLTR +AELPLFDTDERMDKAKEAVA +>GCF_020097155_PROKKA_01798 +M----------------------------------------------------------- +-------------------------------AEGGLGSDGVFVGQDLYSGGSFVYDPWVL +YARGIITAPNLVLAGIVGSGKSSLAKSLYTRSLPFGRRVYVPGDPKGEHTAVAEAVGGKA +IVLGHGLHTRLNPLDEGHRPGG------LTDQEWASTVASRRRDLIGALAETVLARGLTP +LEHTAIDLALTATV----AENEVPILPMVVDHILTPSHDPGGRLAEDGRLVGHALRRLVA +GDLAGLFDGPSTVAFDPDLPMISLDLSRVTENS-TLISVLMTCSSAWMESALLDPNGGQR +WVIYDEAWRLMSHPALLKRMDAHWRLARHYGIANMLIFHKLSDLDNVGDEGSAMRSLANS +LLANAETRIVYRQESDQLGPTATALGLTGTEQTLLPNLGVGQGLWRIKNRSFVIQHQLHP +GELELFDTSSRL---TAGVK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002134.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcf2772bf5b40f0db47d2611bd34ad8c7e9768b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002134.fa @@ -0,0 +1,24 @@ +>GCF_002008305_PROKKA_00598 +MRRERGNNSVLEGDNPAETALIWLIGPAVLLYGAYLLAGFLAGRIHCGAATKPDSLFAPL +GFLVGEHDPAAFGATAQGCTATTGGVIGWLIGLGVLALVLIGVAVTAWSRYQQSDKKFIK +ELREREGLARSAEITKTVGRKSVLSRVKKVRPSIKKPAITDGAMRLGKAEGVDVFASYEE +SVVLIGPPRSGKGVHLLIGAILDAPGPVITTSSRADNLGATAELRKKKGPVALFDPQGLT +GQPSTLKWSPITGCEEPRVANQRAASLIGASGLGSSSSNAEWQAPAITIMECLLHAAALG +ERTVDDLMRWGNNPAEAKEAVKILTEHPKAALNWNLVLKGIIEGDPKLLQSKWFGVEGAV +KGLSVPEVRDVLRPNRFEETLDIDKFLTECGTLYIVGTKTGGSSAGPFLIAMMDAITERA +RELAAKSPGNRLDPPLSLVLDEIANISGAWPGLTQLMADGGGVGISPFAVFQSMAQARNE +WGEQQAQALFDAATVKVQLGGASNVSDLEQFAKLAGQRKIMRTSKSRGKDHTSVSEQIHD +TEVVSVAELRRLPFGWGVLLNRNGRPILMQMTRWWDRKDGKQIKEAAGRYSKALLAELES +KDPAP-STPTDADRAEDSVAALDPVPETAPAIPVR +>GCF_020097155_PROKKA_02243 +M----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------LEA------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------IARTSKSCGKDHTSVSEQIHD +TEVVSVAELRRLPFGWGILLNRNGRPILMRMTRWWDRKDGKQIKEAAGRYSKALLAELES +KDPAPSSTPTDADRAEESVAASDPVPEAAPAIPVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002135.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec9791fa36704ecdf3c848c699f56991a37ed96f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002135.fa @@ -0,0 +1,8 @@ +>GCF_002008305_PROKKA_00599 +MGRFGLHRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGITLTRAGTLDLHH +VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVARM +VRQSQA +>GCF_020097155_PROKKA_02242 +MGRFGLYRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGVTLTEAGTLDLHH +VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVVRM +IRQSQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002136.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6297a03794d4a078d3a66f923c4a25a3944fb2a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002136.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00601 +M----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------IPV------------------------------------------------ +------------------------------------------------KDLIKAR-EDWD +FEREVALDEQSSVERELASANGHLSRLKEALIERGLASLLWGAQHEDVASVPDLVQDTSE +AVLAAQMYLADWLVLPD--SAVRHLEDIDTAPEAYNWGNKAWRGFRALAAYAQDRASGWD +KGGFWEWCASGPVLGWPATSKKLSMTESEGVQTSGKFKGTRDFKVDPAVDSSGEITMLAH +LKISEGGGNLAPRVYFYDDTNGATKKVHIGLVGPHYLVPNKSTN-- +>GCF_023573625_PROKKA_00187 +MAVGYRAIFAVSPREDALAIARESVHSWLVDKLNRARPEVRQQALELDFNAPFAVQLSDE +IHVSNTRAHGDNGQLQQLIRLDESSAPGETWRVNITADRNDVGGVRQQTIMVELDPLHLD +AETAVMRAAPPRFVREMLTQHVLRSGTTVLTATPKALRGSEGGREAYRAVIDPLRQAQAV +IAAQPPGSDMTIWQAAVASLTRQAMGITTALTLDKDALDQFNRRLPRNLQLQPGEVRTFA +PHVDLDDPADSLRHRSLGPGTFARHIKPRVKDGVTVPEVDPTFASVHARRARMYALEQPL +PDSIRSMRQQVRTGELREERDRAAGLVTGFSTVRVRPAAPAPAASPHRPGAGKRPSPTPT +SGRLGASGAIPVPRPLPPSQEKVAEASSATPVAPAEAPQASAPSSITPVPAWQKTLVQLV +WSTLGTEEITKEAIELLAEQLAASGRREQVADEQIANAVREAEIAAAQHDDLRARLEDAE +LAAAAEQEERESLARE-------VEHLRRKAIEAERYEDLVVPEATDEEAKPSTFDDLIE +RIQSERFTTHEYVVFTGDMKKVNEVEAIDIVGRHL---SSCWEFVLTLEGYARAKKDGFN +-GGVHQYLTSGEVDGKRCSPGKHASLESESVKSNAAQRRERLLPVPKNVDRSGAVHMWAH +FKCSKDGTK-SPRMHYYDDTDN-TGKIYIGYIGPH--LTNRQTSSM diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002137.fa new file mode 100644 index 0000000000000000000000000000000000000000..d2feb868d8e02f341314d56604bf4b4884860851 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002137.fa @@ -0,0 +1,6 @@ +>GCF_002008305_PROKKA_00835 +MVSMSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFV +FGLGPRQVPWWREVFGL-------------IRIQGVVGV--------------------- +>GCF_003691675_PROKKA_00567 +---MSRPPEPRPAPAPTARAAAARPATPPGVQGRWARRAAGGLIGVSVLLAAWSFALPFV +FGLGPRQVPWWREVFDVNHEANLTAWWSSGLLLLGAAGFTTVGLVRRALGRTGGGACSRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002138.fa new file mode 100644 index 0000000000000000000000000000000000000000..56860596fa625e3b42a11e0ef8ab7d3b573c15c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002138.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_00883 +MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQVAEEVRGVFGIRWGDRPAHA +RPADALGLAGGPARTRPGSASLTGRGAAAVGADPEAAARLERVLGLADTSRTERGGRAVG +VVAAPDVRAALAAAGHRVVPLVPGTAAAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL +ELRGAVSAAAARGVTVWVLSRGRHQHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA +PQGIADVLAACPEESA +>GCF_003691675_PROKKA_00605 +MPAGKSIRRVARAGARLLPPEQRRRVRRTGGALLRRLPPQLAEEVRGVFGIRWGAPPAHA +RPADALGLAGGQARARPGNASLTGRGAAAVGADPEAAARLERALGLADTSRTEQGGRAVG +VVAAPDVRAALATAGHRVVPLVPGTAGAVAERVEAVVVDVDGVDGPWAGALDAAGAALYL +ELRGAVSAAAARGVTVWVLSRGRHRHRLGALALLHAEDVIVVEAGADRTPLHFTEDPGDA +PQGIADVLAACPEESA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002140.fa new file mode 100644 index 0000000000000000000000000000000000000000..fce1cb0ecb378a6dbf81b8446a5287c227a47062 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002140.fa @@ -0,0 +1,14 @@ +>GCF_002008305_PROKKA_00890 +MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG +VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE +RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP +FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT +VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH +VSMAEGLATLRVAEAMIASAHTGESIRL +>GCF_003691675_PROKKA_00612 +MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG +VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE +RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP +FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT +VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH +VSMAEGLATLRVAEAMIASAHTGESIRL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002141.fa new file mode 100644 index 0000000000000000000000000000000000000000..d366c2d3b2316bf047d2b7dcba9693d1caac257c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002141.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00892 +MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL +RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA +EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV +VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG +GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL +AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP +LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN +STSPIPVDRVTAALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA +EFDAMAEAAYRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE +GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDMLAEHGLADRPGLR +ITTVPLEWYVPATRTVVGVVLLGGKYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN +RVGLGVARSSEAIRAGIVTLVRDGAPGMAEAQRSQSWAVRVATARAALED +>GCF_003691675_PROKKA_00614 +MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL +RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA +EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV +VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG +GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL +AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP +LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN +STSPIPVGRVTSALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA +EFDAMAAAADRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE +GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDLLAEHGLADRPGLR +ITTVPLEWYVPATRTVVGVVLLGGEYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN +RVGLGVARSSEAIRAGIAALVRDGAPGMAEAQRSQSWAARVATARASAED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002142.fa new file mode 100644 index 0000000000000000000000000000000000000000..05da3c22ff9f036a96ec2d96dc04a038eee35c18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002142.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_00893 +MAVATPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVSHRTTFNLGRYGSV +PILRVPVTFRRHLAWQTLHGTARPDVTDWSAVLDPEEAAAMTAWDLAHEVGAGLLQAVVR +GLSPHALPDRARGRLGRAARRLGRLGPARGRRDPAAMRGRRALKNFAAGRTGAWREVWPL +IADYEDGFLRALIDLAPDLVHVHDRHPLPAAAAYDHYRAARGLPPVPWVYDAHEWLPGQM +MPGPVDQRIAWKAAEAELIHEADAVVAVTDELAERMREYHALQERPVTVINGPWGTQLPM +GPAERLPLRTELGLSDDVPLLVYLGKLAAVRGVGTLVDALPLLPGVHIAFVGSPDPDARQ +GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVPTKLRECLLA +GLPLTVSDLREQARFVREQGVGTVFAPGDAADLARAVRDLLARRTELTAAARSPEIAARH +GWEAAERALHGLWRRLVPTPAAPPPVEIAPDPAREPQPRGLLVVGDPPTVRPLADAWPAG +AGPVTLRPPRDFPEGRGLVVGGPEAVWGVLQDWVTDDRAHGTVLIGGEGPLWGRAEQSPV +HELLSLRARGRQVALVAGERILAGVERRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ +AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGRDGASAPRSVLILPGDRTSAE +SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFHGDVVVAPLHTEDLEVAALQALAAGSA +VVAGPPVTPAPDECAPPVTETDDATLLATVLGLLEETSAAAGERRERAREHHARLHAPEA +VLVRLQALLSPAETTDGPAAV +>GCF_003691675_PROKKA_00615 +MPVDTPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVFHRTTFNLGRYGSV +PILRVPVTFRRHLAWQTLHGTARPDATDWSAVLDPEEAAAMTAWDLAHETGAGLPQAVVR +GLSPHALPDGARGRLGRAARRLDRLGPARGRRGPAATRGRRALKNFAAGRTGAWREVWPL +IADYEDGFLRALIDLAPDIVHVHDLHPLPAAAAYDRYRAARGLPPVPWVYDAHEWLPGQM +MPGPVDQRIAWKAAEAELIHEADAVVAVTDGLADRMREYHALQERPVTVINGPWGAQVPM +DPAERLPLRTELGLSDDVPLLVYVGKLAEVRGVRTLVDALPLLPGVHVAYVGSPDPGARQ +GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVATKLRECLLA +GLPLIVSDLREQARFVRDQGVGTVFAPGDAADLARAVRALLARQAELTAAARAPEITARH +GWEAAERALHGLWRRLVPTPAAPQPVEIAPDPARDPRPRGLLVVGDPPTVRPLLDAWPAD +AGSATQRPPRDVPEGRGLAVGGPEAVWGVLQDWVTDDRAHGTVLSGGEGPLWGRAEQSPV +HELLSLRARGRHVALVAGERILAGIDRRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ +AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGHDGASAPRSVLILPGDRTSAE +SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFRSDVVVAPLHTGELEIAALQALAAGSA +VVAGPPVTAAPDGCAPPVIETDDATLLATVLSLLEETSAAARERRERAHEHHARLHAPEA +VLVRLQALLSPAETTDGPAAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002147.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ce1ef0a19bacf32b049ac77f572d60417968977 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002147.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00954 +MATIQTRTNKAGRTTYRVGFYEAGRFQWLPALAREAGAQRVKAIVEDPRQGPTVARRILE +AQVDSAPGMPTLAEFFPRYIEHRGLRCTPGTLAGYEAEAARTFLPRLGELPVDMIDRRTV +AEWIRWQLQQPTARWRAVAARAAAATPPRPEPPLATVSPKTVRNAHALLSAVLGLAVQEG +ILPANPARGADLPDDDVEEERGIFSRAEWARFYAAISESYQPLLIVLLVTGARWGEATAL +QVRDLDVAASVIHVRRAWKKGKEGAVLGVPKTARGRRTIMLPDWAVETLEPLAAGRAADE +FLLTVPGGGVIHRTNFVERHWKPALAAAGIAKHLTPHSLRHTFASWALMDGVPAQVVQHR +LGHESLQTTSRVYAHLLLDAQRAAVDAIGWEPPPGA +>GCF_005280335_PROKKA_01933 +MATISTRTSKKGVTTFRVGYYEGGRFRQMPAMLSETGARRIKAIIEDPAQGPDVARRLLE +AHADGAEDVPTLAQCLDRYVEARAVRCSEGTLAGYRREAARTFLPRLGQLPVTAIDRPAV +QDWIRWQMTQPTARSRAAAERAARAGTPAPS--LEPVSPKTVRNAHSLLSSILYLAVQDG +LIPTNPAHGQDLPADDVEEEKDIFTRPEWDRFYRAMTPHFQPLLALLITSGARWGEATAL +QVRDLDVDAGVIHVRRAWKKGAQGVVLGTPKTQRGRRAIMLPDHVVAMLTPLAAGRPPED +FLLTSPTGRVIHRTNFVERHWKPALAAAGITKDLSPHSARHTFASWALMEGVAPQIVQHR +LGHESLETTSRRYAHLLLDAQRAAVDAIGWRPSPGT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002148.fa new file mode 100644 index 0000000000000000000000000000000000000000..6fb9775b7151152455f7b1e0a9df19055c56f5f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002148.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_00968 +MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEQGAVTRRGA +AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG +DSPVRVFTVEVGEVKRLAAGYAGIALLASLPPERRRAEVDAVVARPPRRWNLTDDGALHD +LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV +AEVLRAAATRLAEIGG +>GCF_003691675_PROKKA_00681 +MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEEGAVTRRGA +AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG +DSPVRVFTVEVGEVKRLAAGYAGIALLAALPPERQRAEVDAVVARPPRRWNLTDDGALHD +LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV +AEVLRAAATRLAEIGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002149.fa new file mode 100644 index 0000000000000000000000000000000000000000..8756781b7059e6b1f63394687a1becf78f5c0055 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002149.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_00969 +MPLTASTVTRTVSVDGASVTCHDSVTPGELDRPLVLVHGTGGTTASHFGHLFPMMATRTR +VIAVDWAPTADPAADLTVDLLVGQVRAVVDELLGPDAAFDLLGYSLGAVVAGQLAADLGR +RVENLVLVAGWATTDVHQRLRNEVWRHLYATSPDALARYTAFCGLSPLALRSLTPAMLDG +ALASLTADEFTARQMDLNARVDVADRLSAVTARTLIVSCAEDIMVPPHHQYELLGIIDDA +RLTTMTSGHAFFLERPAELMQIVDLYLREPDRHPAGAIIPETHA +>GCF_003691675_PROKKA_00682 +MPLTASTVTRTVSVDGASVTCHDSVTPGELDRPLVLVHGTGGTTASHFGHLFPMMATRTR +VFAVDWAPPADPAADLTVDLLVGQVRAAVDELLGPDAAFDLLGYSLGAVVAGQLAADLGR +RVENLVLVAGWATTDVHQRLRNEVWRHLYATSPDALARYTAFCGLSPLALRSLTPAMLDG +ALASLTADEFTARQMDLNARVDVADRLSAVTARTLIVSCAEDIMVPPHHQYELLGIIDDA +RLTTMTSGHAFFLERPAELMQIVDLYLREPDRHPAGAIIPETHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002152.fa new file mode 100644 index 0000000000000000000000000000000000000000..7858954583faf0599ac25fe117eaea162e4dcde9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002152.fa @@ -0,0 +1,14 @@ +>GCF_002008305_PROKKA_01389 +MIRVEAGMSTARFCQLFDMPERTWRRWQAKARTGTAVKGPWPQPGRQAARELVVKHALAH +PAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKAAFATEPSG +PNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIELALADYEA +MFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVRTRVKTPGQ +NGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRPKEVHLGLA +DPTTPTFKTKEILPTT +>GCF_003691675_PROKKA_01121 +----------------------------------------------------MVKHALAH +PAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKAAFATEPSG +PNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIELALADYEA +MFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVRTRVKTPGQ +NGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRPKEVHLGLA +DPTTPTFKTKEILPTT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002154.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002154.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c9414b406672ca764a5341dec09c164aae5bb83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002154.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_01493 +MTTTTPKTARQLRAEWQAEIARREAEIVAAERAEARRIDEALRRAGRARVAAVETLYEML +GIDEQTKTRTRRDGSVQTVRADLDEAERAERLVAAVAALLEGAAGTRSAPAGGAEAVPDE +AAQMVPEEPSGALAPLPPAAGGESAEPDPEEDEAHASDDAEEPVSDEGDEAAREEDAYAE +EPAYGTVSDDLHEAGWQA +>GCF_005280335_PROKKA_02201 +M--TTTKTARQLRAEWQAEIARREAEIAAAEREEDRRTDEALRRAGRARVAAVEILYELL +GVDEQTTTRTRRDGSIQTVRVDRDETERAERLVDAVRALLAHCDGLRSAPA--------- +-------ESAPTSAPLPSPAGLD-ATVSGREQTAHAE---SESTSDEG------------ +---------------WAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002158.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5d0fdf78b40b4cd2d3dac484b642c9c790052d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002158.fa @@ -0,0 +1,6 @@ +>GCF_002008305_PROKKA_01497 +MSAPATAVTFPGVTLFLPDGVMTGDLTYDARTSQLAITYADGETEVLSIDLTLEGYVAAP +GEALIKDWSEHSGFTAALVDAGIVMRVETLQIGPFDSRAYRVLVLTEAVTGR +>GCF_005280335_PROKKA_02209 +MSASTATATFPGVTLFLPDGVMVGDLIYDARTSQLAIVYSDGETEVLSIDLTLEGYLPTP +GEALIKDWSEHSGVTSALVDAGLVMRTETLVVGPFSSRAYRVLVLTPEVTGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002163.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c866a972cc1c0c8c277c04e9e2143ade5197bdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002163.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_01608 +------------------------------------------------------------ +---MSFLIPSVPVSCGCRREVREETGLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPL +TAADVAAIRLQEDEASEHSFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVD +QPAG +>GCF_003691675_PROKKA_01320 +MVNLLLSVTFACGVAIAGLHVVNRRFIAPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAA +LAVLAWLILAVRTV----RARRAGHKLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPL +TAADVAAIRLQEDEASEHRFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVD +QPAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002164.fa new file mode 100644 index 0000000000000000000000000000000000000000..2560f01213768aa0770cbaf6e67dd7a1d1dcab7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002164.fa @@ -0,0 +1,8 @@ +>GCF_002008305_PROKKA_01613 +-------------------------------------------MSGNAFQDLPFPVSGPI +LGSVGERFRLETASDEGTATFSAGGTEGGTYSCGAGQTLLIGDSALLCRAVGENSLDFTI +SRPR +>GCF_005280335_PROKKA_01276 +MRTRVTTSLLGLGLTAAALVGCQTQTWISMCFTDATLRSCEVSVSGNAFQDLPFPVSGPI +LGGVGDRFRLETASVEGTATFSA----GGTYSCGAGQTLLIGDSALLCRAVGENSLDFTI +SRTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002167.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002167.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c38f7401f67bc5cd5fcb6e08515c3f4e72fe766 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002167.fa @@ -0,0 +1,8 @@ +>GCF_002008305_PROKKA_01789 +MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL +IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE +WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEATAGRRA +>GCF_005280335_PROKKA_01087 +MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL +IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE +WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEAPAGRRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002168.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002168.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b646c3e4561c42fdf6f6aa84cd936c45d0257a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002168.fa @@ -0,0 +1,20 @@ +>GCF_002008305_PROKKA_01792 +MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG +NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD +SGSAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALIIYTSGTTGRPKGALFDH +HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI +ATLERERATIFFGVPTMLAYMLRSPRLAASDLSHLRGILYGAAPMPASTAEALVAALPHV +HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM +RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE +VENALAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH +ELVLREIPRNLSGKILKHRLRADLTEPGVPA +>GCF_005280335_PROKKA_01084 +MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG +NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD +SGPAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALNIYTSGTTGRPKGALFDH +HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI +ATLERERATIFFGVPTMLAYMLRSPRMAASDLSHLRGILYGAAPMPASTAEALVAALPHV +HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM +RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE +VENSLAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH +ELVVREIPRNLSGKILKHRLRADLTEPGDPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002171.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2947b6044970d7841297358d05faefad67d7b2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002171.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_01796 +MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA +FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC +DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV +AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS +DDAAEGMSAFAQKRRPVFGSR +>GCF_005280335_PROKKA_01080 +MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA +FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC +DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV +AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS +DDAAEGMSAFAQKRRPVFGSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002177.fa new file mode 100644 index 0000000000000000000000000000000000000000..60ad56ac16ac431ef61a10b31caf0a8caf26fb5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002177.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_02061 +MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG +DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG +TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG +TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC +>GCF_020097155_PROKKA_02221 +MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG +DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG +TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG +TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002179.fa new file mode 100644 index 0000000000000000000000000000000000000000..c88be1764fa98e4594c32b3b326ac23014b432c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002179.fa @@ -0,0 +1,14 @@ +>GCF_002008305_PROKKA_02215 +MLRPRLARPTALLTAGLAALALLTGCSVDGDAAAGSSA------------GSPSAASSSS +GASSSGRVSDGAAPSSSRAAGSSSAVASASRAVESSQAAEASRAAAASREAEKSAAAAAA +EASRSAEAEAEAVAEAEREAEASAEVEVGAAEEESAASAGGDGLSAEGQQAVRQAQSYLS +FTAFSRSGLIDQL-EFEGFSNADATAAVDSLDVDYAAQAVKQAQSYLTHTAFSRTGLIDQ +L-EFEGYSNADATAAVDGLGIDYNEQAAKQAQSYLSHSAFSRAGLIDQLM-FEGYSASQA +EYGVDAAGL +>GCF_005280335_PROKKA_00529 +MLRPRHTRPALLLTAGLTSLALLTGCA-DGDPAPGAAATTAAATTAAATSSAPTTQAASS +SPASSPRTSSAAASSSAKASDAAAAASSSAAAASASEAAESSRAAEAEAEASRE-AEAEA +EAARAREAEESAAAEAEREAEAAATV------EEDSSTTAGEGTVSSG-QAVRAAKNYLE +VLPFSRDGLVHQLVAGDGYSDADAAAAVDSLTVDYEAQARRAAQNYLDVLPFSRDGLVHQ +LIAGDEYSDADAAAAVDSLTVDYQEQAARAAQNYLDVMPFSRDGLIRQLMDGDDYSASQA +EYGVDAVGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002180.fa new file mode 100644 index 0000000000000000000000000000000000000000..d622458db839d614d0b4805161a11fb2fb5d2b68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002180.fa @@ -0,0 +1,20 @@ +>GCF_002008305_PROKKA_02230 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------MSAGRITVVKGDERLASIPLERVSAVVVHGNVDLSGALLRELMWRGLP +CVWCTGAGRVVGWTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGG +MPAVVKRLRSATRLASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVG +RGATDPLNIALNYGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPV +VDSAILAAFNNGELGRLSFTHVLGGARLTQS----------------------------- +--------------------------- +>GCF_023573625_PROKKA_02165 +MDEKAPKVAQIQQGVADHARVDVPTTREAQTMRGIDVRDPSLGLHGRVDRVERLPSGRLR +VVEHKATPVKRAVRINDANRLQLVLQTMALESQGNTVEDAEVYFTTHHRRVPVEISAADR +KAARDAVASARSVVNGETAPAPLLGDPRCMRCSHASVCLPEERQEEEVLSRIVPPDPAGE +TLHLTVPGSRASMSAGRITVVKGDERLASIPLERVLAVVVHGNVDLSGALLRELMWRGLP +CVWCTGAGRVVGWTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGG +MPAVVKRLRSATRQASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVG +RGATDPLNIALNYGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPV +VDSAILAAFNNGELGRLSFTHVLGGARLTQTGRRKVIAAVERRLGTEFKHPVFGYRVTWR +RAIEVQARMFLGVLDGSQEVYKGVRVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002183.fa new file mode 100644 index 0000000000000000000000000000000000000000..c62a965673d8ff585cc475ede19f26dfffdde392 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002183.fa @@ -0,0 +1,20 @@ +>GCF_002008305_PROKKA_02236 +MGGLVISADFPLGVYTGHGPDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL +AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG +GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRRDRNA +SLRAVPGAVRQAMPSPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHATLPPRDHLRS +GIFAPVEHHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG +RYAPSVAPPANRVALHLAPGDLPNLPFSDGRDRFLVLVPRGMPGPALGMLASALAGVRRV +VTSEHQLTVAPEEIEVYDGTEFWKAPTEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA +WSLGNVLRDVEPAFATKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR +LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS +>GCF_023573625_PROKKA_02168 +MGGLVISADFPLGVYTGHGSDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL +AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG +GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRCDRNA +SLRAVPGAVRQAMPNPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHAALPPRDHLRS +GIFASVEQHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG +RYAPSDAPPANRVALHLVPGDLPALPFSDGRDRFLVLVPRGMPGPALGMLASAVAGVRRV +VTSEHQLTVAPEEIEVYDGAQFWKAPPEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA +WSLGNVLRDLEPAFTTKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR +LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002184.fa new file mode 100644 index 0000000000000000000000000000000000000000..3220423c92c58d6da43596956de2016ab188d41f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002184.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02237 +MSDFDTLSLEDLLAACAPGGSTSLLSETPLRPAGGPGAVIAPAKVIEGRGEPTYAYERRM +ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE +SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST +RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA +QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA +LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS +RALAPITDEVAVQVFEAALAHAKSVAGVEWNGQTIQLVGDPAILGAASTDDVEV +>GCF_023573625_PROKKA_02169 +MSDFDTLSLEDLLAACAPGGSTSLLSETPLQPAGGPGAVIAPAKVIEGRGEPTYAYERRM +ELDEAGQPRPVWTVVVDSKQSVSNRDEDAIISARRDQGTPEGEALRKVPTIEVRYGEAVE +SDLSLPHRAFDGHIRAATLDGAPVTQTEAYRALRDATKLDARALLDAAPTALVLGAWDST +RKSHQGRYQSCMTGEIIGVLADQDQEGGAPRTNRRAAGRVDPVAASVKPSAKDVEALVKA +QAGELSAKLQDKVLAEAKKKGETGSSMSTLGLGHIPPVLGELGGVACRSIMRRRLLSFSA +LRQLRFGGTTEQDVACRALLAAYALLGMALSDRELHLRANCHLVESDEPTVTLDLRYGKS +RALAPITDEVAVQVFEAALAHAESVAGVEWNGQTIQLVGDPAILGAASTDDAEV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002186.fa new file mode 100644 index 0000000000000000000000000000000000000000..b65275267180d3a60ef0ed3a5adf915f9525cd78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002186.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_02250 +MTWISANLDFILSLTWRHIAIASPVVLLSLLISVPLGRLANATGWGRRLIVGGSSLLYAI +PSLAVFVILPGLVGTKILDPLNVVIALTLYGVALLTRSASEAFDAVDDELLTAATAQGHS +AWQRFWRVELPLAGESLLAGTRVVSASTLSLVSVGALIGVQSLGTLFTEGYARSFVTEIV +VGIVGTVILAVVFDLVLVALAALLMPWTRRAKVRKASGRRRSSQDTTTTALATVPDLAVQ +EG-RR +>GCF_020097155_PROKKA_00457 +MTWIAENLDLILDLTLRHVALAVPAILLSVLIAVPLGRAANVSRWGRRLAVGGSSLLYAI +PSLAVFVILPGLIGTRILDPLNVVIALTLYGAALLTRSASEAFDALDPDVLHAATAQGHS +PSQRFWGVELPLAGESLLAGTRVVSASTLSLVSVGALIGVPSLGTLFTEGYARAFLTEIL +VGIAGTVLLAVLFDAALVALAAALMPWTRRGR-RTVPAPEDARHDAALTDAVTDPVTAPA +EGVTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002187.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002187.fa new file mode 100644 index 0000000000000000000000000000000000000000..c3bcf34f8e07e59dc46dac7e0cd6f4dbd3c77fb2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002187.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_02260 +MPDLPACLEREPLTRAVVTGYAAKVTAEDRAVQRDAFIAAMVWGYGRVGYGPSRVERIMA +QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES +DIAPVLDSVVRAWFAEHAKDVDVRIGGGWTYPRKYATYVETMQAWGEELKIPADDVERLI +FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGAGDDAEPHLQALEDVIADAE +DRAPDEA +>GCF_023573625_PROKKA_02191 +MPDLPACLECEPLTRAVVTGYAAKVTAEDLAVQRDAFIAAMVWGYGRVGYGPSRVERIMA +QPGFEEQLADVTRITLEQGGPAAFEHIRQQRKSGVGCLKHLGAAFGTKYLYFLTKAHRES +DIAPVLDSVVRAWFAEHVKDVDVRIGGGWTYPDRYRTYVTTMQAWGEELKIPADDVERLI +FLQQQDATQEPWRESWSSAAADPEAGELLEALRLALADLGARDDAEPHLQALEDVIADAE +DRAPDEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002189.fa new file mode 100644 index 0000000000000000000000000000000000000000..83c5d577ee6373ab1f3179e17d2c3a332249e09b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002189.fa @@ -0,0 +1,6 @@ +>GCF_003691675_PROKKA_00016 +M----SAPLPS-----HLTIVQSADLLQVSRDTIRRLIASGDLKAYRIGPSTNRRRPIRV +DRDSLLALREPVTSLAALKAGEAA +>GCF_005280335_PROKKA_00035 +MAAAASKPRPSFDPRPRLTIAEVADYTGTSPSSVRRWIARGELRAYKYGP-----RAIRI +DPADVDAMRQPVTSLADLRGGDAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002190.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a88a05ee464727fbb0991f0ef039971ed763fb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002190.fa @@ -0,0 +1,16 @@ +>GCF_003691675_PROKKA_00018 +MATPRKLPRGITLNPSGRYRVKLYAQDREFSLGTFAALADAKAALAVAQGEVARGTFIPP +AERRRALKAEAEAASARAAAESRTVRQLADAFLAWKEGAGLAWGSVYTYRRHLEGHFLPE +FGDRAVGAVTTVDLNAWLDRLESDHGASVAPEVHGTVTALFKFAAGQARDLPRGFTPWIT +ASPVPALTRTRRRE----HRQVTILAPSELARLSELMTYPE-DRALILTAGWCALRIGEA +LALRRRHVVTDDAGRLMLRIETQVQARGRGLYEAPPKSEAGRRTIYVPALAREALTAHLA +QHVGATAEALLFSRRGGGNRLNNPNTIGKRLKSAVDLLNREREDAGAEPLGRFTFHGLRH +TGLTRMGQQGATEAELMAFAGHSDPKAVRIYQHAERNRLAALADRMTGEDA +>GCF_005280335_PROKKA_00034 +MPKPQRLPRGVDRLPGGGYRARLTVDGYQHTIGSFATLGDARAALDIARGEKARGTFVPP +AVTRARLKAEKEARRAQAAADSRTVRDMAEAWLSWQTERGLKLGSVYTYRRHLEAHFLPT +FGDRPVGEVTALDLNAWLDALEESKGHAGAAQIHRVVAALFKWATGDAAELPRTFTPWLL +TSPVPPLAARRLRRPNLPQRNRETLTDAELSALADLM--PEADRLAVLLSGWCALRIGEV +LALRRRHVTTDPDGTAWVRVESQVQARGSGVREESPKSDAGRREVPVPPVIAADLAAHLD +THAAPGPDGLLFPRVGGGNGLNNPNTVRKRFNAALAALNAQRAEAGENPVENFTWHGLRH +TALTRLGQAGATTAELKAYAGHSDGKSVEVYQHAERRRLAALI-----QDV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002191.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b9d3e42c5581f5843aaafb5f5f56a1dbcb2870f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002191.fa @@ -0,0 +1,24 @@ +>GCF_003691675_PROKKA_00093 +MSDRLRDLVLAFAGGTASASQVDLILEAGGLDDDLVQAVSRLRQEGRLARRQREAARILV +DAATLITGARDMDEILELICRRTRLLLDSDMAYVSLNDVDQGQTYIRTTDGVLTSAYRNL +RMPLGTGILGQAAGGATVSQTGDYLDDTSFPHIPAVDEAVRGEGVVSILAATLRVRGRRI +GALLVADRRPRTYTPDEVDLITQTAGLSAVALSRNEEMRDLQTALDDLTVAREEIESKNV +LLSRLGRLDQELFSVLREEASPADLAEVIGQAIGTEVKALFPADLPAHRTPAAPVVSEHP +CQDSPNGMATLVRAFTGHRELGALEAHGSLDRDERFLFERGATALTALLLAQERGWATQM +QQQHRLVKDLENASTETWRSVAGRLAPHRLQEGGTVRVLAVRTEQLQDTRMALRELLARR +GGVSSIRYEVLRVISPNLTGRELHELLVSRDRSAAVCEQEALLMPEDIRVSLQGVQRTVR +-AMAALNITG--VADPRWDLGLTGLAVAQLPPATVDRLVYRALEPLLSYDRQQGTELTHT +AWSFLECDGRVSVAAERLHIHPNTLRQRIGRIGTLLGEDWHQGSHRTDLHLAL------- +------------------RLHRVQSASRTG +>GCF_020097155_PROKKA_00837 +M----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +----------------------------------------AFLGPGEHFRDLPGAFRTLE +NALAVSRVAGGLHAVDASTVGAVGMVLAGAGEASKD-VTARPLAPLRDLPPQRASALRET +ALAYLDAGTNVAETSRRLFLHRNTVLQRLEQLGAVLGPDWHTPPRSLDLHLALLSAARDD +GGAPGAPPVRSQPRRRAEELRRPRSPAARC diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002193.fa new file mode 100644 index 0000000000000000000000000000000000000000..593aa39dd2de8aece8ec8d0c0d79f20142c45731 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002193.fa @@ -0,0 +1,12 @@ +>GCF_003691675_PROKKA_00241 +MRSLMRMRTPRDIAAG---VLATVRRADPPVIWGAEPMNGGNFLYLWATAWARRRETGRP +WLVRYKPKMEPWLTEFPALRDLTVREEDVSFRQERTVEWGQQTYQDWFFRDLLDFARERL +LTSSGFQVRLKQVDRGAVVVNVRRGDYYSDPVHRANFGFDVAGYVRAAVARVPRDEAGRI +ILVSDDVDWCRENLGFLSAWGEVGTIPGEHDMFNDLAQLAGGRHLVLANSTFSYWGGYLA +SAMPVNDRPQSVQAPLHFNRLYARGESPLLLPQWQAIPDDAF---------I +>GCF_005280335_PROKKA_02433 +MARC-------DLAAARGRALSLVRTQQPFVIWGAEPMNGGNYLYLWATAWARQRHTGEQ +WLVRHKPKMDPWLEEFPLLRALTVDEADVGWRQRRTVEWGQQAGQDFRFKDLRDFARELL +LASESFRSRMAARPGDAMVVNVRRGDYYADAGLRAVFGFDIPGYVHAALRRIPAERQERV +VVVSDDPDWCAANLGFLGRERSVVFMPTPHDMFEDLAQLAVARDLILANSTFSYWGGYLA +SARSAQERPRTVFAPLHFNRLYSDGESPLLLPEWTAIPDDEFSTPDRIQGEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002195.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b471b9e983406b1cd8fee91a19d43b6e4e6e433 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002195.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_00300 +MSTERDALFQGVEGAGGPSQAAGEDMSASETSDTATACHSGVQVEQQTDSQVNTGRADAE +AVRQSHGGAKRRRGGGGRLDTRFDDATLAALRTRAKRLGLAPSTWVRTVVRDALHASRSE +ELDAAVAAQLLGVEERVQASADARELAAQVRPLAINVNDLDRRARAGEPVALSAEVPELI +ELLHEVRALLGDRAAS +>GCF_005280335_PROKKA_02368 +MSADQHPLFQGIEGGGAPSQAGLEDTSVSDVSDRPTACHSGVQVEQQADSQVKTGRADAE +AVRQSHGGAKRRRGGGGRLDTRFDEATLGALRTRAERLGLAPSTWVRSVVRDALHASRSE +ELDAAVAAHLLGVEARVQASADARELAAQVRPLAINVNDLDRRARAGEAVALSAEVPELI +ELLREVRTLLGDRTAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002196.fa new file mode 100644 index 0000000000000000000000000000000000000000..7dbf34d77699a9292432eb3f918c2dee334be5e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002196.fa @@ -0,0 +1,18 @@ +>GCF_003691675_PROKKA_00301 +-------MAKQENNPTSIGLTQYLDPSYWAWAAEDPNGAALLQQGAEAILAYVVQRLEAT +GCQVVEAYGIVHDKDEREVWSDTEKALVVEPKPEHLHAVIKFASRAKSAPLDRLAFGIGV +EPQYVEKPGRGRYAFDNMLSYLTHVKYADKHQYAPSEVATVRGPDYLGIDAQRRETWLKG +RAHVKKKIVAENFEDMRERVLQGEITRDQIMLTDELFDIYSRHQREIDDALSAYGQRRAY +RAAAKLRAGEFSTHVVFVHGDAGIGKTRFATDFITEAINAANAHGERWQVYRAATGNPLD +DWRGEEVLLLDDLRASAMDANDWLLLLDPYNASPAKARYKNKGEVAPRLIVITATIEPVE +FFYYARQKGNVDEALDQFIRRLASVVKVYRADDINRYLVQHIGKIEPYEWHQCSVPTAAH +TPGMYGNAYHQNVG-SRELTYGPETSAEHDAEGAVAELLGGLAVRSPDVPLALIGGAA +>GCF_005280335_PROKKA_02369 +MSRAVVAVAKQENNPTSIGLTQYLDPSYWTWAAEDANGAALLQQGAGPILTYIVQRLEAV +GCEVVEAYGIVHDKDEREVWSDTEKALVVEPKPDHLHAVIKFASRSKSAPLDRLAFGIGV +EPQYVEKPGRGRYAFDNMLSYLTHVKYADKHQYAPSEVATVRGPDYLGIDALRRETWLKG +RAHVKKRVVAENFEDMRERVLQGEITRDQIMLTDGLFDIYSRHQREIDDALSAYGQRRAY +RAAAKLRAGDFSTHVVFVHGDAGIGKTRFATDFIMAAIDAANANGERWQVYRAATGNPLD +DWRGEEVLLLDDLRASAMDANDWLLLLDPYNASPAKARYKNKGEVAPRLIVITATIEPVE +FFFYARQKGNVDEALDQFIRRLASVVKVFRADDINRYLVQHIGKIEPYEWHQCSLPAAAH +TPGVNGNSYHQQVAPSRELTYGPETSAEHDAESAVVELLSGLAVRSPDVPLALIGGAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002198.fa new file mode 100644 index 0000000000000000000000000000000000000000..b53195b00753b76595213b9505763ae8045d798d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002198.fa @@ -0,0 +1,6 @@ +>GCF_003691675_PROKKA_00304 +MTRKHLGFLNFGHWIHRP-----GAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQR +MFSSPFPILAAMAARTERISLGTGVIDLR +>GCF_005280335_PROKKA_02362 +MTKKHLGFLNFGHWIHRDPVGGRPAEPDATAALDDVVQMAVDAEAAGLDGAWIRIHHFQR +MFSSPFPILTAMAARTQRIHLGTGVIDLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002201.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d8d066016842506bff99118c6a93b79d0b03ac5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002201.fa @@ -0,0 +1,8 @@ +>GCF_003691675_PROKKA_00331 +MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR +RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS +KRLSDMP +>GCF_020097155_PROKKA_02232 +MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR +RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS +KRLSDMP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002202.fa new file mode 100644 index 0000000000000000000000000000000000000000..d33b85e87fe01684d860de81e5e824c6f900a543 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002202.fa @@ -0,0 +1,28 @@ +>GCF_003691675_PROKKA_00367 +MVMS--------------------------------------------------LSRV-- +--------LWKV------------------------------------------------ +------------------------------------------------------------ +---------------RSKAPTV----TASVQGTVSVTGEGYTTIR-DSTCGAGNFLNLAY +AKLREIETDLLADQRRRTGSQDLSLDVSLDQRIHIDRFYGIEINWWPAKIAETAMFLVDH +QANRQLAAALGQAPVRLPIKITATIYQHDALTLDWSQALPKPAGRTFVFGNPPFLGDHTR +TAAQLALMQAAWGEGKQLSRLDFVTSWHALTLRLLAERDGEWAFVTTNSIVQGDQPARLF +APIFAAGWRIKFAHRTFAWDSQAPGKAAVHCVIIGFTRDPGTKARLFKYEHARGEAREVP +GVKTINAYLVDGPNVLVDKRSTPLAPDLPEVTYGSKPADAGNLVVTAEQYQAVMADPVMA +PYVRPYVGAVELIRGQQRWCLWLADMDPDAPSHSPELKRRLEGVAAERAKSKAASTRDWA +RFPHLFRQRGLVSDVPFVGIPEVSSEARAYLPVAHFEPDVIISNKVYGALDPDGIVFAVA +SSSMFITWMKTVGGRMKSDLSFSSTITWNGFPLPALTDKDRAALARAAEKVLEARALHPR +RSLAQHYAPLGMDPALVKAHDGLDAVMDKIMGAPRRCRTELERQELLFARYAQLTS +>GCF_020097155_PROKKA_02209 +MTKTEEQEASIAAAQLMASMFTALVGDEVDVPVGEEAPEDAEEEEFATQQASILLTRLLF +LLYGDDAGLWEADLFQRWVEWDTTADNLGPQLDALFRVLNTPENRRRGVPDSLARFPYVN +GGIFDGTSTAGFLTRDFRDALVAACRFRWTQISPAVFGSMFQLVKSKQARRGDGEHYTSE +ENILKTIGPLFLDEYRARADRLIQNKTTTRREVIGLIEEIASNIYVDPACGAGNFLNLAY +AKLREIETDLLADQRRRTGSQDLSLDVSLDQRIHIDRFYGIEINWWPAKIAETAMFLVDH +QANRQLAAALGQAPVRLPIKITATIYQHDALTLDWAQALPVPAGRTFVFGNPPFLGDHTR +TAAQLALMQAAWGEGKQLSRLDFVTSWHALTLRLLAERDGEWAFVTTNSIVQGDQPARLF +APIFAAGWRIKFAHRTFAWDSQAPGKAAVHCVIIGFTRDRDAKARLFKYEHARGEAREVP +GVKTINAYLVDGPDVLVQKRSTPLAPDMPEVVYGSKPTDDGNLIVTAEQYQAVMADPVMA +PYVRPYVGAVELIRGQRRWCLWLTDMDPDAPSRSPELKRRLEGVATERAKSKAASTRDWA +RFPHLFRQRGLVSDVPFVGIPEVSSEGRAYLPVAHFEPDVIISNKVYGAVDPYGIVFAVA +SSSMFITWMKTVGGRLESRISFSSTITWNGFPLPALTDKDRASLAKAGQKVLEARALHPE +RSLAQHYAPLSMDPVLVRAHDGLDTVMDKIMGAPRRCRTELERQELLFTRYAELTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002203.fa new file mode 100644 index 0000000000000000000000000000000000000000..26b4d7829cba91fbb968245642ac7f0a06cc47d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002203.fa @@ -0,0 +1,6 @@ +>GCF_003691675_PROKKA_00374 +MSVTKGLLVRLEALPGKEDEVQEFLGIGRGLVEEEPATVAWFAIRLGPSSFGIFDVFPDD +AGRDAHLSGAVAKALGEQT--GKLFSEPTIEKLDVLASKLPA +>GCF_020097155_PROKKA_01211 +MSVTKGLLVRFDALPGKEDDVKDFLDSGRALVAEEPATIAWFAIRLGPSSFGIFDVLPED +AGRDAHLSGPVAVALGGQTGAGALFSEPTIEKLDVLGSKLPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002205.fa new file mode 100644 index 0000000000000000000000000000000000000000..25021c01a3af6ac27faba03165b262ab76560621 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002205.fa @@ -0,0 +1,34 @@ +>GCF_003691675_PROKKA_00766 +MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT +GMGAEVFGPPAVANDVAARQMDLDGAARRAFDALDDAEDRAWFTRFADGVNAGLDAGARR +APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA +DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG +VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDVRVAHTPR +GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR +RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP +HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA +LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG +DAAAWVGAALAERGPEPLRAALGITASTRDLVRAAVAAVDDAAEPPGPDGAARTWGEAHA +LTPFLFTHEHPGGPDEPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV +FDLGDRTRSRWVVPFGASGLGGGHVTDQLDAWAAGRLLPVPSRPVPPSAGSGVAPARSVP +GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD +FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR +ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRDV +R +>GCF_023573625_PROKKA_00994 +MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT +GMSAEVFGPPAVANDVAARQMDLDGAARQAFNALDDAEDRAWFTRFADGVNAGLDAGARR +APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA +DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG +VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDLRVAHTPR +GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR +RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP +HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA +LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG +DAAAWVGAALAERGPEPLRAALGVAASTRDLVRAAVAAVGDAAEPPGPDDTARTWGAAHA +LTPFLFTHEHPGGPDVPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV +FDLGDRTRSRWVVPFGASSLGGGHVTDQLDAWAAGRLLPVPSGPVPPSAGSGVAPARSVP +GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD +FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR +ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRAV +H diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002207.fa new file mode 100644 index 0000000000000000000000000000000000000000..d8de7f89b451bbb5f013ca17eec75f1ee3884b7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002207.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_00768 +MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE +YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDVGLHVLVAPTDTPVP +GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI +ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA +>GCF_023573625_PROKKA_00996 +MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE +YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDIGLHVLVAPTDTPVP +GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI +ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002208.fa new file mode 100644 index 0000000000000000000000000000000000000000..60c69ff4601d19fc3ae1dfe80b2d607c1b19b7ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002208.fa @@ -0,0 +1,18 @@ +>GCF_003691675_PROKKA_00769 +MSPASTSPRRVLAIGLGPFNLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP +FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYA +TTVTAVRWDDQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEESARVGAS +PVVHTGEYMGRREDIAGAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG +QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEYTIEDVYHALYERQVGPLDPA +RLWPGTSVTDARLVAGPGAPRVEVTLRDEETGVTGGHVVDRVVAGTGYRHPDHPFLEPVR +HLLRAEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRQ +VYAQAESIAFQDFGAVAAGVR +>GCF_023573625_PROKKA_00997 +MSPASTSPRRVLAIGLGPFDLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP +FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYG +TTVTAVRWDEQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEEAVRVGAS +PVVHTGEYMGRREDIVEAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG +QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEHTIEDVYHALYERQVGPLDPA +RLWPGTSVADARLVAGQGAPRVEVTLRDEETGVTARHVVDRVVAGTGYRHPDHPFLEPVR +HLLRVEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRE +VYAQAESIAFQDFGAVAAGVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002218.fa new file mode 100644 index 0000000000000000000000000000000000000000..a42f69d5c44c6dc5e4dd3ec8b55b896195a50ba0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002218.fa @@ -0,0 +1,6 @@ +>GCF_003691675_PROKKA_01861 +MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN +VWLTRQGA +>GCF_023573625_PROKKA_02091 +MSIRYPLGYVENERKVYPQGYARERVSPGGDGEGRHDQETSAGGVSQMISLRIGRQNYRN +VWLTRQGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002219.fa new file mode 100644 index 0000000000000000000000000000000000000000..6327a858809f9254eda4d53f6880440c877ae276 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002219.fa @@ -0,0 +1,12 @@ +>GCF_003691675_PROKKA_01953 +MTTLQRLRAEVARRYAALGLPAWPDPHPDGAPPREEEYSRVTDPQRYRIAAARARVWAEV +LAEAGAVVVPDPVRGIPLDEAGRADLAAPVDRALRVAPPAGVDGASPWWLLETDVPQDDD +GGVLPVIRVAVGAPRQVHALLPDCGCDACDPGSDELLEAVDQAVV--------------- +---------RADGTAEALGRVPGWSFEALTDACRDLAAGGRPRLPRGTRR-----WCGRA +K +>GCF_020097155_PROKKA_00433 +-------------------------------------------------MTARARVWAEV +LAETGAVVVPDPVRGIPLDEAGRADLTVPVDRALRVAPPAGVDGASPWWLLETDVPQDDD +GGVLPVIRVAVGAPGQVHALLPDCGCDACGPGSDELLEAVDQAVASAVGTGVNLRGRHGL +RRRDWHVHWRSDGTAEGQGRVPGWPFEALKDACRDLAAGGRPRLPRGTEATVRAGWFPEA +- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002220.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5861470ceb7a8ef007037202eb0e2bd8eff932b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002220.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_01969 +MTAPQLHLPRTVVSDQTDRAVDLLGHYFTPGKFIGGRWDGFDPSGTRAASANVFTSDDVA +SAALLNTPVPGHAVVHLLITQRVHFAGLLEAVGPDRDFIDVDPDPSGKDMAPVYELYEAL +KTLPKIGPTIASKLVARKRPRLFPIIDAELRQTVFHETRKDGYVGRALLHAEFSAQERTI +WQRLASYHSAASLPTEVSVLRVFDVLAWMEAKAYWGPVP +>GCF_005280335_PROKKA_00458 +MTAPQLHLPRTVASDQTERAVDLLQLYFKSRKFIGSQWDGFDPSGRRAASANVFTADDVA +SAALLNTPVPGHAVVHLLITQRERFSELLRIVGPDRDFIDADPDPSGKDMAPVYELYEAL +KDLPKIGPTIASKLVARKRPRLFPIIDSDLRRTVFHETRKDGHVGRALLHADFSAQERTM +WQRLESYRCAAALPAEVTTLRVFDVLAWMEAKAY----- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002222.fa new file mode 100644 index 0000000000000000000000000000000000000000..5321b7f4c063ddd01f04effb7f7dc27e1a4ef572 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002222.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_01985 +MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFQLTLAPG +VPWTEPKVSPCASTLFTNPTRLSVTTDNSAFYYRITNLRADSTVTDVTASVLVQKSVVDK +LSNG-----LTWTSE-TKDWSNPTLDVSGAK----YIDNGIEYYRYYSTLRTAVPAPVSG +TITLPRIQWYSNCSTNLLTQAQSTGVMANGRGSAVVNGTPLVNVGTYVRLTPRPAG +>GCF_023573625_PROKKA_02233 +MSESTSAAPQPSQSVPSRRRVASSLAWAVPTVVAAAAAPAEAASPLPRIDRVFSIRRATT +AAVPGASVSACGS----GSTRLSVTTDDVNTYYRIANVRTGSTVTDVTASVLVQKDMVDA +METGKNPTTFTWTSSATPSWSTPVREVSGTGSPVLYTNNGIQYYRYVSKLSTPVPAPVSG +TITLPIIGWYSNCSTTL------AGVSVNGRGSAVVNGTPLVNVGTYRQL------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002223.fa new file mode 100644 index 0000000000000000000000000000000000000000..8de0e1bccc4bbab5ace13c60474c0126d273f769 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002223.fa @@ -0,0 +1,4 @@ +>GCF_003691675_PROKKA_02024 +MRVTSPQTLISAVFEAAERATNDLTHLIPDLDRDRAEYAVASVLLEEAWLSNR +>GCF_023573625_PROKKA_01147 +MRATNQQALITAVFEAAERATDSITHLVPDLDRDRAEYALVSVLLEEAWVAQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002229.fa new file mode 100644 index 0000000000000000000000000000000000000000..ac05fe14924a454a9c94192c043555cee4e87982 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002229.fa @@ -0,0 +1,24 @@ +>GCF_003691675_PROKKA_02228 +M----TSPLDIEDVDLSETTRQRPDYFHPD---LYAEQPPAERPGEKHRGQLRIAHRLAE +AHSGRL----------------MYVNGLGWHVWDG----QRWAPDETAAAERAVHD---- +--------------VLRSALAESH------------DG---------------------- +DRNLREDVRRCETAAGIRGVLDIAATLEGVRVAVDALDADPHLLNVANGTLDLRTRTLRP +HDPADRLTRVCRGAWTAGESDGM----------WS--DFLARVLPDDAERAYFQRVIGQA +VFGA-VREHLFPVLTGTGANGKGTAYTAIAHALGDYAAIIDPDLLMTSARGPGG---PEM +MQLFGARLVIGSETEEGKPLD-AALMKRLTGGDPITA--RHLYQAPVTWEPSHQFLYVTN +HLPKVKGNDPAVWRRVRVLPFDVVIPPADRDPALPERLREAADAVVTWAVRGWWDYLDA- +GGMGEPEAVKAATDAYAVQSDAVRRFIADACVIAPGASARTRELHTAWTAWAAA--DGAE +PLAEKKF----GAELDRLGY----------------------------------PTTRTR +AG-----SVRQGIGLLADDD +>GCF_005280335_PROKKA_02200 +MSVRESRPTQADETALKAFTGAEDEVTNFDGVVSYEEEPPAGFLAEPRSGLSPTARPDTE +EHAEAVLAGLSSLSATDSEILQLATTHFVERMWDGTPGTTRHLLDLCAAVARRLGDRKHD +GAPRFYAPRALPVSAVAAMLAHLHRYCVVDLGLPASDGVAPLLVRYADDGPLEGTYSRVT +EASLYVDALALEPESSPKQMEELFARL-AARSQVVHRCSDPNLVPVANGIFDYRTKTLRE +FDP--ELVFLFKAATRYVDAPPMPMIVQPDGTDWNPVDWMASLAPDPEVRHLLWEVTGAL +LRPLNAWDKWLALISPEGRNGKGT-------LLAMWRALLGPDAHKSATLASFGADFPDI +EGLNEKSAILTDENDVGRYLESSATLKSIVTGDVLSAPVKHSKAVPVAFQ--GLMVQCMN +DLPRAKDKSSSFYRRLLAVPMEANFTEATENKAIKHDYVQRPE-VLEWVLHHVLVEMEAF +TSFSEPAACAALKDDVRDANDPVRVFVAEFIDQFAWDLVPTTFAHDLYKAWLVRRWPNTH +PVNEAEFIRQVSGHMAEYGWEHKKNVRVSSRMHSHEPLINEYDLRAWMNPAYNGPDPVKR +AAPLLKPSYR---GWVRIEP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002231.fa new file mode 100644 index 0000000000000000000000000000000000000000..41ce8e9eda6fd8112db7c228d8f533034e22e203 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002231.fa @@ -0,0 +1,6 @@ +>GCF_003691675_PROKKA_02300 +MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS +AAVSTVMSTAVSESDR +>GCF_023573625_PROKKA_00284 +MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS +AAVSTVMSTAVSESDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002234.fa new file mode 100644 index 0000000000000000000000000000000000000000..e92d45b262b6fcd2b35181b0420f39d3b22eacf9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002234.fa @@ -0,0 +1,16 @@ +>GCF_003691675_PROKKA_02303 +MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP +GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA +SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ +LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS +QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG +LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP +WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS +>GCF_023573625_PROKKA_00287 +MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP +GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA +SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ +LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS +QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG +LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP +WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002241.fa new file mode 100644 index 0000000000000000000000000000000000000000..5aa227eb799111e5ee0ef7f6107482eeb0615316 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002241.fa @@ -0,0 +1,20 @@ +>GCF_005280335_PROKKA_00094 +MADIDLTAAPATPEAATGQLTPLASLGRAAAVFGDREAVVYGALRWDYAQFAAHVQSFAR +ALRGRIEPGQTVAAILPNVPAMLAAHFAVPLAGGVLCALNPRLTPRELEYILEHAEARVV +LADADVAEDVRGVVERIGTGAAVAEVVDPEAGHAQPDDGRLTYEALVAEGADGADLPWTV +PDERLPITLNYTSGTTGRPKGVRYTHRSAQLTAVANVLSQEFDAQTRYLWTLPMFHCNGW +TRPWSVTAAGGTHVCLRAVRQDPIWDAFEREGITHLCGAPIVAASIIEAERAHPVEQKIR +MAAAGAAPPPSVIAALEGLNITPVHVYGLTETHGPFTICEPQPGWAELSRPDRAQVMARQ +GVALPLVGEVAVVDMDMNPVPADGQTLGEVVMRGDGVMLGYFKNPEATEEAFRGGWFHSG +DLGVMHPDGYIQLRDRAKDIIISGGENISSIEVEGVVAAHPAVADVAVVGVQDDRWGERP +VAYVVFRSGVERPDDAALRAHCREHLAGFKVPDRFVPVEEMPRTATGKIRKNELRQG +>GCF_020097155_PROKKA_00065 +MDVTQDTLAPELAVARTEPLTPLAFLGRAAAVFGDREAVVYGDMRWSYAELAAHVQSLAR +ALTARIEPGQTVAAILPNVPAMLAAHYAVPLAGGVLTALNPRLTPRELEYILEHAEARVV +LADGDVAAEVRGVVEQIGTGAAVAEVVDAAAGHAAPDAGLLTYDALLAEGAEGEDLPWAV +ADETAPITLNYTSGTTGRPKGVRYTHRSAHQTAVANVITQGYDGATRYLWTLPMFHCNGW +TRPWAVTAAAGTHVCLRAVRMDPIWDALDDEGVTHLCGAPIVAAMIIESERAHPVDREIR +MAAAGAAPPPSVIAALEGLNITPVHVYGLTETHGPFTICEPQPGWAELDRAARAQVMARQ +GVAMPMVGQVAVVDMDMNPVPADGRTMGEVVMRGEGVMLGYYKNPEATAEAFRGGWFHSG +DLGVMHPDGYIQLRDRAKDIIISGGENISSIEVEGVLHAHPAVTDVAVVGVSDERWGERP +VAYLVLDPASGPLDVEALRAHCREHLAGFKVPDRFEVVEEMPRTATGKIRKNELRRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002244.fa new file mode 100644 index 0000000000000000000000000000000000000000..2693d576ed4c8fa7a9f2631a113016fab40acad1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002244.fa @@ -0,0 +1,24 @@ +>GCF_005280335_PROKKA_00117 +MNPTFSRRTGLRTLAAAVVAGTVTIQAPAVLARTAASTPA--AGADGFRVLPYLMEPTAT +SMDLVWFSEREVPGTVVVSGPGLGDNHRGGRTRPAGTRVSTPEFQPLLAYTEKERAQSIK +GLAQGSWLLGPASYKHRVSLTGLKAGKEYRYTVTQGGQRHTAAFRTADDGANWSDLRLIA +FSDTETEPYGRIENREWELSMVTPYTEGSLPRPGEGSVWHQTFGSTTRYGQFTLKYPLTQ +DVALRENIRHIDAAAPDLLLVAGDLGQGGGYQPGWDEFFRHFAGEHSDIASRVPLITSLG +NWETFAALNDGYGTAADRSPVVRSRNKYHAYFERTSAGTDRENPRFRGSYYRTDHGPLTI +LTLDSTNGVPDESVGAGLLSGAPFSGDDRNLTAATMPSDTQGSFTQAEYEAAFPTVFPGS +TPADADLPVLNPGHEQWAWTERQLADARAAGRIVIVEFHHAAYSVGVHGTPPNHEFPDDQ +SGVAMRVYTPLFEKYGVAVVISGHDEMFQRSWVDEDGDGVGFHSYDVGVAADGLRGEQYA +KDASGQWKPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGREAEM +TLTPMYVFPILDDEYRLVRTERRAYDDVQTVRFDRRGVPKPRR +>GCF_020097155_PROKKA_00085 +MNPAFSRRTGLRALAAAVVTGTVATTAPAALAKTAQHAPAVPAGADGFRVLPYLMEPTAT +SMDLVWFSERPVAGTVVVSGPGLGNNHGNGRTRPAGTRVSAPELQPLLAYTQKELTQTLT +GLPQGSWLLGAENWKHRVSLAGLKPGKEYTYTVTQGGRRHTASFRTADDGRDWSDLRLIA +FSDTETEPYGRIENREWELSQVTPYTEGSLPRPGEGSLWQQTFGSTVRYGAFTLKYPLTQ +DVGLRENIAHIDAADPDLLLVAGDLGQGSAYQPGWDEFFRHVAGEHSDIASRVPLITALG +NWETFAALNGGYGTPADRSPVVRSRNKYHAYFERTGAGTDRQNPRFRGSYYRTDHGPLTI +ITLDSTNGVPDESVN-GPLSGAPISGDDRGLTAATMPTDTQGSFTQAEYEAAFPKVFPGS +TPADADLPVFNPGHAQWAWAEEQLADARAKGQIILVEFHHVPLSIGEHGTPPNHAVPDDQ +SGVAMRVYAPLLEKHGVAVVISGHDEMFQRSWVDADGDGVGFHSYDVGVASDGLRGEKYA +KNAAGEYEPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGQSAEM +TLTPMYVFPILDSQYRLVRTERRAYGDVQLIRFDRNGVPLPRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002247.fa new file mode 100644 index 0000000000000000000000000000000000000000..0dc9912b8d431bc355ac6ce916245ec87580438a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002247.fa @@ -0,0 +1,6 @@ +>GCF_005280335_PROKKA_00224 +MTDEQDAVDGRAGVPSWRVIADRISAEHRAADDGPIDEVDPADFDLDEDCCLGGCCAKGI +AYLDAVEQAAARRARRTRA +>GCF_023573625_PROKKA_00172 +MTDEQDAADGRAGVPSWRAIADRISAEHRAGDDGPIDEVDPADFDLDEDCCLGGCCAKGL +AYLDAVERAAARRARRTRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002249.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b957818f3c436042b9e4e1134abeaa1b66eaf21 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002249.fa @@ -0,0 +1,6 @@ +>GCF_005280335_PROKKA_00290 +MADMGNKFDKLKGDAKEGLGKATGDDRLRAEGKTESTAAGAKDAVQNAGDKVKDAAAGIK +DGLSKDR +>GCF_020097155_PROKKA_00236 +MADMGNTFDKLKGDAKGAVGEATGDSHLEAEGRTESAAASAKDAARSAGDAVKGAAEGVK +NAVSRD- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002251.fa new file mode 100644 index 0000000000000000000000000000000000000000..961d20eb9577b8bc94d0a67c314ed348e1577976 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002251.fa @@ -0,0 +1,14 @@ +>GCF_005280335_PROKKA_00343 +MQRIVPNIWCDGTADAAAEFYLRAFAGLPGTAHVRTDRYPTEGLLDFQRPLAGKTLTQEL +DLAGHRFILVNAGDEFAPNPSISFFVNADPSRMDDPRGTLDALWAELTDGGRVLMDLGPY +PHSEHYGWVEDRHGVSWQLMLTDPAGDPRPVIIPQLMFCGPAQNRAAEALDHYLAVFDDA +TPGQRVTYGDMGHVPEGGPVEAGSIVFADARLRGEWVAAMDSAVAQDFTFTEGVSLMVQC +RDQAEIDRLWEALSAVPEAEQCGWLKDRWGVSWQIVPEDMGELMERPGAFEALLGMKKLV +IADF---- +>GCF_020097155_PROKKA_00477 +------------------------------------------------------------ +------------------------------------------------------------ +--------------------MSDAAAGAPQLISPFLWF----HDGAEEALRYYVDVFPDS +EIEEIQRYPDESLDPHYAGM-AGKVISAWVRLGGVRFGALDGGPA--FTLSEAVSFVVAC +RDQEEIDRYWAALSHVPEAEQCGWCKDRFGVSWQIIPADMGRLLQSPAQIQAMMAMRKIE +VAALEALA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002254.fa new file mode 100644 index 0000000000000000000000000000000000000000..d3b62499ee10af43c9da246c1a612064b3a1a608 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002254.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_00350 +MAPRPTPIRSVLQVFALDCPDPPALAAFYAGLLGWRVVEDRPDDEWVNVLPPEHEPQTMK +LAFQLVPDHREPTWPEGDVPQQAHLDFHVPALAEAVPLAEAAGARRHPVQPAEDGSWVVF +TDPAGHLFCLCQA---- +>GCF_020097155_PROKKA_02481 +MDTQNAPV-ARLAMITLDAPDAAALGTFYQAVLGWPVAY---EGDGVVMLA---GPGGVN +LGIGTVEDYTAPRWPDTG-RKQYHLDLAAEDVAAAAARCVALGATRPDHQPGE--TWTVL +LDPAGHPFCVTDAANWG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002256.fa new file mode 100644 index 0000000000000000000000000000000000000000..73facf3bbccfb9c7c413a16c3c92236fd8120184 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002256.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_00394 +MWVHHLDVSYRAVKSRPASARALRDTILIEELKRIHAENYGVYGVRKMHHAMRRAGWEIG +RDQVARLMKLASVEGVRRGRK-------PIITRPAGEPDARPDLVERCFTAERPNQLWGL +P +>GCF_020097155_PROKKA_00663 +-------MSYRAAKTRPASTRALRDEILIKEIRRVHAENYCVYGVRKMHHAMRRAGWEIG +RDQVRRPGGSGRIHCPRRSLRRACLFRFPQIAIEHHWP-----------VRERE------ +- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002257.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d71fbc7e534d5ab943639e389adcaa8b478d828 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002257.fa @@ -0,0 +1,4 @@ +>GCF_005280335_PROKKA_00395 +MIAFIDEHRDQFGVEAICRTLRATECGFITST +>GCF_020097155_PROKKA_00664 +MIAFIDEHRERFGVEAICRVLSATECGFITST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002261.fa new file mode 100644 index 0000000000000000000000000000000000000000..72a26e458de84bcf7fe43094b5d8eb29e1187f14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002261.fa @@ -0,0 +1,12 @@ +>GCF_005280335_PROKKA_00484 +MVTHTDLMTIGEFSSLSRLSVRMLRHYDAHGVLVPEHVDAHSGYRRYAPAQLRDAADIRN +LRDVGLGVSAITALLAARGTSTWTDALALQRCT-LVEELHAARERLSLIDRML-----TP +GEIPMTIQLNRTAVPAMTVVALRGTVPSYSDEGRLWERLMPALQQQGIRPVGPCGVIEHD +DEYREADVDLSVYCPVAPGTRAEGPLVVLQLPERDCLVAHVIGPYTQISQAHDLIVQRME +AEGLAARQDGTLASNVFNRYLVTPDQAAPEDLVTEVCRPLA +>GCF_005280335_PROKKA_02684 +M------------------SRRMLRHWEQEGLLSPALVDPVTGYRRFQATQLGRIRAIAE +LRDLGFSLSEIRQLLDPQIAHSSLERILMQQADRLRDQITEASARLAQVQHRVDTIQKKA +QEISMNLSL--TPLPELSLQGASTTVLDETDIGSAVARL------RDLVPHDQGDLILLF +DGTSPDQITVTAATADGATTPGLQPVSAPLAPQGATVTFPT--PPSSVADAWVLIDAELE +KRG--------LASGGVYRQIISPDGSTT---LQAAVHARD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002262.fa new file mode 100644 index 0000000000000000000000000000000000000000..f20149b4e2999aeaa602512c0f431a416e761e04 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002262.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_00491 +MDEDQGKILATHRQELRRGTLVVACL-------LACRTPRYGYALLEHLAD---ARLDAE +ANTLYPLLRRLEGQGLLQAEWNTDEPRP-RKYYRTTPEGEAIVAELRGDWLRLTDSMTRL +GKDPS--------- +>GCF_005280335_PROKKA_00765 +MNEPTDRPPSGTAPEAWPSAWVRAALEPAILGSLA-GGPLHGYGIAHALADHGFGRL--R +GGSLYPVLGRLEEAGHITARWAPGDAGPGRKDYELTDAGRAAYRDAVANWRRLGDALADL +GATPRLTAQEGTAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002271.fa new file mode 100644 index 0000000000000000000000000000000000000000..91a6430170eb01883ac15debdee554c804ebff13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002271.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_00558 +MSETIERAYPHAPTADDAPLDTAALAVCTTVLQQGAADLRRRFGPVLGEAVVDRQIEDSL +EELRRSGVPRTHRESTAIHFAESRLLALAETTGVVEPSVPRVLFVCLQNAGRSQLAAALL +AERAGDAVRVSSAGSRPTPEVHDDVAPVLSEIGADPAAAYPKPVTPELLAAADYVISLGC +SDECRERTGVEVRDWPVGDPAEADWERLQEIVADIERRVDALWAEIQGRFAA +>GCF_020097155_PROKKA_00485 +MAEAHPAVAGTGPSPSTGPLPRIGEHV--GILAHGAAELRRVFGPALGEETVDRIVEESA +AGLSPAAADPAHRESIAVRFAHDRLASLADARGVTRSGVPHVLFVCVQNAGRSQLAAALL +AERAGDAVRVSSAGSQPAGRIHGNVQPVLTAHGADPARIFPKPITEEVLASADYVITMGC +GDDCPVRLGQDARDWPVGDPAEVDWDRLQEIVADIEVRVDALWREISG---A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002277.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9b6089dc79e2cca56a9416a2ad8731d8f30419c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002277.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_00644 +MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYARE +PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQVFR +AQVTLRPRSEGRGCEADLDWWESRLGALPAQMREWARS +>GCF_020097155_PROKKA_02224 +MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYAQE +PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQEFR +AQVTLRPRSQGRGCQADLDWWESRLGALPAQMREWARS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002281.fa new file mode 100644 index 0000000000000000000000000000000000000000..f22ff225adc223cc6494c0c72e9b8303498c4809 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002281.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_00713 +MTQRRTRWRSAASQDAEYRAHWKA-AASADVGTPDALTWAVLGDSAAVGVGAARVEESYV +AQVAAGVAERTGRPVRVLNLAVSGATAAHVLADQLPLLPADGVDAVTCVVGGNDVAWPVR +FRVDRFAAPLEKIAQRLPAGATLGTVPVFRIPPYESRVECANAAVRVIAARHGLGVADVH +AATRRTSLRHQVSMLSHDLFHPNGAGYRDWARAVLPEVLRQVRGEAPTR +>GCF_023573625_PROKKA_02032 +MPS-PSGWQ--AQHDADYRAHWHALAARAD---PDALTWVVLGDSAAVGIGAESVERTYV +AQVAERVAAETGRPVRVVNLAVSGAMAKDVLADQLPLMPASGVDAVTCVVGGNDVTWAWR +FREAAFEEPLEAIARALPAGATLGLVPTFRIPPFEARVRRANTVVRRVAARHGLGVADVH +AATWRRNLRHQVSRLARDLFHPNGAGYEDWAAAVAPEVLRQVRGQAPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002285.fa new file mode 100644 index 0000000000000000000000000000000000000000..f05546a2a009684873e7e89f06bbabab46863858 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002285.fa @@ -0,0 +1,14 @@ +>GCF_005280335_PROKKA_00773 +M--------AGGEAAVAWILGALRRELGAANLGEEDLEIVVERDRVWGSLWTVTAQGRRF +WFKRPHACLRREVPLRRVLSARAPGELLSTVAACAETGWQLTADQGPVLAQRARED-GPS +HYVELARSLARVQKSLTAADVA----ELRNIGLPVFETGDAVARLDEQLGWFSGLPAGHP +AQCTAAERERAIEGMSVLVERWAVDARMLEGVVPELSVDHNDLHGGNAFVTAEG-VRLSD +WGDTVLAHPFASLRALLVPVRNVFETEAMEQIRGAYLAEWGLGEDVG-DVLDLAMMLAVP +QRLSCWSALADADAWAEYAEYIAPLWREIGTPVAEVEVP +>GCF_020097155_PROKKA_02404 +MTGTGVLDVAGRTAARDWIAGVL-------DLPAAALTVRVVRERSWGDVWRLSSPAGVH +WFKAPHPRLRGEVPLRALLESRAAERVLPLVAADHERGWQLTADAGRTLAALARDDAGAP +RPGEVARLYAGLAGALAAMQEAVGEDDLRGRGLTEFDPAKAELSLLRELAPFRALPAAHP +AHCTAEEEARAVAVRAALAMRW----EDCGGPADPLGLDHNDLHGGNAFLGADGRVLVSD +VGDAVLGHPGASLRALLVPVRAEHGADAAETVRTAWLAARGQDHAAGRERLELAMLLAVP +QRLRAWGALRSPETWAAYAEWITALWRDIGTPVDQLTTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002287.fa new file mode 100644 index 0000000000000000000000000000000000000000..7cedb9afcc677465b66a5d572ab017b33053b5f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002287.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_00852 +MALFRKTAAWGATAAGAVALAAAAMAATWTGPGYTVVNDHSNIFDYKGSIKTTSCVRQSD +GTHLIGGYIRYVQGGRDTGRLWTPTATSCGQTVSRSTTFKDSLALNAPKTQFYYGLNKAP +YGALSEPLGGN +>GCF_020097155_PROKKA_00789 +MG---------------------------------------------------------- +-------------------------DSRCGQTVSCSTTFGDSLGLNAPRTYFNFDLNDVP +YGALSEPVDGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002289.fa new file mode 100644 index 0000000000000000000000000000000000000000..38face0e29e9b6bd52f2e2918507ef08a726cfe6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002289.fa @@ -0,0 +1,14 @@ +>GCF_005280335_PROKKA_00883 +MPDSPAPPGAAPSELVPRAFAERIARRPADPLLAA---AGGEAVSGEAWLARLPHLVEER +LAAWNLTLDPDAPGAPWTGHGALVLPVRRHTLRPAVLKLTWPHLEARHEHLALRLWDGAG +AVRLHAASPPDGALLLERLDADWPLTLEPVLDACVAVGGLLRALDRPATPQFDAVAVKAE +RWDGTLAAPVAAVPRRLQVQARSHLRRLVDSAPEPRLVHEDLHDGNVLAPLPDDGPSGAA +PDARRGHVARRGRWLAIDPKPVAGEGAYAVAPIVWNRPEVTAAAHNARIHVRLRADVVAE +AAGLDEERVRAWTFVRLVLNAVDAAHEGPSADEWRARMIALAGHFAS +>GCF_020097155_PROKKA_00825 +MPASP-PEILVP---IPPEFAADIADRPADPLLAAAPDAAAQPLSGEQWLARLPRILAGR +LTAWDLTLDPDVPGAPWAGTSALVVPVRLPTRRPAVLKVTWPHLEARHEHLALRLWDGAG +AVRLHAADPRDGALLLERLDAGRPLSAEPILDACEVVGGLLRTLARSATPQFDAVADRGA +RWLDTLAAPVAQVPRRLQVQARSHLRDLLDSAPPPRLLHEDLHDGNVL----------AA +PSPADGGEAARGPWLAIDPKLVAGEPAYAVAPIVWSRPEATARAHHARVHVRMRADVVAE +AAGLDGERVRAWTFVRLVLRAVDAAGRGEAGDEVRARMITLAGHFAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002291.fa new file mode 100644 index 0000000000000000000000000000000000000000..51ea4bb3a13b2696348e49971f0c9443b18242fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002291.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_00908 +MSTRSSI----PDAVDTDRTAGTIELLEPPREAVEWMASPAPATDLWWTATVCGEADPDW +HRLET------------------------------------------------------- +-------------------------TVAETIEVLVSWAQGHGLPLPYGAALRTYGNPPDL +GL--VA +>GCF_023573625_PROKKA_01870 +MSAPGSITADGARGLATHRAPGAVELVEPPREAVEWMASSAPATDLWWTATVCGEEDPGW +HRLESAAQIADLVHALTDPRDKLILEDEPPTRYAQIMLLGDGLFMVEIAKRFEGLGAYNW +RIGRGRAADEAANDPQDLVQPLQELTAAETVEVLVSWAQGHGLPLPYGAALRTYGTPPDP +GLGFDS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002295.fa new file mode 100644 index 0000000000000000000000000000000000000000..844856f29b2ccd092e2ed2e31f44fbfec2643960 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002295.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_00944 +M------------SEPERTRPETTPDGHHIVVDGRKWRAQDPHIPEALAGELVKGLMAAR +RLVRTDPTTARPRVQDAKVALGERGDPWWEPTPEGTRERLAAAMRTLLRQRDEGKTICPS +DAARVAGGEAWRDLMDEARAVAAELHAAGAVEVRQRGERVDSAAARGPIRLAAGPQL-G +>GCF_020097155_PROKKA_01225 +MTGEPITPSDPEHSGPERTGPEHTPDGHFIIVDGRRWRATDPDIPEALRAELVKELMAAR +RLVKSRGDAARVRVQDAKVALGERGDPWWEPTEQGRRDRLAAAMRTLLRQRGEDRTICPS +DAARVVGGEDWRDLMPVAREVAGTLAEEGVVVVTRKGAAVDVATARGPVRIAAGPALET diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002297.fa new file mode 100644 index 0000000000000000000000000000000000000000..004a1e113083668d80637f9e9fc6bc95167551b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002297.fa @@ -0,0 +1,22 @@ +>GCF_005280335_PROKKA_00960 +MAQNTAGEGLLESIRQGYSFEDATVTLGAAVVDGQVHADAPVRLPLRMMNRHGLVAGATG +TGKTKTLQMMAEQLSSAGVPVFLADVKGDLSGLAVAGEASEKLAERTTATGMPWQSQAYP +VEFLALGGDGVGVPVRATVDAFGPVLLSRIMELNETQESSLQLMFHWADQRGLAMDDLAD +LKAVVTHLTSDEGKADLKGLGGVATSTANVILREVTGLEAAGMAAFFGVPEFETAELLRV +APDGRGVISCLELPTLAAKPQLFSTFMVWLLADLFAELPEAGDLDQPKLVFFLDEAHLLF +DGASKAFLDAITTTVRLIRSKGVGLFFVTQTPQDLPAEVLGQLANRVQHALRAFTPQDAK +ALKQTVQTFPTTEYDLAETLTSAKVGEAVVTVMDPEGAPTPVALTRMWSPQSAMEPAPEE +AMRQIVGASALLPVYGTAQDRESASEVLSAQAAA-----AAPSTGGSARGSAAGAGDTRV +ADGHGGGTVVSGVDLGDIEALRREEEKATARARKEADKPSDFERAMGNFMKSAGTQLGRE +VVRSVLGTRGRRGGGLLGGLFRR +>GCF_020097155_PROKKA_00900 +MAENTA---LLDTLRAGYTFDDPTITLGAAVVDGEVHADVPVRLPLRMMNRHGLVAGATG +TGKTKTLQMMAEQLSAAGVPVFLADVKGDLSGLATAGTASDTLTERTRATGMPWQAQAYP +VEFYALGGDGVGVPVRATVDSFGPVLLSRIMELNETQESCLQLMFHWADQRDLPLDDLKD +LKAVVVHLTSDEGKADLKGLGGVSTATANVILRKVTGLEASGMDQFFGVPEFETAELLRV +APDGRGVVSCLELPTLQSKPELFSTFMIWLLADLFAELPEAGDLDKPKLVFFLDEAHLLF +DGASRAFLEAITTTVRLIRSKGVGLFFITQTPKDVPGDVLAQLANRVQHALRAFTPEDAK +ALKATVQTFPKTDYDLEEVLTGAKVGEAVVTVMDPDGAPTPVALTRMWSPQSTMGPTPED +AMKAAVAASPLMGQYGTAQERESAAEKLAAQAAAPQGETAVPATGESAR----------- +---DGGNVTVSGVDLGNIEEIRREEDARARRAQEKADKPSDFEKAMGNFMKSAGTQIGRE +VVRSVFGTRRRSGGGLLGGLF-G diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002299.fa new file mode 100644 index 0000000000000000000000000000000000000000..2059a23acf8b88ad23d382d29c534034d0448083 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002299.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_01005 +MDPVSTPTDPHRHPAPDARVRV------QAGDAVVADGPLWARAALFAVPAVWLGLLIGI +SLIEAPLKFTAPGITIPLGLGIGRRVFFAMNLVEVVLAVVLLVALARVLGRPRGLTVPGP +GRLWLGGLTAAGLLAVKAVAIRPFLNRRTDRVLAGVDDGGSSWHYLYIAVDGLLILTVVA +LIVAVARHLLVRTTAA- +>GCF_020097155_PROKKA_00949 +---MSVP--PHPTPAPDAPRPLPGAAPREAGNAVVVGGPRGARALLLAVPGVWLGLLVGI +SLIEAPLKFTAPGITIPLGLGIGRRVFFAMNLVEAVLAVVLLVALAKSLGRPRELTAPGP +GRLWLGGLTAAGLLAVKAVFIRPFLNRRTDMVLAGVDDGGSLWHYAYVAVDGLLILTVIA +LIVLAARHLLPASPGAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002300.fa new file mode 100644 index 0000000000000000000000000000000000000000..06e65dba8d4d5607f97e6ee317224df4cb8877d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002300.fa @@ -0,0 +1,16 @@ +>GCF_005280335_PROKKA_01011 +MTDAGPQGPAVPVRTRRVAHPGRVTAVVLVVAALVAAAFLAGRFFQPPSTAADNEAAATP +IDVWAHAEERVIDDGSSYVATVAAGRTRTVTVAADGPAVVLRQAAEVGEMVRPGDAAGEV +SGVAYVFLPEPLALYRDLTEGDRGEDVASLQRALRQTGRWTATDGVFGDSTARALRETFR +GAGSPLPEDEPVTVGWRQFIPVSDDGAVVTAAATYGATL------TEDRPLLELQVSAPT +IRFTADVTQATALEKGQEVEVSGAFGSLHGTIAKIGEFAAAEGSERAGHPVTVAFDATAE +DAPPVGQSVTVSTTAAEDVPAMLTVPQTAVRVEGASSYVVVQVPASAREGSASSAPAERR +VPVTVERTGGGYAAVSGDLAPGDRVKVS +>GCF_020097155_PROKKA_00954 +----------------------------MLVLALLAASFVAGRFFQPPTT-ADPAAVARP +IDVWAAVEQRAVDTTASFAGTVAAGKTRSVAVQAEGPAVVLRQTAKPGESVRPGDVAGEV +SGVTYVFLAEPLALYRDLTEGDEGEDVASLQRALQKAGHATDTDGVLDSGTARALRELFA +EAGDPLPEDAPVTVSWHQFIPLGKDGAQVTAAAGVVSALYPAWVASRQRPADALR----- +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------G diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002303.fa new file mode 100644 index 0000000000000000000000000000000000000000..8aa9420c9f07c50b082305ede6af54180f162b54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002303.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_01039 +MTKIAIITGSTRPNRLNRQVADWVLERANGR---GDAAEYELVDIADFDLPLLDEPMPAA +WQQYAN--EHTKAWSAKIAEFDGFVFVTPEYNHSLAPALANALSYLNAEWANKAAGIVGY +GSAMGVRATEHLRAILSELQVAHVQKHGMFSLFTDFKDFAEFQPTELQAASVDPMFDQLL +SWTEAMKTVRQG +>GCF_005280335_PROKKA_01321 +M-RLGIVIGSVREGRFGAQVGAWVEEVARGLDTGGRDAEWDVLDVAAFDLPIMTD---EG +WAQDEDGPAEVHRWRDAVAACDGFVFISPEYNRNIPGAFKNAFDLLSAQWKDKALALVAY +GGLGGVRATEAWRFTVAAYNMHVVGDSVQLVRRADFPD-ETFARTEHHDKTLSRVLTRLV +DLTEATAALR-G diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002305.fa new file mode 100644 index 0000000000000000000000000000000000000000..e49c7fcf5d49029ae0788d753debb09eaaa26edf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002305.fa @@ -0,0 +1,20 @@ +>GCF_005280335_PROKKA_01212 +M------------------------------VLGFG----------------------GS +TVLILVVGLVYATAIRALPRTGGGVLFAVLSAGRIPGFIAGWSLALGYIGIIAMNASAVS +LIFRVTFPGLLSHGKLLEVAGWEVYLAEVLVSILFIWVFALLNMKGVEFSGRFQFWAVVT +MLTCIAVLGVSAVYAFLTKNIELPAAVPSGQSPLTSVVVILAIAPWALSSKVPLVRAWAA +ILRSPDLMDNPP------------------------------------------------ +-------------------------LHGAG------------------------------ +-------VGPP---AGCRG--------------------------------RRTRMGGG- +------------------LHLSDSTGSIR----------------------RCATPG--- +---------RR +>GCF_005280335_PROKKA_01871 +MSHVTSSPPATGPGLKKTLSSLDAYAMGFGAMIGFGWVVLVGGWLKDAGTLGSIIAIVSG +GLIMTVVALVYAELVAAIPKAGGEHHYLLRGMGARWSFLGSWGITGGYISIVAFEAVALP +RTAAYIWPEIESI-PLWNAFGSDVYLVWALVGAGAAVVITWINYIGVKLAGIVQTIVVAT +LLVIGALLVFGAGTGGSVANFEPLFTDARG------LFTVMIVVPF-------LFVGFDV +IPQSAEELNMPPRRMGVMIIVSVAAATLWYIMVILTNASSMPREQLVNADLVTADAMAAL +FHSPAMANVLLVGGMAGILTSWIALLMGAARLLYAMGVSGMLPRWFGHIHPKYRTPSNAV +LFIGVLSIAAPFFGAGALGWFVDSGSPSIVFTYMMVCIVFLLLRRREPEMDRPFRAGGAT +AGRVLGVTGVILTAGLLSLYIPGMPASIAPMAYAFFGLWWLLGLVFLFRIPRGITPGEDA +EERLLERLARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002307.fa new file mode 100644 index 0000000000000000000000000000000000000000..25db883fe010e91de4e06b4e5efdb41898cefb39 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002307.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_01272 +MVKKLEQNMGADAMRAATGRDHAGWRAVLQDAGAQQWS-HPRIAAYLVE--------EHG +VDGWWAQGITVDYEQAHQGRLPGQQADGTFSVGLTRTVPGERLEALARVEAAV------- +SAVHGEPHGRNLTASQPVVR--WR--LPDGGRLAAAAQA-PNKTGTPVNLTMQRLPDAAA +VEPTRRALEELLEAA------RSGEGPVATPGR +>GCF_020097155_PROKKA_02055 +MSTSPARGANLNAIAEATGLTFEDWAAWLDARGARDLTVHAEIVGLVLERMRSGETAEVG +SPEWWAQGVTVAYEQHIGRRRPGQRADGTFAVTASRILEGTREEVHARAVGAVRAALSDG +GALRGVGLAKEPTESATATRLFWRAVLADGTRAELATEPRPQTAGKPAK---------AA +VVATHSRAASAEEAAAWKAFWRN--LPAAL--- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002310.fa new file mode 100644 index 0000000000000000000000000000000000000000..de88a3361b1eebc2ed96fcf4e20c3e9ec537a307 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002310.fa @@ -0,0 +1,12 @@ +>GCF_005280335_PROKKA_01311 +MTVQKFPVFPAGTLEHVCKLIAELYTGNELTRIMSEIPLRDDLGEGNTKWRRLACAVSKN +QAHTQSGNAVIALVSASMRPERTLDRADAARLTRDQLNQVLSLVGYRVRD--DGRVARA- +------SRARSTDEAEKRTEHLRGLLERGGAHREVLTYCRPELLRKDYYEAVFEAIKGLG +SRLRQLTGVDGDGYALVEDAMAGSTPRIRLNALQTRTQRDEQRGVANLTKGLFSAFRNPA +AHEPRIEWTLSEQDALDVLGTLSMIHRRLDMA-----------TVEAL +>GCF_005280335_PROKKA_02210 +M--QRAGLTPVTIIKN-----------------------------------RGSANEERI +EVQAQLQNSSLAMFAI----EDPLFEGDHVEMPDPRGGQMVKVVRKLVQHPMPANMARAF +GGSNGYAEVTWGESAAVRQAPVR-RLELEGLHPEVVRVSSALFADEQFDSAVTEAMKSLE +IRVRRLAASTLSGAPLMQEAFRPKEPKLDVAVEEGRSGEDEREGFFHLFRGAMVGIRNPK +AHE--LAHGDNPFEALEALALASMLHRRLDIAAGRLECADDSVTVLDQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002311.fa new file mode 100644 index 0000000000000000000000000000000000000000..84eab6d55b8a2c62acef1de9ceb69fe2cd85e2f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002311.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_01319 +M----DNVGIAVRDLEEAVAFFEDLGLTVLGRDEVSGEFAETAVGLEGNHAKIALLATPD +GHGKVELMQYLNPEPVEAEPTRPNEIGMHRIAFAVDDLDAALAAAVRHGCRPLRGVARYE +DAFLLTYVRGPSGILVMLAQELKAGE +>GCF_020097155_PROKKA_01227 +MGIRFENVGIAVEDLEEAVDFFQGLGLVVVGRDEVQGEWADTAVGLDGNHARIALLTAPD +GGPGVELFEYLHPEALPTPDTLPHMIGMHRVAFRVDDLDAALAACDRRGYAPLRGVADYE +GVFRLTYVRGPSGIVVMLAQATGEG- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002317.fa new file mode 100644 index 0000000000000000000000000000000000000000..b109f203d8dd46c3150ae503f49ac7e491979e0b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002317.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_02013 +-----MTTPAPTSRSDWAEYNAAQAGRGRIRPLTARAVDAL-AADADLGARHAVELGCGA +GVEARHLLALGLTVSTIDADPSIAPAMAALAAGGALDHRTGRIEDWDPLPAADLVLANAA +LPFVPRHAFDAVWSRIRAALAPGGVLAVDLFGAEDDWSSNAGTYLTRPEVEDLVRGLEVV +ELTERSERGPAFSGPKHWHVFTVIARARRRPSDRSPV +>GCF_020097155_PROKKA_01290 +MGDTALMIATPTSSSDWNSYNAARAGTSAVRPLTERALTALRATHQNLSGLRAVELGSGA +GIEARRLLQEGLTVHTIDVDASVEERMHELTSLGVLEHRTGLIEEWDPLPLADLILANAS +LPFIPRAHFAPVWERLRQALLPGGILAVDLFGCEDTWASDQGTYLTLQEVERLLDALEVI +ELNERNEEGRSFDGIKHWHTFTVIAR--------RTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002319.fa new file mode 100644 index 0000000000000000000000000000000000000000..06c83bce6c5775649e52e7432645b6e8381f062a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002319.fa @@ -0,0 +1,16 @@ +>GCF_005280335_PROKKA_02277 +MADAVQ----------VC------------------------------------------ +------------------------------------------------------------ +AFNST-------------------------YTASQGPAVPCSSSAR---------EREDA +LLDALD--VDP----PGSWWSRAAELARPRTVVAGDPPREDWLAVPLRRDGPLATTGDLG +RAAAVGLVIREDGPLWDEDLVRTLTPPPICPKVLEVRTPADWLRLVEAWPEAASKATAEI +LARHTGLDGRWLVPRWTAVAEQWDAVHLSIGAWARSAGVVQPVGEGSAWTMCAGWDPDAT +FWLTAQPTVASEQVLPTLTPAEALDGLA------------------------G +>GCF_020097155_PROKKA_01291 +MKASVQDLLPGPRGRRLCLEAARMLSHRVADLVFWLGYELDPDRGISSLVMWPPGGGALE +AGARPAVSIDQVAQALADLDLSGLTDGVVQAALVGSVMSARYWQEPDGEDVLAGHPDIHA +ALEAVAAGVLGSAAARHWGSPRAAAQWVIDWRAFEDPA-PVPRDARRVLAAWAREERRQE +VRAAAEHPVDPTANFSGTWWS----IPQGAVVSVGQIP-----------TGLDLVEDDIG +AEAATVIPVRGAG------------------RTYEVRGPGDWIRLCRRFPLEVSASRRHD +WYRVTGRSGRWVIPDWEQVASEWDAVHLTTLGYLSAATRALPVEAGVA-TVLAGWDPDTT +VWL-ADAVRESEEPRQCWQRVSGDDGWARCVPVRDVGSEGPARGRGASPPVEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002326.fa new file mode 100644 index 0000000000000000000000000000000000000000..342b072a08d491cd67ca4a95ffc03a8f7dc177fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002326.fa @@ -0,0 +1,14 @@ +>GCF_005280335_PROKKA_02652 +MATLAEQVQGERMARVALSMIAEPNDPITGYVLARHGGVETLRLIESDDEVPGLARADTL +MWRERLTARVTPGLLDQMAQA-ERHGFGTLIPADKEWPAGLNDLSDRAPYLLWTRGAVSF +LMTALSDRATITGARAATAYGEQVAGELAAGLADEERVVVSGGAYGIEGAAHKSVLAASG +QTIAVLAGGLDRPYPAGHSELLNRIGDVGLLVSELPPGAAPTRHRFLARNRLLAALSGAT +VIPEAGPRSGSMTTVIAARELSRGVGAVPGPVTSVASAGPNELIKQGFASLVTQPSDVID +LLDADRTPDRTVTRPEVGREFG-HRHPSPGTPGRSL +>GCF_020097155_PROKKA_01771 +MSGVAGLGVDERRARVVLALLAEPDDPVTGGLLRRLGAVETLGLLDTDTTVPGLGRVDGQ +VWRDRLTSQGRLDGLDQRLRVLEESGIVILIPGDAQWPRALDDLGERAPYVLFVRGAASF +LARPMQDLVTVTGSRAASAYGEYVAAELAGDLANRERVLVAGGAYGVESAVHRAALAAGG +DTIAVLAGGVDRPYPSGNRDLLDRVGDVGALVSELPPGSVPTRHRFLARSRLLGAMSAAT +VVVEAGARSGAIGVAAEAHQLGRQVGAVPGPVTSVTSHGPHELLRAGHARLVTSAADVEE +L-----TANRATHRPGLSADFTRHTAPAAGPPERSL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002328.fa new file mode 100644 index 0000000000000000000000000000000000000000..03d114ce3919bcaa7fa3acd78bba05278d9385b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002328.fa @@ -0,0 +1,16 @@ +>GCF_005280335_PROKKA_02675 +MSNTERDPKEQVCENGPGAAPTGQEESLREARFTDGLSAGVAEAAGDAGAVVEILEPREV +PLGGPRAMPVQRTLPQRARSLIGAWCFLDFYGPDDVSATGGMDVPRHPHTGLATVSWLFE +GRIDHADSAGNWATVRPGEVNLMNAGTGITHTEYSTDDTSGLHGAQLWYALPDAHRFSAP +ALHSHRPEPVAGEGWTARVFLGDLLGESSPVPTYIPLTGAELRLEPGATARIAVPQDHEH +GLLTVSGAVTLQGADVPAAHLGYVGTGTAELTVTAGEEPVIALLIGGEPLGEQIIMWWNF +VGRSHEEVVRWRSAYQQEMGFEAPEDGSPLASAAARALRGGDGALGSPVQGALLDALVGT +AYDDGRAFPQFGDFPPDPKPPIPAPPLPNTRMRLRG +>GCF_020097155_PROKKA_02487 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +-----------------------------------------------------MDALRGA +AYDDGRAFPQFGDFPPDPKPPIRAPPLPHTRMRPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002330.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ff7f519a9b81010b56f97cc954d17b19740cc22 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002330.fa @@ -0,0 +1,12 @@ +>GCF_020097155_PROKKA_00051 +MAAVPDSLKLEGARFVGRSLRGARFIDSDLSHVRARGVMLDGADFDSPWLLDGEGSLVVN +GVDVAPLVEVELNRRFPGRAQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSV +EGEWSFSQTLRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYE +QVLAVRSERLAQVREFLASVDDAGLDEERRHPWSPEYPETVRSCLHVILEEEWEHLRYAL +RDLDALDDAAAQGR +>GCF_020097155_PROKKA_01208 +MPAL-------SAGACG------------------------------------------- +-------------------TQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSV +EGEWSFSQTLRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYE +QVLAVRSERLAQVREFLESVDDAA------------------------------------ +----------AQGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002331.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff72e4e6e5e6ae1f7dd3425a5009c97f41ed620a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002331.fa @@ -0,0 +1,12 @@ +>GCF_020097155_PROKKA_00053 +MRLIALPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEE +VAGEALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHSQGRYPLED +TVSAFHQLVEDGKIRYWGVSNFDHRDLADLQDVPGSSGLATDQVLYNLSRRGPEYDLLPW +CADHQLPVMAYSPIEQGRILHDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQ +HVRDNATALDVELTRDDLDALDRAFPPPSGPRPLEML +>GCF_023573625_PROKKA_01995 +---MTLPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEE +VVGEALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHWQGRYPLQD +TVAAFHQLVEDGKIRYWGVSNFDHRALAELQDVPGSSGLATDQVLYNLSRRGPEYDLLPW +CTDHQLPVMAYSPIEQGRILDDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQ +HVRDNATALDVQLTREDLDALDRAFPPPSGP--VKSF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002332.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e0b4ab91d41c95a16d6b11e5a2ec9c7921a5718 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002332.fa @@ -0,0 +1,18 @@ +>GCF_020097155_PROKKA_00147 +MSTLRTHRRRAALGSFIGTTIEWYDFYLYGLAAALVFNVQFFPGQTAFGATLASFATLAV +GVVLRPLGGIVAGHFGDRVGRKALLVISLLLMGGASMLIGVLPTFAQAGWWAVAGLVLLR +CLQGVSAGMEWGGAALMSVEHAPAGRRGLFGSFTQVGSSAGMLLATGAFSLVKLVTTDEQ +FAAFGWRLPFLASGLLVVVGLAIRLGVEDSAEFRVHRDVGTVSRAPVVELLRHHARPVLV +TAGLRLGQNGLYYLVTAYLVSYLVLRGADDGVLVSAIMVASAIGLLSTPFWGAVSDRVGR +ARVSRVGYALTAVAGWVLFAVVDAGALAVLPLVVVLVINVAHDSVYGPQAAWFSEQFPVR +VRYSGVNLGYQLGTVVGGGFAPFIAALLYEAGGHTPWLIAAYLTLLATLSLIATRFARDP +VARPETDLVADDAAILAPQADGP-------AAVVPA--DRAPVTLETR +>GCF_023573625_PROKKA_00200 +MSTLRTHRRRAVLGSFIGTTIEWYDFYLYGLAAALVFNVQFFPGQTAFGATLASFATLAV +GVVLRPLGGIVAGHFGDRVGRKALLVISLLLMGGASMLIGVLPTFAQAGWWAVAGLVLLR +CLQGLSAGMEWGGAALMSVEHAPADRRGLFGSFTQVGSSAGMLLATGAFSLVKLATTDEQ +FAAFGWRLPFLASGLLVVVGLAIRLGVEDSAEFRVHRDAGTVSRAPVVELLRHHARPVLV +TAGLRLGQNGLYYLVTAYLVSYLVLRGADDGVLVSAIMVASAIGLVSTPFWGAVSDRVGR +ARVSRVGYALTAVAGWVLFAVVDAGALAVLPLVVVLVINVAHDSVYGPQAAWFAEQFPVR +VRYSGVNLGYQLGTVVGGGFAPFIAALLYEVGGHTPWLIAAYLTLLATLSLIASRFARDP +VARPETDLVADDAAILAAQADGPAVDAAPGAAAVTARPDRAPVTLETR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002334.fa new file mode 100644 index 0000000000000000000000000000000000000000..e31f93cfa849e58cc2f9a8a5827073078ec90c14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002334.fa @@ -0,0 +1,18 @@ +>GCF_020097155_PROKKA_00307 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------MRQDAGAQTVGNVVSTIAVSAGTGALA +GSVLPGLGNVVGFAAGVVSGVAMAVPVADTDGDGQKDSVAEMAGDVAEGAWNWIRGK +>GCF_020097155_PROKKA_00335 +MTTSYVTKVGMSEWESADSMDQLAHGVTVAASSLAEVVSDQDATWQSLGNHYEGDGEGDL +VNGFFVPVENAARVVLAAEALDKAFLDFSNALRGLWADRRVFETEVDTYNSMYGAQAIET +LPPGVDSWRAALASMPADLERRYQQAASTCASAVRTIDIEALDLDSVSEGRPGQLGREIV +AEAAKNALPLDPENPSTSALGLLDVARVREPWLRFDDVIPETWQARFMGLNVGPLGASVY +AGGAAMVRAAQTRSWAPLRNVPLAMSMTMRNYSNDMAALALRYEDPRKFRRPTWPAFKSQ +FLDGLPVTGFIRSTVPLWGKRTPATVGAPAPAMAGAYRVESRGAFRLNAGVKGLGAAGTL +VGAGLTYRDEYDQQLRENQAETPGASREEVESEARQDAGAQTAGNVLSTIAVSAGTGALA +GSVLPGPGNVVGFAAGVVSGVAMAVPVKDTDGDGQKDSVAEVAGDLAEGAWNWIRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002335.fa new file mode 100644 index 0000000000000000000000000000000000000000..7b75e79789984de6d6622735cdf1daba6c83e370 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002335.fa @@ -0,0 +1,6 @@ +>GCF_020097155_PROKKA_00323 +MTQTPTPHLAGPSPVKVGLLVLAICAVGGVIIGAVAGLTDGGSVENMFIGAVYAGFIGFF +LPGLPAALIAGLVAAARGRRRG +>GCF_020097155_PROKKA_00343 +MDQD------------------------------VATEAEQTVSED---GAVYAGVIGLF +---LPAALIAALVAAARGRRRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002336.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed0878834219a23e8d42227d9c2ac395f166796b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002336.fa @@ -0,0 +1,8 @@ +>GCF_020097155_PROKKA_00324 +MPEYDFETYPTTPDAMAKYLQEREAAGNPMTGEEALAYSDWSRERGRAIQAKIDARKTPE +ER---EEFRRFAEEFERQCLEDEKRFAEEAAREAAEDAERAAQGKRPIKRERDIVTPKGF +SGIGVTPRGW +>GCF_020097155_PROKKA_00344 +MTKYNFEAYPTEPESMAKYLHEREAAGKPITRAEGEAYIEWSLAKEQEITERKE-RMSPA +ERAGHEGFQREEEPMGAIFDLEDARSEVEALVEAAEDAERAAAGKRPLKRERDIVTPEGF +SGMGVTPRGW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002339.fa new file mode 100644 index 0000000000000000000000000000000000000000..52f21730bb6e2c2d04b01db551516802c6827352 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002339.fa @@ -0,0 +1,12 @@ +>GCF_020097155_PROKKA_00345 +M-ETFWGLTTPAWTAIYTLLTAGLLVAAIVAGLYAKRQWETARDAQVEATRPYVLVTLEP +GERSMAMVDFVIRNIGVRPAYNVTISIEPHLLRAREEGGNEMAAMRLLHEPTAMIPPGQV +TRMFYDRMSDR--SGRDDLPVHHTAVVSYVDSS------GREWTDTFDLDLRVLEGGMFH +SYDDLHTVSQTL---KKMARTLDRSRVLKEGEMDVVAVTENRADH-QVRTLLEEYHRQVE +IANLHRGKPGYVDRVRSFDARAESIAEQLRALGVSVQGAPQD +>GCF_023573625_PROKKA_01145 +MDDTFWGMSATGWTAYYTLLTAGLLLVAIAAALYARNQVQIARAAQREATRPYIIVTAEP +SPIGWRVMDLVIRNIGQRPAYNVKVSLTPEPVRANETPGAPISEVQWLREPIPMLAPGQE +LRTFYDAMEERLNSGRSDLPTSHDYSVEYDEGTVAAKKGKRDHRDSGVVDLNAMAGAMQP +DVYNIHHVASALRDIKKEVAKMNRSGTYIQPASEVRDILDQRGPRTKPRSTV-------- +--------PGPLPAERS----------ALRRLYDRFTGR--- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002340.fa new file mode 100644 index 0000000000000000000000000000000000000000..70453a5154a7922f3917d76bb7f01dec9885329e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002340.fa @@ -0,0 +1,22 @@ +>GCF_020097155_PROKKA_00425 +M--------------------------------------------------------GK- +----------------VRGDQAVQS----------------LQPHKVL---------DSD +SSHGRLIRQQGERVPTDGDFTLSDRAQKEIVKLFIASESSLEGRTIGEWFSEDFFESNFW +TYWATMFAFETWHSLAEMRRYLLRFVHAIDGLADFSALKFNRYDQYDSMVKPLLAYLEPH +GVDFRYSTTVRDVRVETADGKVRAERLLLTVDGVQQEQEVGEDDLVSVTNGSITESTTYG +DHHTPAPSTTEPGGSWTLWENLAEQSPLFGRPGVFYRGLPERSWFVSATATVESREVEEH +IERLTQRPLHDGKVNTGGIVTATDSPWMLSFTVHRQPHFPTQRPDQTIVWIHALYSDTEG +AYVKKPVTECTGEEITQEWLYHLGVPEDRIPEPAAQESVNTVLVYMPFITSYFMPRRAGD +RPAVMPEGSMNLAFIGNFAESPTRDTVFTTEYSVRTAMEAVYTLFDVERGVPEVFASATD +LRELI------------------------------------------- +>GCF_020097155_PROKKA_01186 +MQYTAGNYEAFARPRPAQHAQETKAYIVGSGLAGLAAAVFLIRDAGVPGANVTILEKGEI +AGGALDGLDVPEKGFVIRGGRELENHMECLWDMMRSIPSLELEDASVLDEFYWLNKDDPN +YSLRRATVRRGEDAGHEGRFDLPKRAQKDLLKIFLAERAEMEGKRIDEVMGREFLDSPFW +MYWRTMFAFEEWHSALEFKLYLHRFIHHIGGLPDFTALKFTKYNQYESFVLPLMHYLTEH +GVVFRSGTEVLDVDFAHRNGEIRATAIRCRRDGAEETIELGEHDLALMTIGSLVDNSDEG +DHHTPAALNEGPAPAWDLWKRIAKKDPAFGRPEVFCSSIEETKW-ESATVTTLDERIPAY +IERIAQRDPFSGRVVTGGIVTAEDSSWLLSWTVNRQPHFKKQPKDQIVVWVYGLFVDVDG +DYVKKPLAQCTGEEITQEWLYHLGVPVEEIPELAAT-GARCVPVMMPYVTSFFMPRRAGD +RPQVVPEGAANFAFLGQFAET-GRDTIFTTEYSVRTGMEAVYELLDVERGVPETWGSTYD +VRDLLEASARMRDGKKVEMPGPAALRGYLRGKLEHGEIGQLLEEHGLI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002341.fa new file mode 100644 index 0000000000000000000000000000000000000000..a1a7d1b6588a7dfa0ed7e7a25c1587867ba60c6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002341.fa @@ -0,0 +1,4 @@ +>GCF_020097155_PROKKA_00620 +MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVISEPADQ +>GCF_023573625_PROKKA_01018 +MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIR-----------------M diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002342.fa new file mode 100644 index 0000000000000000000000000000000000000000..7966d5d132a366362e21e84a45744bc8321d63de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002342.fa @@ -0,0 +1,12 @@ +>GCF_020097155_PROKKA_00628 +MAINWRRAQYLLAEDLTDIPVRYIDELFGSNGIALGPENPQDVDTSVRRARMRRYLTTLD +LDTNRADQQRFADVMAERYRKIALVHQHGNTDETQWKLERWTTLLRAAGFQVDTTALSVT +WPPGPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS +RDKTYTATESLTKLVSRAQASLGMSPKDLGGEQPEVRRLLQSLQGIAAPISTLRNDTNVH +HGAEVVPQWVRPRHARLVLGAAQLWCQTVLETLSDPTAPWRVTDAAAQR +>GCF_020097155_PROKKA_00696 +MAINWRRAQYLLAEDLTDFPVRYIDELFDGNGIALGPENPQDVDTSVRRARMRRYLTTLD +LDINRADQQRFADVLAERYREIALVHQHGNTGETQWNLDRWTTTLQAAGFRVDTTALSVT +WPPDPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS +RGETYTATESLTKLVSRAQTSLGMSPKGLGGEQPEVRQLLQSLQGIAVPISTLRNDTNVH +HGAEVVPQWVRPRHARLVVGAAQLWCQTVLETLSDPTAPWRVVDAAAQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002345.fa new file mode 100644 index 0000000000000000000000000000000000000000..5dcb447a78c39c151602894a842886accf0c5987 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002345.fa @@ -0,0 +1,28 @@ +>GCF_020097155_PROKKA_00636 +M--NFSVDLNIGDRVLTDAGPARVKSMWALGVELETINEPAKLVPWTDLIIRPTIDGQAQ +AVDAALHPWWDQLPEKVQQDAIFKMECVLEILTGFRSGLASLAQPHEPVVPFGPFSQASV +SAQCEAMARLVSFEKSADRELMRRVQDGELDSPGVTPRAVHHWVRRWQASGLRGLVDGRA +LRSAQGFGALDPRFLKIAEQEFARFDGSASATNRQEIHRRIQVRMHAEGITDAHLPQRLV +SDYLSHRFAQLGKTTRAHRSRRHRKISSTASAALHHLGHCATDVTRADNLVYDEFTGKPM +SVEIATIMSVPARVIVAVRVFPKSVSATEVALLLYDAMRPQSMLIDQDGASDWRWCGVPT +SLQLPEQASPLANDPASG-LGEHAIPAMTPTHLRMDNGSIFRSEQLRRLALHWSITLSHS +RGTRPTDNPHIERFHETLQRFYQQLPGYKGRNVSERGSWTGVVAEAPLLTAADLERRLRQ +FIALDYHRRPHTGLTLPGAPEVNISPLEMFDWILATTGRIHVPQHPDLIYQFLPTRWLTP +GHAGVEYKNMTYDAAVLDEFRSKIPGRFRDEDAKVPFHYDPRDATRLWFRHPDTDRIHEI +PWRNRHLLHAPLTDVVRDEARRRIRARGGPKALTGALIDRQLIEEIGHLAHTRADETWTT +TMAASRMRFDQARRDHDEAALAHRLTTPEAPTD-LEHGGRHLRLVPPDAMPDRT--ATNG +LAGLFEPWPDYAQE----I +>GCF_023573625_PROKKA_02218 +MRAQMSAPIQAGDSILTEHGPVEVIAPQSTGLLVRAPGGQETLITHAQVIPRRFQNGTIA +GVMASLYPLWDQLDQAVRDDALFKLECVNEVNTGYRRGVASLALEGEPFYPFGPGWGVSL +RARYQAMARLVSLEKRVDRVLMRRVYDGEVQRPEIGLRTLQSWGESFEEHGLRGLIDGRA +LRKVQDFGVIDVRYRQAADEVFGQFDGEISAVNQQEIQRRIYALLRQRGQSDVQVPDRLE +SDFLRHYYRRLGKGTRAHRSRSLRKIATTSSAALHHPGYCASDVTRADNLVTDEYTGKPI +SVEICTIISVPTRVVVALRVFPRSVTSFELGLVLYDAMRPFSMVAADGAIDDWRWCGVPT +GLQMSAPQCPRHVKEDEGPLGVHYIPAVTPVEMHTDHGSTYISDQFRTLLQQFGITLSLT +RGGRPTDNPHIERFHETLQRAYQQLPGYKGRNVSERGSVVGVQADEPLLTARQLEAYLRA +FVAVDYHRRPHTGLIWPGTEEQALTPLEMFDAMLASTGRLHYPQHPDLIYQFLPIRWLTI +RHAGVEYKNMAYDAEVLDEFRDCRAGAFRDKDAAAPFHYDPRDTTRLWFRHPETDRIHEI +PWRGRHLLYAPMVEIVRDQALAQIRRRAGRRH-SAKVSMLELIDEIGQLATAPRDETWAH +KLSAARMRWDQGQRDHDEVAHARALQQAHVPKPRTSRAGRDHLLSLPGGRTEDTPPAGFG +LADLSEPWPDYPEEHDELA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002346.fa new file mode 100644 index 0000000000000000000000000000000000000000..6fc7cfc742840101b7b30e711e2c06c563e54469 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002346.fa @@ -0,0 +1,12 @@ +>GCF_020097155_PROKKA_00637 +MSQLMGDAGGGPATPWSHLEFSTPEGPVLCHPTDPLPDLGTIMSVRTPRSHALSRHVPVQ +TFSATNTDVVAVESGLEQELVLVLDRDPAQDRLVGQPLTVTWARQSGGTRRHTPDLLTLT +HEGAVTVWDVRPEGRRDPKFWEAARCTRAVCEHNGWTYELFGGLPEVHAINLRWLSSYRH +SMPWYADLRDTLERLACTNSATIGTLLGADDGSGELISAMWHWAWDGRLQLDLTRPLKTS +TPVRWEPR +>GCF_023573625_PROKKA_02219 +M----------------------------------------------------------- +--------------------------------------------------------LSLD +RDGQVCLWDARPSRRQDEEFLEAARTTEACARLLGWDYRVHAGHGPAYEANLRWLSAFRA +LKPWYPEAEQRLGQLLAHGERSVQEVFAVDDGTGELISGLWHHVWAGRVETDLDSPLCGA +SILRWVG- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002349.fa new file mode 100644 index 0000000000000000000000000000000000000000..9432db1b1c049800536651c4be13a852c66a5ce9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002349.fa @@ -0,0 +1,10 @@ +>GCF_020097155_PROKKA_00667 +MDLAPSSSPTIELSWHADLTPGQLDDLNRLFAAEYLEDFGEWDPDQPYGYAPHDMHVIAT +LDAQTVGHIGWARRSITVGDHHVTIAGVGGVLVTPSGRGHHLGQRLMRAAVDSMRAHSDA +EFGYLGCHESVVPFYVSCGWRRIVAAERYIGLNGQPSESAQGDPLLVMPLRNAKQPWSAG +EIDLQGRPW +>GCF_020097155_PROKKA_00699 +MDLVPSSSLKIELTWHTDLTPGQLDDLNRLFAAEYREDYGEWDPDQPYGYAPHDMHVIAT +LDAQTVGHIGWARRSIAVGARPVTIAGVGGVLVAPSGRGHHVGQRLMRSAVDSMRVHSDA +EFGYLGCDESVVPFYVSCGWQRIVAAERSIGRGGQPTQSTQGEPLLVMPLRGTEQLWPAG +EIDLRGRPW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002351.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0cc7613daa96b1abf0b70582327e37034787188 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002351.fa @@ -0,0 +1,4 @@ +>GCF_020097155_PROKKA_00669 +MPRRDSHQDLRQKLEAVETKISHHLFQSPGIAESLRIVDQSTGKEADAVDAVLTSRGPA +>GCF_023573625_PROKKA_02015 +MPRRDSHQDLRQKLEAVETKISHHLFQSPGIAESLRIVDQSTGKEADAVDAVLTSRGPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002355.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f166d5aff94fc796a0f4fdf99ce539e29fcaa82 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002355.fa @@ -0,0 +1,10 @@ +>GCF_020097155_PROKKA_00939 +MHGEERSTRAALERAGHVGLASRIGLDGTLVPPDGRAGPGAPDAAGVGYASRVPEQRIIA +RRSLGNAPTRPDGLRLASLAALGEEQFSTHMLAASGGDPFDTSTEESALEDLLEIIEGAG +DHFDPHAWYVVGDGEGEIGVVLPQPLPDKPGTGTVFYVAVLPSRRGRGKGRQLHQFGLSE +LARRGCTEYVGSTSVDNAPMVAVFQANGCELEH +>GCF_020097155_PROKKA_01294 +M----------------------------------------------------------- +------------------------------------------------------------ +--------------------------------------AVLPSRRGQGMGRRLHALGLAE +LARRGARKYIGSTGRKKAAMVAVSRANDCIVEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002359.fa new file mode 100644 index 0000000000000000000000000000000000000000..1971d0cafbdac2b97c06bbb081e16c93f180cdb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002359.fa @@ -0,0 +1,10 @@ +>GCF_020097155_PROKKA_01196 +MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIRKHNPNLSGTAESAGRVGM +RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT +AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV +TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDAISTPEAVDY +>GCF_023573625_PROKKA_01533 +MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIREHNPDLSGTADSAGRVGM +RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT +AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV +TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDTISTPEAVDY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002360.fa new file mode 100644 index 0000000000000000000000000000000000000000..464d04555514613b0a7711c3d0341f710ca5f5f8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002360.fa @@ -0,0 +1,16 @@ +>GCF_020097155_PROKKA_01197 +MTEPVTYTPDIEHSVDREEDLTREILAQMGAAQRRTAGEHKHAHRDAHAKSHAVLKATLE +VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL +DSHNQDFLMVNFPTLAFGTVARYQEMLGLLEKNSQSPELLQRLTTGAARVVRGAVETVGG +TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASANVRALTGQDMKVKDFSS +ISEIVADFFSRESAEYVLRAQLATDAERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS +HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPTSLDEI +PD +>GCF_023573625_PROKKA_01532 +MTEPVKYTPDIEHSVDREEDLTREILAQMGAAQRRAAGEHKHAHRDAHAKSHAVLKATLE +VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL +DSHNQDFLMVNFPTLAFGTVARYKEMLSLLEKNSQSPELLQRLTTGAARVVRGAVETVGG +TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASENVRALTGQDMKVEDFSS +ISEIVADFFSRESAEYVLRAQLATDPERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS +HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPSSLDDI +PD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002362.fa new file mode 100644 index 0000000000000000000000000000000000000000..80bcd002f7701f122aedfdf8367ff271e817dee7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002362.fa @@ -0,0 +1,6 @@ +>GCF_020097155_PROKKA_01788 +M-------------------NIYPDFGAFGDNTTLHTVIGALLTFVLVTAVLTMLISGIT +WAIATANGNHTTATKARTGLLVALGTATLAGAGITWLNWLINLGDQL +>GCF_020097155_PROKKA_01790 +MLDLMTSVLPTLPMMLPMEVDITPNDDGLPGIAQLRNIVAAVMTIGLILSVLALIISAIV +WGFGANSSNPHLAGRGKVGVLVSCGAAIICGAAVTLINFFWNVGQSV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002364.fa new file mode 100644 index 0000000000000000000000000000000000000000..4fa68dda5da1717c5fe118b52fe9b0ce7d6da490 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002364.fa @@ -0,0 +1,16 @@ +>GCF_020097155_PROKKA_01885 +MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLGETLLVLGPQVATAFAGFID +LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF +TECFNETLPEELNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL +VRTWLVEHEGQQQSAATPARQTKTREAWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG +KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGEARRFDQLQVEVDGVDRLVKELPLSGS +YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI +AD +>GCF_023573625_PROKKA_00900 +MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLDETLLILGRQVATAFGGFID +LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF +AECFNETLPEEVNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL +ARTWLVEHEGQQQSAATPARQTKTREVWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG +KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGVARRFDQLQVEVDGVDRLVKELPLSGS +YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI +AD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002368.fa new file mode 100644 index 0000000000000000000000000000000000000000..fa327095cf4301632e84afb0ae992a2ebb0f4651 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002368.fa @@ -0,0 +1,28 @@ +>GCF_020097155_PROKKA_02315 +MALHVGLYSPWNTTDPRAWSGVISPMAEALRDVFDVTVIPPVGQRDARGERIRTRLRGMT +GRRSLPTHTMATARLRSAVLAHQLRRHTGAPLDALVTIAASTDVLSLPDDLPIVQVTDAT +FPAIRGFYPLATGLGRRNEREGMRVEEAGAQATDRYLVASEWAALSLTDVVGVAPHRVTV +APFGPGTPPPADARRREPGSSLRVLAVIADWERKRGDDIVAAVARAREFRDLTLTIVGRA +PEGLPSWVNAPGVVDRARLAELYRGHDVLVDLALANAAGVVMTDALASGLPVIATHVGGV +DTIVRDGKTGWLVQPSGAVDATARVLTTL----DAAAVTRASAAALADARARLSWRAWAA +TADEVVRAAVAERRGQASPEAQRRRALMVTPILPSTGGQESAGEHLVNDIAQVI-AERSE +LTMLSSDGPANRRALERGVAFAHRLLTSAPLRCDRLPRLLGVAPALNARTVEQVRGLVAS +ADLVDLQWEESALLLGPLRRMNADARIVVTLHDVLSQRFARQRELQSSRLRKGVWAARQA +AATMLEAHIVREADAVVVLSQKDADLLPKRGRRARIHVVPPAITGPLRPLR---DGTGAP +FLLFVAYMARWENEDAMHWFVTEILPRVRAEAPDVRVAVAGGGLRDHVVAELEANDVEVL +GFVHDLEPLYEEASAVVVPLRYGAGVKFKVVDALVRGVPVVTTTVGNEGIHPADAAIVAD +EPAAFAEAVTAVLANLPCAERYARSRATDVAREFGPNRFRARLQEVYR +>GCF_023573625_PROKKA_00517 +MTPRIGLYSPWDLTDPRAWSGAAHQMAEALAAVADVEIVPPVQVDDAPLERARTRARGAR +GRRSLPRHTMATARRRSQALSQALEARVGPSLDALVAIAGSTDVLRIPANLPLVQVTDAT +FPAICGFYPMATGLGRRGEREGQRVEHASAVRTDRWAVASQWAADSLVADVGVPASAVRV +APFGPGVTPTSAPRVRRPQRPMRVLAVIADWQRKRGDAVVDAVQQARRHADIELTIVGHA +PDDLPIWVHLEGVVQSDRLSDIYADHDVLLDLASANAAGVVMTDALASGLPVIATRVGGV +ASIVQDGRTGWLVDADRAAEQAANQLRLLGESGGADQVAAASKAAAEDAARRLTWRSWAA +AVMESVEEAV------AAHAATERRIVMISPLLPSAAHQETAGEKLVRQTVDTLTADGAR +VTLVSTPGPANRRAILRGGVPDHRLLSPARRITGRAARLLDLAPVLSPADLAPVRGLLRT +ADVVDLQWEESGILLPALRLTAPGARTVVTLHDVLSQRFARQRDLQLRPARRAVWEARRR +AALAVERLVLAMADDVVVLSDKDAALLSSRG-RARVHVVPPPIPGSLRPERRDLQPTAEP +QLLFVGFMARWANEEGMHWFVTEVLPRIRAELPGARVAVAGGGHRDHVVEELENSEIEVL +GFVEDLEALYNAADIVVVPLLSGAGVKFKVVEALVRGVPVVTTSVGNEGIHPADAALVAD +DPQDFADAVLDVARYPQIAESHARAHASAVAEEFGVAGFRQRIKEIYR