LiteFold/InterPro · Datasets at Hugging Face

IPR019858

19,858

CRISPR-associated protein Cas1, HMARI/TNEAP subtype

CRISPR-assoc_Cas1_HMARI/TNEAP

Family

1,861

false

This entry describes a Cas1 subgroup that includes Cas1 proteins of the related HMARI and TNEAP subtypes of CRISPR/Cas system. The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

[ "GO:0004520", "GO:0046872", "GO:0043571" ]

[ "DNA endonuclease activity", "metal ion binding", "maintenance of CRISPR repeat elements" ]

[ "molecular_function", "molecular_function", "biological_process" ]

3

[ "PANTHER", "NCBIFAM", "CDD" ]

[ "PTHR43219", "TIGR03641", "cd09722" ]

[ "", "cas1_HMARI", "Cas1_I-B" ]

[ 1861, 1644, 1339 ]

3

[]

0

[ "2yzs", "4wj0", "4xtk", "7ei1" ]

4

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147" ]

[ "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with euka...

[ 2007, 2007, 2006, 2011, 2014 ]

5

[ "IPR002729" ]

[]

1

0

1

[ "Archaea", "Bacteria", "metagenomes" ]

[ 267, 1559, 35 ]

3

[]

0

true

Family

CRISPR-associated protein Cas1, HMARI/TNEAP subtype

CRISPR-assoc_Cas1_HMARI/TNEAP

7

IPR019859

19,859

Gliding motility-associated protein GldM

Motility-assoc_prot_GldM

Family

2,018

false

This protein family, GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes [ ]. However, members of this protein family are found also in several members of the Bacteriodetes that appear no...

[]

0

[ "NCBIFAM" ]

[ "TIGR03517" ]

[ "GldM_gliding" ]

[ 2018 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[ "6ey4", "6ey5", "6ey6", "6ys8", "7cmg", "7sat" ]

6

[ "PUB00045359" ]

[ "16199564" ]

[ "Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis." ]

[ 2005 ]

1

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 2005, 13 ]

2

[]

0

true

Family

Gliding motility-associated protein GldM

Motility-assoc_prot_GldM

7

IPR019860

19,860

Gliding motility-associated ABC transporter permease protein GldF

Motility-assoc_ABC_perm_GldF

Family

1,508

false

Members of this protein family are exclusive to the Bacteroidetes phylum. GldF is believed to be a ABC transporter permease protein (along with ATP-binding subunit, GldA and a substrate-binding subunit, GldG) and is linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga joh...

[]

0

[ "NCBIFAM" ]

[ "TIGR03518" ]

[ "ABC_perm_GldF" ]

[ 1508 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00045356" ]

[ "11948149" ]

[ "Mutations in Flavobacterium johnsoniae gldF and gldG disrupt gliding motility and interfere with membrane localization of GldA." ]

[ 2002 ]

1

[]

0

null

[ "Bacteroidota", "ecological metagenomes" ]

[ 1503, 5 ]

2

[]

0

true

Family

Gliding motility-associated ABC transporter permease protein GldF

Motility-assoc_ABC_perm_GldF

6

IPR019861

19,861

Type IX secretion system membrane protein, PorP/SprF family

PorP/SprF_Bacteroidetes

Family

12,603

false

This entry describes a protein family unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Cytophaga johnsonae (Flavobacterium johnsoniae), that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are f...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF11751", "TIGR03519" ]

[ "PorP_SprF", "T9SS_PorP_fam" ]

[ 12601, 12185 ]

2

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00074052", "PUB00074053" ]

[ "19966289", "24257839" ]

[ "A protein secretion system linked to bacteroidete gliding motility and pathogenesis.", "Deletion of the Cytophaga hutchinsonii type IX secretion system gene sprP results in defects in gliding motility and cellulose utilization." ]

[ 2010, 2014 ]

2

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 12447, 29, 127 ]

3

[]

0

true

Family

Type IX secretion system membrane protein, PorP/SprF family

PorP/SprF_Bacteroidetes

8

IPR019862

19,862

Gliding motility-associated protein GldE

Motility-assoc_prot_GldE

Family

1,760

false

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae) and Cytophaga hutchinsonii. GldE was dis...

[]

0

[ "NCBIFAM" ]

[ "TIGR03520" ]

[ "GldE" ]

[ 1760 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00045357" ]

[ "11418556" ]

[ "Cloning and characterization of the Flavobacterium johnsoniae gliding motility genes gldD and gldE." ]

[ 2001 ]

1

[]

0

null

[ "Bacteria", "Homo sapiens", "Siphoviridae sp. ctBLh2", "metagenomes" ]

[ 1725, 1, 1, 33 ]

4

[ "Homo sapiens" ]

[ 1 ]

1

true

Family

Gliding motility-associated protein GldE

Motility-assoc_prot_GldE

7

IPR019863

19,863

Gliding-associated putative ABC transporter substrate-binding GldG

Motility-assoc_ABC-rel_GldG

Family

1,840

false

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldG is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae) and Cytophaga hutchinsonii. Knockouts of...

[]

0

[ "NCBIFAM" ]

[ "TIGR03521" ]

[ "GldG" ]

[ 1840 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00045356" ]

[ "11948149" ]

[ "Mutations in Flavobacterium johnsoniae gldF and gldG disrupt gliding motility and interfere with membrane localization of GldA." ]

[ 2002 ]

1

[]

0

null

[ "Bacteroidota", "Elysia marginata", "ecological metagenomes" ]

[ 1830, 1, 9 ]

3

[]

0

true

Family

Gliding-associated putative ABC transporter substrate-binding GldG

Motility-assoc_ABC-rel_GldG

6

IPR019865

19,865

Gliding motility-associated lipoprotein GldJ

Glid_motil-assoc_lipo_GldJ

Family

1,086

false

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldJ is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae) [ ]. Knockouts of GldJ abolish the g...

[]

0

[ "NCBIFAM" ]

[ "TIGR03524" ]

[ "GldJ" ]

[ 1086 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00045360" ]

[ "15805509" ]

[ "Flavobacterium johnsoniae GldJ is a lipoprotein that is required for gliding motility." ]

[ 2005 ]

1

[]

0

null

[ "Bacteroidota", "Stylophora pistillata", "ecological metagenomes" ]

[ 1077, 1, 8 ]

3

[]

0

true

Family

Gliding motility-associated lipoprotein GldJ

Glid_motil-assoc_lipo_GldJ

9

IPR019866

19,866

Gliding motility-associated lipoprotein GldK

Glid_motil-assoc_lipo_GldK

Family

1,023

false

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldK is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae) [ ]. Knockouts of GldK abolish the g...

[]

0

[ "NCBIFAM" ]

[ "TIGR03525" ]

[ "GldK" ]

[ 1023 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00045359", "PUB00045360" ]

[ "16199564", "15805509" ]

[ "Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis.", "Flavobacterium johnsoniae GldJ is a lipoprotein that is required for gliding motility." ]

[ 2005, 2005 ]

2

[]

0

null

[ "Elysia marginata", "Flavobacteriales", "ecological metagenomes" ]

[ 1, 1016, 6 ]

3

[]

0

true

Family

Gliding motility-associated lipoprotein GldK

Glid_motil-assoc_lipo_GldK

3

IPR019867

19,867

Gliding motility-associated lipoprotein GldK, short form

Glid_motil-assoc_GldK_short

Family

90

false

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldK is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae) [ ]. Knockouts of GldK abolish the g...

[]

0

[ "NCBIFAM" ]

[ "TIGR03529" ]

[ "GldK_short" ]

[ 90 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00045359", "PUB00045360" ]

[ "16199564", "15805509" ]

[ "Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis.", "Flavobacterium johnsoniae GldJ is a lipoprotein that is required for gliding motility." ]

[ 2005, 2005 ]

2

[]

0

null

[ "Cytophagales" ]

[ 90 ]

1

[]

0

true

Family

Gliding motility-associated lipoprotein GldK, short form

Glid_motil-assoc_GldK_short

8

IPR019869

19,869

Gliding motility-associated, peptidyl-prolyl isomerase, GldI

Motility-assoc_PPIase_GldI

Family

835

false

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase ( ) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Cytophaga johnsonae (Flavobacterium johnsoniae...

[]

0

[ "NCBIFAM" ]

[ "TIGR03516" ]

[ "ppisom_GldI" ]

[ 835 ]

1

[ "GP" ]

[ "GenProp0781" ]

[ "GP:GenProp0781" ]

1

[]

0

[ "PUB00045355" ]

[ "15060031" ]

[ "GldI is a lipoprotein that is required for Flavobacterium johnsoniae gliding motility and chitin utilization." ]

[ 2004 ]

1

[]

0

null

[ "Flavobacteriaceae", "ecological metagenomes" ]

[ 831, 4 ]

2

[]

0

true

Family

Gliding motility-associated, peptidyl-prolyl isomerase, GldI

Motility-assoc_PPIase_GldI

7

IPR019870

19,870

Selenium metabolism protein YedF

Se_metab_YedF

Family

1,955

false

Members of this protein family are about 200 amino acids in size, and include the uncharacterised YedF protein of Escherichia coli. This family shares an N-terminal domain, modelled by , with the sulphurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulphide motif, CGXC. Th...

[]

0

[ "NCBIFAM" ]

[ "TIGR03527" ]

[ "selenium_YedF" ]

[ 1955 ]

1

[ "GP" ]

[ "GenProp0726" ]

[ "GP:GenProp0726" ]

1

[]

0

[ "PUB00034422" ]

[ "16930487" ]

[ "Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic." ]

[ 2006 ]

1

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 1921, 34 ]

2

[]

0

true

Family

Selenium metabolism protein YedF

Se_metab_YedF

3

IPR019871

19,871

Diaminopropionate ammonia-lyase, subgroup

DiNH2propionate_NH3-lyase_sub

Family

1,808

false

Members of this protein family are the homodimeric, pyridoxal phosphate enzyme diaminopropionate ammonia-lyase, which adds water to remove two amino groups, leaving pyruvate [ ]. The structure of E. coli diaminopropionate ammonia-lyase has been revealed [ ].

[ "GO:0008838" ]

[ "diaminopropionate ammonia-lyase activity" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR03528" ]

[ "2_3_DAP_am_ly" ]

[ 1808 ]

1

[ "EC", "GP" ]

[ "4.3.1.15", "GenProp0726" ]

[ "EC:4.3.1.15", "GP:GenProp0726" ]

2

[ "4d9g", "4d9i", "4d9k", "4d9m", "4d9n", "5ygr" ]

6

[ "PUB00045881", "PUB00061068" ]

[ "12596860", "22505717" ]

[ "Gene cloning, purification, and characterization of 2,3-diaminopropionate ammonia-lyase from Escherichia coli.", "Crystal structure of Escherichia coli diaminopropionate ammonia-lyase reveals mechanism of enzyme activation and catalysis." ]

[ 2002, 2012 ]

2

[ "IPR010081" ]

[]

1

0

1

[ "Bacteria", "Candidatus Methanomethylicus mesodigestus", "Eukaryota", "metagenomes" ]

[ 1796, 1, 3, 8 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Diaminopropionate ammonia-lyase, subgroup

DiNH2propionate_NH3-lyase_sub

5

IPR019872

19,872

O-phosphoseryl-tRNA(Sec) selenium transferase

Sec-tRNA_Se_transferase

Family

2,353

false

In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalysed by a homologue of the bacterial SelA protein. It converts O-phosphos...

[ "GO:0098621", "GO:0001717" ]

[ "O-phosphoseryl-tRNA(Sec) selenium transferase activity", "conversion of seryl-tRNAsec to selenocys-tRNAsec" ]

[ "molecular_function", "biological_process" ]

2

[ "PIRSF", "PANTHER", "NCBIFAM" ]

[ "PIRSF017689", "PTHR12944", "TIGR03531" ]

[ "SepSecS", "", "selenium_SpcS" ]

[ 1857, 2347, 2030 ]

3

[ "EC", "GP", "METACYC", "REACTOME" ]

[ "2.9.1.2", "GenProp0797", "PWY-6281", "R-HSA-2408557" ]

[ "EC:2.9.1.2", "GP:GenProp0797", "METACYC:PWY-6281", "REACTOME:R-HSA-2408557" ]

4

[ "2z67", "3bc8", "3bca", "3bcb", "3hl2", "4zdl", "4zdo", "4zdp", "7l1t", "7mdl", "8g9z" ]

11

[ "PUB00045882" ]

[ "17142313" ]

[ "RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea." ]

[ 2006 ]

1

[ "IPR008829" ]

[]

1

0

1

[ "Archaea", "Eukaryota", "marine sediment metagenome" ]

[ 45, 2297, 11 ]

3

[ "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 1, 1, 5, 6, 5, 2 ]

6

true

Family

O-phosphoseryl-tRNA(Sec) selenium transferase

Sec-tRNA_Se_transferase

2

IPR019873

19,873

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, DapH

DapH

Family

3,109

false

This enzyme catalyses the transfer of an acetyl group from acetyl-CoA to tetrahydrodipicolinate and is part of the diaminopimelate pathway of lysine biosynthesis. An alternate name is tetrahydrodipicolinate N-acetyltransferase.

[ "GO:0047200", "GO:0009089" ]

[ "tetrahydrodipicolinate N-acetyltransferase activity", "L-lysine biosynthetic process via diaminopimelate" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_01691", "TIGR03532" ]

[ "DapH", "DapD_Ac" ]

[ 2888, 3108 ]

2

[ "EC", "GP", "METACYC" ]

[ "2.3.1.89", "GenProp0787", "PWY-2941" ]

[ "EC:2.3.1.89", "GP:GenProp0787", "METACYC:PWY-2941" ]

3

[ "3cj8", "3r8y" ]

2

[]

0

[]

0

null

[ "Bacteria", "Methanopyrus kandleri", "ecological metagenomes" ]

[ 3099, 2, 8 ]

3

[]

0

true

Family

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, DapH

DapH

1

IPR019874

19,874

Release factor glutamine methyltransferase

RF_methyltr_PrmC

Family

26,117

false

Members of this protein family are HemK, a protein once thought to be involved in heme biosynthesis but now recognised to be a protein-glutamine methyltransferase that modifies the peptide chain release factors [ ]. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by ...

[ "GO:0008168" ]

[ "methyltransferase activity" ]

[ "molecular_function" ]

1

[ "HAMAP", "NCBIFAM" ]

[ "MF_02126", "TIGR03534" ]

[ "RF_methyltr_PrmC", "RF_mod_PrmC" ]

[ 22096, 25860 ]

2

[ "EC", "GP" ]

[ "2.1.1.297", "GenProp0746" ]

[ "EC:2.1.1.297", "GP:GenProp0746" ]

2

[ "1nv8", "1nv9", "1sg9", "1t43", "1vq1", "2b3t", "4dzr" ]

7

[ "PUB00043100" ]

[ "11847124" ]

[ "The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors." ]

[ 2002 ]

1

[ "IPR004556" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "unclassified Caudoviricetes", "unclassified sequences" ]

[ 25267, 353, 2, 495 ]

4

[ "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 1, 3, 1, 2 ]

4

true

Family

Release factor glutamine methyltransferase

RF_methyltr_PrmC

5

IPR019876

19,876

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria

DapD_gammaproteobac

Family

1,689

false

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) is involved in the succinylated branch of the "lysine biosynthesis via diaminopimelate (DAP)" pathway ( ). This entry represents the gammaproteobacteria family of DapD sequences, which is the most closely related to the actinobacterial DapD famil...

[]

0

[ "NCBIFAM" ]

[ "TIGR03536" ]

[ "DapD_gpp" ]

[ 1689 ]

1

[ "EC", "GP" ]

[ "2.3.1.117", "GenProp0786" ]

[ "EC:2.3.1.117", "GP:GenProp0786" ]

2

[ "3r5a", "3r5b", "3r5c", "3r5d" ]

4

[]

0

[ "IPR026586" ]

[]

1

0

1

[ "Bacteria", "metagenomes" ]

[ 1682, 7 ]

2

[]

0

true

Family

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria

DapD_gammaproteobac

6

IPR019880

19,880

4-dedimethylamino-4-oxo-anhydrotetracycline transaminase OxyQ

OxyQ

Family

4,638

false

This family of actinobacterial proteins are involved in the biosynthesis of the tetracycline antibiotic, oxytetracycline. The minimum set of enzymes required for the biosynthesis of anhydrotetracycline, the first intermediate in the synthesis of oxytetracycline, are OxyL, OxyQ, and OxyT. OxyQ catalyzes the conversion o...

[]

0

[ "NCBIFAM" ]

[ "TIGR03539" ]

[ "DapC_actino" ]

[ 4638 ]

1

[ "GP" ]

[ "GenProp0786" ]

[ "GP:GenProp0786" ]

1

[]

0

[ "PUB00055043", "PUB00087301" ]

[ "20418392", "18422316" ]

[ "Methanococci use the diaminopimelate aminotransferase (DapL) pathway for lysine biosynthesis.", "Identifying the minimal enzymes required for anhydrotetracycline biosynthesis." ]

[ 2010, 2008 ]

2

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 4475, 2, 161 ]

3

[]

0

true

Family

4-dedimethylamino-4-oxo-anhydrotetracycline transaminase OxyQ

OxyQ

1

IPR019881

19,881

LL-diaminopimelate aminotransferase-like

DapL-like

Family

419

false

This group of the superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway ( ). Every member of this group is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known aminotransferases, succinylases, d...

[ "GO:0010285", "GO:0009089" ]

[ "L,L-diaminopimelate aminotransferase activity", "L-lysine biosynthetic process via diaminopimelate" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR03540" ]

[ "DapC_direct" ]

[ 419 ]

1

[ "EC", "GP", "METACYC" ]

[ "2.6.1.83", "GenProp0125", "PWY-5097" ]

[ "EC:2.6.1.83", "GP:GenProp0125", "METACYC:PWY-5097" ]

3

[]

0

[ "PUB00043268", "PUB00045445", "PUB00055043" ]

[ "17583737", "17093042", "20418392" ]

[ "Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia.", "L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine.", "Me...

[ 2007, 2006, 2010 ]

3

[ "IPR019942" ]

[]

1

0

1

[ "Bacteria", "Geodia barretti", "Methanobacteriota", "ecological metagenomes" ]

[ 263, 1, 142, 13 ]

4

[]

0

true

Family

LL-diaminopimelate aminotransferase-like

DapL-like

4

IPR019882

19,882

Conserved hypothetical protein CHP03643

CHP03643

Family

2,313

false

This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three ident...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF10985", "TIGR03643" ]

[ "DUF2805", "" ]

[ 2313, 1955 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 2305, 8 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP03643

CHP03643

5

IPR019883

19,883

Lactoylglutathione lyase

Lactoylglutathione_lyase

Family

1,046

false

Members of this protein family share homology with lactoylglutathione lyase (glyoxalase I) and are found mainly in marine members of the gammaproteobacteria, including from Colwellia psychrerythraea (strain 34H / ATCC BAA-681). This family excludes a well-separated, more narrowly distributed paralogous family, exemplif...

[]

0

[ "NCBIFAM" ]

[ "TIGR03645" ]

[ "glyox_marine" ]

[ 1046 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "marine sediment metagenome" ]

[ 1040, 6 ]

2

[]

0

true

Family

Lactoylglutathione lyase

Lactoylglutathione_lyase

9

IPR019884

19,884

YtoQ family protein

YtoQ_family_protein

Family

1,856

false

This entry represents a family of uncharacterised proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF11071", "TIGR03646" ]

[ "Nuc_deoxyri_tr3", "YtoQ_fam" ]

[ 1856, 1818 ]

2

[]

0

[ "8of6" ]

1

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 1751, 62, 43 ]

3

[]

0

true

Family

YtoQ family protein

YtoQ_family_protein

4

IPR019885

19,885

Transcription regulator HTH, AsnC-type, conserved site

Tscrpt_reg_HTH_AsnC-type_CS

Conserved_site

54,079

false

The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily [ ]. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and...

[]

0

[ "PROSITE" ]

[ "PS00519" ]

[ "HTH_ASNC_1" ]

[ 54079 ]

1

[]

0

[ "1i1g", "2cg4", "2dbb", "2gqq", "2l4a", "2p5v", "2p6s", "2p6t", "3i4p" ]

9

[ "PUB00005435", "PUB00011124" ]

[ "7770911", "12675791" ]

[ "The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus.", "The Lrp family of transcriptional regulators." ]

[ 1995, 2003 ]

2

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences", "uncultured Caudovirales phage" ]

[ 1192, 52556, 55, 275, 1 ]

5

[ "Escherichia coli (strain K12)" ]

[ 3 ]

1

true

Conserved_site

Transcription regulator HTH, AsnC-type, conserved site

Tscrpt_reg_HTH_AsnC-type_CS

3

IPR019886

19,886

Sodium symporter small subunit

Na_symporter_ssu

Domain

5,211

false

Proteins matched by this entry are highly hydrophobic bacterial proteins of about 90 amino acids in length. They are usually found immediately upstream (sometimes fused to) a member of the solute:sodium symporter family, and are therefore putative sodium:solute symporter small subunits. They tend to be found in aquatic...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF13937", "TIGR03647" ]

[ "DUF4212", "Na_symport_sm" ]

[ 5207, 5203 ]

2

[ "GP" ]

[ "GenProp0821" ]

[ "GP:GenProp0821" ]

1

[]

0

[]

0

[]

0

null

[ "Archaea", "Bacteria", "Dinophyceae", "unclassified sequences" ]

[ 259, 4813, 52, 87 ]

4

[]

0

true

Domain

Sodium symporter small subunit

Na_symporter_ssu

9

IPR019888

19,888

Transcription regulator AsnC-like

Tscrpt_reg_AsnC-like

Family

118,199

false

The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily [ ]. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and...

[]

0

[ "SMART" ]

[ "SM00344" ]

[ "HTH_ASNC" ]

[ 118199 ]

1

[ "REACTOME" ]

[ "R-HSA-9637628" ]

[ "REACTOME:R-HSA-9637628" ]

1

[ "1i1g", "1ri7", "2cfx", "2cg4", "2cyy", "2dbb", "2e1c", "2e7w", "2e7x", "2efn", "2efo", "2efp", "2efq", "2gqq", "2ia0", "2ivm", "2l4a", "2p5v", "2p6s", "2p6t", "2pmh", "2pn6", "2qz8", "2vbw", "2vbx", "2vby", "2vbz", "2vc0", "2vc1", "2w24", "2w25", "2w29"...

42

[ "PUB00005435", "PUB00011124" ]

[ "7770911", "12675791" ]

[ "The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus.", "The Lrp family of transcriptional regulators." ]

[ 1995, 2003 ]

2

[]

[ "IPR049859" ]

0

1

0

[ "Archaea", "Bacteria", "Eukaryota", "Siphoviridae sp. ctBLh2", "unclassified sequences" ]

[ 6296, 110870, 82, 1, 950 ]

5

[ "Escherichia coli (strain K12)" ]

[ 3 ]

1

true

Family

Transcription regulator AsnC-like

Tscrpt_reg_AsnC-like

9

IPR019889

19,889

DNA helicase, DnaB-like, phage

DNA_helicase_DnaB-like_phg

Family

504

false

Proteins in this entry are phage (or prophage-region) homologues of the bacterial homohexameric replicative DNA helicase DnaB. Some phages rely on host DnaB while others encode their own versions. This entry represents the largest phage-specific clade among the close homologues of DnaB, but there are other phage DnaB h...

[]

0

[ "NCBIFAM" ]

[ "TIGR03600" ]

[ "phage_DnaB" ]

[ 504 ]

1

[ "GP" ]

[ "GenProp0208" ]

[ "GP:GenProp0208" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "Caudoviricetes", "hydrothermal vent metagenome" ]

[ 457, 46, 1 ]

3

[]

0

true

Family

DNA helicase, DnaB-like, phage

DNA_helicase_DnaB-like_phg

3

IPR019891

19,891

Bacteriocin, streptolysin S, precursor

Bacteriocin_streptolysin_S_pre

Family

74

false

This entry represents a family of heterocycle-containing bacteriocin precursors. It includes the hemolytic polypeptide streptolysin S from Streptococcus pyogenes. These small, ribosomally produced polypeptide precursors are extensively processed post-translationally. Bacteriocin genes in general are small, highly diver...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF27786", "TIGR03602" ]

[ "Bacteriocin_streptolysin_S_pre", "streptolysinS" ]

[ 74, 73 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria" ]

[ 74 ]

1

[]

0

true

Family

Bacteriocin, streptolysin S, precursor

Bacteriocin_streptolysin_S_pre

4

IPR019892

19,892

Thiazole/oxazole-forming peptide maturase, SagC family component

Cyclo_dehy_ocin

Family

105

false

Members of this protein family include enzymes related to SagC, a protein involved in thiazole/oxazole cyclodehydration modifications during biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). Recent evidence suggests that the YcaO/SagD-like component, not ...

[]

0

[ "NCBIFAM" ]

[ "TIGR03603" ]

[ "cyclo_dehy_ocin" ]

[ 105 ]

1

[]

0

[]

0

[ "PUB00045446", "PUB00064880" ]

[ "18375757", "22522320" ]

[ "Discovery of a widely distributed toxin biosynthetic gene cluster.", "YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations." ]

[ 2008, 2012 ]

2

[]

0

null

[ "Bacillati", "Thermococcaceae" ]

[ 101, 4 ]

2

[]

0

true

Family

Thiazole/oxazole-forming peptide maturase, SagC family component

Cyclo_dehy_ocin

8

IPR019893

19,893

PQQ-dependent dehydrogenase SndH-like

SndH-like

Family

301

false

PQQ, or pyrroloquinoline-quinone, serves as a cofactor for a number of sugar and alcohol dehydrogenases in a limited number of bacterial species. Most characterised PQQ-dependent enzymes have multiple β-propeller repeats ( ). This entry, however, represents a family of PQQ-dependent dehydrogenases that lack this repeat...

[]

0

[ "NCBIFAM" ]

[ "TIGR03606" ]

[ "non_repeat_PQQ" ]

[ 301 ]

1

[ "GP" ]

[ "GenProp0170" ]

[ "GP:GenProp0170" ]

1

[ "1c9u", "1cq1", "1cru", "1qbi", "5min", "8re0", "8rfk", "8rg1" ]

8

[ "PUB00030195", "PUB00153450" ]

[ "10366508", "16461703" ]

[ "The 1.7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat.", "Pyrroloquinoline quinone-dependent dehydrogenases from Ketogulonicigenium vulgare catalyze the direct conversion of L-sorbosone to ...

[ 1999, 2006 ]

2

[]

0

null

[ "Bacteria", "Nitrososphaeraceae", "marine metagenome" ]

[ 295, 5, 1 ]

3

[]

0

true

Family

PQQ-dependent dehydrogenase SndH-like

SndH-like

3

IPR019894

19,894

Patatin-related protein

Patatin-related_protein

Domain

910

false

Patatins are plant storage proteins capable of phospholipase activity (see ). This entry is found in a family of bacterial proteins of unknown function that contain an N-terminal patatin domain. Regions of strong sequence conservation are separated by regions of significant sequence and length variability. The proteins...

[]

0

[ "NCBIFAM" ]

[ "TIGR03607" ]

[ "" ]

[ 910 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "hydrothermal vent metagenome" ]

[ 903, 3, 4 ]

3

[]

0

true

Domain

Patatin-related protein

Patatin-related_protein

2

IPR019895

19,895

Putative bacteriocin export ABC transporter, lactococcin 972 group

L_ocin_972_ABC

Family

1,044

false

A bacteriocin system gene pair with a fairly wide distribution in bacteria consists of a lactococcin 972 homologue (see ) and a multiple-membrane-spanning putative immunity protein (see ). This entry represents a small clade within the ABC transporters that are encoded adjacent to these bacteriocin system gene pairs an...

[]

0

[ "NCBIFAM" ]

[ "TIGR03608" ]

[ "L_ocin_972_ABC" ]

[ 1044 ]

1

[ "GP" ]

[ "GenProp0809" ]

[ "GP:GenProp0809" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "bioreactor metagenome" ]

[ 1043, 1 ]

2

[]

0

true

Family

Putative bacteriocin export ABC transporter, lactococcin 972 group

L_ocin_972_ABC

1

IPR019896

19,896

Polysaccharide pyruvyl transferase, CsaB

Polysacch_pyruvyl_Trfase_CsaB

Family

1,924

false

The cell surface anchoring B (CsaB) protein of Bacillus anthracis adds a pyruvyl group to peptidoglycan-associated polysaccharide [ ]. This addition is necessary for the non-covalent anchoring of proteins containing an S-layer homology (SLH) domain ( ) to these pyruvylated polysaccharides. The proteins in this entry re...

[]

0

[ "NCBIFAM" ]

[ "TIGR03609" ]

[ "S_layer_CsaB" ]

[ 1924 ]

1

[ "GP" ]

[ "GenProp0811" ]

[ "GP:GenProp0811" ]

1

[]

0

[ "PUB00009913" ]

[ "10970841" ]

[ "Bacterial SLH domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation." ]

[ 2000 ]

1

[]

0

null

[ "Bacteria", "Halobacteriales", "Paulinella", "ecological metagenomes" ]

[ 1906, 3, 2, 13 ]

4

[]

0

true

Family

Polysaccharide pyruvyl transferase, CsaB

Polysacch_pyruvyl_Trfase_CsaB

1

IPR019898

19,898

3-aminoacrylate deaminase RutC

RutC

Family

1,012

false

RutC from E. coli is essential for growth on uracil as sole nitrogen source. Its function is not known, but it is thought to reduce aminoacrylate peracid to aminoacrylate [ ].

[]

0

[ "HAMAP", "NCBIFAM" ]

[ "MF_00831", "TIGR03610" ]

[ "RutC", "RutC" ]

[ 899, 1012 ]

2

[ "GP" ]

[ "GenProp0813" ]

[ "GP:GenProp0813" ]

1

[ "3v4d" ]

1

[ "PUB00056792" ]

[ "20400551" ]

[ "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems." ]

[ 2010 ]

1

[ "IPR006175" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 1009, 3 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

3-aminoacrylate deaminase RutC

RutC

7

IPR019899

19,899

Sodium/solute symporter, VC2705 subfamily

Na/solute_symporter_VC_2705

Family

5,170

false

This family belongs to a larger family of transporters of the sodium:solute symporter superfamily, TC 2.A.21. Members of this strictly bacterial protein subfamily are found almost invariably immediately downstream from a member of family . Occasionally, the two genes are fused.

[]

0

[ "NCBIFAM" ]

[ "TIGR03648" ]

[ "Na_symport_lg" ]

[ 5170 ]

1

[ "GP" ]

[ "GenProp0821" ]

[ "GP:GenProp0821" ]

1

[]

0

[]

0

[ "IPR001734" ]

[]

1

0

1

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 124, 4904, 64, 78 ]

4

[]

0

true

Family

Sodium/solute symporter, VC2705 subfamily

Na/solute_symporter_VC_2705

7

IPR019901

19,901

Ergot alkaloid biosynthesis protein

Ergot_alkaloid_biosynthesis

Family

657

false

Proteins in this family are required in the final stages of the biosynthesis of secondary metabolite such as fungal alkaloids. These include agroclavine dehydrogenase (easG) from ergot ( Claviceps purpurea ), which is required for the biosynthesis of the ergot alkaloid agroclavine, converting the intermediate chanoclav...

[]

0

[ "NCBIFAM" ]

[ "TIGR03649" ]

[ "ergot_EASG" ]

[ 657 ]

1

[ "EC" ]

[ "1.5.1" ]

[ "EC:1.5.1" ]

1

[]

0

[ "PUB00089636", "PUB00089637", "PUB00089638" ]

[ "20735127", "21494745", "28620689" ]

[ "Controlling a structural branch point in ergot alkaloid biosynthesis.", "New insights into ergot alkaloid biosynthesis in Claviceps purpurea: an agroclavine synthase EasG catalyses, via a non-enzymatic adduct with reduced glutathione, the conversion of chanoclavine-I aldehyde to agroclavine.", "Silencing of a ...

[ 2010, 2011, 2017 ]

3

[]

0

null

[ "Bacteria", "Fungi" ]

[ 56, 601 ]

2

[ "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)" ]

[ 1 ]

1

true

Family

Ergot alkaloid biosynthesis protein

Ergot_alkaloid_biosynthesis

2

IPR019902

19,902

Violacein biosynthesis enzyme, VioE

Violacein_biosynth_enz_VioE

Family

72

false

Violacein is a purple-coloured pigment produced by bacteria such as Chromobacterium violaceum. Violacein exhibits significant biological activities, such as strong inhibition of several tumor cell lines, as well as antibacterial and trypanocidal activities. Violacein is synthesised from two molecules of tryptophan by t...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR03650", "cd16330" ]

[ "violacein_E", "LolA_VioE" ]

[ 72, 68 ]

2

[]

0

[ "2zf3", "2zf4", "3bmz" ]

3

[ "PUB00055019" ]

[ "17176066" ]

[ "In vitro biosynthesis of violacein from L-tryptophan by the enzymes VioA-E from Chromobacterium violaceum." ]

[ 2006 ]

1

[]

0

null

[ "Bacteria" ]

[ 72 ]

1

[]

0

true

Family

Violacein biosynthesis enzyme, VioE

Violacein_biosynth_enz_VioE

9

IPR019904

19,904

Peroxiredoxin OsmC

Peroxiredoxin_OsmC

Family

9,718

false

Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription ...

[ "GO:0004601", "GO:0006979" ]

[ "peroxidase activity", "response to oxidative stress" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR03562" ]

[ "osmo_induc_OsmC" ]

[ 9718 ]

1

[]

0

[ "1nye", "1qwi", "1ukk" ]

3

[ "PUB00008206" ]

[ "8820643" ]

[ "Growth-phase-dependent expression of the osmotically inducible gene osmC of Escherichia coli K-12." ]

[ 1996 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 49, 9570, 23, 76 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Peroxiredoxin OsmC

Peroxiredoxin_OsmC

6

IPR019905

19,905

Peroxiredoxin OsmC-like protein, Firmicutes

OsmC-like_firmicutes

Family

898

false

Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription ...

[]

0

[ "NCBIFAM" ]

[ "TIGR03563" ]

[ "perox_SACOL1771" ]

[ 898 ]

1

[]

0

[]

0

[ "PUB00008206" ]

[ "8820643" ]

[ "Growth-phase-dependent expression of the osmotically inducible gene osmC of Escherichia coli K-12." ]

[ 1996 ]

1

[]

0

null

[ "Bacteria" ]

[ 898 ]

1

[]

0

true

Family

Peroxiredoxin OsmC-like protein, Firmicutes

OsmC-like_firmicutes

8

IPR019906

19,906

Large ribosomal subunit protein uL6, bacteria

Ribosomal_uL6_bact

Family

28,602

false

Large ribosomal subunit protein uL6 was previously known as L6. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform...

[ "GO:0003735", "GO:0019843", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "rRNA binding", "translation", "ribosome" ]

[ "molecular_function", "molecular_function", "biological_process", "cellular_component" ]

4

[ "HAMAP", "PRINTS", "NCBIFAM" ]

[ "MF_01365_B", "PR00059", "TIGR03654" ]

[ "Ribosomal_uL6_B", "RIBOSOMALL6", "L6_bact" ]

[ 24437, 28501, 25655 ]

3

[]

0

[ "1c04", "1eg0", "1ml5", "1nkw", "1nwx", "1nwy", "1rl6", "1sm1", "1vvj", "1vy4", "1vy5", "1vy6", "1vy7", "1xbp", "2j28", "2rdo", "2zjp", "2zjq", "2zjr", "3bbx", "3cf5", "3dll", "3j3v", "3j3w", "3j5l", "3j6b", "3j7z", "3j8g", "3j9w", "3j9y", "3j9z", "3ja1"...

1,117

[ "PUB00001241", "PUB00007068", "PUB00007069", "PUB00007070" ]

[ "8262035", "11297922", "11290319", "11114498" ]

[ "Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein.", "Atomic structures at last: the ribosome in 2000.", "The ribosome in focus.", "The end of the beginning: structural studies of ribosomal proteins." ]

[ 1993, 2001, 2001, 2000 ]

4

[ "IPR000702" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 24225, 3939, 438 ]

3

[ "Arabidopsis thaliana", "Escherichia coli (strain K12)", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)", "Schizosaccharomyces pombe (strain 972 / ATCC 24843)", "Zea mays" ]

[ 6, 1, 1, 10, 1, 1, 11 ]

7

true

Family

Large ribosomal subunit protein uL6, bacteria

Ribosomal_uL6_bact

6

IPR019907

19,907

Large ribosomal subunit protein uL6, archaea

Ribosomal_uL6_arc

Family

907

false

This protein family represents the archaeal ribosomal protein uL6. Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in ac...

[ "GO:0003735", "GO:0019843", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "rRNA binding", "translation", "ribosome" ]

[ "molecular_function", "molecular_function", "biological_process", "cellular_component" ]

4

[ "HAMAP", "NCBIFAM" ]

[ "MF_01365_A", "TIGR03653" ]

[ "Ribosomal_uL6_A", "uL6_arch" ]

[ 841, 896 ]

2

[]

0

[ "1ffk", "1jj2", "1k73", "1k8a", "1k9m", "1kc8", "1kd1", "1kqs", "1m1k", "1m90", "1n8r", "1nji", "1q7y", "1q81", "1q82", "1q86", "1qvf", "1qvg", "1s72", "1vq4", "1vq5", "1vq6", "1vq7", "1vq8", "1vq9", "1vqk", "1vql", "1vqm", "1vqn", "1vqo", "1vqp", "1w2b"...

92

[ "PUB00007068", "PUB00007069", "PUB00007070" ]

[ "11297922", "11290319", "11114498" ]

[ "Atomic structures at last: the ribosome in 2000.", "The ribosome in focus.", "The end of the beginning: structural studies of ribosomal proteins." ]

[ 2001, 2001, 2000 ]

3

[ "IPR000702" ]

[]

1

0

1

[ "Archaea", "Eukaryota", "unclassified sequences" ]

[ 887, 4, 16 ]

3

[]

0

true

Family

Large ribosomal subunit protein uL6, archaea

Ribosomal_uL6_arc

8

IPR019908

19,908

Endodeoxyribonuclease toxin RalR

Toxin_RalR

Family

482

false

RalR was originally thought to inhibit restriction modification [ ] but instead is part of a toxin/antitoxin system and functions as a non-specific DNase [ ]. Toxin RalR functions as a non-specific endonuclease that cleaves methylated and unmethylated DNA. The adjacent gene product, RalA (for RalR antitoxin), functions...

[]

0

[ "NCBIFAM" ]

[ "TIGR03655" ]

[ "anti_R_Lar" ]

[ 482 ]

1

[]

0

[]

0

[ "PUB00045450", "PUB00074292" ]

[ "7476171", "24748661" ]

[ "Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12.", "RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system in Escherichia coli." ]

[ 1995, 2014 ]

2

[]

0

null

[ "Bacteria", "Methanospirillum lacunae", "Viruses", "metagenomes" ]

[ 377, 1, 87, 17 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Endodeoxyribonuclease toxin RalR

Toxin_RalR

1

IPR019909

19,909

Haem uptake protein IsdC

Haem_uptake_protein_IsdC

Family

463

false

Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for haem scavenging from hemoproteins [ ]. The IsdB protein is only observed in Staphylococcus and consists of an N-terminal hydrophobic signal sequence, a pair of tandem NEAT (NEAr Transporter, )...

[ "GO:0030492", "GO:0015886", "GO:0009274" ]

[ "hemoglobin binding", "heme transport", "peptidoglycan-based cell wall" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "NCBIFAM" ]

[ "TIGR03656" ]

[ "IsdC" ]

[ 463 ]

1

[ "GP" ]

[ "GenProp0828" ]

[ "GP:GenProp0828" ]

1

[ "2k78", "2o6p" ]

2

[ "PUB00041777", "PUB00045368", "PUB00045371" ]

[ "17229211", "18676371", "18467329" ]

[ "Haem recognition by a Staphylococcus aureus NEAT domain.", "Demonstration of the iron-regulated surface determinant (Isd) heme transfer pathway in Staphylococcus aureus.", "Pathway for heme uptake from human methemoglobin by the iron-regulated surface determinants system of Staphylococcus aureus." ]

[ 2007, 2008, 2008 ]

3

[]

0

null

[ "Bacilli" ]

[ 463 ]

1

[]

0

true

Family

Haem uptake protein IsdC

Haem_uptake_protein_IsdC

2

IPR019910

19,910

Luciferase-like, F420-dependent oxidoreductase, MSMEG4879, predicted

Lucif-like_OxRdtase_MSMEG_4879

Family

2,009

false

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor [ ]. Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a...

[]

0

[ "NCBIFAM" ]

[ "TIGR03564" ]

[ "F420_MSMEG_4879" ]

[ 2009 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00014322", "PUB00014323", "PUB00014324", "PUB00014325" ]

[ "8703001", "7776372", "12445781", "10891279" ]

[ "The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.", "Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution.", "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD.", "Structure of coenzyme F(420)...

[ 1996, 1995, 2002, 2000 ]

4

[]

0

null

[ "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 1937, 6, 66 ]

3

[]

0

true

Family

Luciferase-like, F420-dependent oxidoreductase, MSMEG4879, predicted

Lucif-like_OxRdtase_MSMEG_4879

4

IPR019911

19,911

Alkanesulphonate monooxygenase, FMN-dependent

Alkanesulphonate_mOase_FMN-dep

Family

4,550

false

This entry represents a distinct group of proteins within the wider luciferase-like family of monooxygenases, including SsuD from E.coli and MsuD from P.fluorescens which are closely related [ , , ]. They catalyse the desulphonation of aliphatic sulfonates in an FMN-dependent fashion [ , ]. SsuD converts alkanesulfonat...

[ "GO:0008726" ]

[ "alkanesulfonate monooxygenase activity" ]

[ "molecular_function" ]

1

[ "HAMAP", "NCBIFAM" ]

[ "MF_01229", "TIGR03565" ]

[ "Alkanesulf_monooxygen", "alk_sulf_monoox" ]

[ 4396, 4541 ]

2

[ "EC", "GP", "GP" ]

[ "1.14.14.5", "GenProp0934", "GenProp1424" ]

[ "EC:1.14.14.5", "GP:GenProp0934", "GP:GenProp1424" ]

3

[ "1m41", "1nqk", "7jv3", "7jw9", "7jyb", "7k14", "7k64" ]

7

[ "PUB00014324", "PUB00019571", "PUB00103479" ]

[ "12445781", "10049377", "34029591" ]

[ "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD.", "A novel reduced flavin mononucleotide-dependent methanesulfonate sulfonatase encoded by the sulfur-regulated msu operon of Pseudomonas aeruginosa.", "Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond c...

[ 2002, 1999, 2021 ]

3

[ "IPR050172" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 4537, 4, 9 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Alkanesulphonate monooxygenase, FMN-dependent

Alkanesulphonate_mOase_FMN-dep

1

IPR019912

19,912

FMN reductase, MsuE-like

FMN_Rdtase_MsuE-like

Family

1,888

false

This entry represents a protein family that uses NAD(P)H to reduce FMN and regenerate FMNH2. Family members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulphonate monooxygenase.

[]

0

[ "NCBIFAM" ]

[ "TIGR03566" ]

[ "FMN_reduc_MsuE" ]

[ 1888 ]

1

[ "EC", "METACYC", "METACYC" ]

[ "1.5.1.42", "PWY-681", "PWY-7723" ]

[ "EC:1.5.1.42", "METACYC:PWY-681", "METACYC:PWY-7723" ]

3

[ "4c76" ]

1

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 1876, 6, 6 ]

3

[]

0

true

Family

FMN reductase, MsuE-like

FMN_Rdtase_MsuE-like

4

IPR019913

19,913

Pyrimidine utilisation protein RutD

Pyrimidine_utilisation_RutD

Family

1,204

false

RutD is encoded within the Rut operon which allows growth on pyrimidines as sole nitrogen source [ ]. The function of this protein is not known, but it is necessary for growth on pyrimidines, and cells lacking RutD produce much less of the Rut pathway intermediate malonic semialdehyde than normal [ ]. It is thought tha...

[ "GO:0016811", "GO:0006212" ]

[ "hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides", "uracil catabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00832", "TIGR03611" ]

[ "RutD", "RutD" ]

[ 1097, 1204 ]

2

[ "EC", "GP", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC" ]

[ "3.5.1.-", "GenProp0813", "PWY-1822", "PWY-5497", "PWY-5784", "PWY-5846", "PWY-6409", "PWY-6899", "PWY-7018", "PWY-7403", "PWY-7430", "PWY-7496", "PWY-7571", "PWY-7652", "PWY-7771", "PWY-7821", "PWY-7850", "PWY-8229", "PWY-8293", "PWY-8402", "PWY-8418", "PWY-8431", "PWY-8...

[ "EC:3.5.1.-", "GP:GenProp0813", "METACYC:PWY-1822", "METACYC:PWY-5497", "METACYC:PWY-5784", "METACYC:PWY-5846", "METACYC:PWY-6409", "METACYC:PWY-6899", "METACYC:PWY-7018", "METACYC:PWY-7403", "METACYC:PWY-7430", "METACYC:PWY-7496", "METACYC:PWY-7571", "METACYC:PWY-7652", "METACYC:PWY-777...

24

[ "3v48" ]

1

[ "PUB00033899", "PUB00056792" ]

[ "16540542", "20400551" ]

[ "A previously undescribed pathway for pyrimidine catabolism.", "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems." ]

[ 2006, 2010 ]

2

[]

0

null

[ "Acyrthosiphon pisum", "Pseudomonadota", "ecological metagenomes" ]

[ 1, 1200, 3 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Pyrimidine utilisation protein RutD

Pyrimidine_utilisation_RutD

2

IPR019914

19,914

Pyrimidine monooxygenase RutA

Pyrimidine_monooxygenase_RutA

Family

1,500

false

Pyrimidine monooxygenase RutA catalyzes the pyrimidine ring opening between N-3 and C-4 by an unusual flavin hydroperoxide-catalyzed mechanism to yield ureidoacrylate peracid [ , ]. It cleaves pyrmidine rings directly by adding oxygen atoms, making a toxic ureidoacrylate peracid product which can be spontaneously reduc...

[ "GO:0004497", "GO:0006212" ]

[ "monooxygenase activity", "uracil catabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_01699", "TIGR03612" ]

[ "RutA", "RutA" ]

[ 1471, 1494 ]

2

[ "EC", "GP" ]

[ "1.14.99.46", "GenProp0813" ]

[ "EC:1.14.99.46", "GP:GenProp0813" ]

2

[ "5wan", "6sgg", "6sgl", "6sgm", "6sgn", "6tee", "6tef", "6teg" ]

8

[ "PUB00033899", "PUB00056792", "PUB00056808" ]

[ "16540542", "20400551", "20369853" ]

[ "A previously undescribed pathway for pyrimidine catabolism.", "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.", "Catalysis of a flavoenzyme-mediated amide hydrolysis." ]

[ 2006, 2010, 2010 ]

3

[ "IPR050172" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes", "leotiomyceta" ]

[ 1412, 8, 80 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Pyrimidine monooxygenase RutA

Pyrimidine_monooxygenase_RutA

3

IPR019915

19,915

Transcription regulator, pyrimidine utilisation, RutR

Tscrpt_reg_pyr_util_RutR

Family

262

false

This entry represents a subset of the TetR family of transcriptional regulators. These proteins are encoded in operons responsible for the import and catabolism of pyrimidines, primarily uracil [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR03613" ]

[ "RutR" ]

[ 262 ]

1

[ "GP" ]

[ "GenProp0813" ]

[ "GP:GenProp0813" ]

1

[ "3loc", "4jyk", "4x1e", "4xk4", "6z1b" ]

5

[ "PUB00033899" ]

[ "16540542" ]

[ "A previously undescribed pathway for pyrimidine catabolism." ]

[ 2006 ]

1

[ "IPR050109" ]

[]

1

0

1

[ "Bacteria" ]

[ 262 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Transcription regulator, pyrimidine utilisation, RutR

Tscrpt_reg_pyr_util_RutR

9

IPR019916

19,916

Ureidoacrylate amidohydrolase RutB

RutB

Family

1,081

false

This entry represents the RutB subfamily of isochorismatases, which are peroxyureidoacrylate/ureidoacrylate amidohydrolases. They are encoded in operons responsible for the import and catabolism of pyrimidines, particularly uracil [ ].

[ "GO:0016811" ]

[ "hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides" ]

[ "molecular_function" ]

1

[ "HAMAP", "NCBIFAM" ]

[ "MF_00830", "TIGR03614" ]

[ "RutB", "RutB" ]

[ 1037, 1078 ]

2

[ "EC", "GP" ]

[ "3.5.1.110", "GenProp0813" ]

[ "EC:3.5.1.110", "GP:GenProp0813" ]

2

[ "8bkd", "8bll", "8blm", "8bln", "8byw" ]

5

[ "PUB00033899" ]

[ "16540542" ]

[ "A previously undescribed pathway for pyrimidine catabolism." ]

[ 2006 ]

1

[]

0

null

[ "Opisthokonta", "Pseudomonadati", "marine sediment metagenome" ]

[ 3, 1076, 2 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Ureidoacrylate amidohydrolase RutB

RutB

6

IPR019917

19,917

FMN reductase (NADH) RutF

RutF

Family

884

false

The Rut pathway allows cells to use pyrimidines as sole nitrogen source. The function of RutF in this pathway is to reduce FMN, producing FMNH2 which is subsequently used by RutA in opening the pyrimidine ring [ , , ].

[ "GO:0008752" ]

[ "FMN reductase [NAD(P)H] activity" ]

[ "molecular_function" ]

1

[ "HAMAP", "NCBIFAM" ]

[ "MF_00833", "TIGR03615" ]

[ "RutF", "RutF" ]

[ 848, 768 ]

2

[ "EC", "GP", "METACYC", "METACYC" ]

[ "1.5.1.42", "GenProp0813", "PWY-681", "PWY-7723" ]

[ "EC:1.5.1.42", "GP:GenProp0813", "METACYC:PWY-681", "METACYC:PWY-7723" ]

4

[]

0

[ "PUB00033899", "PUB00056792", "PUB00056808" ]

[ "16540542", "20400551", "20369853" ]

[ "A previously undescribed pathway for pyrimidine catabolism.", "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.", "Catalysis of a flavoenzyme-mediated amide hydrolysis." ]

[ 2006, 2010, 2010 ]

3

[]

0

null

[ "Pseudomonadota", "marine sediment metagenome" ]

[ 882, 2 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

FMN reductase (NADH) RutF

RutF

1

IPR019918

19,918

Pyrimidine permease RutG, predicted

Pyrimidine_permease_RutG_pred

Family

561

false

This entry represents a set of proteins that are part of the wider uracil-xanthine permease family. They are encoded in operons responsible for the import and catabolism of pyrimidines, primarily uracil, and are predicted to function as pyrimidine permeases [ , ].

[ "GO:0015218", "GO:0006864" ]

[ "pyrimidine nucleotide transmembrane transporter activity", "pyrimidine nucleotide transport" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR03616" ]

[ "RutG" ]

[ 561 ]

1

[ "GP" ]

[ "GenProp0813" ]

[ "GP:GenProp0813" ]

1

[]

0

[ "PUB00033899", "PUB00056792" ]

[ "16540542", "20400551" ]

[ "A previously undescribed pathway for pyrimidine catabolism.", "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems." ]

[ 2006, 2010 ]

2

[ "IPR006042" ]

[]

1

0

1

[ "Enterobacteria phage VT2-Sa", "Gammaproteobacteria" ]

[ 1, 560 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Pyrimidine permease RutG, predicted

Pyrimidine_permease_RutG_pred

3

IPR019919

19,919

Luciferase-like, F420-dependent oxidoreductase, MSMEG2256, predicted

Lucif-like_OxRdtase_MSMEG_2256

Family

2,090

false

F420 is a flavin derivative that functions as a redox coenzyme in methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea (strain 34H / ATCC BAA-681), Rhodopseudomonas palustris (strain HaA2), amongst others. A number of luciferase-like protein subfamilies appear only in F420-pos...

[]

0

[ "NCBIFAM" ]

[ "TIGR03617" ]

[ "F420_MSMEG_2256" ]

[ 2090 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00014322", "PUB00014323", "PUB00014324", "PUB00014325" ]

[ "8703001", "7776372", "12445781", "10891279" ]

[ "The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.", "Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution.", "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD.", "Structure of coenzyme F(420)...

[ 1996, 1995, 2002, 2000 ]

4

[ "IPR050564" ]

[]

1

0

1

[ "Archaea", "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 26, 1934, 9, 121 ]

4

[]

0

true

Family

Luciferase-like, F420-dependent oxidoreductase, MSMEG2256, predicted

Lucif-like_OxRdtase_MSMEG_2256

3

IPR019920

19,920

F420-binding domain, putative

F420-binding_dom_put

Domain

15,382

false

It has been estimated that just over ten percent of all genome-sequenced prokaryotes, including most actinomycetes, use F420 as a redox coenzyme. This entry represents a set of predicted F420-binding enzymes. The Rv1155 protein from Mycobacterium tuberculosis has been crystallised and its structure shown to broadly res...

[]

0

[ "NCBIFAM" ]

[ "TIGR03618" ]

[ "Rv1155_F420" ]

[ 15382 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[ "1rfe", "1w9a", "1xxo", "1y30", "2aq6", "2asf", "3f7e", "4qvb", "5jab" ]

9

[ "PUB00032214" ]

[ "15620716" ]

[ "Crystal structure of the conserved hypothetical protein Rv1155 from Mycobacterium tuberculosis." ]

[ 2005 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Geodia barretti", "metagenomes" ]

[ 280, 14963, 4, 135 ]

4

[]

0

true

Domain

F420-binding domain, putative

F420-binding_dom_put

7

IPR019921

19,921

Luciferase-like, F420-dependent oxidoreductase, Rv2161c, predicted

Lucif-like_OxRdtase_Rv2161c

Domain

12,469

false

F420 is a flavin derivative that functions as a redox coenzyme in methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea (strain 34H / ATCC BAA-681), Rhodopseudomonas palustris (strain HaA2), amongst others. A number of luciferase-like protein subfamilies appear only in F420-pos...

[]

0

[ "NCBIFAM" ]

[ "TIGR03619" ]

[ "F420_Rv2161c" ]

[ 12469 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00014322", "PUB00014323", "PUB00014324", "PUB00014325" ]

[ "8703001", "7776372", "12445781", "10891279" ]

[ "The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.", "Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution.", "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD.", "Structure of coenzyme F(420)...

[ 1996, 1995, 2002, 2000 ]

4

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 129, 11817, 36, 487 ]

4

[]

0

true

Domain

Luciferase-like, F420-dependent oxidoreductase, Rv2161c, predicted

Lucif-like_OxRdtase_Rv2161c

4

IPR019922

19,922

Luciferase-like, F420-dependent oxidoreductase, MSMEG4141, predicted

Lucif-like_OxRdatse_MSMEG_4141

Family

3,729

false

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor [ ]. Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a...

[]

0

[ "NCBIFAM" ]

[ "TIGR03620" ]

[ "F420_MSMEG_4141" ]

[ 3729 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00014322", "PUB00014323", "PUB00014324", "PUB00014325" ]

[ "8703001", "7776372", "12445781", "10891279" ]

[ "The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.", "Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution.", "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD.", "Structure of coenzyme F(420)...

[ 1996, 1995, 2002, 2000 ]

4

[]

0

null

[ "Bacteria", "unclassified sequences" ]

[ 3657, 72 ]

2

[]

0

true

Family

Luciferase-like, F420-dependent oxidoreductase, MSMEG4141, predicted

Lucif-like_OxRdatse_MSMEG_4141

7

IPR019923

19,923

Luciferase-like, F420-dependent oxidoreductase, MSMEG2516, predicted

Lucif-like_OxRdtase_MSMEG_2516

Family

2,218

false

Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor [ ]. Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a...

[]

0

[ "NCBIFAM" ]

[ "TIGR03621" ]

[ "F420_MSMEG_2516" ]

[ 2218 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[ "9g64", "9gkh", "9gm0", "9gnc", "9gnd" ]

5

[ "PUB00014322", "PUB00014323", "PUB00014324", "PUB00014325" ]

[ "8703001", "7776372", "12445781", "10891279" ]

[ "The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions.", "Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution.", "Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD.", "Structure of coenzyme F(420)...

[ 1996, 1995, 2002, 2000 ]

4

[ "IPR050172" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 2143, 75 ]

2

[]

0

true

Family

Luciferase-like, F420-dependent oxidoreductase, MSMEG2516, predicted

Lucif-like_OxRdtase_MSMEG_2516

3

IPR019925

19,925

DNA repair protein, predicted

DNA_repair_protein_predicted

Family

680

false

This entry represents a family of bacterial proteins which are about 900 amino acids in length. They are homologous to the AddB protein ( ), which repairs double-strand DNA breaks via homologous recombination, and are predicted to function in DNA repair.

[]

0

[ "NCBIFAM" ]

[ "TIGR03623" ]

[ "" ]

[ 680 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 647, 33 ]

2

[]

0

true

Family

DNA repair protein, predicted

DNA_repair_protein_predicted

5

IPR019927

19,927

Large ribosomal subunit protein uL3, bacteria/organella

Ribosomal_uL3_bact_org

Family

31,219

false

This entry represents bacterial, mitochondrial and chloroplast uL3 proteins. The organelle proteins typically contain a transit peptide sequence located N-terminal to the region covered by this entry. Ribosomal protein L3 (also known as uL3) is one of the proteins from the large ribosomal subunit. In Escherichia coli, ...

[ "GO:0003735", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "translation", "ribosome" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "HAMAP", "PANTHER", "NCBIFAM" ]

[ "MF_01325_B", "PTHR11229", "TIGR03625" ]

[ "Ribosomal_uL3_B", "", "L3_bact" ]

[ 25493, 31196, 29844 ]

3

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-BTA-5389840", "R-BTA-5419276", "R-BTA-9937383", "R-CEL-5389840", "R-CEL-5419276", "R-CEL-9937383", "R-HSA-5368286", "R-HSA-5389840", "R-HSA-5419276", "R-HSA-9937383", "R-MMU-5389840", "R-MMU-5419276", "R-MMU-9937383", "R-RNO-5389840", "R-RNO-5419276", "R-RNO-9937383" ]

[ "REACTOME:R-BTA-5389840", "REACTOME:R-BTA-5419276", "REACTOME:R-BTA-9937383", "REACTOME:R-CEL-5389840", "REACTOME:R-CEL-5419276", "REACTOME:R-CEL-9937383", "REACTOME:R-HSA-5368286", "REACTOME:R-HSA-5389840", "REACTOME:R-HSA-5419276", "REACTOME:R-HSA-9937383", "REACTOME:R-MMU-5389840", "REACTOM...

16

[ "1nkw", "1nwx", "1nwy", "1sm1", "1vvj", "1vy4", "1vy5", "1vy6", "1vy7", "1xbp", "2ftc", "2j28", "2ogm", "2ogn", "2ogo", "2rdo", "2zjp", "2zjq", "2zjr", "3bbx", "3cf5", "3dll", "3iy9", "3j3v", "3j3w", "3j5l", "3j6b", "3j7y", "3j7z", "3j8g", "3j9m", "3j9w"...

1,294

[ "PUB00001418", "PUB00001424", "PUB00002601", "PUB00007068", "PUB00007069", "PUB00007070", "PUB00087081" ]

[ "1597181", "1499563", "2406244", "11297922", "11290319", "11114498", "24675956" ]

[ "YmL9, a nucleus-encoded mitochondrial ribosomal protein of yeast, is homologous to L3 ribosomal proteins from all natural kingdoms and photosynthetic organelles.", "Primary structures of ribosomal proteins L3 and L4 from Bacillus stearothermophilus.", "Organization and nucleotide sequence of a gene cluster cod...

[ 1992, 1992, 1990, 2001, 2001, 2000, 2014 ]

7

[ "IPR000597" ]

[]

1

0

1

[ "Bacteria", "Candidatus Methanofastidiosum methylothiophilum", "Eukaryota", "unclassified sequences" ]

[ 24698, 1, 6046, 474 ]

4

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 7, 1, 2, 2, 1, 7, 6, 1, 8, 5, 1, 1, 12 ]

13

true

Family

Large ribosomal subunit protein uL3, bacteria/organella

Ribosomal_uL3_bact_org

7

IPR019928

19,928

Large ribosomal subunit protein uL3, archaea

Ribosomal_uL3_arc

Family

953

false

This entry represents archaeal uL3 proteins. Ribosomal protein L3 (also known as uL3) is one of the proteins from the large ribosomal subunit. In Escherichia coli, L3 is known to bind to the 23S rRNA and may participate in the formation of the peptidyltransferase centre of the ribosome. It belongs to a family of riboso...

[ "GO:0003735", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "translation", "ribosome" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "HAMAP", "NCBIFAM" ]

[ "MF_01325_A", "TIGR03626" ]

[ "Ribosomal_uL3_A", "L3_arch" ]

[ 771, 938 ]

2

[]

0

[ "1ffk", "1jj2", "1k73", "1k8a", "1k9m", "1kc8", "1kd1", "1kqs", "1m1k", "1m90", "1ml5", "1n8r", "1nji", "1q7y", "1q81", "1q82", "1q86", "1qvf", "1qvg", "1s72", "1vq4", "1vq5", "1vq6", "1vq7", "1vq8", "1vq9", "1vqk", "1vql", "1vqm", "1vqn", "1vqo", "1vqp"...

98

[ "PUB00001418", "PUB00001424", "PUB00002601", "PUB00007068", "PUB00007069", "PUB00007070", "PUB00087081" ]

[ "1597181", "1499563", "2406244", "11297922", "11290319", "11114498", "24675956" ]

[ "YmL9, a nucleus-encoded mitochondrial ribosomal protein of yeast, is homologous to L3 ribosomal proteins from all natural kingdoms and photosynthetic organelles.", "Primary structures of ribosomal proteins L3 and L4 from Bacillus stearothermophilus.", "Organization and nucleotide sequence of a gene cluster cod...

[ 1992, 1992, 1990, 2001, 2001, 2000, 2014 ]

7

[ "IPR045077" ]

[]

1

0

1

[ "Archaea", "Eukaryota", "ecological metagenomes" ]

[ 907, 21, 25 ]

3

[]

0

true

Family

Large ribosomal subunit protein uL3, archaea

Ribosomal_uL3_arc

2

IPR019929

19,929

Iron-regulated surface determinant protein IsdB

Iron-reg_IsdB

Family

37

false

Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for haem scavenging from hemoproteins [ ]. The IsdB protein is only observed in Staphylococcus and consists of an N-terminal hydrophobic signal sequence, a pair of tandem NEAT (NEAr Transporter, )...

[ "GO:0015232", "GO:0015886", "GO:0005618" ]

[ "heme transmembrane transporter activity", "heme transport", "cell wall" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "NCBIFAM" ]

[ "TIGR03657" ]

[ "IsdB" ]

[ 37 ]

1

[ "GP" ]

[ "GenProp0828" ]

[ "GP:GenProp0828" ]

1

[]

0

[ "PUB00041777", "PUB00045368", "PUB00045371", "PUB00058917", "PUB00060964" ]

[ "17229211", "18676371", "18467329", "21574663", "19398548" ]

[ "Haem recognition by a Staphylococcus aureus NEAT domain.", "Demonstration of the iron-regulated surface determinant (Isd) heme transfer pathway in Staphylococcus aureus.", "Pathway for heme uptake from human methemoglobin by the iron-regulated surface determinants system of Staphylococcus aureus.", "Unique h...

[ 2007, 2008, 2008, 2011, 2009 ]

5

[]

0

null

[ "Staphylococcus" ]

[ 37 ]

1

[]

0

true

Family

Iron-regulated surface determinant protein IsdB

Iron-reg_IsdB

5

IPR019930

19,930

Iron-regulated surface determinant protein H

IsdH

Family

36

false

HarA (also known as isdH) is a haem-binding NEAT-domain (NEAr Transporter, ) protein which has been shown to bind to the haptoglobin-hemoglobin complex in order to extract haem from it. HarA has also been reported to bind haemoglobin directly [ ]. HarA (also known as IsdH) contains three NEAT domains as well as a sorta...

[ "GO:0020037" ]

[ "heme binding" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR03658" ]

[ "IsdH_HarA" ]

[ 36 ]

1

[ "GP" ]

[ "GenProp0828" ]

[ "GP:GenProp0828" ]

1

[]

0

[ "PUB00043982", "PUB00045368" ]

[ "16762363", "18676371" ]

[ "Solution structure of the NEAT (NEAr Transporter) domain from IsdH/HarA: the human hemoglobin receptor in Staphylococcus aureus.", "Demonstration of the iron-regulated surface determinant (Isd) heme transfer pathway in Staphylococcus aureus." ]

[ 2006, 2008 ]

2

[]

0

null

[ "Staphylococcus" ]

[ 36 ]

1

[]

0

true

Family

Iron-regulated surface determinant protein H

IsdH

5

IPR019931

19,931

LPXTG cell wall anchor motif

LPXTG_anchor

Conserved_site

38,182

false

Surface proteins from Gram-positive cocci are covalently linked to the bacterial cell wall by sortase, a membrane-anchored transpeptidase that cleaves proteins between the threonine and the glycine of a conserved LPxTG motif, with the formation of a thioester between the conserved cysteine of sortase and the threonine ...

[]

0

[ "PFAM", "PROFILE" ]

[ "PF00746", "PS50847" ]

[ "Gram_pos_anchor", "GRAM_POS_ANCHORING" ]

[ 26492, 29827 ]

2

[ "GP", "REACTOME" ]

[ "GenProp0626", "R-HSA-8876493" ]

[ "GP:GenProp0626", "REACTOME:R-HSA-8876493" ]

2

[ "4z1p", "5xxz", "5xya", "5xyr", "7woi", "8xvp", "8xvq" ]

7

[ "PUB00007890", "PUB00007952", "PUB00007953" ]

[ "10427003", "11856734", "9423856" ]

[ "Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall.", "Anchoring of surface proteins to the cell wall of Staphylococcus aureus. III. Lipid II is an in vivo peptidoglycan substrate for sortase-catalyzed surface protein anchoring.", "A comprehensive genetic study of streptoco...

[ 1999, 2002, 1998 ]

3

[]

0

null

[ "Archaea", "Bacteria", "Caudoviricetes", "Eukaryota", "unclassified sequences" ]

[ 25, 37932, 29, 75, 121 ]

5

[ "Homo sapiens", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)" ]

[ 1, 1 ]

2

true

Conserved_site

LPXTG cell wall anchor motif

LPXTG_anchor

7

IPR019932

19,932

Conserved hypothetical protein CHP03543

CHP03543

Family

1,305

false

Members of this protein family contain two full and two partial repeats of a domain found at the N terminus of Bacillus subtilis cell-division initiation protein DivIVA. The portion repeated four times in these proteins includes the motif GYxxxxVD.

[]

0

[ "NCBIFAM" ]

[ "TIGR03543" ]

[ "divI1A_rptt_fam" ]

[ 1305 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 1296, 9 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP03543

CHP03543

3

IPR019933

19,933

DivIVA domain

DivIVA_domain

Domain

19,747

false

This entry describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologues, toward the N terminus. It is also found as a repeated domain in other proteins. This domain forms a parallel coiled-coil which is capped with two unique crossed and intertwined loops, exposing hydrophobic a...

[]

0

[ "NCBIFAM" ]

[ "TIGR03544" ]

[ "DivI1A_domain" ]

[ 19747 ]

1

[]

0

[ "2wuj", "2wuk", "4ug1", "4ug3", "6gp7", "6gpz", "6gqa", "6gqn", "6lfa", "7o39", "8e2b", "8e2c", "9pv2" ]

13

[ "PUB00054393", "PUB00151021" ]

[ "20502438", "32695423" ]

[ "Features critical for membrane binding revealed by DivIVA crystal structure.", "Structural basis of self-assembly in the lipid-binding domain of mycobacterial polar growth factor Wag31." ]

[ 2010, 2020 ]

2

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 19529, 5, 213 ]

3

[]

0

true

Domain

DivIVA domain

DivIVA_domain

4

IPR019934

19,934

Conserved hypothetical protein CHP03545

CHP03545

Family

397

false

This entry represents a relatively rare but broadly distributed uncharacterised protein family from bacterial species with outer membranes. In many of these genomes, members of this family are encoded as part of a two-gene pair.

[]

0

[ "NCBIFAM" ]

[ "TIGR03545" ]

[ "" ]

[ 397 ]

1

[ "GP" ]

[ "GenProp0790" ]

[ "GP:GenProp0790" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 391, 6 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP03545

CHP03545

2

IPR019935

19,935

Conserved hypothetical protein CHP03546

CHP03546

Family

385

false

Members of this family are uncharacterised proteins, usually encoded by a gene adjacent to a member of family , which is also uncharacterised.

[]

0

[ "NCBIFAM" ]

[ "TIGR03546" ]

[ "" ]

[ 385 ]

1

[ "GP" ]

[ "GenProp0790" ]

[ "GP:GenProp0790" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 378, 7 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP03546

CHP03546

9

IPR019936

19,936

N-acetylneuraminate epimerase, proteobacteria

NanM_proteobact

Family

1,322

false

This entry represents N-acetylneuraminate epimerase from Escherichia coli (NanM, also known as YjhT) and similar proteobacterial proteins. NanM converts alpha-N-acetylneuranimic acid (Neu5Ac) to the beta-anomer, accelerating the equilibrium between the alpha- and beta-anomers. This enzyme probably facilitates sialidase...

[]

0

[ "HAMAP", "NCBIFAM" ]

[ "MF_01195", "TIGR03547" ]

[ "NanM", "muta_rot_YjhT" ]

[ 716, 1322 ]

2

[ "EC" ]

[ "5.1.3.24" ]

[ "EC:5.1.3.24" ]

1

[ "2uvk" ]

1

[ "PUB00045883", "PUB00099659" ]

[ "18063573", "33895133" ]

[ "Sialic acid mutarotation is catalyzed by the Escherichia coli beta-propeller protein YjhT.", "The metalloprotein YhcH is an anomerase providing N-acetylneuraminate aldolase with the open form of its substrate." ]

[ 2008, 2021 ]

2

[ "IPR056734" ]

[]

1

0

1

[ "Bacteria" ]

[ 1322 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

N-acetylneuraminate epimerase, proteobacteria

NanM_proteobact

1

IPR019938

19,938

YcaO domain protein

YcaO_dom_prot

Family

1,775

false

This family consists of remarkably well-conserved proteins from gamma and beta Proteobacteria, heavily skewed towards organisms of marine environments. Its gene neighbourhood is not conserved. This family has an OsmC-like N-terminal domain. It shares a YcaO domain, frequently associated with ATP-dependent cyclodehydrat...

[]

0

[ "NCBIFAM" ]

[ "TIGR03549" ]

[ "" ]

[ 1775 ]

1

[]

0

[]

0

[ "PUB00064880" ]

[ "22522320" ]

[ "YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations." ]

[ 2012 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 1768, 2, 5 ]

3

[]

0

true

Family

YcaO domain protein

YcaO_dom_prot

2

IPR019939

19,939

CofG family

CofG_family

Family

4,650

false

This entry represents either a subunit (CofG/subunit 1) or the N-terminal domain of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO [ ]. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineag...

[ "GO:0016765", "GO:0051539" ]

[ "transferase activity, transferring alkyl or aryl (other than methyl) groups", "4 iron, 4 sulfur cluster binding" ]

[ "molecular_function", "molecular_function" ]

2

[ "HAMAP", "SFLD", "NCBIFAM" ]

[ "MF_01611", "SFLDF00294", "TIGR03550" ]

[ "FO_synth_sub1", "7_8-didemethyl-8-hydroxy-5-dea", "F420_cofG" ]

[ 4565, 4574, 4626 ]

3

[ "EC", "GP", "METACYC", "METACYC", "METACYC" ]

[ "4.3.1.32", "GenProp0792", "PWY-5198", "PWY-8112", "PWY-8113" ]

[ "EC:4.3.1.32", "GP:GenProp0792", "METACYC:PWY-5198", "METACYC:PWY-8112", "METACYC:PWY-8113" ]

5

[]

0

[ "PUB00045884" ]

[ "14593448" ]

[ "Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F(420) biosynthesis." ]

[ 2003 ]

1

[ "IPR034405" ]

[]

1

0

1

[ "Archaea", "Bacteria", "Eukaryota", "metagenomes" ]

[ 658, 3755, 112, 125 ]

4

[]

0

true

Family

CofG family

CofG_family

5

IPR019940

19,940

CofH family

CofH_family

Family

4,239

false

This enzyme (CofH), together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases [ ]. CofH catalyzes the radical-mediated synthesis of 5-amino-5-(4-hydroxybenzyl)-6-(D-ribitylimino)-5...

[ "GO:0016765" ]

[ "transferase activity, transferring alkyl or aryl (other than methyl) groups" ]

[ "molecular_function" ]

1

[ "HAMAP", "SFLD", "NCBIFAM" ]

[ "MF_01612", "SFLDF00293", "TIGR03551" ]

[ "FO_synth_sub2", "((2_3_4_5-tetrahydroxypentyl)a", "F420_cofH" ]

[ 4069, 3068, 4193 ]

3

[ "EC", "GP", "METACYC", "METACYC", "METACYC" ]

[ "2.5.1.147", "GenProp0792", "PWY-5198", "PWY-8112", "PWY-8113" ]

[ "EC:2.5.1.147", "GP:GenProp0792", "METACYC:PWY-5198", "METACYC:PWY-8112", "METACYC:PWY-8113" ]

5

[]

0

[ "PUB00045884", "PUB00092595" ]

[ "14593448", "25781338" ]

[ "Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme F(420) biosynthesis.", "Biosynthetic versatility and coordinated action of 5'-deoxyadenosyl radicals in deazaflavin biosynthesis." ]

[ 2003, 2015 ]

2

[ "IPR020050" ]

[]

1

0

1

[ "Archaea", "Bacteria", "Eukaryota", "metagenomes" ]

[ 503, 3511, 101, 124 ]

4

[]

0

true

Family

CofH family

CofH_family

9

IPR019941

19,941

Transcription regulator LuxR, chaperone HchA-associated

Tscrpt_reg_LuxR_HchA-assoc

Family

246

false

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding ( ) and transcriptional regulator ( ) domains. Members of this family only occur adjacent to the gene hchA (Hsp31, [ , ]) and are found in only a few gammaproteobacteria.

[]

0

[ "NCBIFAM" ]

[ "TIGR03541" ]

[ "reg_near_HchA" ]

[ 246 ]

1

[]

0

[]

0

[ "PUB00060586", "PUB00153445" ]

[ "21696459", "28235098" ]

[ "Hsp31 of Escherichia coli K-12 is glyoxalase III.", "Structural and biochemical studies on Vibrio cholerae Hsp31 reveals a novel dimeric form and Glutathione-independent Glyoxalase activity." ]

[ 2011, 2017 ]

2

[]

0

null

[ "Bacteria" ]

[ 246 ]

1

[]

0

true

Family

Transcription regulator LuxR, chaperone HchA-associated

Tscrpt_reg_LuxR_HchA-assoc

8

IPR019942

19,942

LL-diaminopimelate aminotransferase/aminotransferase ALD1

DapL/ALD1

Family

4,544

false

Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some alg...

[ "GO:0008483" ]

[ "transaminase activity" ]

[ "molecular_function" ]

1

[ "HAMAP", "PANTHER", "NCBIFAM" ]

[ "MF_01642", "PTHR43144", "TIGR03542" ]

[ "DapL_aminotrans_1", "", "DAPAT_plant" ]

[ 3336, 4304, 3860 ]

3

[ "EC", "GP", "METACYC" ]

[ "2.6.1.83", "GenProp0125", "PWY-5097" ]

[ "EC:2.6.1.83", "GP:GenProp0125", "METACYC:PWY-5097" ]

3

[ "2z1z", "2z20", "3asa", "3asb", "3ei5", "3ei6", "3ei7", "3ei8", "3ei9", "3eia", "3eib", "3qgu", "4fl0", "6oxm" ]

14

[ "PUB00045445", "PUB00055043", "PUB00086413", "PUB00086414" ]

[ "17093042", "20418392", "23221596", "27758894" ]

[ "L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine.", "Methanococci use the diaminopimelate aminotransferase (DapL) pathway for lysine biosynthesis.", "Pipecolic acid, an endogenous mediator of defense amplification and priming, i...

[ 2006, 2010, 2012, 2016 ]

4

[]

[ "IPR019881" ]

0

1

0

[ "Archaea", "Bacteria", "Eukaryota", "metagenomes" ]

[ 54, 2638, 1776, 76 ]

4

[ "Arabidopsis thaliana", "Oryza sativa subsp. japonica", "Zea mays" ]

[ 7, 4, 19 ]

3

true

Family

LL-diaminopimelate aminotransferase/aminotransferase ALD1

DapL/ALD1

5

IPR019943

19,943

Coenzyme F420 biosynthesis protein FbiB, C-terminal

F420_FbiB_C

Domain

2,182

false

Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5 to 6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems l...

[ "GO:0016881" ]

[ "acid-amino acid ligase activity" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR03553" ]

[ "F420_FbiB_CTERM" ]

[ 2182 ]

1

[ "EC", "EC", "EC", "GP", "METACYC", "METACYC" ]

[ "1.3.8.17", "6.3.2.31", "6.3.2.34", "GenProp0791", "PWY-5198", "PWY-5199" ]

[ "EC:1.3.8.17", "EC:6.3.2.31", "EC:6.3.2.34", "GP:GenProp0791", "METACYC:PWY-5198", "METACYC:PWY-5199" ]

6

[ "4xom", "4xoo", "4xoq" ]

3

[]

0

[ "IPR029479" ]

[]

1

0

1

[ "Actinomycetes", "freshwater metagenome" ]

[ 2170, 12 ]

2

[]

0

true

Domain

Coenzyme F420 biosynthesis protein FbiB, C-terminal

F420_FbiB_C

7

IPR019944

19,944

F420-dependent glucose-6-phosphate dehydrogenase

F420-dep_G6P_DH

Family

1,567

false

This family consists of the F420-dependent glucose-6-phosphate dehydrogenase of Mycobacterium and Nocardia [ , , ]. It shows homology to several other F420-dependent enzymes rather than to the NAD or NADP-dependent glucose-6-phosphate dehydrogenases [ ].

[]

0

[ "HAMAP", "NCBIFAM" ]

[ "MF_02123", "TIGR03554" ]

[ "F420_G6P_DH", "F420_G6P_DH" ]

[ 1131, 1567 ]

2

[ "EC", "GP", "REACTOME" ]

[ "1.1.98.2", "GenProp0002", "R-HSA-1222541" ]

[ "EC:1.1.98.2", "GP:GenProp0002", "REACTOME:R-HSA-1222541" ]

3

[ "3b4y", "3c8n", "5lxe" ]

3

[ "PUB00045886", "PUB00060753", "PUB00060754", "PUB00060755" ]

[ "9555906", "8631674", "20075070", "10879539" ]

[ "Molecular analysis of the gene encoding F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis.", "Purification of a novel coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Mycobacterium smegmatis.", "Glucose 6-phosphate accumulation in mycobacteria: implications for a novel...

[ 1998, 1996, 2010, 2000 ]

4

[ "IPR019945" ]

[]

1

0

1

[ "Bacteria", "freshwater metagenome" ]

[ 1565, 2 ]

2

[]

0

true

Family

F420-dependent glucose-6-phosphate dehydrogenase

F420-dep_G6P_DH

8

IPR019945

19,945

F420-dependent glucose-6-phosphate dehydrogenase-related

F420_G6P_DH-rel

Family

7,651

false

Members of this protein family include F420-dependent glucose-6-phosphate dehydrogenases ( ) and related proteins. All members of this family come from species that synthesise coenzyme F420, with the exception of those that belong to , a subgroup within this family in which cofactor binding may instead be directed to F...

[]

0

[ "NCBIFAM" ]

[ "TIGR03557" ]

[ "F420_G6P_family" ]

[ 7651 ]

1

[ "EC", "GP", "REACTOME" ]

[ "1.1.98.2", "GenProp0002", "R-HSA-1222541" ]

[ "EC:1.1.98.2", "GP:GenProp0002", "REACTOME:R-HSA-1222541" ]

3

[ "1rhc", "3b4y", "3c8n", "5lxe", "9fp4", "9fpp" ]

6

[ "PUB00055044" ]

[ "20675471" ]

[ "Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria." ]

[ 2010 ]

1

[]

[ "IPR019944", "IPR023907", "IPR031017" ]

0

3

0

[ "Archaea", "Bacteria", "Eukaryota", "metagenomes" ]

[ 348, 7284, 2, 17 ]

4

[]

0

true

Family

F420-dependent glucose-6-phosphate dehydrogenase-related

F420_G6P_DH-rel

3

IPR019946

19,946

5,10-methylenetetrahydromethanopterin reductase

MeH4methanopterin_reductase

Family

593

false

Members of this protein family are 5,10-methylenetetrahydromethanopterin reductase, an F420-dependent enzyme of methanogenesis [ ]. It is restricted to the Archaea.

[ "GO:0018537" ]

[ "coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity" ]

[ "molecular_function" ]

1

[ "HAMAP", "NCBIFAM", "NCBIFAM" ]

[ "MF_01091", "NF002619", "TIGR03555" ]

[ "F420_mer", "PRK02271.1", "F420_mer" ]

[ 586, 589, 251 ]

3

[ "EC", "GP", "METACYC", "METACYC", "METACYC" ]

[ "1.5.98.2", "GenProp0002", "PWY-5209", "PWY-7784", "PWY-8305" ]

[ "EC:1.5.98.2", "GP:GenProp0002", "METACYC:PWY-5209", "METACYC:PWY-7784", "METACYC:PWY-8305" ]

5

[ "1ezw", "1f07", "1z69", "8qpl", "8qpm", "8qq8" ]

6

[ "PUB00071486" ]

[ "2298726" ]

[ "Purification and properties of 5,10-methylenetetrahydromethanopterin reductase, a coenzyme F420-dependent enzyme, from Methanobacterium thermoautotrophicum strain delta H." ]

[ 1990 ]

1

[]

0

null

[ "Archaea", "ecological metagenomes" ]

[ 588, 5 ]

2

[]

0

true

Family

5,10-methylenetetrahydromethanopterin reductase

MeH4methanopterin_reductase

5

IPR019947

19,947

DNA photolyase class 1, 8-HDF type

Photolyase_8HDF

Family

48

false

This entry describes a narrow clade of cyanobacterial deoxyribodipyrimidine photolyase (or DNA photolyase). This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA ph...

[]

0

[ "NCBIFAM" ]

[ "TIGR03556" ]

[ "photolyase_8HDF" ]

[ 48 ]

1

[]

0

[ "1owl", "1owm", "1own", "1owo", "1owp", "1qnf", "1tez" ]

7

[ "PUB00001269", "PUB00076729", "PUB00076730", "PUB00076734", "PUB00076735", "PUB00163231" ]

[ "7813451", "25910181", "26352435", "10896222", "11254140", "22066008" ]

[ "A new class of DNA photolyases present in various organisms including aplacental mammals.", "Binding of Substrate Locks the Electrochemistry of CRY-DASH into DNA Repair.", "Evolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes.", "PhrA, the major photoreactivating factor in the cyanob...

[ 1994, 2015, 2015, 2000, 2001, 2011 ]

6

[ "IPR002081" ]

[]

1

0

1

[ "Cyanophyceae" ]

[ 48 ]

1

[]

0

true

Family

DNA photolyase class 1, 8-HDF type

Photolyase_8HDF

7

IPR019949

19,949

N-acetyl-S-alkylcysteine monooxygenase-like

CmoO-like

Family

22,898

false

This entry represents a family of prokaryotic alkanal monooxygenase, including Luciferase-like monooxygenase from Escherichia coli (YhbW) and N-acetyl-S-alkylcysteine monooxygenase from Bacillus subtilis (CmoO). CmoO is involved in a cysteine salvage pathway from S-alkylcysteine, which is likely important in the catabo...

[]

0

[ "NCBIFAM" ]

[ "TIGR03558" ]

[ "oxido_grp_1" ]

[ 22898 ]

1

[]

0

[ "4us5" ]

1

[ "PUB00103904", "PUB00106750" ]

[ "35584544", "24554499" ]

[ "Cysteine Dealkylation in <i>Bacillus subtilis</i> by a Novel Flavin-Dependent Monooxygenase.", "Insights into the bioactivity of mensacarcin and epoxide formation by MsnO8." ]

[ 2022, 2014 ]

2

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 251, 22509, 25, 113 ]

4

[ "Arabidopsis thaliana", "Escherichia coli (strain K12)" ]

[ 1, 1 ]

2

true

Family

N-acetyl-S-alkylcysteine monooxygenase-like

CmoO-like

2

IPR019950

19,950

M protein-type anchor motif

M_anchor

Conserved_site

851

false

Viruses, parasites and bacteria are covered in protein and sugar molecules that help them gain entry into a host by counteracting the host's defences. One such molecule is the M protein produced by certain streptococcal bacteria [ ]. M proteins embody an anchor motif that is now known to be shared by many Gram-positive...

[]

0

[ "PRINTS" ]

[ "PR00015" ]

[ "GPOSANCHOR" ]

[ 851 ]

1

[]

0

[]

0

[ "PUB00002106", "PUB00003798", "PUB00080447" ]

[ "2188957", "2287281", "26866233" ]

[ "Sequence and structural characteristics of the trypsin-resistant T6 surface protein of group A streptococci.", "Conservation of a hexapeptide sequence in the anchor region of surface proteins from gram-positive cocci.", "M Protein and Other Surface Proteins on Streptococci" ]

[ 1990, 1990, 0 ]

3

[]

0

null

[ "Lactobacillales" ]

[ 851 ]

1

[]

0

true

Conserved_site

M protein-type anchor motif

M_anchor

3

IPR019951

19,951

F420-dependent oxidoreductase-predicted, Rv3520c

F420_OxRdatse_Rv3520c_pred

Family

5,831

false

Members of this protein family are predicted to be oxidoreductases dependent on coenzyme F420. The family includes a single member in Mycobacterium tuberculosis (Rv3520c/MT3621) but four in Mycobacterium smegmatis. Prediction that this family is F420-dependent is based primarily on Partial Phylogenetic Profiling vs. F4...

[]

0

[ "NCBIFAM" ]

[ "TIGR03559" ]

[ "F420_Rv3520c" ]

[ 5831 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00055044" ]

[ "20675471" ]

[ "Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria." ]

[ 2010 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 5668, 9, 154 ]

3

[]

0

true

Family

F420-dependent oxidoreductase-predicted, Rv3520c

F420_OxRdatse_Rv3520c_pred

2

IPR019952

19,952

F420-dependent oxidoreductase-predicted, Rv1855c

F420_OxRdatse_Rv1855c_pred

Family

7,752

false

Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea (strain 34H / ATCC BAA-681), Rhodopseudomonas palustris (strain HaA2), amongst others. Partial phylogenetic profiling identifies protein subfamilies, within th...

[]

0

[ "NCBIFAM" ]

[ "TIGR03560" ]

[ "F420_Rv1855c" ]

[ 7752 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[]

0

[ "IPR050172" ]

[]

1

0

1

[ "Archaea", "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 83, 7530, 4, 135 ]

4

[]

0

true

Family

F420-dependent oxidoreductase-predicted, Rv1855c

F420_OxRdatse_Rv1855c_pred

5

IPR019953

19,953

Organic hydroperoxide resistance protein famiy

OHR

Family

17,104

false

The OsmC-like proteins ( ) contain several deeply split clades of homologous proteins. This clade includes the protein Ohr, or organic hydroperoxide resistance protein.

[ "GO:0006979" ]

[ "response to oxidative stress" ]

[ "biological_process" ]

1

[ "PANTHER", "NCBIFAM" ]

[ "PTHR33797", "TIGR03561" ]

[ "", "organ_hyd_perox" ]

[ 17082, 16183 ]

2

[]

0

[ "1n2f", "1usp", "1zb8", "1zb9", "2bjo", "2ql8", "3eer", "3i07", "3lus", "4mh4", "4noz", "4xx2", "6d9n", "6eb4", "6ebc", "6ebd", "6ebg", "6ecy", "6ed0", "6mjn", "6uhw", "9jx6", "9jxc", "9k1j" ]

24

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 16368, 712, 24 ]

3

[]

0

true

Family

Organic hydroperoxide resistance protein famiy

OHR

7

IPR019954

19,954

Ubiquitin conserved site

Ubiquitin_CS

Conserved_site

30,823

false

This entry represents the conserved central region of Ubiquitin and related proteins. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) ...

[]

0

[ "PROSITE" ]

[ "PS00299" ]

[ "UBIQUITIN_1" ]

[ 30823 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-110312", "R-BTA-110314", "R-BTA-110320", "R-BTA-1169091", "R-BTA-1234176", "R-BTA-1253288", "R-BTA-1295596", "R-BTA-1358803", "R-BTA-156827", "R-BTA-168638", "R-BTA-174048", "R-BTA-174084", "R-BTA-174113", "R-BTA-174154", "R-BTA-174178", "R-BTA-174184", "R-BTA-179409", "R-BT...

[ "REACTOME:R-BTA-110312", "REACTOME:R-BTA-110314", "REACTOME:R-BTA-110320", "REACTOME:R-BTA-1169091", "REACTOME:R-BTA-1234176", "REACTOME:R-BTA-1253288", "REACTOME:R-BTA-1295596", "REACTOME:R-BTA-1358803", "REACTOME:R-BTA-156827", "REACTOME:R-BTA-168638", "REACTOME:R-BTA-174048", "REACTOME:R-BT...

1,452

[ "1aar", "1bt0", "1c3t", "1cmx", "1d3z", "1f9j", "1fxt", "1g6j", "1nbf", "1ndd", "1ogw", "1otr", "1p3q", "1q0w", "1q5w", "1r4m", "1r4n", "1s1q", "1sif", "1tbe", "1ubi", "1ubq", "1ud7", "1uzx", "1v80", "1v81", "1v86", "1wgg", "1wr1", "1wr6", "1wrd", "1wx9"...

1,286

[ "PUB00015619", "PUB00015620", "PUB00015621", "PUB00015622", "PUB00015623", "PUB00015624" ]

[ "15454246", "14998368", "15556404", "15525528", "12646216", "15564047" ]

[ "The ubiquitin-mediated protein degradation pathway in cancer: therapeutic implications.", "Getting into position: the catalytic mechanisms of protein ubiquitylation.", "Polyubiquitin chains: polymeric protein signals.", "Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene si...

[ 2004, 2004, 2004, 2004, 2003, 2004 ]

6

[]

0

null

[ "Bacteria", "Eukaryota", "Viruses", "metagenomes" ]

[ 112, 30349, 246, 116 ]

4

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 95, 5, 16, 29, 76, 49, 4, 59, 59, 6, 7, 48 ]

12

true

Conserved_site

Ubiquitin conserved site

Ubiquitin_CS

7

IPR019957

19,957

ABC transporter, high-affinity heme uptake system protein IsdE

ABC_transptr_haem-bd_IsdE

Family

855

false

This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localised to the cell wall and bearing the NEAT (NEAr Transporter, ) haem-binding domain [ , ]. IsdE has been shown to bind heme and is involved in the process of scavenging haem for the purpose of obtaining iron [ , ].

[ "GO:0020037", "GO:0015886", "GO:0016020" ]

[ "heme binding", "heme transport", "membrane" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "NCBIFAM" ]

[ "TIGR03659" ]

[ "IsdE" ]

[ 855 ]

1

[ "GP" ]

[ "GenProp0828" ]

[ "GP:GenProp0828" ]

1

[ "2q8p", "2q8q", "5joq" ]

3

[ "PUB00045368", "PUB00045369", "PUB00045372", "PUB00045373" ]

[ "18676371", "18715872", "17929943", "17666394" ]

[ "Demonstration of the iron-regulated surface determinant (Isd) heme transfer pathway in Staphylococcus aureus.", "The IsdC protein from Staphylococcus aureus uses a flexible binding pocket to capture heme.", "Heme binding properties of Staphylococcus aureus IsdE.", "Heme coordination by Staphylococcus aureus ...

[ 2008, 2008, 2007, 2007 ]

4

[]

0

null

[ "Acyrthosiphon pisum", "Bacteria" ]

[ 1, 854 ]

2

[]

0

true

Family

ABC transporter, high-affinity heme uptake system protein IsdE

ABC_transptr_haem-bd_IsdE

9

IPR019958

19,958

Small ribosomal subunit protein uS9, archaea

Ribosomal_uS9_arc

Family

815

false

This entry represents the archaeal small ribosomal subunit protein uS9. uS9 proteins adopt a β/α/β fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [ ]. Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codon...

[ "GO:0003735", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "translation", "ribosome" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "HAMAP", "NCBIFAM" ]

[ "MF_00532_A", "TIGR03627" ]

[ "Ribosomal_uS9_A", "uS9_arch" ]

[ 780, 814 ]

2

[]

0

[ "4v4n", "4v6u", "5jb3", "5jbh", "6skf", "6skg", "6sw9", "6swc", "6swe", "6th6", "6tmf", "7zag", "7zah", "7zai", "7zhg", "8hkx", "8hky", "8hkz", "8hl1", "8hl2", "8hl3", "8hl4", "8hl5", "8wkp", "8wq2", "8wq4", "9e71", "9e7f", "9fhl", "9fny", "9fnz", "9fo0"...

43

[ "PUB00001585", "PUB00007068", "PUB00007069", "PUB00007070", "PUB00034480" ]

[ "2332055", "11297922", "11290319", "11114498", "8722013" ]

[ "The primary structure of rat ribosomal protein S16.", "Atomic structures at last: the ribosome in 2000.", "The ribosome in focus.", "The end of the beginning: structural studies of ribosomal proteins.", "Structures of prokaryotic ribosomal proteins: implications for RNA binding and evolution." ]

[ 1990, 2001, 2001, 2000, 1995 ]

5

[ "IPR000754" ]

[]

1

0

1

[ "Archaea", "unclassified sequences" ]

[ 797, 18 ]

2

[]

0

true

Family

Small ribosomal subunit protein uS9, archaea

Ribosomal_uS9_arc

2

IPR019960

19,960

Type I secretion C-terminal target domain, VC_A0849 subclass

T1SS_VCA0849

Domain

5,818

false

This entry represents a C-terminal domain associated with secretion by type 1 secretion systems (T1SS). Members of this subclass do not include the RtxA toxin of Vibrio cholerae and its homologues, although the two classes of proteins share large size, occurrence in genomes with T1SS, regions with long tandem repeats, ...

[]

0

[ "NCBIFAM" ]

[ "TIGR03661" ]

[ "T1SS_VCA0849" ]

[ 5818 ]

1

[]

0

[ "5juh" ]

1

[]

0

[]

0

null

[ "Bacteria", "Escherichia phage 4MG", "Eukaryota", "Halocatena marina", "metagenomes" ]

[ 5791, 1, 16, 1, 9 ]

5

[]

0

true

Domain

Type I secretion C-terminal target domain, VC_A0849 subclass

T1SS_VCA0849

4

IPR019961

19,961

Small ribosomal subunit protein uS11, archaea

Ribosomal_uS11_arc

Family

833

false

This entry represents archaeal ribosomal uS11 proteins. Small ribosomal subunit protein uS11, previously known as Ribosomal protein S11 [ ], plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. Ribosomes are the particles that cat...

[ "GO:0003735", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "translation", "ribosome" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "NCBIFAM" ]

[ "TIGR03628" ]

[ "arch_S11P" ]

[ 833 ]

1

[]

0

[ "4cvn", "4cw7", "4v4n", "4v6u", "5jb3", "5jbh", "6skf", "6skg", "6sw9", "6swc", "6swd", "6th6", "6tmf", "7zag", "7zah", "7zai", "7zhg", "8hkx", "8hky", "8hkz", "8hl1", "8hl2", "8hl3", "8hl4", "8hl5", "8wkp", "8wq2", "8wq4", "9e71", "9e7f", "9fhl", "9fny"...

45

[ "PUB00001562", "PUB00007068", "PUB00007069", "PUB00007070", "PUB00086615" ]

[ "3191988", "11297922", "11290319", "11114498", "14568531" ]

[ "Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family.", "Atomic structures at last: the ribosome in 2000.", "The ribosome in focus.", "The end of the beginning: structural studies of ribosomal pr...

[ 1988, 2001, 2001, 2000, 2003 ]

5

[ "IPR001971" ]

[]

1

0

1

[ "Archaea", "Eukaryota", "unclassified sequences" ]

[ 808, 8, 17 ]

3

[]

0

true

Family

Small ribosomal subunit protein uS11, archaea

Ribosomal_uS11_arc

1

IPR019962

19,962

Conserved hypothetical protein CHP03663

CHP03663

Family

756

false

This entry represents a protein family found in bacteria and archaea, almost always in the same genomes as members of family , and frequently as a nearby gene. The few invariant residues in this family, found toward the N terminus, include a dipeptide DE, a tripeptide HGP, and two different Arg residues. Up to three me...

[]

0

[ "PANTHER", "NCBIFAM" ]

[ "PTHR41710", "TIGR03663" ]

[ "", "" ]

[ 752, 686 ]

2

[ "GP" ]

[ "GenProp0830" ]

[ "GP:GenProp0830" ]

1

[]

0

[ "PUB00099992" ]

[ "32706435" ]

[ "Agl22 and Agl23 are involved in the synthesis and utilization of the lipid-linked intermediates in the glycosylation pathways of the halophilic archaeaon Haloarcula hispanica." ]

[ 2020 ]

1

[]

[ "IPR016950" ]

0

1

0

[ "Bacteria", "Methanobacteriota", "ecological metagenomes" ]

[ 225, 494, 37 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP03663

CHP03663

4

IPR019963

19,963

Futalosine hydrolase

FL_hydrolase_MqnB

Family

2,558

false

This enzyme catalyses the conversion of futalosine to de-hypoxanthine futalosine in a pathway for the biosynthesis of menaquinone distinct from the pathway observed in E. coli [ , ].

[ "GO:0016799", "GO:0009234" ]

[ "hydrolase activity, hydrolyzing N-glycosyl compounds", "menaquinone biosynthetic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00991", "TIGR03664" ]

[ "MqnB", "fut_nucase" ]

[ 2465, 2552 ]

2

[ "EC", "GP", "METACYC" ]

[ "3.2.2.26", "GenProp0829", "PWY-7374" ]

[ "EC:3.2.2.26", "GP:GenProp0829", "METACYC:PWY-7374" ]

3

[]

0

[ "PUB00045374", "PUB00074051" ]

[ "18801996", "19420717" ]

[ "An alternative menaquinone biosynthetic pathway operating in microorganisms.", "Enzymatic properties of futalosine hydrolase, an enzyme essential to a newly identified menaquinone biosynthetic pathway." ]

[ 2008, 2009 ]

2

[]

0

null

[ "Bacteria", "Phytophthora kernoviae 00238/432", "Stenosarchaea group", "ecological metagenomes" ]

[ 2531, 1, 11, 15 ]

4

[]

0

true

Family

Futalosine hydrolase

FL_hydrolase_MqnB

4

IPR019964

19,964

KH domain protein, archaea

KH_domain_protein_archaea

Family

925

false

This family of proteins is universal among 41 archaeal genomes analysed [ ] and is not observed outside of the archaea. The proteins contain a single KH domain, which is likely to confer the ability to bind RNA.

[]

0

[ "NCBIFAM" ]

[ "TIGR03665" ]

[ "arCOG04150" ]

[ 925 ]

1

[]

0

[ "1tua", "2e3u", "3aev" ]

3

[ "PUB00045375" ]

[ "18042280" ]

[ "Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea." ]

[ 2007 ]

1

[]

0

null

[ "Archaea", "ecological metagenomes" ]

[ 886, 39 ]

2

[]

0

true

Family

KH domain protein, archaea

KH_domain_protein_archaea

6

IPR019965

19,965

PPOX class F420-dependent enzyme, family Rv2061, putative

PPOX_F420-dep_Rv2061_put

Family

3,486

false

A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F4...

[]

0

[ "NCBIFAM" ]

[ "TIGR03666" ]

[ "Rv2061_F420" ]

[ 3486 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00055044" ]

[ "20675471" ]

[ "Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria." ]

[ 2010 ]

1

[]

0

null

[ "Archaea", "Bacteria", "ecological metagenomes" ]

[ 57, 3363, 66 ]

3

[]

0

true

Family

PPOX class F420-dependent enzyme, family Rv2061, putative

PPOX_F420-dep_Rv2061_put

9

IPR019966

19,966

F420-dependent enzyme, PPOX class, family Rv3369, probable

F420-dep_enz_PPOX_Rv3369

Family

461

false

A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F4...

[]

0

[ "NCBIFAM" ]

[ "TIGR03667" ]

[ "Rv3369" ]

[ 461 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00055044" ]

[ "20675471" ]

[ "Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria." ]

[ 2010 ]

1

[]

0

null

[ "Bacteria", "uncultured organism" ]

[ 460, 1 ]

2

[]

0

true

Family

F420-dependent enzyme, PPOX class, family Rv3369, probable

F420-dep_enz_PPOX_Rv3369

1

IPR019967

19,967

F420-dependent enzyme, PPOX class, family Rv0121, probable

F420-dep_enz_PPOX_Rv0121

Family

1,519

false

A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F4...

[]

0

[ "NCBIFAM" ]

[ "TIGR03668" ]

[ "Rv0121_F420" ]

[ 1519 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[ "4zky", "5jv4" ]

2

[ "PUB00055044" ]

[ "20675471" ]

[ "Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria." ]

[ 2010 ]

1

[]

0

null

[ "Archaea", "Bacteria", "ecological metagenomes" ]

[ 27, 1475, 17 ]

3

[]

0

true

Family

F420-dependent enzyme, PPOX class, family Rv0121, probable

F420-dep_enz_PPOX_Rv0121

3

IPR019968

19,968

Urea ABC transporter, substrate-binding protein

Urea_ABC_transptr_substrate-bd

Family

376

false

Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea...

[]

0

[ "NCBIFAM" ]

[ "TIGR03669" ]

[ "urea_ABC_arch" ]

[ 376 ]

1

[ "GP" ]

[ "GenProp0743" ]

[ "GP:GenProp0743" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "Halobacteriales", "marine sediment metagenome" ]

[ 272, 102, 2 ]

3

[]

0

true

Family

Urea ABC transporter, substrate-binding protein

Urea_ABC_transptr_substrate-bd

7

IPR019969

19,969

DNA-directed RNA polymerase subunit Rpo2

RNAP_Rpo2

Family

1,086

false

This entry represents the archaeal DNA-directed RNA polymerase subunit Rpo2 (previously known as subunit B), it is the homologue of eukaryotic Rpb2 [ ]. DNA-directed RNA polymerases, also known as DNA-dependent RNA polymerases, are responsible for the polymerisation of ribonucleotides into a sequence complementary to t...

[ "GO:0003677", "GO:0003899", "GO:0008270", "GO:0006351" ]

[ "DNA binding", "DNA-directed RNA polymerase activity", "zinc ion binding", "DNA-templated transcription" ]

[ "molecular_function", "molecular_function", "molecular_function", "biological_process" ]

4

[ "NCBIFAM" ]

[ "TIGR03670" ]

[ "rpoB_arch" ]

[ 1086 ]

1

[ "EC" ]

[ "2.7.7.6" ]

[ "EC:2.7.7.6" ]

1

[ "2pmz", "2waq", "2wb1", "2y0s", "3hkz", "4ayb", "4qiw", "4v8s", "6kf3", "6kf4", "6kf9", "7ok0", "7oq4", "7oqy", "8cro", "8oki", "8orq", "8p2i", "8rbo", "9bct", "9bcu" ]

21

[ "PUB00059148", "PUB00059149" ]

[ "19419240", "19880312" ]

[ "Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.", "Archaeal RNA polymerase." ]

[ 2009, 2009 ]

2

[]

0

null

[ "Archaea", "Geodia barretti", "unclassified sequences" ]

[ 1068, 1, 17 ]

3

[]

0

true

Family

DNA-directed RNA polymerase subunit Rpo2

RNAP_Rpo2

4

IPR019970

19,970

Large ribosomal subunit protein uL4, archaea

Ribosomall_uL4-arc

Family

869

false

This entry represents the large ribosomal subunit protein uL4 found in archaea. One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assemb...

[ "GO:0003735", "GO:0019843", "GO:0006412", "GO:0005840" ]

[ "structural constituent of ribosome", "rRNA binding", "translation", "ribosome" ]

[ "molecular_function", "molecular_function", "biological_process", "cellular_component" ]

4

[ "HAMAP", "NCBIFAM" ]

[ "MF_01328_A", "TIGR03672" ]

[ "Ribosomal_uL4_A", "rpl4p_arch" ]

[ 820, 869 ]

2

[]

0

[ "1ffk", "1jj2", "1k73", "1k8a", "1k9m", "1kc8", "1kd1", "1kqs", "1m1k", "1m90", "1ml5", "1n8r", "1nji", "1q7y", "1q81", "1q82", "1q86", "1qvf", "1qvg", "1s72", "1vq4", "1vq5", "1vq6", "1vq7", "1vq8", "1vq9", "1vqk", "1vql", "1vqm", "1vqn", "1vqo", "1vqp"...

98

[ "PUB00026405", "PUB00106464" ]

[ "11483524", "22306461" ]

[ "The kink-turn: a new RNA secondary structure motif.", "Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution." ]

[ 2001, 2012 ]

2

[ "IPR045240" ]

[]

1

0

1

[ "Archaea", "ecological metagenomes" ]

[ 858, 11 ]

2

[]

0

true

Family

Large ribosomal subunit protein uL4, archaea

Ribosomall_uL4-arc

9

IPR019971

19,971

Large ribosomal subunit protein uL14, archaea

Ribosomal_uL14_arc

Family

756

false

This protein is part of the 50S ribosomal subunit. It forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in two inter-subunit bridges [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR03673" ]

[ "uL14_arch" ]

[ 756 ]

1

[]

0

[ "1ffk", "1jj2", "1k73", "1k8a", "1k9m", "1kc8", "1kd1", "1kqs", "1m1k", "1m90", "1n8r", "1nji", "1q7y", "1q81", "1q82", "1q86", "1qvf", "1qvg", "1s72", "1vq4", "1vq5", "1vq6", "1vq7", "1vq8", "1vq9", "1vqk", "1vql", "1vqm", "1vqn", "1vqo", "1vqp", "1w2b"...

92

[ "PUB00045897" ]

[ "17599351" ]

[ "Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements." ]

[ 2007 ]

1

[ "IPR000218" ]

[]

1

0

1

[ "Archaea", "ecological metagenomes" ]

[ 745, 11 ]

2

[]

0

true

Family

Large ribosomal subunit protein uL14, archaea

Ribosomal_uL14_arc

4

IPR019972

19,972

Large ribosomal subunit protein uL14, conserved site

Ribosomal_uL14_CS

Conserved_site

43,156

false

This entry represents the large ribosomal subunit protein uL14 (formerly known as L14) from all domains of life. In eubacteria, uL14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities. Based on amino-acid sequence homolo...

[]

0

[ "PROSITE" ]

[ "PS00049" ]

[ "RIBOSOMAL_L14" ]

[ 43156 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-156827", "R-BTA-1799339", "R-BTA-6791226", "R-BTA-72689", "R-BTA-72706", "R-BTA-975956", "R-BTA-975957", "R-CEL-156827", "R-CEL-1799339", "R-CEL-72689", "R-CEL-72706", "R-CEL-975956", "R-CEL-975957", "R-DME-156827", "R-DME-1799339", "R-DME-72689", "R-DME-72706", "R-DME-97595...

[ "REACTOME:R-BTA-156827", "REACTOME:R-BTA-1799339", "REACTOME:R-BTA-6791226", "REACTOME:R-BTA-72689", "REACTOME:R-BTA-72706", "REACTOME:R-BTA-975956", "REACTOME:R-BTA-975957", "REACTOME:R-CEL-156827", "REACTOME:R-CEL-1799339", "REACTOME:R-CEL-72689", "REACTOME:R-CEL-72706", "REACTOME:R-CEL-9759...

70

[ "1c04", "1ffk", "1jj2", "1k73", "1k8a", "1k9m", "1kc8", "1kd1", "1kqs", "1m1k", "1m90", "1ml5", "1n8r", "1nji", "1nkw", "1nwx", "1nwy", "1q7y", "1q81", "1q82", "1q86", "1qvf", "1qvg", "1s72", "1sm1", "1vq4", "1vq5", "1vq6", "1vq7", "1vq8", "1vq9", "1vqk"...

1,818

[ "PUB00007068", "PUB00007069", "PUB00007070", "PUB00015240" ]

[ "11297922", "11290319", "11114498", "15299380" ]

[ "Atomic structures at last: the ribosome in 2000.", "The ribosome in focus.", "The end of the beginning: structural studies of ribosomal proteins.", "Crystallization and preliminary X-ray diffraction studies of bacterial ribosomal protein L14." ]

[ 2001, 2001, 2000, 1994 ]

4

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 829, 22044, 19896, 387 ]

4

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 18, 1, 1, 2, 1, 7, 1, 2, 14, 4, 3, 3, 22 ]

13

true

Conserved_site

Large ribosomal subunit protein uL14, conserved site

Ribosomal_uL14_CS

6

IPR019973

19,973

Flap endonuclease, archaea

Flap_endonuc_arc

Family

964

false

This entry represents an endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment [ ]. It has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities and cleaves the junction between single and...

[ "GO:0016788" ]

[ "hydrolase activity, acting on ester bonds" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR03674" ]

[ "fen_arch" ]

[ 964 ]

1

[]

0

[ "1a76", "1a77", "1b43", "1mc8", "1rxv", "1rxw", "2izo", "3ory", "4wa8" ]

9

[ "PUB00054247" ]

[ "9852084" ]

[ "Characterization of FEN-1 from Xenopus laevis. cDNA cloning and role in DNA metabolism." ]

[ 1998 ]

1

[ "IPR023426" ]

[]

1

0

1

[ "Archaea", "Bacteria", "ecological metagenomes" ]

[ 941, 3, 20 ]

3

[]

0

true

Family

Flap endonuclease, archaea

Flap_endonuc_arc

5

IPR019974

19,974

XPG conserved site

XPG_CS

Conserved_site

14,122

false

Xeroderma pigmentosum (XP) [ ] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic comp...

[ "GO:0016788" ]

[ "hydrolase activity, acting on ester bonds" ]

[ "molecular_function" ]

1

[ "PROSITE", "PROSITE" ]

[ "PS00841", "PS00842" ]

[ "XPG_1", "XPG_2" ]

[ 11607, 10266 ]

2

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-110362", "R-BTA-174437", "R-BTA-5651801", "R-BTA-5685939", "R-BTA-69166", "R-CEL-5651801", "R-CEL-5685939", "R-CEL-69166", "R-DDI-110362", "R-DDI-5651801", "R-DDI-69166", "R-DME-5358565", "R-DME-5651801", "R-DME-5685939", "R-DME-5693607", "R-DME-6804756", "R-DME-69166", "R-D...

[ "REACTOME:R-BTA-110362", "REACTOME:R-BTA-174437", "REACTOME:R-BTA-5651801", "REACTOME:R-BTA-5685939", "REACTOME:R-BTA-69166", "REACTOME:R-CEL-5651801", "REACTOME:R-CEL-5685939", "REACTOME:R-CEL-69166", "REACTOME:R-DDI-110362", "REACTOME:R-DDI-5651801", "REACTOME:R-DDI-69166", "REACTOME:R-DME-5...

80

[ "1b43", "1mc8", "1rxv", "1rxw", "1ul1", "2izo", "3ory", "3q8k", "3q8l", "3q8m", "3qe9", "3qea", "3qeb", "4q0r", "4q0w", "4q0z", "4q10", "4wa8", "5fv7", "5k97", "5kse", "5um9", "5uzv", "5v04", "5v05", "5v06", "5v07", "5v08", "5v09", "5v0a", "5v0b", "5v0c"...

64

[ "PUB00002851", "PUB00004160", "PUB00004189", "PUB00004415", "PUB00005433", "PUB00097845" ]

[ "8206890", "8247134", "8090225", "8464724", "8160271", "32821917" ]

[ "Isolation of active recombinant XPG protein, a human DNA repair endonuclease.", "Yeast excision repair gene RAD2 encodes a single-stranded DNA endonuclease.", "XPG endonuclease makes the 3' incision in human DNA nucleotide excision repair.", "Evolutionary conservation of excision repair in Schizosaccharomyce...

[ 1994, 1993, 1994, 1993, 1994, 2020 ]

6

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Viruses", "metagenomes" ]

[ 621, 6, 13457, 11, 27 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 27, 1, 11, 8, 18, 21, 3, 9, 6, 4, 3, 21 ]

12

true

Conserved_site

XPG conserved site

XPG_CS

2

IPR019975

19,975

Transcription termination factor CPSF1, archaea

aCPSF1

Family

1,012

false

This entry represents the Factor that terminates transcription in archaea (FttA), also known as archaeal Cleavage and Polyadenylation Specificity Factor 1 (aCPSF1), and similar sequences mainly found in archaea. FttA is a homologue of eukaryotic CPSF73 (Cleavage and Polyadenylation Specificity Factor 73 kDa subunit) an...

[ "GO:0003723" ]

[ "RNA binding" ]

[ "molecular_function" ]

1

[ "HAMAP", "NCBIFAM" ]

[ "MF_00870", "TIGR03675" ]

[ "FttA", "arCOG00543" ]

[ 983, 1012 ]

2

[]

0

[ "2xr1", "2ycb", "3af5", "3af6", "9bct", "9bcu" ]

6

[ "PUB00045375", "PUB00095180", "PUB00106760", "PUB00160283" ]

[ "18042280", "32857850", "23222134", "32094586" ]

[ "Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.", "The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.", "Archaeal β-CASP ribonucleases of the aCPSF1 family are orthologs of the euka...

[ 2007, 2020, 2013, 2020 ]

4

[ "IPR050698" ]

[]

1

0

1

[ "Archaea", "Bacteria", "Geodia barretti", "ecological metagenomes" ]

[ 982, 3, 1, 26 ]

4

[]

0

true

Family

Transcription termination factor CPSF1, archaea

aCPSF1

5