LiteFold/InterPro · Datasets at Hugging Face

IPR013353

13,353

Type III secretion system chaperone YscB

T3SS_YscB

Family

129

false

Members of this family include YscB of Yersinia and functionally equivalent (but differently named) proteins from type III secretion systems of other pathogens that affect animal cells. In Yersinia pestis, the secretion of effector proteins, termed Yersinia outer proteins (Yops), is regulated by the activity of the Yop...

[ "GO:0030254" ]

[ "protein secretion by the type III secretion system" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02513" ]

[ "type_III_yscB" ]

[ 129 ]

1

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "1xkp" ]

1

[ "PUB00020751", "PUB00069641" ]

[ "15701523", "23355975" ]

[ "Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis.", "The SycN/YscB chaperone-binding domain of YopN is required for the calcium-dependent regulation of Yop secretion by Yersinia pestis." ]

[ 2005, 2013 ]

2

[ "IPR010261" ]

[]

1

0

1

[ "Bacteria" ]

[ 129 ]

1

[]

0

true

Family

Type III secretion system chaperone YscB

T3SS_YscB

3

IPR013354

13,354

Type III secretion system needle length determinant, C-terminal domain

T3SS_YscP_C

Domain

184

false

Proteins with this domain include YscP of the Yersinia type III secretion system and equivalent proteins in other pathogenic bacterial type III secretion systems. The entry describes the conserved C-terminal region. The N-terminal regions are poorly conserved, variable in length and often contain low-complexity sequenc...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02514", "cd17467" ]

[ "type_III_yscP", "T3SS_YscP_C" ]

[ 173, 178 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "5cuk" ]

1

[ "PUB00106697", "PUB00106698", "PUB00141077", "PUB00141295", "PUB00141296", "PUB00141297", "PUB00141298", "PUB00141299" ]

[ "19055526", "20643949", "23028376", "26589798", "23935040", "18641141", "18424518", "16102009" ]

[ "The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome.", "Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP).", "The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into h...

[ 2009, 2010, 2012, 2016, 2013, 2008, 2008, 2005 ]

8

[ "IPR021136" ]

[]

1

0

1

[ "Diploscapter pachys", "Pseudomonadati" ]

[ 1, 183 ]

2

[]

0

true

Domain

Type III secretion system needle length determinant, C-terminal domain

T3SS_YscP_C

8

IPR013355

13,355

Type IV pilus secretin PilQ

Pilus_4_PilQ

Family

6,678

false

A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus...

[]

0

[ "NCBIFAM" ]

[ "TIGR02515" ]

[ "IV_pilus_PilQ" ]

[ 6678 ]

1

[]

0

[ "3jc8", "3jc9", "4av2", "6ve2", "6ve3", "6ve4", "6w6m" ]

7

[ "PUB00068649", "PUB00084373" ]

[ "16707682", "10547691" ]

[ "Escherichia coli competence gene homologs are essential for competitive fitness and the use of DNA as a nutrient.", "DNA uptake in bacteria." ]

[ 2006, 1999 ]

2

[ "IPR001775" ]

[]

1

0

1

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

[ 6603, 6, 2, 67 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type IV pilus secretin PilQ

Pilus_4_PilQ

4

IPR013356

13,356

Type II secretion system protein GspD

T2SS_GspD

Family

6,887

false

General secretion pathway protein D (GspD) is the secretin component of the type II secretion system. GspD is closely homologous to the type IV pilus outer membrane secretin PilQ ( ) and to the type III secretion system pore YscC/HrcC ( ). The N-terminal part of GspD extends into the periplasm and may interact with sec...

[ "GO:0015628", "GO:0015627", "GO:0019867" ]

[ "protein secretion by the type II secretion system", "type II protein secretion system complex", "outer membrane" ]

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

3

[ "NCBIFAM" ]

[ "TIGR02517" ]

[ "type_II_gspD" ]

[ 6887 ]

1

[ "GP", "REACTOME" ]

[ "GenProp0053", "R-HSA-9760173" ]

[ "GP:GenProp0053", "REACTOME:R-HSA-9760173" ]

2

[ "5wln", "5wq7", "5wq8", "5wq9", "5zdh", "6hcg", "6i1x", "6i1y" ]

8

[ "PUB00051842", "PUB00093998", "PUB00094002", "PUB00094004" ]

[ "19217396", "30767847", "28258547", "22523076" ]

[ "Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody.", "Architecture, Function, and Substrates of the Type II Secretion System.", "1H, 15N and 13C resonance assignments and secondary structure of PulG, the major pseudopilin from Klebsiella oxyt...

[ 2009, 2019, 2017, 2012 ]

4

[ "IPR001775" ]

[]

1

0

1

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

[ 6773, 13, 101 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type II secretion system protein GspD

T2SS_GspD

6

IPR013357

13,357

Acetaldehyde dehydrogenase, acetylating

Acetaldehyde_DH_acetylating

Family

1,246

false

Aldehyde dehydrogenases ( and ) are enzymes which oxidize a wide variety of aliphatic and aromatic aldehydes using NAD(P) as a cofactor. In eukaryotes, at least twenty distinct aldehyde dehydrogenase families have been classified [ ]. Many aldehyde dehydrogenases have also been found in prokaryotic species. A glutamic ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02518" ]

[ "EutH_ACDH" ]

[ 1246 ]

1

[ "GP", "GP" ]

[ "GenProp0292", "GenProp0294" ]

[ "GP:GenProp0292", "GP:GenProp0294" ]

2

[ "3k9d", "5j78", "5j7i" ]

3

[ "PUB00033217", "PUB00033864" ]

[ "11154732", "8419288" ]

[ "Role of aldehyde dehydrogenases in endogenous and xenobiotic metabolism.", "Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600." ]

[ 2000, 1993 ]

2

[]

0

null

[ "Bacteria", "bioreactor metagenome" ]

[ 1241, 5 ]

2

[]

0

true

Family

Acetaldehyde dehydrogenase, acetylating

Acetaldehyde_DH_acetylating

4

IPR013358

13,358

Pilus biogenesis, MshL

Pilus_biogenesis_MshL

Family

1,642

false

Proteins containing this region are predicted secretins, that is, outer membrane pore proteins associated with delivery of proteins from the periplasm to the outside of the cell. Related proteins include the GspD type II secretion family, the YscC/HrcC family type III secretion family, and the PilQ type IV pilus format...

[]

0

[ "NCBIFAM" ]

[ "TIGR02519" ]

[ "pilus_MshL" ]

[ 1642 ]

1

[]

0

[]

0

[]

0

[ "IPR001775" ]

[]

1

0

1

[ "Bacteria", "Symbiodinium necroappetens", "unclassified sequences" ]

[ 1605, 1, 36 ]

3

[]

0

true

Family

Pilus biogenesis, MshL

Pilus_biogenesis_MshL

2

IPR013359

13,359

Pilus formation type IVB, outer membrane PilN

Pilus_4B_PilN

Family

1,105

false

Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. Proteins in this entry appear to be secretins for pilus formation, although they are quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus,...

[]

0

[ "NCBIFAM" ]

[ "TIGR02520" ]

[ "pilus_B_mal_scr" ]

[ 1105 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Plasmid R64", "Pseudomonadota", "metagenomes" ]

[ 1, 1101, 3 ]

3

[]

0

true

Family

Pilus formation type IVB, outer membrane PilN

Pilus_4B_PilN

3

IPR013360

13,360

Pilus biogenesis/stability type IV, PilW

Pilus_4_PilW

Family

4,615

false

Proteins in this entry are designated PilF [ ] and PilW [ ]. This outer membrane protein is required both for pilus stability and for pilus functions such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

[]

0

[ "NCBIFAM" ]

[ "TIGR02521" ]

[ "type_IV_pilW" ]

[ 4615 ]

1

[]

0

[ "2fi7", "2ho1", "2vq2" ]

3

[ "PUB00020773", "PUB00020782" ]

[ "15612916", "8973346" ]

[ "Type IV pilus biogenesis in Neisseria meningitidis: PilW is involved in a step occurring after pilus assembly, essential for fibre stability and function.", "Identification of a gene, pilF, required for type 4 fimbrial biogenesis and twitching motility in Pseudomonas aeruginosa." ]

[ 2005, 1996 ]

2

[]

0

null

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

[ 4556, 3, 56 ]

3

[]

0

true

Family

Pilus biogenesis/stability type IV, PilW

Pilus_4_PilW

4

IPR013361

13,361

Pilus biogenesis CpaD

Pilus_CpaD

Family

1,287

false

Proteins in this entry consist of a pilus biogenesis protein, CpaD, from Caulobacter, and homologues in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function of the homologues is not known.

[]

0

[ "NCBIFAM" ]

[ "TIGR02522" ]

[ "pilus_cpaD" ]

[ 1287 ]

1

[]

0

[]

0

[]

0

[ "IPR019027" ]

[]

1

0

1

[ "Eukaryota", "Pseudomonadati", "metagenomes" ]

[ 2, 1271, 14 ]

3

[]

0

true

Family

Pilus biogenesis CpaD

Pilus_CpaD

6

IPR013362

13,362

Pilus modification type IV, PilV

Pilus_4_PilV

Family

4,091

false

Pilus systems categorized as type IV pilins differ greatly from one another, with some showing greater similarity to type II or type III secretion systems than to each other. Members of this protein family represent the PilV protein of type IV pilus systems found in Pseudomonas aeruginosa PAO1, Pseudomonas syringae pv....

[]

0

[ "NCBIFAM" ]

[ "TIGR02523" ]

[ "type_IV_pilV" ]

[ 4091 ]

1

[]

0

[]

0

[]

0

[]

0

null

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

[ 4025, 5, 61 ]

3

[]

0

true

Family

Pilus modification type IV, PilV

Pilus_4_PilV

2

IPR013363

13,363

Dot/Icm secretion system ATPase DotB

Dot_Icm_DotB

Family

88

false

Proteins in this entry are the DotB component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/I...

[]

0

[ "NCBIFAM" ]

[ "TIGR02524" ]

[ "dot_icm_DotB" ]

[ 88 ]

1

[]

0

[ "6geb" ]

1

[]

0

[]

0

null

[ "Gammaproteobacteria", "marine sediment metagenome" ]

[ 87, 1 ]

2

[]

0

true

Family

Dot/Icm secretion system ATPase DotB

Dot_Icm_DotB

9

IPR013364

13,364

ATPase, plasmid transfer, TraJ

ATPase_plasmid-transfer_TraJ

Family

547

false

Proteins in this entry are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase ( ) of a type-IV secretion-like system of the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii.

[]

0

[ "NCBIFAM" ]

[ "TIGR02525" ]

[ "plasmid_TraJ" ]

[ 547 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Ecdysozoa", "Plasmid R64", "Pseudomonadota" ]

[ 2, 1, 544 ]

3

[]

0

true

Family

ATPase, plasmid transfer, TraJ

ATPase_plasmid-transfer_TraJ

9

IPR013365

13,365

Dot/Icm secretion system IcmQ

Dot_Icm_IcmQ

Family

106

false

Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/I...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09475", "TIGR02527" ]

[ "Dot_icm_IcmQ", "dot_icm_IcmQ" ]

[ 106, 102 ]

2

[]

0

[ "3fxd", "3fxe", "4eyy" ]

3

[ "PUB00020742" ]

[ "15661013" ]

[ "The Legionella IcmS-IcmW protein complex is important for Dot/Icm-mediated protein translocation." ]

[ 2005 ]

1

[]

0

null

[ "Gammaproteobacteria", "marine sediment metagenome" ]

[ 104, 2 ]

2

[]

0

true

Family

Dot/Icm secretion system IcmQ

Dot_Icm_IcmQ

3

IPR013366

13,366

Ethanolamine utilisation EutJ

EutJ

Family

2,007

false

Salmonella typhimurium is capable of growth on ethanolamine as a sole source of carbon nitrogen and energy [ ]. During growth on this compound the cells form a multimolecular structure known as a metabolosome, which is similar to the carboxysome used by some photosynthetic bacteria to fix CO2, and is thought to contain...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02529", "cd24047" ]

[ "EutJ", "ASKHA_NBD_EutJ" ]

[ 2006, 1693 ]

2

[ "GP" ]

[ "GenProp0292" ]

[ "GP:GenProp0292" ]

1

[ "3h1q" ]

1

[ "PUB00002263", "PUB00009955", "PUB00014698", "PUB00020756", "PUB00097901", "PUB00100312" ]

[ "7868611", "10464203", "3045078", "16291677", "29531136", "27063436" ]

[ "Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster.", "The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins.", "Ethanolamine utili...

[ 1995, 1999, 1988, 2005, 2018, 2016 ]

6

[]

0

null

[ "Bacteria", "unclassified sequences" ]

[ 1998, 9 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Ethanolamine utilisation EutJ

EutJ

3

IPR013367

13,367

Flagellar, putative

Flagellar_put

Family

1,814

false

Proteins in this entry are encoded in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function of this protein is unknown...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF12611", "TIGR02530" ]

[ "Flagellar_put", "flg_new" ]

[ 1780, 1779 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 1800, 14 ]

2

[]

0

true

Family

Flagellar, putative

Flagellar_put

7

IPR013369

13,369

Type II secretion system protein GspE

T2SS_GspE

Family

5,746

false

GspE is a cytoplasmic hexameric ATPase of the type II secretion system. It contains three domains (N1E, N2E and CTE) of which the N1E domain is associated with the cytoplasmic domain of the inner membrane protein GspL [ ]. The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-neg...

[ "GO:0005524", "GO:0015628", "GO:0015627" ]

[ "ATP binding", "protein secretion by the type II secretion system", "type II protein secretion system complex" ]

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

3

[ "NCBIFAM" ]

[ "TIGR02533" ]

[ "type_II_gspE" ]

[ 5746 ]

1

[ "EC", "GP" ]

[ "7.4.2.8", "GenProp0053" ]

[ "EC:7.4.2.8", "GP:GenProp0053" ]

2

[ "1p9r", "1p9w", "4ksr", "4kss", "4pht" ]

5

[ "PUB00051842", "PUB00093998", "PUB00094002", "PUB00094003", "PUB00094004" ]

[ "19217396", "30767847", "28258547", "25092625", "22523076" ]

[ "Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody.", "Architecture, Function, and Substrates of the Type II Secretion System.", "1H, 15N and 13C resonance assignments and secondary structure of PulG, the major pseudopilin from Klebsiella oxyt...

[ 2009, 2019, 2017, 2014, 2012 ]

5

[]

0

null

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

[ 5665, 8, 73 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type II secretion system protein GspE

T2SS_GspE

9

IPR013370

13,370

Muconate/chloromuconate cycloisomerase

Chloromuconate_cycloisomerase

Family

2,829

false

This family consists of muconate cycloisomerase (or Muconate Lactonizing Enzyme (MLE); ) and chloromuconate cycloisomerase (or chloromuconate lactonizing enzymes (Cl-MLEs); ), enzymes that often overlap in specificity. It does not include more distantly related proteins such as mandelate racemase ( ). MLE, a homooctame...

[ "GO:0018849", "GO:0018850", "GO:0030145" ]

[ "muconate cycloisomerase activity", "chloromuconate cycloisomerase activity", "manganese ion binding" ]

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

3

[ "SFLD", "NCBIFAM", "CDD" ]

[ "SFLDG01258", "TIGR02534", "cd03318" ]

[ "(chloro)muconate_cycloisomeras", "mucon_cyclo", "MLE" ]

[ 2727, 2773, 2506 ]

3

[ "EC", "GP" ]

[ "5.5.1", "GenProp0711" ]

[ "EC:5.5.1", "GP:GenProp0711" ]

2

[ "1bkh", "1f9c", "1muc", "1nu5", "2chr", "2muc", "3ct2", "3dgb", "3fcp", "3fj4", "3i4k", "3i6e", "3muc", "4m0x" ]

14

[ "PUB00069767", "PUB00080864", "PUB00080865", "PUB00080866" ]

[ "15581566", "8987982", "8905091", "4599397" ]

[ "Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity.", "The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.", "The beta-ketoadipate pathway and the biology of self-identity.", "The beta-ketoadipate pathw...

[ 2005, 1996, 1996, 1973 ]

4

[]

0

null

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

[ 2824, 2, 3 ]

3

[]

0

true

Family

Muconate/chloromuconate cycloisomerase

Chloromuconate_cycloisomerase

7

IPR013372

13,372

Ethanolamine utilization, putative

Eut_put

Family

368

false

Proteins in this entry are encoded in operons for the polyhedral organelle-based degradation of ethanolamine. This family is not found in proteobacterial species, which otherwise have the same suite of genes in the eut operon. Proteobacteria have two genes that are not found in other species which encode proteins which...

[]

0

[ "PIRSF", "NCBIFAM" ]

[ "PIRSF034981", "TIGR02536" ]

[ "Eut_put", "eut_hyp" ]

[ 315, 164 ]

2

[ "GP" ]

[ "GenProp0292" ]

[ "GP:GenProp0292" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "bioreactor metagenome" ]

[ 365, 3 ]

2

[]

0

true

Family

Ethanolamine utilization, putative

Eut_put

4

IPR013373

13,373

Flagellin/pilin, N-terminal site, archaea

Flagellin/pilin_N_arc

Conserved_site

3,918

false

This entry describes a hydrophobic N-terminal conserved site of archaeal flagellins and pilins [ ]. This site is directly analogous to the bacterial N-terminal methylation site , which has a cleavage motif resembling G^FxxxE followed by a strongly hydrophobic sequence. The bacterial domain is a recognition site for cle...

[]

0

[ "NCBIFAM" ]

[ "TIGR02537" ]

[ "arch_flag_Nterm" ]

[ 3918 ]

1

[]

0

[ "3j1r", "5kyh", "5o4u", "5tfy", "5z1l", "7ofq", "7txi", "8cwm", "8fj5", "8fk7", "8gi2", "8rey", "8rh5", "9eq7", "9esm", "9etu" ]

16

[ "PUB00069628" ]

[ "23794623" ]

[ "Novel archaeal adhesion pilins with a conserved N terminus." ]

[ 2013 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Saline Natrinema sp. J7-1 virus 2", "unclassified sequences" ]

[ 3822, 32, 1, 63 ]

4

[]

0

true

Conserved_site

Flagellin/pilin, N-terminal site, archaea

Flagellin/pilin_N_arc

8

IPR013374

13,374

ATPase, type IV, pilus assembly, PilB

ATPase_typ4_pilus-assembl_PilB

Family

4,233

false

This model describes a protein involved in type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly, and is closely related to GspE ( ) of type II secretio...

[ "GO:0016887", "GO:0009297" ]

[ "ATP hydrolysis activity", "pilus assembly" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02538" ]

[ "type_IV_pilB" ]

[ 4233 ]

1

[]

0

[ "3jc8", "5tsg", "5tsh", "5zfr", "6olj" ]

5

[]

0

[]

0

null

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

[ 4176, 8, 49 ]

3

[]

0

true

Family

ATPase, type IV, pilus assembly, PilB

ATPase_typ4_pilus-assembl_PilB

5

IPR013375

13,375

O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea

Sep_Cys-tRNA_synth_arc

Family

309

false

Aminoacylation of tRNA(Cys) with Cys, and cysteine biosynthesis in the process, happens in Methanocaldococcus jannaschii and several other archaea by misacylation of tRNA(Cys) with O-phosphoserine (Sep), followed by modification of the phosphoserine to cysteine. In some species, direct tRNA-cys aminoacylation also occu...

[ "GO:0043766" ]

[ "Sep-tRNA:Cys-tRNA synthase activity" ]

[ "molecular_function" ]

1

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

[ "MF_01675", "NF006810", "TIGR02539" ]

[ "Sep_Cys_tRNA_synth", "PRK09331.1", "SepCysS" ]

[ 282, 309, 301 ]

3

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

[ "2.5.1.73", "GenProp0304", "PWY-6308" ]

[ "EC:2.5.1.73", "GP:GenProp0304", "METACYC:PWY-6308" ]

3

[ "2e7i", "2e7j", "3wkr", "3wks", "5x6b" ]

5

[ "PUB00020741" ]

[ "15790858" ]

[ "RNA-dependent cysteine biosynthesis in archaea." ]

[ 2005 ]

1

[ "IPR008829" ]

[]

1

0

1

[ "Archaea", "ecological metagenomes" ]

[ 300, 9 ]

2

[]

0

true

Family

O-phosphoseryl-tRNA:Cys-tRNA synthase, archaea

Sep_Cys-tRNA_synth_arc

4

IPR013376

13,376

Glutathione peroxidase Gpx7, putative

Glut_perox_Gpx7

Family

1,657

false

This model represents one of several families of known and probable glutathione peroxidases. It is restricted to animals and designated GPX7.

[ "GO:0004602", "GO:0006979" ]

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

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02540" ]

[ "gpx7" ]

[ 1657 ]

1

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

[ "1.11.1.9", "PWY-4081", "R-BTA-3299685", "R-DRE-3299685", "R-HSA-3299685", "R-MMU-3299685" ]

[ "EC:1.11.1.9", "METACYC:PWY-4081", "REACTOME:R-BTA-3299685", "REACTOME:R-DRE-3299685", "REACTOME:R-HSA-3299685", "REACTOME:R-MMU-3299685" ]

6

[ "2p31", "3cyn", "3kij" ]

3

[]

0

[ "IPR000889" ]

[]

1

0

1

[ "Chordata" ]

[ 1657 ]

1

[ "Danio rerio", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 2, 4, 3, 5 ]

4

true

Family

Glutathione peroxidase Gpx7, putative

Glut_perox_Gpx7

9

IPR013377

13,377

Peptidoglycan hydrolase FlgJ

FlgJ

Family

5,293

false

FlgJ is a flagellum-specific muramidase which hydrolyses the peptidoglycan layer to assemble the rod structure in the periplasmic space [ ]. The N-terminal region of this protein acts directly in flagellar rod assembly, while the C-terminal region is a flagellum-specific muramidase (peptidoglycan hydrolase) required fo...

[ "GO:0016798", "GO:0044780" ]

[ "hydrolase activity, acting on glycosyl bonds", "bacterial-type flagellum assembly" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02541" ]

[ "flagell_FlgJ" ]

[ 5293 ]

1

[ "EC", "GP", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "...

[ "3.2.1.-", "GenProp0885", "PWY-1921", "PWY-5821", "PWY-5976", "PWY-6527", "PWY-6717", "PWY-6735", "PWY-6737", "PWY-6749", "PWY-6784", "PWY-6821", "PWY-6848", "PWY-6855", "PWY-6906", "PWY-6972", "PWY-7056", "PWY-7057", "PWY-7074", "PWY-7091", "PWY-7133", "PWY-7134", "PWY-7...

[ "EC:3.2.1.-", "GP:GenProp0885", "METACYC:PWY-1921", "METACYC:PWY-5821", "METACYC:PWY-5976", "METACYC:PWY-6527", "METACYC:PWY-6717", "METACYC:PWY-6735", "METACYC:PWY-6737", "METACYC:PWY-6749", "METACYC:PWY-6784", "METACYC:PWY-6821", "METACYC:PWY-6848", "METACYC:PWY-6855", "METACYC:PWY-690...

32

[ "2zyc", "3k3t", "3vwo", "5dn4", "5dn5" ]

5

[ "PUB00005848", "PUB00020765" ]

[ "10049388", "11554792" ]

[ "Peptidoglycan-hydrolyzing activity of the FlgJ protein, essential for flagellar rod formation in Salmonella typhimurium.", "The role in flagellar rod assembly of the N-terminal domain of Salmonella FlgJ, a flagellum-specific muramidase." ]

[ 1999, 2001 ]

2

[]

0

null

[ "Bacteria", "Opisthokonta", "unclassified sequences" ]

[ 5244, 6, 43 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Peptidoglycan hydrolase FlgJ

FlgJ

7

IPR013378

13,378

Internalin B-like, B-repeat

InlB-like_B-rpt

Repeat

8,736

false

This entry represents the B-repeat described in internalins of Listeria species [ , , ]. These are 70-residue repeats, found in one copy in internalin B, three in internalin A and two in internalin H [ , ]. The B-repeat plays an important role in protein-protein interactions, as it probably binds a host cell receptor a...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09479", "TIGR02543" ]

[ "Flg_new", "List_Bact_rpt" ]

[ 8290, 6114 ]

2

[ "REACTOME", "REACTOME" ]

[ "R-HSA-8875360", "R-HSA-8876493" ]

[ "REACTOME:R-HSA-8875360", "REACTOME:R-HSA-8876493" ]

2

[ "1m9s", "2y5p", "2y5q", "7nms", "7pv8", "7pv9" ]

6

[ "PUB00016543", "PUB00055671", "PUB00106890" ]

[ "11575932", "21345802", "35234145" ]

[ "Internalins from the human pathogen Listeria monocytogenes combine three distinct folds into a contiguous internalin domain.", "Fold and function of the InlB B-repeat.", "A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat." ]

[ 2001, 2011, 2022 ]

3

[]

0

null

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

[ 175, 8293, 74, 22, 172 ]

5

[ "Arabidopsis thaliana" ]

[ 2 ]

1

true

Repeat

Internalin B-like, B-repeat

InlB-like_B-rpt

6

IPR013380

13,380

Type 3 secretion system ATPase SctN

ATPase_T3SS_SctN

Family

1,974

false

Proteins in this entry are found in a variety of bacteria, and are ATPases that occurs as a cytoplasmic component of the type III secretion system (T3SS) found in many pathogenic bacteria. This entry includes SctN (also known as YscN) from Yersinia enterocolitica, which is a component of the Yop (Yersinia outer protein...

[ "GO:0005524", "GO:0046961", "GO:0006754", "GO:0030254", "GO:0005737", "GO:0030257" ]

[ "ATP binding", "proton-transporting ATPase activity, rotational mechanism", "ATP biosynthetic process", "protein secretion by the type III secretion system", "cytoplasm", "type III protein secretion system complex" ]

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

6

[ "NCBIFAM" ]

[ "TIGR02546" ]

[ "III_secr_ATP" ]

[ 1974 ]

1

[ "EC", "GP" ]

[ "7.4.2.8", "GenProp0052" ]

[ "EC:7.4.2.8", "GP:GenProp0052" ]

2

[ "6njo", "6njp" ]

2

[ "PUB00034695", "PUB00097931", "PUB00097932" ]

[ "16672607", "25591178", "28653671" ]

[ "Characterization of the Yersinia enterocolitica type III secretion ATPase YscN and its regulator, YscL.", "Composition, formation, and regulation of the cytosolic c-ring, a dynamic component of the type III secretion injectisome.", "A dynamic and adaptive network of cytosolic interactions governs protein expor...

[ 2006, 2015, 2017 ]

3

[ "IPR005714" ]

[]

1

0

1

[ "Bacteria", "Opisthokonta", "metagenomes" ]

[ 1963, 2, 9 ]

3

[]

0

true

Family

Type 3 secretion system ATPase SctN

ATPase_T3SS_SctN

7

IPR013381

13,381

CRISPR-associated protein Cse1

CRISPR-assoc_prot_Cse1

Family

3,496

false

This entry represents the Cse1 family of Cas proteins, which includes CT1972 from Chlorobium tepidum [ ]. These proteins are found in the CRISPR/Cas subtype Escherichia coli regions of many bacteria (most of which are mesophiles), and not in Archaea. This is also known as CasA, or Cse1 Type I-E [ ]. The CRISPR-Cas syst...

[]

0

[ "PFAM", "NCBIFAM", "CDD" ]

[ "PF09481", "TIGR02547", "cd09669" ]

[ "CRISPR_Cse1", "casA_cse1", "Cse1_I-E" ]

[ 3433, 3013, 738 ]

3

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

[ "GenProp0021", "GenProp0315", "GenProp1179" ]

[ "GP:GenProp0021", "GP:GenProp0315", "GP:GenProp1179" ]

3

[ "3wvo", "4an8", "4ej3", "4f3e", "4h3t", "4qyz", "4tvx", "4u7u", "5cd4", "5h9e", "5h9f", "5u07", "5u0a", "6c66", "8yb6", "8yha", "8zlu", "8zm3", "8zp7", "9jxs" ]

20

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00078085" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "24459147", "21552286" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2014, 2011 ]

7

[]

0

null

[ "Bacteria", "Methanomicrobia", "Opisthokonta", "unclassified sequences", "virus sp. ctHG14" ]

[ 3442, 20, 4, 29, 1 ]

5

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

CRISPR-associated protein Cse1

CRISPR-assoc_prot_Cse1

2

IPR013382

13,382

CRISPR-associated protein Cse2

CRISPR-assoc_prot_Cse2

Family

3,170

false

This entry represents the Cse2 family of Cas proteins, which includes CT1973 from Chlorobium tepidum. These proteins are found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea [ ]. This is also known as CasB or Cse2 Type I-E [ ]. The CRISPR-Cas system is a prok...

[]

0

[ "PFAM", "NCBIFAM", "CDD" ]

[ "PF09485", "TIGR02548", "cd09670" ]

[ "CRISPR_Cse2", "casB_cse2", "Cse2_I-E" ]

[ 3144, 3070, 230 ]

3

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

[ "GenProp0021", "GenProp0315", "GenProp1179" ]

[ "GP:GenProp0021", "GP:GenProp0315", "GP:GenProp1179" ]

3

[ "2zca", "3wa8", "4h79", "4h7a", "4qyz", "4tvx", "4u7u", "5cd4", "5h9e", "5h9f", "5u07", "5u0a", "6c66", "8yb6", "8yha", "8zlu", "8zm3", "8zp7", "9jxs" ]

19

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00078085" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "24459147", "21552286" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2014, 2011 ]

7

[]

0

null

[ "Bacteria", "Dikarya", "Methanomicrobia", "unclassified sequences" ]

[ 3128, 4, 17, 21 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

CRISPR-associated protein Cse2

CRISPR-assoc_prot_Cse2

2

IPR013383

13,383

CRISPR-associated protein DxTHG, conserved site

CRISPR-assoc_prot_DxTHG_CS

Conserved_site

688

false

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. This entry represents a conserved site found in two otherwise substantially different families of Cas proteins [ ]. This site includes the motif [VI...

[]

0

[ "NCBIFAM" ]

[ "TIGR02549" ]

[ "CRISPR_DxTHG" ]

[ 688 ]

1

[]

0

[ "2i71", "4eog", "6o6s", "6o6v", "6o6x", "6o6y", "6o6z", "6o71", "6ov0", "8y6z", "8y75", "8y7g" ]

12

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "24459147" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2014 ]

6

[]

0

null

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

[ 138, 543, 7 ]

3

[]

0

true

Conserved_site

CRISPR-associated protein DxTHG, conserved site

CRISPR-assoc_prot_DxTHG_CS

9

IPR013384

13,384

Flagellar hook-associated protein 3

Flagell_FlgL

Family

9,556

false

FlgL (or hook-associated protein 3, HAP3) proteins are flagellar hook-associated proteins encoded in bacterial flagellar operons [ , ]. An N-terminal region of about 150 residues and a C-terminal region of about 85 residues are conserved in this family, though members show considerable length heterogeneity between thes...

[ "GO:0071973", "GO:0009424" ]

[ "bacterial-type flagellum-dependent cell motility", "bacterial-type flagellum hook" ]

[ "biological_process", "cellular_component" ]

2

[ "NCBIFAM" ]

[ "TIGR02550" ]

[ "flagell_flgL" ]

[ 9556 ]

1

[ "GP" ]

[ "GenProp0882" ]

[ "GP:GenProp0882" ]

1

[ "2d4x", "3pwx", "5kay", "5yti", "5ziz", "5zj0", "7c7z", "9go6" ]

8

[ "PUB00076711", "PUB00076712" ]

[ "8158647", "12940991" ]

[ "A mutant hook-associated protein (HAP3) facilitates torsionally induced transformations of the flagellar filament of Escherichia coli.", "The type III secretion chaperone FlgN regulates flagellar assembly via a negative feedback loop containing its chaperone substrates FlgK and FlgL." ]

[ 1994, 2003 ]

2

[]

0

null

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

[ 9458, 11, 87 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Flagellar hook-associated protein 3

Flagell_FlgL

7

IPR013385

13,385

Type III secretion system apparatus protein YscQ/HrcQ/SpaO

T3SS_SpaO/YscQ/SpaO

Family

2,779

false

Proteins in this entry are encoded within type III secretion operons and are involved in many different functions. For example, YscQ in Yersinia is essential for YOPs secretion [ ] and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae [ ]. SpaO is involved in a secretory pathway res...

[ "GO:0030254" ]

[ "protein secretion by the type III secretion system" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02551" ]

[ "SpaO_YscQ" ]

[ 2779 ]

1

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "3uep" ]

1

[ "PUB00001240", "PUB00016760", "PUB00020771", "PUB00161231" ]

[ "8404849", "9721292", "8169210", "25994170" ]

[ "Cognate gene clusters govern invasion of host epithelial cells by Salmonella typhimurium and Shigella flexneri.", "Negative regulation of hrp genes in Pseudomonas syringae by HrpV.", "The lcrB (yscN/U) gene cluster of Yersinia pseudotuberculosis is involved in Yop secretion and shows high homology to the spa g...

[ 1993, 1998, 1994, 2015 ]

4

[]

[ "IPR003283", "IPR061286" ]

0

2

0

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

[ 2775, 2, 2 ]

3

[ "Zea mays" ]

[ 1 ]

1

true

Family

Type III secretion system apparatus protein YscQ/HrcQ/SpaO

T3SS_SpaO/YscQ/SpaO

6

IPR013387

13,387

Type III secretion system, PrgH/EprH

T3SS_PrgH/EprH

Family

764

false

In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion [ ] and is a structural component of the needle complex, which is the core component of type III secretion sy...

[]

0

[ "NCBIFAM" ]

[ "TIGR02554" ]

[ "PrgH" ]

[ 764 ]

1

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "2y9j", "3gr0", "3gr1", "3j1x", "3j6d", "4g1i", "5tcp", "5tcr", "6duz", "6pem", "6pep", "6q14", "6q15", "6q16", "6uot", "6uov", "7ah9", "7ahi" ]

18

[ "PUB00020739", "PUB00020743" ]

[ "15528446", "7476203" ]

[ "Structural insights into the assembly of the type III secretion needle complex.", "PhoP/PhoQ transcriptional repression of Salmonella typhimurium invasion genes: evidence for a role in protein secretion." ]

[ 2004, 1995 ]

2

[ "IPR019029" ]

[]

1

0

1

[ "Pseudomonadota" ]

[ 764 ]

1

[]

0

true

Family

Type III secretion system, PrgH/EprH

T3SS_PrgH/EprH

4

IPR013388

13,388

Type III secretion apparatus protein OrgA/MxiK

T3SS_OrgA/MxiK

Family

833

false

This protein is encoded by genes which are found in type III secretion operons, and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus [ ]. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09482", "TIGR02555" ]

[ "OrgA_MxiK", "OrgA_MxiK" ]

[ 833, 598 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[]

0

[ "PUB00020740", "PUB00020748", "PUB00020770" ]

[ "12864857", "8063389", "10816487" ]

[ "MxiK and MxiN interact with the Spa47 ATPase and are required for transit of the needle components MxiH and MxiI, but not of Ipa proteins, through the type III secretion apparatus of Shigella flexneri.", "Identification and characterization of a Salmonella typhimurium oxygen-regulated gene required for bacterial...

[ 2003, 1994, 2000 ]

3

[]

0

null

[ "Bacteria" ]

[ 833 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type III secretion apparatus protein OrgA/MxiK

T3SS_OrgA/MxiK

5

IPR013389

13,389

CRISPR-associated protein Cas8b

CRISPR-assoc_prot_Cas8b

Family

647

false

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. This entry represents a minor class of Cas proteins, known as Cas8b [ ], found in at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihy...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09484", "TIGR02556" ]

[ "Cas_TM1802", "cas_TM1802" ]

[ 647, 275 ]

2

[ "GP" ]

[ "GenProp0021" ]

[ "GP:GenProp0021" ]

1

[]

0

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00085160" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "24459147", "28238733" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2014, 2017 ]

7

[]

0

null

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

[ 201, 436, 10 ]

3

[]

0

true

Family

CRISPR-associated protein Cas8b

CRISPR-assoc_prot_Cas8b

7

IPR013390

13,390

Type III secretion protein HpaP

T3SS_HpaP

Family

385

false

This entry represents proteins encoded by genes which are always found in type III secretion operons [ ], which are described as SctP (Secretion and Cellular Translocation P) proteins in many pathogenic bacteria. Lineage-specific names for SctP include HpaP in Ralstonia solanacearum, YscP in Yersinia, HrpP in Pseudomon...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09483", "TIGR02557" ]

[ "HpaP", "HpaP" ]

[ 382, 295 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[]

0

[ "PUB00020779", "PUB00104257", "PUB00106704" ]

[ "12730176", "26520801", "29345052" ]

[ "Characterization of the Xanthomonas axonopodis pv. glycines Hrp pathogenicity island.", "Type III Secretion: Building and Operating a Remarkable Nanomachine.", "HpaP, a novel regulatory protein with ATPase and phosphatase activity, contributes to full virulence in Xanthomonas campestris pv. campestris." ]

[ 2003, 2016, 2018 ]

3

[]

0

null

[ "Capitella teleta", "Pseudomonadati", "organismal metagenomes" ]

[ 1, 377, 7 ]

3

[]

0

true

Family

Type III secretion protein HpaP

T3SS_HpaP

5

IPR013391

13,391

Type III secretion protein HrpB2

T3SS_HrpB2

Family

305

false

This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09487", "TIGR02558" ]

[ "HrpB2", "HrpB2" ]

[ 305, 189 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[]

0

[]

0

[]

0

null

[ "Pseudomonadota", "plant metagenome" ]

[ 301, 4 ]

2

[]

0

true

Family

Type III secretion protein HrpB2

T3SS_HrpB2

8

IPR013392

13,392

Type III secretion protein HrpB7

T3SS_HrpB7

Family

299

false

This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09486", "TIGR02559" ]

[ "HrpB7", "HrpB7" ]

[ 299, 134 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[]

0

[]

0

[]

0

null

[ "Alexandrium andersonii", "Pseudomonadota" ]

[ 1, 298 ]

2

[]

0

true

Family

Type III secretion protein HrpB7

T3SS_HrpB7

9

IPR013393

13,393

Type III secretion protein HrpB4

T3SS_HrpB4

Family

322

false

This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09502", "TIGR02560" ]

[ "HrpB4", "HrpB4" ]

[ 322, 141 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[]

0

[]

0

[]

0

null

[ "Pseudomonadota", "plant metagenome" ]

[ 317, 5 ]

2

[]

0

true

Family

Type III secretion protein HrpB4

T3SS_HrpB4

1

IPR013394

13,394

Type III secretion system, HrpB1/HrpK

T3SS_HrpB1/HrpK

Family

472

false

This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09613", "TIGR02561" ]

[ "HrpB1_HrpK", "HrpB1_HrpK" ]

[ 472, 227 ]

2

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "Ricinus communis", "plant metagenome" ]

[ 466, 1, 5 ]

3

[]

0

true

Family

Type III secretion system, HrpB1/HrpK

T3SS_HrpB1/HrpK

3

IPR013395

13,395

CRISPR-associated Cas3, Yersinia-type

CRISPR-assoc_Cas3_yers

Family

933

false

This entry represents the Yersinia-type Cas3 family of helicases. The Yersinia-type Cas3 helicases differ from the more common Cas3 proteins by being considerably larger, though they still share a number of motifs, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromo...

[]

0

[ "NCBIFAM" ]

[ "TIGR02562" ]

[ "cas3_yersinia" ]

[ 933 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0310" ]

[ "GP:GenProp0021", "GP:GenProp0310" ]

2

[ "5b7i", "5gqh", "8flj", "9p11", "9p1d" ]

5

[ "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

[]

0

null

[ "Anopheles coluzzii", "Bacteria", "metagenomes" ]

[ 1, 927, 5 ]

3

[]

0

true

Family

CRISPR-associated Cas3, Yersinia-type

CRISPR-assoc_Cas3_yers

3

IPR013396

13,396

CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST

CRISPR-assoc_prot_Csy4

Family

1,300

false

This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4. In Pseudomonas aeruginosa, crRNA biogenesis requires the endoribonuclease Csy4, which binds and ...

[ "GO:0004519", "GO:0043571" ]

[ "endonuclease activity", "maintenance of CRISPR repeat elements" ]

[ "molecular_function", "biological_process" ]

2

[ "PFAM", "NCBIFAM", "CDD" ]

[ "PF09618", "TIGR02563", "cd09739" ]

[ "Cas_Csy4", "cas_Csy4", "Cas6_I-F" ]

[ 1297, 1230, 972 ]

3

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0310" ]

[ "GP:GenProp0021", "GP:GenProp0310" ]

2

[ "2xli", "2xlj", "2xlk", "4al5", "4al6", "4al7", "5o6u", "5o7h", "5uz9", "6b44", "6b45", "6b46", "6b47", "6b48", "6lnb", "6lnc", "6ne0", "6pif", "6pig", "6pij", "6uvn", "6v9q", "6vbw", "6vqv", "6vqw", "6vqx", "6w1x", "6whi", "7ecv", "7elm", "7eln", "7eqg"...

64

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00061193", "PUB00071890" ]

[ "17442114", "17379808", "16545108", "21699496", "22522703", "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, 2012, 2014 ]

6

[]

0

null

[ "Bacteria", "Reticulomyxa filosa", "unclassified Mohonavirus", "unclassified sequences" ]

[ 1285, 1, 2, 12 ]

4

[]

0

true

Family

CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST

CRISPR-assoc_prot_Csy4

4

IPR013397

13,397

Type I-F CRISPR-associated protein Csy1

CRISPR-assoc_prot_Csy1

Family

973

false

This entry represents type I-F CRISPR-associated protein Csy1 (CRISPR/Cas Subtype Ypest protein 1, also known as Cas8f), typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. Csy1 is part of the type I-F CRISPR system yersinia (Csy) su...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09611", "TIGR02564" ]

[ "Cas_Csy1", "cas_Csy1" ]

[ 973, 826 ]

2

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0310" ]

[ "GP:GenProp0021", "GP:GenProp0310" ]

2

[ "5uz9", "6b44", "6b45", "6b47", "6b48", "6ne0", "6vqv", "6vqw", "6vqx", "6w1x", "6whi", "7ecv", "7ecw", "7elm", "7eln", "7eqg", "7jzw", "7jzx", "7jzy", "7jzz", "7t3j", "7t3k", "7t3l", "7taw", "7tax", "7we6", "7yhs", "8w1p", "8ydb", "8yeo", "8yh9", "8z0k"...

35

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00106900", "PUB00106901", "PUB00106902" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "32170016", "34432044", "28985564" ]

[ "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, 2020, 2021, 2017 ]

8

[]

0

null

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

[ 961, 5, 7 ]

3

[]

0

true

Family

Type I-F CRISPR-associated protein Csy1

CRISPR-assoc_prot_Csy1

6

IPR013398

13,398

Type I-F CRISPR-associated protein Csy2

CRISPR-assoc_prot_Csy2

Family

1,165

false

This entry represents ty I-F CRISPR-associated protein Csy2 (also known as Cas5f), typified by YPO2464 of Yersinia pestis, which is part of the type I-F CRISPR system yersinia (Csy) surveillance complex in which the binding of target dsDNA leads to large quaternary and tertiary structural changes in the complex that ar...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09614", "TIGR02565" ]

[ "Cas_Csy2", "cas_Csy2" ]

[ 1165, 918 ]

2

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0310" ]

[ "GP:GenProp0021", "GP:GenProp0310" ]

2

[ "5uz9", "6b44", "6b45", "6b47", "6b48", "6lnb", "6lnc", "6ne0", "6pif", "6pig", "6pij", "6uvn", "6v9q", "6vbw", "6vqv", "6vqw", "6vqx", "6w1x", "6whi", "7ecv", "7ecw", "7elm", "7eln", "7eqg", "7jzw", "7jzx", "7jzy", "7jzz", "7t3j", "7t3k", "7t3l", "7taw"...

56

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00106900", "PUB00106901", "PUB00106902" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "32170016", "34432044", "28985564" ]

[ "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, 2020, 2021, 2017 ]

8

[]

0

null

[ "Bacteria", "Steinernema glaseri", "unclassified Mohonavirus", "unclassified sequences" ]

[ 1149, 1, 2, 13 ]

4

[]

0

true

Family

Type I-F CRISPR-associated protein Csy2

CRISPR-assoc_prot_Csy2

1

IPR013399

13,399

Type I-F CRISPR-associated protein Csy3

CRISPR-assoc_prot_Csy3

Family

1,201

false

This entry represents type I-F CRISPR-associated protein Csy3 (also known as Cas7f) [ ], typified by YPO2463 of Yersinia pestis. Csy3 is part of the type I-F CRISPR system yersinia (Csy) surveillance complex in which the binding of target dsDNA leads to large quaternary and tertiary structural changes in the complex th...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09615", "TIGR02566" ]

[ "Cas_Csy3", "cas_Csy3" ]

[ 1201, 1159 ]

2

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0310" ]

[ "GP:GenProp0021", "GP:GenProp0310" ]

2

[ "5uz9", "5xlo", "5xlp", "6b44", "6b45", "6b46", "6b47", "6b48", "6kqr", "6lnb", "6lnc", "6ne0", "6pif", "6pig", "6pij", "6uvn", "6v9q", "6vbw", "6vqv", "6vqw", "6vqx", "6w1x", "6whi", "7ecv", "7ecw", "7elm", "7eln", "7eqg", "7jzw", "7jzx", "7jzy", "7jzz"...

62

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00106900", "PUB00106901", "PUB00106902" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "32170016", "34432044", "28985564" ]

[ "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, 2020, 2021, 2017 ]

8

[]

0

null

[ "Bacteria", "Ecdysozoa", "unclassified Mohonavirus", "unclassified sequences" ]

[ 1182, 3, 2, 14 ]

4

[]

0

true

Family

Type I-F CRISPR-associated protein Csy3

CRISPR-assoc_prot_Csy3

8

IPR013401

13,401

Type III secretion regulator, YopN/LcrE/InvE/MxiC

T3SS_LcrE

Domain

1,443

false

This protein is found in type III secretion operons and, in Yersinia, is localized to the cell surface and is involved in the Low-Calcium Response (LCR), possibly by sensing the calcium concentration [ ]. In Salmonella, the gene is known as InvE and is believed to perform an essential role in the secretion process and ...

[ "GO:0030254", "GO:0050709", "GO:0009986" ]

[ "protein secretion by the type III secretion system", "negative regulation of protein secretion", "cell surface" ]

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

3

[ "NCBIFAM" ]

[ "TIGR02568" ]

[ "LcrE" ]

[ 1443 ]

1

[ "GP" ]

[ "GenProp0052" ]

[ "GP:GenProp0052" ]

1

[ "1xkp", "1xl3", "2vix", "2vj4", "2vj5", "4nrh", "4p3z", "4p40", "6gx7", "7yyg" ]

10

[ "PUB00020751", "PUB00020764", "PUB00020775", "PUB00049756", "PUB00106892" ]

[ "15701523", "12169593", "1857212", "18304577", "25056950" ]

[ "Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis.", "Salmonella type III secretion-associated protein InvE controls translocation of effector proteins into host cells.", "The surface-located YopN protein is involved in calcium signal transduction in ...

[ 2005, 2002, 1991, 2008, 2014 ]

5

[]

[ "IPR010812" ]

0

1

0

[ "Bacteria", "Beauveria bassiana D1-5", "ecological metagenomes" ]

[ 1440, 1, 2 ]

3

[]

0

true

Domain

Type III secretion regulator, YopN/LcrE/InvE/MxiC

T3SS_LcrE

3

IPR013402

13,402

Conserved hypothetical protein CHP02569

CHP02569

Family

1,136

false

This entry has so far only been found in Actinobacteria, including at least five species of Mycobacterium, three of Corynebacterium, and Nocardia farcinica -always in a single copy per genome. The function is unknown.

[]

0

[ "NCBIFAM" ]

[ "TIGR02569" ]

[ "TIGR02569_actnb" ]

[ 1136 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Lipomyces orientalis", "freshwater metagenome" ]

[ 1134, 1, 1 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP02569

CHP02569

5

IPR013403

13,403

Type I-U CRISPR-associated RAMP protein Csb1/Cas7u

CRISPR-assoc_prot_Csb1/Cas7u

Family

570

false

Members of this family, previously called Csx4 and now called Csb1 or Cas7u, are found in association with CRISPR repeats and other CRISPR-associated (cas) genes. Its CRISPR/Cas type, now called type I-U, originally was designated Dpsych. It was first seen in the genomes of Geobacter sulfurreducens PCA and Desulfotalea...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09617", "TIGR02570" ]

[ "Cas_GSU0053", "cas7_GSU0053" ]

[ 570, 500 ]

2

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0469" ]

[ "GP:GenProp0021", "GP:GenProp0469" ]

2

[ "8ane" ]

1

[ "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

[]

0

null

[ "Bacteria", "Methanobacteriati", "unclassified sequences" ]

[ 553, 7, 10 ]

3

[]

0

true

Family

Type I-U CRISPR-associated RAMP protein Csb1/Cas7u

CRISPR-assoc_prot_Csb1/Cas7u

2

IPR013404

13,404

Competence operon E, ComEB

Competence_ComEB

Family

1,724

false

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use compone...

[]

0

[ "NCBIFAM" ]

[ "TIGR02571" ]

[ "ComEB" ]

[ 1724 ]

1

[ "GP" ]

[ "GenProp0311" ]

[ "GP:GenProp0311" ]

1

[]

0

[ "PUB00019328", "PUB00052316", "PUB00052317" ]

[ "7968523", "8901420", "10361283" ]

[ "Characterization of comE, a late competence operon of Bacillus subtilis required for the binding and uptake of transforming DNA.", "Who's competent and when: regulation of natural genetic competence in bacteria.", "Mutational analysis of ComS: evidence for the interaction of ComS and MecA in the regulation of ...

[ 1993, 1996, 1999 ]

3

[ "IPR015517" ]

[]

1

0

1

[ "Bacillota", "Trichuris trichiura", "bioreactor metagenome" ]

[ 1721, 1, 2 ]

3

[]

0

true

Family

Competence operon E, ComEB

Competence_ComEB

8

IPR013406

13,406

Conserved hypothetical protein CHP02574, addiction module

CHP02574_addiction_mod

Family

3,040

false

This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins ( ). It is likely that this protein and its partner comprise some form ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09720", "TIGR02574" ]

[ "Unstab_antitox", "stabl_TIGR02574" ]

[ 3020, 1432 ]

2

[ "GP" ]

[ "GenProp0321" ]

[ "GP:GenProp0321" ]

1

[ "8c26" ]

1

[ "PUB00020763" ]

[ "10547685" ]

[ "Addiction modules and programmed cell death and antideath in bacterial cultures." ]

[ 1999 ]

1

[]

0

null

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

[ 2961, 3, 5, 71 ]

4

[]

0

true

Family

Conserved hypothetical protein CHP02574, addiction module

CHP02574_addiction_mod

8

IPR013407

13,407

CRISPR-associated protein Cmr2

CRISPR-assoc_prot_Cmr2

Family

942

false

This entry is encoded within the CRISPR-associated RAMP module, a set of six genes found together in prokaryotic genomes [ ]. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six genes (but not those encoding this entry) contain RAMP domains, and b...

[]

0

[ "NCBIFAM" ]

[ "TIGR02577" ]

[ "cas_TM1794_Cmr2" ]

[ 942 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0316" ]

[ "GP:GenProp0021", "GP:GenProp0316" ]

2

[ "3ung", "3ur3", "3w2v", "3w2w", "3x1l", "4doz", "4h4k", "4w8y", "6s6b", "6s8b", "6s8e", "6s91", "6sh8", "6shb", "6sic", "9arw" ]

16

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00065747", "PUB00071890" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "22405013", "24459147" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2012, 2014 ]

7

[]

0

null

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

[ 111, 821, 10 ]

3

[]

0

true

Family

CRISPR-associated protein Cmr2

CRISPR-assoc_prot_Cmr2

6

IPR013408

13,408

CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1

Cas10/Csm1

Family

921

false

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. This entry represents Csm1 (CRISPR/Cas Subtype Mtube Protein 1), which is a single-strand-specific deoxyribonuclease (ssDNase) which digests both li...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02578", "cd09680" ]

[ "cas_TM1811_Csm1", "Cas10_III" ]

[ 921, 351 ]

2

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

[ "2.7.7.-", "GenProp0021", "GenProp0318", "PWY-6322", "PWY-6626", "PWY-6749", "PWY-6955", "PWY-6998", "PWY-7127", "PWY-7419", "PWY-7529", "PWY-7706", "PWY-7719", "PWY-7735", "PWY-7737", "PWY-7769", "PWY-7888", "PWY-7904", "PWY-8117", "PWY-8179" ]

[ "EC:2.7.7.-", "GP:GenProp0021", "GP:GenProp0318", "METACYC:PWY-6322", "METACYC:PWY-6626", "METACYC:PWY-6749", "METACYC:PWY-6955", "METACYC:PWY-6998", "METACYC:PWY-7127", "METACYC:PWY-7419", "METACYC:PWY-7529", "METACYC:PWY-7706", "METACYC:PWY-7719", "METACYC:PWY-7735", "METACYC:PWY-7737"...

20

[ "4uw2", "6ifk", "6ifl", "6ifn", "6ifr", "6ifu", "6ify", "6ifz", "6ig0", "6iqw", "6kbd", "6kc0", "6mua", "6mur", "6mus", "6mut", "6muu", "6nud", "6nue", "6o73", "6o74", "6o75", "6o78", "6o79", "6o7b", "6o7d", "6o7e", "6o7h", "6o7i", "6xn3", "6xn4", "6xn5"...

56

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00091685" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "29979631" ]

[ "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, 2018 ]

6

[]

0

null

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

[ 79, 825, 17 ]

3

[]

0

true

Family

CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1

Cas10/Csm1

6

IPR013409

13,409

CRISPR-associated protein Crn3/Csx3

CRISPR-assoc_prot_Crn3/Csx3

Family

263

false

This entry represents the Crn3/Csx3 family of Cas proteins, which is encoded in CRISPR-associated gene cluster near CRISPR repeats in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09620", "TIGR02579" ]

[ "Cas_csx3", "cas_csx3" ]

[ 263, 120 ]

2

[ "GP" ]

[ "GenProp0021" ]

[ "GP:GenProp0021" ]

1

[ "3wzg", "3wzh", "3wzi", "6vjg", "6yud", "9mud", "9mue", "9muo", "9mw9" ]

9

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00106706", "PUB00106707" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "26106927", "32597755" ]

[ "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, 2015, 2020 ]

7

[]

0

null

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

[ 27, 229, 4, 3 ]

4

[]

0

true

Family

CRISPR-associated protein Crn3/Csx3

CRISPR-assoc_prot_Crn3/Csx3

1

IPR013410

13,410

CRISPR-associated RAMP Cmr4

CRISPR-assoc_RAMP_Cmr4

Family

1,323

false

This entry represents the CRISPR system Cmr endoribonuclease Cmr4 which is part of the broad RAMP superfamily collection of CRISPR-associated proteins. The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system [ , , ]. Cmr4 is required for target-cle...

[]

0

[ "PANTHER", "NCBIFAM" ]

[ "PTHR36700", "TIGR02580" ]

[ "", "cas_RAMP_Cmr4" ]

[ 1322, 1074 ]

2

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0316" ]

[ "GP:GenProp0021", "GP:GenProp0316" ]

2

[ "3x1l", "4rdp", "4w8w", "4wnz", "6s6b", "6s8b", "6s8e", "6s91", "6sh8", "6shb", "6sic", "9arw" ]

12

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00088224", "PUB00106893", "PUB00106894" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "25280103", "25541196", "32730741" ]

[ "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, 2014, 2015, 2020 ]

8

[]

0

null

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

[ 161, 1147, 15 ]

3

[]

0

true

Family

CRISPR-associated RAMP Cmr4

CRISPR-assoc_RAMP_Cmr4

3

IPR013411

13,411

CRISPR-associated RAMP protein Csx7

CRISPR-assoc_RAMP_Csx7

Family

262

false

This entry represents a family of Cas proteins that are found in the RAMP-2 subtype of CRISPR/cas locus which includes the representative protein SSO1426 from Saccharolobus solfataricus P2, was designated Csx7 in [ ]. The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key ele...

[]

0

[ "NCBIFAM" ]

[ "TIGR02581" ]

[ "cas_cyan_RAMP" ]

[ 262 ]

1

[ "GP" ]

[ "GenProp0021" ]

[ "GP:GenProp0021" ]

1

[ "8bmw" ]

1

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "24459147" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2014 ]

6

[]

0

null

[ "Archaea", "Bacteria", "anaerobic digester metagenome" ]

[ 89, 172, 1 ]

3

[]

0

true

Family

CRISPR-associated RAMP protein Csx7

CRISPR-assoc_RAMP_Csx7

5

IPR013412

13,412

CRISPR-associated RAMP Csm3

CRISPR-assoc_RAMP_Csm3

Family

893

false

This entry represents the Csm3 (CRISPR/cas Subtype Mtube, protein 3) family of Cas proteins encoded by genes found in the mtube subtype CRISPR/cas locus and designated. This is also known as Csm3 Type III-A [ , ]. Csm3 binds unstructured RNAs in a sequence non-specific manner, which suggests that it interacts with the ...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02582", "cd09684" ]

[ "cas7_TM1809", "Csm3_III-A" ]

[ 893, 54 ]

2

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0318" ]

[ "GP:GenProp0021", "GP:GenProp0318" ]

2

[ "4n0l", "4qts", "5yjd", "6ae2", "6ifk", "6ifl", "6ifn", "6ifr", "6ifu", "6ify", "6ifz", "6ig0", "6iqw", "6mur", "6mus", "6mut", "6muu", "6nbt", "6nud", "6nue", "6o7e", "6o7h", "6o7i", "6xn3", "6xn4", "6xn5", "6xn7", "7uzw", "7uzx", "7uzy", "7uzz", "7v00"...

52

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00078085", "PUB00106895", "PUB00106896" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "21552286", "30759237", "24157656" ]

[ "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, 2011, 2019, 2013 ]

8

[]

0

null

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

[ 83, 797, 13 ]

3

[]

0

true

Family

CRISPR-associated RAMP Csm3

CRISPR-assoc_RAMP_Csm3

3

IPR013413

13,413

CRISPR-associated protein, NE0113

CRISPR-assoc_prot_NE0113

Family

394

false

This entry represents a minor family of Cas proteins that are now called Csm6 and previously called Csx6, with both CARF (CRISPR-associated Rossman Fold) and HEPN domains, is a ring nuclease for cyclic-oligoadenylates that are generated as second messengers involved in activation of CRISPR systems [ , ]. The CRISPR-Cas...

[]

0

[ "NCBIFAM" ]

[ "TIGR02584" ]

[ "cas_NE0113" ]

[ 394 ]

1

[ "GP" ]

[ "GenProp0021" ]

[ "GP:GenProp0021" ]

1

[]

0

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00085051", "PUB00106708" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "24817877", "31326273" ]

[ "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, 2014, 2019 ]

7

[]

0

null

[ "Bacteria", "unclassified sequences" ]

[ 388, 6 ]

2

[]

0

true

Family

CRISPR-associated protein, NE0113

CRISPR-assoc_prot_NE0113

6

IPR013414

13,414

CRISPR-associated protein Cas7, subtype I-B/Tneap

Cas7/Cst2/DevR_sub_I-B/Tneap

Family

1,003

false

This entry represents a family of DevR (Cas7)-type Cas proteins that includes DevR from Myxococcus xanthus. DevR is a key regulator of development. DevR mutants are incapable of fruiting body development [ ]. The expression of DevR appears to be regulated through a number of means, including both location and autorepre...

[]

0

[ "NCBIFAM" ]

[ "TIGR02585" ]

[ "cas_Cst2_DevR" ]

[ 1003 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0317" ]

[ "GP:GenProp0021", "GP:GenProp0317" ]

2

[]

0

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "24459147" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2014 ]

6

[ "IPR010154" ]

[ "IPR016581" ]

1

0

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

[ 114, 882, 7 ]

3

[]

0

true

Family

CRISPR-associated protein Cas7, subtype I-B/Tneap

Cas7/Cst2/DevR_sub_I-B/Tneap

1

IPR013415

13,415

CRISPR-associated protein Cas5/Cmx5/DevS

Cas5_Cmx5_DevS

Family

118

false

This entry represents a family of Cas5 proteins that includes DevS from Myxococcus xanthus, as well as related proteins from Leptospira interrogans and Gemmata obscuriglobus. Cas5 is a key regulator of development that is encoded in a cluster of CRISPR-associated (cas) genes, and in the special case of M. xanthus has t...

[ "GO:0051607" ]

[ "defense response to virus" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02586" ]

[ "cas5_cmx5_devS" ]

[ 118 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0922" ]

[ "GP:GenProp0021", "GP:GenProp0922" ]

2

[ "8fcj", "8fcu", "8fd2", "8fd3", "8ff4", "8ff5" ]

6

[ "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

[]

0

null

[ "Bacteria" ]

[ 118 ]

1

[]

0

true

Family

CRISPR-associated protein Cas5/Cmx5/DevS

Cas5_Cmx5_DevS

7

IPR013416

13,416

Conserved hypothetical protein CHP02587, putative integral membrane

CHP02587_IM

Family

594

false

Members of this protein family are found in Anabaena sp. (strain PCC 7120), Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. The proteins appear to span the membrane seven times.

[]

0

[ "NCBIFAM" ]

[ "TIGR02587" ]

[ "" ]

[ 594 ]

1

[]

0

[]

0

[]

0

[ "IPR024464" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 592, 2 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP02587, putative integral membrane

CHP02587_IM

2

IPR013417

13,417

Conserved hypothetical protein CHP02588

CHP02588

Family

819

false

The function of this protein is unknown. It often found as part of a two-gene operon with , a protein that appears to span the membrane seven times. It has so far been found in the bacteria Anabaena sp. (strain PCC 7120), Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09624", "TIGR02588" ]

[ "DUF2393", "" ]

[ 530, 289 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 805, 14 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP02588

CHP02588

5

IPR013418

13,418

Type I-C CRISPR-associated protein Cas7/Csd2

CRISPR-assoc_prot_Cas7/Csd2

Family

2,172

false

This entry represents one of two closely related subfamilies that belong to the larger family of CRISPR-associated protein TM1801. Members are the type I-C CRISPR-associated protein Cas7/Csd2 of the Dvulg subtype of the CRISPR/cas system [ , ]. A related entry is , the Csh2 protein of the Hmari CRISPR subtype. The CRIS...

[ "GO:0043571" ]

[ "maintenance of CRISPR repeat elements" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02589" ]

[ "cas_Csd2" ]

[ 2172 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0313" ]

[ "GP:GenProp0021", "GP:GenProp0313" ]

2

[ "7kha", "8dej", "8dex", "8dfa", "8dfo", "8dfs", "8g9s", "8g9t", "8g9u", "8gaf", "8gam", "8gan" ]

12

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00106897", "PUB00106898" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "33230133", "36805026" ]

[ "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, 2020, 2023 ]

7

[ "IPR006482" ]

[]

1

0

1

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

[ 2125, 2, 18, 27 ]

4

[]

0

true

Family

Type I-C CRISPR-associated protein Cas7/Csd2

CRISPR-assoc_prot_Cas7/Csd2

3

IPR013419

13,419

Type I-B CRISPR-associated protein Cas7/Csh2

CRISPR-assoc_prot_Cas7/Csh2

Family

564

false

This entry represents one of two closely related subfamilies that belong to the larger family of CRISPR-associated protein TM1801. Members are the type I-B CRISPR-associated protein Cas7/Csh2 of the Hmari subtype of the CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. A re...

[ "GO:0043571" ]

[ "maintenance of CRISPR repeat elements" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02590" ]

[ "cas_Csh2" ]

[ 564 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0320" ]

[ "GP:GenProp0021", "GP:GenProp0320" ]

2

[ "7xz3" ]

1

[ "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

[ "IPR006482" ]

[]

1

0

1

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

[ 200, 359, 5 ]

3

[]

0

true

Family

Type I-B CRISPR-associated protein Cas7/Csh2

CRISPR-assoc_prot_Cas7/Csh2

7

IPR013420

13,420

Type I-B CRISPR-associated protein Cas8b/Csh1, C-terminal

CRISPR-assoc_prot_Cas8b/Csh1_C

Domain

423

false

This entry is found in the C-terminal region of a family of type I-B CRISPR-associated protein Cas8b/Csh1 of the Hmari subtype, [ ]. Except for some sequences from halophilic archaea, this domain contains a pair of CXXC motifs. The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. T...

[]

0

[ "NCBIFAM" ]

[ "TIGR02591" ]

[ "cas_Csh1" ]

[ 423 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0320" ]

[ "GP:GenProp0021", "GP:GenProp0320" ]

2

[]

0

[ "PUB00020781", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890" ]

[ "16292354", "17442114", "17379808", "16545108", "21699496", "24459147" ]

[ "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.", "Evolutionary conservation of sequence and secondary structures in CRISPR repeats.", "CRISPR provides acquired resistance against viruses in prokaryotes.", "A putative RNA-interference-base...

[ 2005, 2007, 2007, 2006, 2011, 2014 ]

6

[]

0

null

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

[ 148, 271, 4 ]

3

[]

0

true

Domain

Type I-B CRISPR-associated protein Cas8b/Csh1, C-terminal

CRISPR-assoc_prot_Cas8b/Csh1_C

8

IPR013421

13,421

Type I-B CRISPR-associated protein Cas5, HALMA

CRISPR-assoc_prot_Cas5_HALMA

Family

717

false

This entry represents a Cas5 family of Cas proteins unique to the hmari subtype of cas genes and CRISPR repeats, which is the only subtype present in Haloarcula marismortui ATCC 43049. The hmari type, though uncommon, is also found in the Aquificae, Thermotogae, Firmicutes, and Dictyoglomi. The CRISPR-Cas system is a p...

[]

0

[ "NCBIFAM" ]

[ "TIGR02592" ]

[ "cas_Cas5h" ]

[ 717 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0320" ]

[ "GP:GenProp0021", "GP:GenProp0320" ]

2

[]

0

[ "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

[ "IPR021124" ]

[]

1

0

1

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

[ 188, 523, 6 ]

3

[]

0

true

Family

Type I-B CRISPR-associated protein Cas5, HALMA

CRISPR-assoc_prot_Cas5_HALMA

4

IPR013422

13,422

CRISPR-associated protein Cas5, N-terminal

CRISPR-assoc_prot_Cas5_N

Domain

7,666

false

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. This entry represents a shared N-terminal region, of about 43 amino acids in length, found in a number of Cas proteins. This region is widely distri...

[]

0

[ "NCBIFAM" ]

[ "TIGR02593" ]

[ "CRISPR_cas5" ]

[ 7666 ]

1

[ "GP" ]

[ "GenProp0021" ]

[ "GP:GenProp0021" ]

1

[ "3kg4", "3vzh", "3vzi", "4f3m", "4n77", "4qyz", "4r0j", "4tvx", "4u7u", "5cd4", "5h9e", "5h9f", "5u07", "5u0a", "6c66", "7kha", "7r21", "7r2k", "7tr6", "7tr8", "7tr9", "7tra", "8dej", "8dex", "8dfa", "8dfo", "8dfs", "8fcj", "8fcu", "8fd2", "8fd3", "8ff4"...

56

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00043290", "PUB00060621", "PUB00071890" ]

[ "17442114", "17379808", "16545108", "16079334", "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, 2005, 2011, 2014 ]

6

[]

0

null

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

[ 478, 7101, 24, 63 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Domain

CRISPR-associated protein Cas5, N-terminal

CRISPR-assoc_prot_Cas5_N

4

IPR013423

13,423

Conserved hypothetical protein CHP02594

CHP02594

Family

1,686

false

This entry is so far restricted mostly to proteobacteria, although it is found in some other bacteria. Its function is unknown.

[]

0

[ "NCBIFAM" ]

[ "TIGR02594" ]

[ "" ]

[ 1686 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Opisthokonta", "Viruses", "metagenomes" ]

[ 1497, 2, 172, 15 ]

4

[]

0

true

Family

Conserved hypothetical protein CHP02594

CHP02594

5

IPR013425

13,425

Autotransporter-associated beta strand repeat

Autotrns_rpt

Repeat

15,193

false

This Autotransporter-associated β strand repeat model represents a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters ( ). The repeats occur with a periodicity of 60 to 100 r...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF12951", "TIGR02601" ]

[ "PATR", "autotrns_rpt" ]

[ 14022, 14981 ]

2

[]

0

[ "5ke1", "8axg", "8e7f" ]

3

[ "PUB00077770", "PUB00106899" ]

[ "25869731", "28268178" ]

[ "The passenger-associated transport repeat promotes virulence factor secretion efficiency and delineates a distinct autotransporter subtype.", "Structural insights into the architecture of the Shigella flexneri virulence factor IcsA/VirG and motifs involved in polar distribution and secretion." ]

[ 2015, 2017 ]

2

[]

0

null

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

[ 15111, 2, 29, 51 ]

4

[ "Escherichia coli (strain K12)", "Mus musculus" ]

[ 2, 1 ]

2

true

Repeat

Autotransporter-associated beta strand repeat

Autotrns_rpt

3

IPR013426

13,426

Exosortase, EpsH-like

EpsH-like

Family

2,725

false

Members of this family are designated exosortase, analogous to sortase in cell wall sorting mediated by LPXTG domains in Gram-positive bacteria. The phylogenetic distibution of the proteins in this entry is nearly perfectly correlated with the distribution of the proteins having the PEP-CTERM anchor motif [ ]. Members ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02602" ]

[ "8TM_EpsH" ]

[ 2725 ]

1

[ "GP", "GP" ]

[ "GenProp0326", "GenProp0652" ]

[ "GP:GenProp0326", "GP:GenProp0652" ]

2

[]

0

[ "PUB00034422" ]

[ "16930487" ]

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

[ 2006 ]

1

[ "IPR019127" ]

[ "IPR017540", "IPR017544", "IPR026488", "IPR026491", "IPR026492" ]

1

5

0

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

[ 2663, 2, 14, 46 ]

4

[]

0

true

Family

Exosortase, EpsH-like

EpsH-like

7

IPR013427

13,427

Haem-binding domain, putative

Haem-bd_dom_put

Domain

4,926

false

This entry represents a protein domain found predominantly in bacterial species. A large number of paralogues exist in some of the species that contain it. For example, more than twenty copies are found in Rhodopirellula baltica SH 1 and Verrucomicrobium spinosum DSM 4136. This domain is approximately 140 amino acids l...

[]

0

[ "NCBIFAM" ]

[ "TIGR02603" ]

[ "CxxCH_TIGR02603" ]

[ 4926 ]

1

[]

0

[ "7zs0", "7zs1", "7zs2", "9fbk" ]

4

[]

0

[ "IPR009056" ]

[]

1

0

1

[ "Bacteria", "Symbiodiniaceae", "ecological metagenomes" ]

[ 4820, 12, 94 ]

3

[]

0

true

Domain

Haem-binding domain, putative

Haem-bd_dom_put

9

IPR013429

13,429

Putative regulatory protein FmdB, zinc ribbon domain

Regulatory_FmdB_Zinc_ribbon

Domain

15,046

false

This entry represents a putative zinc β-ribbon domain of about 41 amino acids found in several small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein,...

[]

0

[ "PFAM", "SMART", "NCBIFAM" ]

[ "PF09723", "SM00834", "TIGR02605" ]

[ "Zn_ribbon_8", "CxxC_CXXC_SSSS", "CxxC_CxxC_SSSS" ]

[ 14100, 14877, 14650 ]

3

[]

0

[]

0

[ "PUB00020777" ]

[ "8841393" ]

[ "Molecular characterisation of formamidase from Methylophilus methylotrophus." ]

[ 1996 ]

1

[]

0

null

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

[ 97, 13846, 12, 411, 680 ]

5

[]

0

true

Domain

Putative regulatory protein FmdB, zinc ribbon domain

Regulatory_FmdB_Zinc_ribbon

9

IPR013430

13,430

Toxin-antitoxin system, antidote protein, HigA

Toxin_antidote_HigA

Family

11,886

false

Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in...

[ "GO:0003677" ]

[ "DNA binding" ]

[ "molecular_function" ]

1

[ "PANTHER", "NCBIFAM" ]

[ "PTHR36924", "TIGR02607" ]

[ "", "antidote_HigA" ]

[ 11395, 11686 ]

2

[ "GP", "GP" ]

[ "GenProp0321", "GenProp0322" ]

[ "GP:GenProp0321", "GP:GenProp0322" ]

2

[ "2eby", "2icp", "2ict", "3cec", "3trb", "4mct", "4mcx", "6cf1", "6chv", "6f8h", "6f8s", "6fix", "6jpi", "6lb3", "7csv", "7csw", "7csy", "9chl", "9chn" ]

19

[ "PUB00021015", "PUB00106709" ]

[ "11322821", "26987441" ]

[ "Specific protein-DNA and protein-protein interaction in the hig gene system, a plasmid-borne proteic killer gene system of plasmid Rts1.", "The HigB/HigA toxin/antitoxin system of Pseudomonas aeruginosa influences the virulence factors pyochelin, pyocyanin, and biofilm formation." ]

[ 2001, 2016 ]

2

[]

0

null

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

[ 11457, 89, 3, 43, 294 ]

5

[ "Escherichia coli (strain K12)" ]

[ 2 ]

1

true

Family

Toxin-antitoxin system, antidote protein, HigA

Toxin_antidote_HigA

1

IPR013431

13,431

Delta-60 repeat

Delta_60_rpt

Repeat

4,996

false

This repeat often occurs in tandem, up to as many as 13 times, in proteins from Bdellovibrio bacteriovorus, Azotobacter vinelandii, Geobacter sulfurreducens, Pirellula sp. 1, Myxococcus xanthus, amongst others, many of which are Deltaproteobacteria. The length of the repeat ranges from about 57 to 61 amino acids -this ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF17164", "TIGR02608" ]

[ "DUF5122", "delta_60_rpt" ]

[ 4797, 3188 ]

2

[]

0

[]

0

[]

0

[]

0

null

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

[ 41, 4827, 14, 3, 111 ]

5

[]

0

true

Repeat

Delta-60 repeat

Delta_60_rpt

3

IPR013432

13,432

Putative addiction module antidote

Doc_partner

Family

1,445

false

Members of this family are putative addiction module antidote proteins encoded by genes that appear recurrently in two-gene operons, where the other gene encodes a Doc (death-on-curing) protein ( ). Many family members contain an AbrB-like domain ( ). Note that these proteins tend to be found on bacterial chromosomes, ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02609" ]

[ "doc_partner" ]

[ 1445 ]

1

[ "GP" ]

[ "GenProp0321" ]

[ "GP:GenProp0321" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "Ricinus communis", "metagenomes" ]

[ 1425, 1, 19 ]

3

[]

0

true

Family

Putative addiction module antidote

Doc_partner

7

IPR013433

13,433

Putative polyhydroxyalkanoic acid system protein

PHA_gran_rgn

Family

2,828

false

Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins at found at the surface of PHA granules. These proteins have so far been predominantly found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09650", "TIGR02610" ]

[ "PHA_gran_rgn", "PHA_gran_rgn" ]

[ 2828, 1844 ]

2

[ "GP" ]

[ "GenProp0055" ]

[ "GP:GenProp0055" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "Fungi", "ecological metagenomes" ]

[ 2811, 2, 15 ]

3

[]

0

true

Family

Putative polyhydroxyalkanoic acid system protein

PHA_gran_rgn

5

IPR013434

13,434

Conserved hypothetical protein CHP02611

CHP02611

Family

2,231

false

Proteins in this entry are Actinobacterial proteins of about 150 amino acids in length, with three predicted transmembrane helices and an unusual motif with consensus sequence PGPGW.

[]

0

[ "NCBIFAM" ]

[ "TIGR02611" ]

[ "" ]

[ 2231 ]

1

[]

0

[]

0

[]

0

[ "IPR019099" ]

[]

1

0

1

[ "Bacteria", "freshwater metagenome" ]

[ 2230, 1 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP02611

CHP02611

5

IPR013435

13,435

Mobile mystery protein A

Mobile_mystery_prot_A

Family

560

false

Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02612" ]

[ "mob_myst_A" ]

[ 560 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 547, 13 ]

2

[]

0

true

Family

Mobile mystery protein A

Mobile_mystery_prot_A

8

IPR013436

13,436

Mobile mystery protein B

Mobile_mystery_prot_B

Family

639

false

Proteins in this family, designated mobile mystery protein B, are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are always found together with mobile m...

[]

0

[ "NCBIFAM" ]

[ "TIGR02613" ]

[ "mob_myst_B" ]

[ 639 ]

1

[]

0

[]

0

[]

0

[ "IPR040198" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 617, 22 ]

2

[]

0

true

Family

Mobile mystery protein B

Mobile_mystery_prot_B

4

IPR013438

13,438

Sporulation stage V, protein E

SpoVE

Family

1,630

false

Like FtsW, SpoVE proteins are encoded in a peptidoglycan operon context, but found only in endospore-forming bacteria such as Bacillus, Geobacillus and Oceanobacillus. In these genera they are part of a larger set of paralogs (not just the pair FtsW and RodA) and are required specifically for sporulation, not for viabi...

[]

0

[ "NCBIFAM" ]

[ "TIGR02615" ]

[ "spoVE" ]

[ 1630 ]

1

[]

0

[]

0

[]

0

[ "IPR013437" ]

[]

1

0

1

[ "Bacillati", "metagenomes" ]

[ 1623, 7 ]

2

[]

0

true

Family

Sporulation stage V, protein E

SpoVE

2

IPR013440

13,440

Tryptophanase

TNase

Family

1,124

false

Proteins in this entry belong to the beta-eliminating lyase family and are thought to act as tryptophanases ( ) (also known as L-tryptophan indole-lyases). The genes encoding these proteins are, as a rule, found with a tryptophanase leader peptide TnaC encoded upstream.

[ "GO:0009034", "GO:0006568" ]

[ "tryptophanase activity", "L-tryptophan metabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00544", "TIGR02617" ]

[ "Tryptophanase", "tnaA_trp_ase" ]

[ 1101, 557 ]

2

[ "EC", "GP" ]

[ "4.1.99.1", "GenProp0456" ]

[ "EC:4.1.99.1", "GP:GenProp0456" ]

2

[ "1ax4", "2c44", "2oqx", "2v0y", "2v1p", "4up2", "4w1y", "4w4h", "5d8g", "5w19", "5w1b", "8v2k", "8v4a", "8v6p", "8v9p", "9blv", "9bnj", "9dy7" ]

18

[]

0

[ "IPR011166" ]

[]

1

0

1

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

[ 6, 1107, 5, 6 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Tryptophanase

TNase

8

IPR013441

13,441

Tyrosine phenol-lyase

Tyr_phenol_ly

Family

393

false

Tyrosine phenol-lyases ( ) (beta-tyrosinase), are pyridoxal-phosphate enzymes which are closely related to tryptophanase ( ) (see ). Both belong to the beta-eliminating lyase family.

[ "GO:0050371", "GO:0006570" ]

[ "tyrosine phenol-lyase activity", "tyrosine metabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00543", "TIGR02618" ]

[ "Tyr_phenol_lyase", "tyr_phenol_ly" ]

[ 343, 393 ]

2

[ "EC" ]

[ "4.1.99.2" ]

[ "EC:4.1.99.2" ]

1

[ "1c7g", "1tpl", "2ez1", "2ez2", "2tpl", "2vlf", "2vlh", "2ycn", "2ycp", "2yct", "2yhk", "6dur", "6dvx", "6dxv", "6dyt", "6dz5", "6ecg", "6mls", "6mme", "6mo3", "6mpd", "6mqq", "6nv8", "7fjk", "7tcs", "7tdl", "9j3u" ]

27

[]

0

[ "IPR011166" ]

[]

1

0

1

[ "Alveolata", "Bacteria", "ecological metagenomes" ]

[ 2, 384, 7 ]

3

[]

0

true

Family

Tyrosine phenol-lyase

Tyr_phenol_ly

9

IPR013442

13,442

CRISPR system ring nuclease SSO1393-like

SSO1393-like

Domain

480

false

This entry represents a conserved region of about 150 amino acids found in a family of Cas proteins, such as ring nuclease SSO1393 from Saccharolobus solfataricus [ ]. The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09651", "TIGR02619" ]

[ "Cas_APE2256", "" ]

[ 480, 334 ]

2

[ "GP" ]

[ "GenProp0021" ]

[ "GP:GenProp0021" ]

1

[ "3qyf", "7pq2", "7pq3", "7pq6", "7pqa", "8phb", "8phj" ]

7

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00091682" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "30232454" ]

[ "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, 2018 ]

6

[]

0

null

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

[ 98, 378, 4 ]

3

[]

0

true

Domain

CRISPR system ring nuclease SSO1393-like

SSO1393-like

5

IPR013443

13,443

CRISPR-associated protein Csx16

CRISPR-assoc_prot_Csx16

Family

233

false

This entry represents the CRISPR-associated protein Csx16 which has not been experimentally characterised but seems to be distantly related to DUF1874 (AcrIII-1) family proteins, which are potent ring nucleases [ ]. The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key eleme...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09652", "TIGR02620" ]

[ "Cas_VVA1548", "cas_VVA1548" ]

[ 233, 213 ]

2

[ "GP" ]

[ "GenProp0021" ]

[ "GP:GenProp0021" ]

1

[]

0

[ "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890", "PUB00106903" ]

[ "17442114", "17379808", "16545108", "21699496", "24459147", "32735657" ]

[ "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, 2020 ]

6

[]

0

null

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

[ 224, 2, 3, 4 ]

4

[]

0

true

Family

CRISPR-associated protein Csx16

CRISPR-assoc_prot_Csx16

5

IPR013444

13,444

Helicase Cas3, CRISPR-associated, Anaes-subtype

Helicase_Cas3_CRISPR-ass_Anaes

Family

568

false

This entry represents a subfamily of Cas3 DEAH-box helicases found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. The proteins include both DEAH and HD motifs. Cas3 is one of four protein families (Cas1 to Cas4) that are associated with CRISPR...

[]

0

[ "NCBIFAM" ]

[ "TIGR02621" ]

[ "cas3_GSU0051" ]

[ 568 ]

1

[ "GP", "GP" ]

[ "GenProp0021", "GenProp0469" ]

[ "GP:GenProp0021", "GP:GenProp0469" ]

2

[]

0

[ "PUB00009737", "PUB00043286", "PUB00043287", "PUB00043288", "PUB00060621", "PUB00071890" ]

[ "11952905", "17442114", "17379808", "16545108", "21699496", "24459147" ]

[ "Identification of genes that are associated with DNA repeats in prokaryotes.", "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: computati...

[ 2002, 2007, 2007, 2006, 2011, 2014 ]

6

[]

0

null

[ "Bacteria", "Methanobacteriati", "unclassified sequences" ]

[ 554, 7, 7 ]

3

[]

0

true

Family

Helicase Cas3, CRISPR-associated, Anaes-subtype

Helicase_Cas3_CRISPR-ass_Anaes

5

IPR013446

13,446

Glucose-1-phosphate cytidylyltransferase-like

G1P_cyt_trans-like

Family

6,654

false

Alpha-D-Glucose-1-phosphate cytidylyltransferase, also known as CDP-glucose pyrophosphorylase, is the product of the rfbF gene and produces CDP-D-glucose from alpha-D-Glucose-1-phosphate and MgCTP as substrate [ , , ]. CDP-D-Glucose is the precursor for synthesising four of the five naturally occurring 3,6-dideoxy suga...

[ "GO:0047343" ]

[ "glucose-1-phosphate cytidylyltransferase activity" ]

[ "molecular_function" ]

1

[ "PANTHER", "CDD" ]

[ "PTHR47183", "cd02524" ]

[ "", "G1P_cytidylyltransferase" ]

[ 6654, 4873 ]

2

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

[ "2.7.7.33", "PWY-5833", "PWY-5940", "PWY-8139" ]

[ "EC:2.7.7.33", "METACYC:PWY-5833", "METACYC:PWY-5940", "METACYC:PWY-8139" ]

4

[ "1tzf", "1wvc" ]

2

[ "PUB00021018", "PUB00037809", "PUB00080743", "PUB00080755" ]

[ "15634670", "15292268", "10406840", "8144449" ]

[ "Kinetic and structural analysis of alpha-D-Glucose-1-phosphate cytidylyltransferase from Salmonella typhi.", "Molecular structure of alpha-D-glucose-1-phosphate cytidylyltransferase from Salmonella typhi.", "Evolutionary considerations in relating oligosaccharide diversity to biological function.", "Cloning,...

[ 2005, 2004, 1999, 1994 ]

4

[]

[ "IPR046981" ]

0

1

0

[ "Archaea", "Bacteria", "Eukaryota", "Siphoviridae sp. ctHip2", "unclassified sequences" ]

[ 47, 6385, 8, 1, 213 ]

5

[]

0

true

Family

Glucose-1-phosphate cytidylyltransferase-like

G1P_cyt_trans-like

8

IPR013447

13,447

Rhamnulose-1-phosphate aldolase

Rhamnulose-1-P_Aldolase

Family

2,022

false

Proteins in this entry match the enzyme RhaD, rhamnulose-1-phosphate aldolase ( ).

[ "GO:0008994", "GO:0019301" ]

[ "rhamnulose-1-phosphate aldolase activity", "rhamnose catabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00770", "TIGR02624" ]

[ "RhaD", "rhamnu_1P_ald" ]

[ 2022, 1670 ]

2

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

[ "4.1.2.19", "GenProp0457", "GenProp1529" ]

[ "EC:4.1.2.19", "GP:GenProp0457", "GP:GenProp1529" ]

3

[ "1gt7", "1ojr", "2uyu", "2uyv", "2v29", "2v2a", "2v2b", "2v9e", "2v9f", "2v9g", "2v9i", "2v9l", "2v9m", "2v9n", "2v9o", "9dgh" ]

16

[]

0

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 2020, 2 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Rhamnulose-1-phosphate aldolase

Rhamnulose-1-P_Aldolase

9

IPR013448

13,448

L-rhamnose mutarotase

L-rhamnose_mutarotase

Family

3,599

false

This entry contains rhamnose mutarotase from Escherichia coli, previously designated YiiL as an uncharacterised protein, and close homologues associated with rhamnose dissimilation operons in other bacterial genomes. Mutarotase is a term for an epimerase that changes optical activity. This enzyme was shown experimental...

[ "GO:0016857", "GO:0005737" ]

[ "racemase and epimerase activity, acting on carbohydrates and derivatives", "cytoplasm" ]

[ "molecular_function", "cellular_component" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_01663", "TIGR02625" ]

[ "L_rham_rotase", "YiiL_rotase" ]

[ 3338, 3418 ]

2

[ "EC", "GP" ]

[ "5.1.3.32", "GenProp0457" ]

[ "EC:5.1.3.32", "GP:GenProp0457" ]

2

[ "1x8d", "2qlw", "2qlx", "6hhn" ]

4

[ "PUB00020761", "PUB00020762" ]

[ "15876375", "15060078" ]

[ "Structural insights into the monosaccharide specificity of Escherichia coli rhamnose mutarotase.", "NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration." ]

[ 2005, 2004 ]

2

[ "IPR008000" ]

[]

1

0

1

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

[ 3557, 18, 24 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

L-rhamnose mutarotase

L-rhamnose_mutarotase

1

IPR013449

13,449

Rhamnulokinase

Family

6,919

false

Rhamnulokinase ( ) is an enzyme that catalyses the second step in rhamnose catabolism. It catalyses the ATP-dependent phosphorylation of L-rhamnulose to produce L-rhamnulose-1-phosphate and ADP. Rhamnulokinase exists as a monomer composed of two large domains. The ATP binding site is located in the cleft between the tw...

[ "GO:0008993", "GO:0019301" ]

[ "rhamnulokinase activity", "rhamnose catabolic process" ]

[ "molecular_function", "biological_process" ]

2

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

[ "MF_01535", "TIGR02627", "cd07771" ]

[ "Rhamnulokinase", "rhamnulo_kin", "ASKHA_NBD_FGGY_RhaB-like" ]

[ 1872, 2596, 6919 ]

3

[ "EC", "GP" ]

[ "2.7.1.5", "GenProp0457" ]

[ "EC:2.7.1.5", "GP:GenProp0457" ]

2

[ "2cgj", "2cgk", "2cgl", "2uyt", "4c23" ]

5

[]

0

[]

0

null

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

[ 64, 6767, 4, 84 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Rhamnulokinase

5

IPR013450

13,450

L-fuculokinase

Fuculokinase

Family

1,244

false

Proteins in this entry are L-fuculokinases including the Escherichia coli enzyme [ ]. They catalyse the second step in fucose catabolism and belong to the FGGY family of carbohydrate kinases. These enzymes are encoded by the kinase (K) gene of the fucose (fuc) operon.

[ "GO:0008737", "GO:0005975" ]

[ "L-fuculokinase activity", "carbohydrate metabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00986", "TIGR02628" ]

[ "Fuculokinase", "fuculo_kin_coli" ]

[ 1147, 1244 ]

2

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

[ "2.7.1.51", "GenProp0458", "GenProp1589", "GenProp1680" ]

[ "EC:2.7.1.51", "GP:GenProp0458", "GP:GenProp1589", "GP:GenProp1680" ]

4

[]

0

[ "PUB00074166" ]

[ "13905785" ]

[ "The metabolism of L-fucose. I. The purification and properties of L-fuculose kinase." ]

[ 1962 ]

1

[ "IPR000577" ]

[]

1

0

1

[ "Bacteria" ]

[ 1244 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

L-fuculokinase

Fuculokinase

9

IPR013451

13,451

L-rhamnose catabolism isomerase

L_rhamnose_iso

Family

914

false

These enzymes are isomerases in the pathway of L-rhamnose catabolism, as found in Pseudomonas stutzeri and in a number of the Rhizobiales, and are distinct from the L-rhamnose isomerases of Escherichia coli (see ). They catalyze the isomerisation step in rhamnose catabolism. Genetic evidence in Rhizobium leguminosarum ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02629" ]

[ "L_rham_iso_rhiz" ]

[ 914 ]

1

[ "GP" ]

[ "GenProp0457" ]

[ "GP:GenProp0457" ]

1

[ "2hcv", "2i56", "2i57", "3itl", "3ito", "3itt", "3itv", "3itx", "3ity", "3iud", "3iuh", "3iui", "3m0h", "3m0l", "3m0m", "3m0v", "3m0x", "3m0y", "4gji", "4gjj" ]

20

[]

0

[]

0

null

[ "Effrenium voratum", "Pseudomonadati", "ecological metagenomes" ]

[ 1, 908, 5 ]

3

[]

0

true

Family

L-rhamnose catabolism isomerase

L_rhamnose_iso

7

IPR013452

13,452

Xylose isomerase, bacterial-type

XylA_bac

Family

8,231

false

Xylose isomerase (XI) ( ) catalyses the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose [ ].

[ "GO:0009045" ]

[ "xylose isomerase activity" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR02630" ]

[ "xylose_isom_A" ]

[ 8231 ]

1

[ "EC", "GP" ]

[ "5.3.1.5", "GenProp1656" ]

[ "EC:5.3.1.5", "GP:GenProp1656" ]

2

[ "1a0c", "1a0d", "1a0e", "4xkm", "5nh4", "5nh5", "5nh6", "5nh7", "5nh8", "5nh9", "5nha", "5nhb", "5nhc", "5nhd", "5nhe", "5nhm", "5yn3", "6int", "6t8e", "6t8f" ]

20

[ "PUB00162408" ]

[ "25981595" ]

[ "Bacterial xylose isomerases from the mammal gut Bacteroidetes cluster function in Saccharomyces cerevisiae for effective xylose fermentation." ]

[ 2015 ]

1

[ "IPR001998" ]

[]

1

0

1

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

[ 7310, 870, 6, 45 ]

4

[ "Arabidopsis thaliana", "Escherichia coli (strain K12)", "Oryza sativa subsp. japonica", "Zea mays" ]

[ 6, 1, 3, 9 ]

4

true

Family

Xylose isomerase, bacterial-type

XylA_bac

6

IPR013453

13,453

Xylose isomerase, actinobacteria

XylA_actinobac

Family

3,008

false

This is an enzyme which as well as interconverting D-xylose and D-xylulose, is also active as a D-glucose isomerase. It is tetrameric and dependent on a divalent cation, either Mg2+, Co2+ or Mn2+, as characterised in Arthrobacter [ ]. Enzymes in this entry differ substantially from the D-xylose isomerases of .

[ "GO:0009045", "GO:0042732" ]

[ "xylose isomerase activity", "D-xylose metabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02631" ]

[ "xylA_Arthro" ]

[ 3008 ]

1

[ "EC" ]

[ "5.3.1.5" ]

[ "EC:5.3.1.5" ]

1

[ "1bhw", "1bxb", "1bxc", "1clk", "1did", "1die", "1dxi", "1gw9", "1mnz", "1muw", "1o1h", "1oad", "1qt1", "1s5m", "1s5n", "1xib", "1xic", "1xid", "1xie", "1xif", "1xig", "1xih", "1xii", "1xij", "1xim", "1xin", "1xis", "1xla", "1xlb", "1xlc", "1xld", "1xle"...

187

[ "PUB00020769" ]

[ "1854338" ]

[ "D-Xylose (D-glucose) isomerase from Arthrobacter strain N.R.R.L. B3728. Purification and properties." ]

[ 1991 ]

1

[ "IPR001998" ]

[]

1

0

1

[ "Acrobeloides nanus", "Bacteria", "metagenomes" ]

[ 1, 2942, 65 ]

3

[]

0

true

Family

Xylose isomerase, actinobacteria

XylA_actinobac

8

IPR013454

13,454

Bifunctional rhamnulose-1-phosphate aldolase/alcohol dehydrogenase

Bifunc_RhaD/ADH

Family

4,585

false

Rhamnose is a methyl-pentose sugar which is found as a constituent of pectin within the cell walls of dicotyledonous plants and has also been found in the mucilage of a number of legume plants [ ]. RhaD from Rhizobium leguminosarum bv. trifolii is encoded by a gene occurring in a rhamnose utilisation cluster, and is ne...

[]

0

[ "NCBIFAM" ]

[ "TIGR02632" ]

[ "RhaD_aldol-ADH" ]

[ 4585 ]

1

[ "GP", "GP" ]

[ "GenProp0457", "GenProp1662" ]

[ "GP:GenProp0457", "GP:GenProp1662" ]

2

[]

0

[ "PUB00020766", "PUB00020780" ]

[ "11386373", "15576793" ]

[ "Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source.", "A genetic locus necessary for rhamnose uptake and catabolism in Rhizobium leguminosarum bv. trifolii." ]

[ 2001, 2004 ]

2

[]

0

null

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

[ 4544, 2, 39 ]

3

[]

0

true

Family

Bifunctional rhamnulose-1-phosphate aldolase/alcohol dehydrogenase

Bifunc_RhaD/ADH

7

IPR013455

13,455

Xylose import ATP-binding protein XylG

ABC_transptr_XylG

Family

1,631

false

Several bacterial species use the enzymes xylose isomerase and xylulokinase for xylose utilisation. This entry represents the ATP-binding cassette (ABC) subunit of the known, or predicted, high-affinity xylose ABC transporter used for xylose import [ ]. The genes encoding these proteins, which closely resemble other su...

[ "GO:0005524", "GO:0015614", "GO:0015753", "GO:0016020" ]

[ "ATP binding", "ABC-type D-xylose transporter activity", "D-xylose transmembrane transport", "membrane" ]

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

4

[ "NCBIFAM" ]

[ "TIGR02633" ]

[ "xylG" ]

[ 1631 ]

1

[ "EC" ]

[ "7.5.2.10" ]

[ "EC:7.5.2.10" ]

1

[]

0

[ "PUB00004290", "PUB00014769", "PUB00017894", "PUB00017895", "PUB00017896", "PUB00017897", "PUB00017898", "PUB00017899", "PUB00025109", "PUB00026406", "PUB00043654", "PUB00043805" ]

[ "9872322", "9873074", "11421269", "1282354", "9640644", "11988180", "11470432", "11402022", "11080142", "11532960", "11421270", "15057456" ]

[ "Crystal structure of the ATP-binding subunit of an ABC transporter.", "Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters.", "ABC transporters: physiology, structure and mechanism--an overview.", "ABC transporters: from microorgani...

[ 1998, 1999, 2001, 1992, 1998, 2002, 2001, 2001, 2000, 2001, 2001, 2004 ]

12

[]

0

null

[ "Bacteria", "Eukaryota" ]

[ 1629, 2 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Xylose import ATP-binding protein XylG

ABC_transptr_XylG

5

IPR013456

13,456

D-xylose-binding periplasmic protein

XylF

Family

2,911

false

This entry represents the D-xylose-binding periplasmic protein XylF (also known as D-xylose ABC transporter substrate-binding protein) which is a periplasmic (when in Gram-negative bacteria) binding protein for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter [ , , ]. Bacterial high affinity tr...

[ "GO:0048029", "GO:0015753" ]

[ "monosaccharide binding", "D-xylose transmembrane transport" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02634" ]

[ "xylF" ]

[ 2911 ]

1

[]

0

[ "3m9w", "3m9x", "3ma0", "4ywh" ]

4

[ "PUB00021020", "PUB00061627", "PUB00065357", "PUB00071925", "PUB00071938" ]

[ "9657999", "8581399", "20678502", "18310026", "8003968" ]

[ "The D-xylose-binding protein, XylF, from Thermoanaerobacter ethanolicus 39E: cloning, molecular analysis, and expression of the structural gene.", "Molecular genetics of a receptor protein for D-xylose, encoded by the gene xylF, in Escherichia coli.", "Conformational changes and ligand recognition of Escherich...

[ 1998, 1995, 2010, 2008, 1994 ]

5

[]

0

null

[ "Bacteria", "Sar", "ecological metagenomes" ]

[ 2906, 2, 3 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

D-xylose-binding periplasmic protein

XylF

6

IPR013457

13,457

Rhamnose isomerase-related

Rhamnose_iso-rel

Family

2,330

false

The proteins in this entry are closely related to the L-rhamnose isomerases ( ) found in Pseudomonas stutzeri [ ] and in a number of the Rhizobiales. They are encoded in similar genomic contexts, close to genes apparently involved in rhamnose catabolism such as rhamnulose-1-phosphate aldolase ( ), sugar kinases, and su...

[]

0

[ "NCBIFAM" ]

[ "TIGR02635" ]

[ "RhaI_grampos" ]

[ 2330 ]

1

[ "GP" ]

[ "GenProp0457" ]

[ "GP:GenProp0457" ]

1

[]

0

[ "PUB00020768" ]

[ "15184124" ]

[ "Cloning, nucleotide sequence, and overexpression of the L-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli." ]

[ 2004 ]

1

[]

0

null

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

[ 2310, 1, 19 ]

3

[]

0

true

Family

Rhamnose isomerase-related

Rhamnose_iso-rel

8

IPR013458

13,458

Aldose 1-epimerase, bacterial

Ald_epimerase_bac

Family

1,872

false

Aldose 1-epimerase ( ) (also known as mutarotase) participates in the Leloir pathway for galactose/glucose interconversion. It is the enzyme responsible for the anomeric interconversion of D-glucose and other aldoses between their alpha- and beta-forms. The sequence of mutarotase from two bacteria, Acinetobacter calcoa...

[ "GO:0004034", "GO:0006012" ]

[ "aldose 1-epimerase activity", "galactose metabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02636" ]

[ "galM_Leloir" ]

[ 1872 ]

1

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

[ "5.1.3.3", "GenProp0143", "GenProp1310", "PWY-6317" ]

[ "EC:5.1.3.3", "GP:GenProp0143", "GP:GenProp1310", "METACYC:PWY-6317" ]

4

[ "1l7j", "1l7k", "1mmu", "1mmx", "1mmy", "1mmz", "1mn0", "1ns0", "1ns2", "1ns4", "1ns7", "1ns8", "1nsm", "1nsr", "1nss", "1nsu", "1nsv", "1nsx", "1nsz" ]

19

[ "PUB00002113" ]

[ "1694527" ]

[ "Carbohydrate utilization in Streptococcus thermophilus: characterization of the genes for aldose 1-epimerase (mutarotase) and UDPglucose 4-epimerase." ]

[ 1990 ]

1

[ "IPR015443" ]

[]

1

0

1

[ "Bacteria", "Opisthokonta" ]

[ 1870, 2 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Aldose 1-epimerase, bacterial

Ald_epimerase_bac

9

IPR013459

13,459

Rhamnose ABC transporter, substrate-binding protein RhaS

RhaS

Family

2,578

false

This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of the gene in Rhizobium leguminosarum [ ] abolishes rhamnose transport and prevents growth on rhamnose as a carbon source. Bacterial high affinity transport systems are involved in active transport of so...

[ "GO:0015762" ]

[ "rhamnose transmembrane transport" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02637" ]

[ "RhaS" ]

[ 2578 ]

1

[ "GP" ]

[ "GenProp0457" ]

[ "GP:GenProp0457" ]

1

[ "4kvf", "5bq3" ]

2

[ "PUB00020780", "PUB00071925", "PUB00071938" ]

[ "15576793", "18310026", "8003968" ]

[ "A genetic locus necessary for rhamnose uptake and catabolism in Rhizobium leguminosarum bv. trifolii.", "Characterization of a Pseudomonas putida ABC transporter (AatJMQP) required for acidic amino acid uptake: biochemical properties and regulation by the Aau two-component system.", "Sequence relationships bet...

[ 2004, 2008, 1994 ]

3

[ "IPR030159" ]

[]

1

0

1

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

[ 2566, 3, 9 ]

3

[]

0

true

Family

Rhamnose ABC transporter, substrate-binding protein RhaS

RhaS

1

IPR013460

13,460

Lactaldehyde reductase

Lactal_redase

Family

3,364

false

The proteins in this entry form a distinct clade of iron-containing alcohol dehydrogenases. The genes encoding these proteins are generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in the production of lactaldehydes, which are reduced by the...

[]

0

[ "NCBIFAM" ]

[ "TIGR02638" ]

[ "lactal_redase" ]

[ 3364 ]

1

[ "GP", "GP" ]

[ "GenProp1370", "GenProp1529" ]

[ "GP:GenProp1370", "GP:GenProp1529" ]

2

[ "1rrm", "2bi4", "2bl4", "5br4", "7qlg", "7qlq", "7qls", "7qnf", "7qnh", "7qni", "7qnj", "7r0p", "7r3d", "7r5t" ]

14

[ "PUB00020754", "PUB00020757" ]

[ "2203757", "3275622" ]

[ "Oxygen regulation of L-1,2-propanediol oxidoreductase activity in Escherichia coli.", "Metabolism of L-fucose and L-rhamnose in Escherichia coli: aerobic-anaerobic regulation of L-lactaldehyde dissimilation." ]

[ 1990, 1988 ]

2

[ "IPR039697" ]

[]

1

0

1

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

[ 3354, 5, 5 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Lactaldehyde reductase

Lactal_redase

7

IPR013461

13,461

ATP-dependent Clp protease ATP-binding subunit ClpA

ClpA

Family

9,444

false

Proteins in this entry are related to ClpA ( ) from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates [ ]. ClpA functions as the regulatory component of the ATP dependent prote...

[ "GO:0016887", "GO:0043335" ]

[ "ATP hydrolysis activity", "protein unfolding" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02639" ]

[ "ClpA" ]

[ 9444 ]

1

[ "GP", "GP" ]

[ "GenProp0251", "GenProp1137" ]

[ "GP:GenProp0251", "GP:GenProp1137" ]

2

[ "1ksf", "1r6b", "6w1z", "6w20", "6w21", "6w22", "6w23", "6w24", "7uiv", "7uiw", "7uix", "7uiy", "7uiz", "7uj0" ]

14

[ "PUB00020738", "PUB00020750", "PUB00020759", "PUB00020760", "PUB00088088" ]

[ "12235156", "10485712", "2186030", "11287666", "28824920" ]

[ "Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.", "Global unfolding of a substrate protein by the Hsp100 chaperone ClpA.", "The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate.", ...

[ 2002, 1999, 1990, 2001, 2017 ]

5

[ "IPR001270" ]

[]

1

0

1

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

[ 9334, 9, 101 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

ATP-dependent Clp protease ATP-binding subunit ClpA

ClpA

6

IPR013462

13,462

Gas vesicle protein GvpN

Gas-vesicle_GvpN

Family

564

false

The GvpN protein is associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy [ , ]. It belongs to a larger family of ATPases [ ].

[ "GO:0000166", "GO:0005524", "GO:0031412", "GO:0031411" ]

[ "nucleotide binding", "ATP binding", "gas vesicle organization", "gas vesicle" ]

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

4

[ "NCBIFAM" ]

[ "TIGR02640" ]

[ "gas_vesic_GvpN" ]

[ 564 ]

1

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

[ "3.6.4.-", "GenProp0460", "PWY-7250" ]

[ "EC:3.6.4.-", "GP:GenProp0460", "METACYC:PWY-7250" ]

3

[]

0

[ "PUB00005841", "PUB00011347", "PUB00033391" ]

[ "9927482", "8606186", "8002589" ]

[ "AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.", "Functional studies of the gvpACNO operon of Halobacterium salinarium reveal that the GvpC protein shapes gas vesicles.", "Wild-type gas vesicle formation requires at least ten genes in the ...

[ 1999, 1996, 1994 ]

3

[]

0

null

[ "Bacteria", "Batrachochytrium dendrobatidis (strain JAM81 / FGSC 10211)", "Stenosarchaea group" ]

[ 461, 1, 102 ]

3

[]

0

true

Family

Gas vesicle protein GvpN

Gas-vesicle_GvpN

6

IPR013465

13,465

Thymidine phosphorylase

Thymidine_Pase

Family

4,096

false

Thymidine phosphorylase (alternate name: pyrimidine phosphorylase) is involved, in Escherichia coli and other Proteobacteria, in (deoxy)nucleotide degradation. It is often encoded in an operon together with a deoxyribose-phosphate aldolase, a phosphopentomutase and a purine nucleoside phosphorylase. In many other linea...

[ "GO:0009032", "GO:0006213" ]

[ "thymidine phosphorylase activity", "pyrimidine nucleoside metabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_01628", "TIGR02643" ]

[ "Thymid_phosp", "T_phosphoryl" ]

[ 4067, 3567 ]

2

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

[ "2.4.2.4", "GenProp1410", "GenProp1631", "PWY-7181" ]

[ "EC:2.4.2.4", "GP:GenProp1410", "GP:GenProp1631", "METACYC:PWY-7181" ]

4

[ "1azy", "1otp", "1tpt", "2tpt", "4ead", "4eaf", "4lhm", "4x46", "4xr5", "4yek", "4yyy", "5ey3" ]

12

[]

0

[ "IPR018090" ]

[]

1

0

1

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

[ 4043, 28, 25 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Thymidine phosphorylase

Thymidine_Pase

7