LiteFold/InterPro · Datasets at Hugging Face

IPR014102

14,102

Phytoene desaturase

Phytoene_desaturase

Family

1,296

false

This entry represents phytoene desaturase (PDS) from plants and cyanobacteria (blue-green algae). It is an essential carotenoid biosynthetic enzyme. It converts phytoene into zeta-carotene via the intermediary of phytofluene by the symmetrical introduction of two double bonds at the C-11 and C-11' positions of phytoene...

[ "GO:0016166", "GO:0016117" ]

[ "phytoene dehydrogenase activity", "carotenoid biosynthetic process" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02731" ]

[ "phytoene_desat" ]

[ 1296 ]

1

[ "EC", "GP" ]

[ "1.3.5.5", "GenProp0758" ]

[ "EC:1.3.5.5", "GP:GenProp0758" ]

2

[ "5mog" ]

1

[ "PUB00089809", "PUB00089810" ]

[ "9914519", "29176862" ]

[ "Two Arabidopsis thaliana carotene desaturases, phytoene desaturase and zeta-carotene desaturase, expressed in Escherichia coli, catalyze a poly-cis pathway to yield pro-lycopene.", "Plant-type phytoene desaturase: Functional evaluation of structural implications." ]

[ 1999, 2017 ]

2

[]

0

null

[ "Cyanophyceae", "Eukaryota" ]

[ 348, 948 ]

2

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

[ 4, 2, 6 ]

3

true

Family

Phytoene desaturase

Phytoene_desaturase

4

IPR014103

14,103

Zeta-carotene desaturase

Zeta_caro_desat

Family

1,088

false

Zeta-carotene desaturase (also known as carotene 7,8-desaturase) catalyses two consecutive desaturations at positions C-7 and C-7' in the pathway from zeta-carotene to lycopene in plants and cyanobacteria [ ].

[ "GO:0016719", "GO:0016117" ]

[ "9,9'-di-cis-zeta-carotene desaturase activity", "carotenoid biosynthetic process" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02732" ]

[ "zeta_caro_desat" ]

[ 1088 ]

1

[ "EC", "GP" ]

[ "1.3.5.6", "GenProp0758" ]

[ "EC:1.3.5.6", "GP:GenProp0758" ]

2

[]

0

[ "PUB00089809" ]

[ "9914519" ]

[ "Two Arabidopsis thaliana carotene desaturases, phytoene desaturase and zeta-carotene desaturase, expressed in Escherichia coli, catalyze a poly-cis pathway to yield pro-lycopene." ]

[ 1999 ]

1

[]

0

null

[ "Cyanophyceae", "Eukaryota" ]

[ 345, 743 ]

2

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

[ 2, 5, 10 ]

3

true

Family

Zeta-carotene desaturase

Zeta_caro_desat

5

IPR014104

14,104

Myxoxanthophyll biosynthesis, C-3',4' desaturase CrtD

Myxoxanthophyll_desat_CrtD

Family

346

false

This entry represents a family of proteins from cyanobacteria. Members of this family include the Slr1293 protein, a carotenoid biosynthesis protein which was shown to be the C-3',4' desaturase (CrtD) of myxoxanthophyll biosynthesis in Synechocystis sp. (strain PCC 6803), and close homologues (presumed to be functional...

[]

0

[ "NCBIFAM" ]

[ "TIGR02733" ]

[ "desat_CrtD" ]

[ 346 ]

1

[]

0

[]

0

[ "PUB00034538" ]

[ "15317766" ]

[ "Slr1293 in Synechocystis sp. strain PCC 6803 Is the C-3',4' desaturase (CrtD) involved in myxoxanthophyll biosynthesis." ]

[ 2004 ]

1

[ "IPR045892" ]

[]

1

0

1

[ "Cyanobacteriota" ]

[ 346 ]

1

[]

0

true

Family

Myxoxanthophyll biosynthesis, C-3',4' desaturase CrtD

Myxoxanthophyll_desat_CrtD

9

IPR014105

14,105

Carotenoid/retinoid oxidoreductase

Carotenoid/retinoid_OxRdtase

Family

14,058

false

Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (4,4'-diaponeurosporene oxygenase or CrtP, and 4,4'-diaponeurosporenoate glycosyltransferase or CrtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most o...

[ "GO:0016117" ]

[ "carotenoid biosynthetic process" ]

[ "biological_process" ]

1

[ "NCBIFAM" ]

[ "TIGR02734" ]

[ "crtI_fam" ]

[ 14058 ]

1

[ "GP" ]

[ "GenProp0758" ]

[ "GP:GenProp0758" ]

1

[ "4dgk", "4rep" ]

2

[ "PUB00062758", "PUB00062759", "PUB00062762", "PUB00088399", "PUB00088401", "PUB00088402" ]

[ "20431015", "21878683", "18948076", "10498735", "15933032", "25326460" ]

[ "Lateral transfer of genes from fungi underlies carotenoid production in aphids.", "Diversification of genes for carotenoid biosynthesis in aphids following an ancient transfer from a fungus.", "Evolution of carotene desaturation: the complication of a simple pathway.", "4,4'-diapophytoene desaturase: catalyt...

[ 2010, 2012, 2009, 1999, 2005, 2015 ]

6

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Mimiviridae sp. ChoanoV1", "metagenomes" ]

[ 552, 12098, 1097, 1, 310 ]

5

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

[ 1 ]

1

true

Family

Carotenoid/retinoid oxidoreductase

Carotenoid/retinoid_OxRdtase

8

IPR014106

14,106

Phosphoribosylaminoimidazole-succinocarboxamide synthase, Vibrio-type

SAICAR_synthase_Vibrio-typ

Family

886

false

This entry represents a protein family of phosphoribosylaminoimidazole-succinocarboxamide synthases (SAICAR synthetase or PUR7), significantly different in sequence from ( ), which is predominantly found in the gammaproteobacteria Vibrio, Pseudoalteromonas, Pseudoalteromonas, Shewanella, Colwellia, and also in the prim...

[ "GO:0004639", "GO:0006164" ]

[ "phosphoribosylaminoimidazolesuccinocarboxamide synthase activity", "purine nucleotide biosynthetic process" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02735" ]

[ "purC_vibrio" ]

[ 886 ]

1

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

[ "6.3.2.6", "GenProp0110", "PWY-6123", "PWY-6124", "PWY-7234" ]

[ "EC:6.3.2.6", "GP:GenProp0110", "METACYC:PWY-6123", "METACYC:PWY-6124", "METACYC:PWY-7234" ]

5

[]

0

[ "PUB00004940", "PUB00070198" ]

[ "1574589", "15641804" ]

[ "De novo purine nucleotide biosynthesis.", "Mechanism of action of Escherichia coli phosphoribosylaminoimidazolesuccinocarboxamide synthetase." ]

[ 1992, 2005 ]

2

[]

0

null

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

[ 868, 16, 2 ]

3

[]

0

true

Family

Phosphoribosylaminoimidazole-succinocarboxamide synthase, Vibrio-type

SAICAR_synthase_Vibrio-typ

9

IPR014107

14,107

Cytochrome c oxidase cbb3-type, CcoQ

Cyt_c_oxidase_cbb3_CcoQ

Family

285

false

Members of this protein family are restricted to the epsilon branch of the Proteobacteria. All members are found in operons containing the other three structural subunits of the cbb3 type of cytochrome c oxidase. These small proteins show remote sequence similarity to the CcoQ subunit in other cytochrome c oxidase syst...

[]

0

[ "NCBIFAM" ]

[ "TIGR02736" ]

[ "cbb3_Q_epsi" ]

[ 285 ]

1

[ "GP" ]

[ "GenProp0483" ]

[ "GP:GenProp0483" ]

1

[]

0

[]

0

[ "IPR008621" ]

[]

1

0

1

[ "Epsilonproteobacteria", "hydrothermal vent metagenome" ]

[ 275, 10 ]

2

[]

0

true

Family

Cytochrome c oxidase cbb3-type, CcoQ

Cyt_c_oxidase_cbb3_CcoQ

7

IPR014108

14,108

Cytochrome c oxidase caa3 type assembly factor CtaG

Caa3-assmbl_CtaG

Family

1,322

false

CtaG is required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis [ ]. This entry represents CtaG from B.subtilis and other Bacilli.

[]

0

[ "NCBIFAM" ]

[ "TIGR02737" ]

[ "caa3_CtaG" ]

[ 1322 ]

1

[]

0

[]

0

[ "PUB00034539" ]

[ "14766920" ]

[ "CtaG is required for formation of active cytochrome c oxidase in Bacillus subtilis." ]

[ 2004 ]

1

[ "IPR019108" ]

[]

1

0

1

[ "Bacilli", "Phytophthora kernoviae 00238/432" ]

[ 1321, 1 ]

2

[]

0

true

Family

Cytochrome c oxidase caa3 type assembly factor CtaG

Caa3-assmbl_CtaG

8

IPR014109

14,109

Type-F conjugative transfer system pilin assembly thiol-disulphide isomerase TrbB

Thiol-disulphide_isomerase_rbB

Family

829

false

This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02738" ]

[ "TrbB" ]

[ 829 ]

1

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00034395", "PUB00034396" ]

[ "16321931", "16138100" ]

[ "F-like type IV secretion systems encode proteins with thioredoxin folds that are putative DsbC homologues.", "Mobile genetic elements: the agents of open source evolution." ]

[ 2005, 2005 ]

2

[ "IPR039555" ]

[]

1

0

1

[ "Eumetazoa", "Gammaproteobacteria" ]

[ 4, 825 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system pilin assembly thiol-disulphide isomerase TrbB

Thiol-disulphide_isomerase_rbB

9

IPR014110

14,110

Type-F conjugative transfer system pilin assembly protein TraF

TraF

Family

948

false

This entry includes TraF; a protein that is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TraF has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm [ ]. Unlike the related protein TrbB ( ), TraF does ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02739" ]

[ "TraF" ]

[ 948 ]

1

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00034395", "PUB00034396", "PUB00034397" ]

[ "16321931", "16138100", "3042757" ]

[ "F-like type IV secretion systems encode proteins with thioredoxin folds that are putative DsbC homologues.", "Mobile genetic elements: the agents of open source evolution.", "The product of the F plasmid transfer operon gene, traF, is a periplasmic protein." ]

[ 2005, 2005, 1988 ]

3

[ "IPR039555" ]

[]

1

0

1

[ "Opisthokonta", "Pseudomonadati" ]

[ 5, 943 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system pilin assembly protein TraF

TraF

6

IPR014111

14,111

Type IV conjugative transfer system protein TraF-like

T4SS_TraF-like

Family

977

false

This entry contains TraF-like proteins that are related to the F-type conjugation system pilus assembly proteins TraF ( )and TrbB ( ) both of which exhibit a thioredoxin fold [ ]. The proteins in this entry have the same length and architecture as TraF, but lack the CXXC-motif found in TrbB that is believed to be respo...

[]

0

[ "NCBIFAM" ]

[ "TIGR02740" ]

[ "TraF-like" ]

[ 977 ]

1

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00034395" ]

[ "16321931" ]

[ "F-like type IV secretion systems encode proteins with thioredoxin folds that are putative DsbC homologues." ]

[ 2005 ]

1

[ "IPR039555" ]

[]

1

0

1

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

[ 968, 4, 5 ]

3

[]

0

true

Family

Type IV conjugative transfer system protein TraF-like

T4SS_TraF-like

2

IPR014112

14,112

Type-F conjugative transfer system pilin chaperone TraQ, proteobacteria

TraQ_proteobacteria

Family

445

false

This entry represents TraQ, a protein that makes a specific interaction with pilin (TraA) to aid its transfer through the inner membrane during the process of F-type conjugative pilus assembly [ , ].

[]

0

[ "NCBIFAM", "PFAM", "PIRSF", "NCBIFAM" ]

[ "NF010287", "PF09679", "PIRSF003265", "TIGR02741" ]

[ "PRK13727.1", "TraQ", "TraQ", "TraQ" ]

[ 413, 445, 177, 310 ]

4

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00034396", "PUB00034398" ]

[ "16138100", "10564517" ]

[ "Mobile genetic elements: the agents of open source evolution.", "Interaction between the F plasmid TraA (F-pilin) and TraQ proteins." ]

[ 2005, 1999 ]

2

[]

0

null

[ "Gammaproteobacteria", "human gut metagenome" ]

[ 444, 1 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system pilin chaperone TraQ, proteobacteria

TraQ_proteobacteria

7

IPR014113

14,113

Type-F conjugative transfer system pilin assembly protein TrbC, subgroup

T4SS_TrbC_subgr

Family

1,564

false

This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA [ , ]. The N-terminal portion of these proteins is heterogeneous.

[]

0

[ "NCBIFAM" ]

[ "TIGR02742" ]

[ "TrbC_Ftype" ]

[ 1564 ]

1

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00034396", "PUB00034399" ]

[ "16138100", "205063" ]

[ "Mobile genetic elements: the agents of open source evolution.", "[Evaluation of the alginat membrane filter method for the Enterovirus concentration in water (author's transl)]" ]

[ 2005, 1977 ]

2

[ "IPR019106" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "Methanosarcina mazei", "metagenomes" ]

[ 1546, 9, 1, 8 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system pilin assembly protein TrbC, subgroup

T4SS_TrbC_subgr

7

IPR014114

14,114

Type-F conjugative transfer system protein TraW

TraW

Family

1,421

false

This entry represents TraW, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [ , ].

[]

0

[ "NCBIFAM" ]

[ "TIGR02743" ]

[ "TraW" ]

[ 1421 ]

1

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00034396", "PUB00034400" ]

[ "16138100", "1355084" ]

[ "Mobile genetic elements: the agents of open source evolution.", "Characterization, localization, and sequence of F transfer region products: the pilus assembly gene product TraW and a new product, TrbI." ]

[ 2005, 1992 ]

2

[]

0

null

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

[ 1409, 6, 6 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system protein TraW

TraW

1

IPR014115

14,115

Type-F conjugative transfer system protein TrbI

TrbI_Ftype

Family

1,132

false

This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [ , ].

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09677", "TIGR02744" ]

[ "TrbI_Ftype", "TrbI_Ftype" ]

[ 1120, 713 ]

2

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00034396", "PUB00034400" ]

[ "16138100", "1355084" ]

[ "Mobile genetic elements: the agents of open source evolution.", "Characterization, localization, and sequence of F transfer region products: the pilus assembly gene product TraW and a new product, TrbI." ]

[ 2005, 1992 ]

2

[]

0

null

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

[ 1123, 5, 4 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system protein TrbI

TrbI_Ftype

1

IPR014116

14,116

Cytochrome c oxidase cbb3 type, accessory protein FixG

Cyt_c_oxidase_cbb3_FixG

Family

9,792

false

Member of this ferredoxin-like protein family, include FixG, CcoG and RdxA,. They are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else;...

[ "GO:0016020" ]

[ "membrane" ]

[ "cellular_component" ]

1

[ "NCBIFAM" ]

[ "TIGR02745" ]

[ "ccoG_rdxA_fixG" ]

[ 9792 ]

1

[ "GP" ]

[ "GenProp0483" ]

[ "GP:GenProp0483" ]

1

[]

0

[ "PUB00017603" ]

[ "8661920" ]

[ "The Bradyrhizobium japonicum fixGHIS genes are required for the formation of the high-affinity cbb3-type cytochrome oxidase." ]

[ 1996 ]

1

[]

0

null

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

[ 9667, 7, 118 ]

3

[]

0

true

Family

Cytochrome c oxidase cbb3 type, accessory protein FixG

Cyt_c_oxidase_cbb3_FixG

9

IPR014117

14,117

Type-IV secretion system protein TraC

TraC-F-type

Family

1,981

false

The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases [ , ].

[]

0

[ "NCBIFAM" ]

[ "TIGR02746" ]

[ "TraC-F-type" ]

[ 1981 ]

1

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[]

0

[ "PUB00034396", "PUB00034402" ]

[ "16138100", "12855161" ]

[ "Mobile genetic elements: the agents of open source evolution.", "F factor conjugation is a true type IV secretion system." ]

[ 2005, 2003 ]

2

[ "IPR025955" ]

[]

1

0

1

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

[ 1967, 7, 7 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-IV secretion system protein TraC

TraC-F-type

4

IPR014118

14,118

Type IV conjugative transfer system protein TraV

T4SS_TraV

Family

2,202

false

This entry represents TraV, a component of a conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK [ , , ]. This protein contains three conserved cysteines in the N-terminal half.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09676", "TIGR02747" ]

[ "TraV", "TraV" ]

[ 2176, 1426 ]

2

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[ "7okn", "7oko", "7spb", "7spc", "7spi", "7spj", "7spk" ]

7

[ "PUB00034396", "PUB00034401", "PUB00034402" ]

[ "16138100", "11722740", "12855161" ]

[ "Mobile genetic elements: the agents of open source evolution.", "Evidence that F-plasmid proteins TraV, TraK and TraB assemble into an envelope-spanning structure in Escherichia coli.", "F factor conjugation is a true type IV secretion system." ]

[ 2005, 2001, 2003 ]

3

[]

0

null

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

[ 2179, 9, 14 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type IV conjugative transfer system protein TraV

T4SS_TraV

9

IPR014119

14,119

Heptaprenyl diphosphate synthase component II

GerC3_HepT

Family

1,093

false

The proteins in this entry are component II of the heterodimeric heptaprenyl diphosphate synthase. They are found proximate to the gene for component I ( ). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis.

[]

0

[ "NCBIFAM" ]

[ "TIGR02748" ]

[ "GerC3_HepT" ]

[ 1093 ]

1

[]

0

[]

0

[]

0

[ "IPR000092" ]

[]

1

0

1

[ "Bacilli" ]

[ 1093 ]

1

[]

0

true

Family

Heptaprenyl diphosphate synthase component II

GerC3_HepT

7

IPR014121

14,121

Type-F conjugative transfer system mating-pair stabilisation protein TraN

TraN_Ftype

Family

3,054

false

TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilisation (adhesin) component of the F-type conjugative plasmid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein [ , , ].

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF06986", "TIGR02750" ]

[ "F_T4SS_TraN", "TraN_Ftype" ]

[ 3054, 929 ]

2

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00020464", "PUB00034396", "PUB00034402" ]

[ "1593622", "16138100", "12855161" ]

[ "Characterization of the F plasmid mating aggregation gene traN and of a new F transfer region locus trbE.", "Mobile genetic elements: the agents of open source evolution.", "F factor conjugation is a true type IV secretion system." ]

[ 1992, 2005, 2003 ]

3

[]

0

null

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

[ 3015, 22, 17 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system mating-pair stabilisation protein TraN

TraN_Ftype

4

IPR014122

14,122

Demethylmenaquinone methyltransferase

MenG_heptapren

Family

769

false

MenG is a generic term for a methyltransferase that catalyses the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone meth...

[ "GO:0008168", "GO:0009234" ]

[ "methyltransferase activity", "menaquinone biosynthetic process" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02752" ]

[ "MenG_heptapren" ]

[ 769 ]

1

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

[ "2.1.1.163", "PWY-5839", "PWY-5844", "PWY-5849", "PWY-5890", "PWY-5891", "PWY-5892", "PWY-5895", "PWY-7996" ]

[ "EC:2.1.1.163", "METACYC:PWY-5839", "METACYC:PWY-5844", "METACYC:PWY-5849", "METACYC:PWY-5890", "METACYC:PWY-5891", "METACYC:PWY-5892", "METACYC:PWY-5895", "METACYC:PWY-7996" ]

9

[]

0

[]

0

[ "IPR004033" ]

[]

1

0

1

[ "Bacteria" ]

[ 769 ]

1

[]

0

true

Family

Demethylmenaquinone methyltransferase

MenG_heptapren

8

IPR014123

14,123

Superoxide dismutase, Nickel-type

Superoxide_dismutase_Ni-type

Family

2,820

false

This entry represents nickel-dependent superoxide dismutase (NiSOD) ( ), a SOD enzyme that uses nickel, rather than iron, manganese, copper, or zinc. All SOD enzymes catalyse the dismutation of toxic superoxide radical anions to oxygen and hydrogen peroxide in order to protect cells from oxidative damage. The catalytic...

[ "GO:0004784", "GO:0016151", "GO:0016209" ]

[ "superoxide dismutase activity", "nickel cation binding", "antioxidant activity" ]

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

3

[ "PFAM", "NCBIFAM" ]

[ "PF09055", "TIGR02753" ]

[ "Sod_Ni", "sodN" ]

[ 2820, 2445 ]

2

[ "GP", "GP" ]

[ "GenProp0213", "GenProp0488" ]

[ "GP:GenProp0213", "GP:GenProp0488" ]

2

[ "1q0d", "1q0f", "1q0g", "1q0k", "1q0m", "1t6i", "1t6q", "1t6u", "3g4x", "3g4z", "3g50", "4ncq" ]

12

[ "PUB00031358", "PUB00035719" ]

[ "15209499", "16756300" ]

[ "Nickel superoxide dismutase structure and mechanism.", "Nickel superoxide dismutase reaction mechanism studied by hybrid density functional methods." ]

[ 2004, 2006 ]

2

[]

0

null

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

[ 4, 2498, 172, 146 ]

4

[]

0

true

Family

Superoxide dismutase, Nickel-type

Superoxide_dismutase_Ni-type

6

IPR014124

14,124

Peptidase S26A, superoxide dismutase maturation protease, nickel-type

Pept_S26A_Sod_Ni_maturase

Family

1,020

false

Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [ ]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identif...

[]

0

[ "NCBIFAM" ]

[ "TIGR02754" ]

[ "sod_Ni_protease" ]

[ 1020 ]

1

[ "GP" ]

[ "GenProp0488" ]

[ "GP:GenProp0488" ]

1

[]

0

[ "PUB00000522", "PUB00003576" ]

[ "8439290", "7845208" ]

[ "Evolutionary families of peptidases.", "Families of serine peptidases." ]

[ 1993, 1994 ]

2

[]

0

null

[ "Bacteria", "freshwater metagenome" ]

[ 1003, 17 ]

2

[]

0

true

Family

Peptidase S26A, superoxide dismutase maturation protease, nickel-type

Pept_S26A_Sod_Ni_maturase

5

IPR014125

14,125

Type-F conjugative transfer system pilin acetylase TraX

TraX_Ftype

Family

799

false

TraX is responsible for the acetylation of the F-pilin TraA during conjugative plasmid transfer. The purpose of this acetylation is unclear, but the reported transcriptional regulation of TraX may indicate that it is involved in the process of pilu extension/retraction [ , , ].

[]

0

[ "NCBIFAM" ]

[ "TIGR02755" ]

[ "TraX_Ftype" ]

[ 799 ]

1

[ "GP" ]

[ "GenProp0484" ]

[ "GP:GenProp0484" ]

1

[]

0

[ "PUB00011624", "PUB00020482", "PUB00034396" ]

[ "8444800", "7768788", "16138100" ]

[ "The Escherichia coli K-12 F plasmid gene traX is required for acetylation of F pilin.", "Characterization of traX, the F plasmid locus required for acetylation of F-pilin subunits.", "Mobile genetic elements: the agents of open source evolution." ]

[ 1993, 1995, 2005 ]

3

[ "IPR008875" ]

[]

1

0

1

[ "Bacteria", "Ecdysozoa" ]

[ 797, 2 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system pilin acetylase TraX

TraX_Ftype

9

IPR014126

14,126

Type-F conjugative transfer system secretin TraK

TraK_Ftype

Family

905

false

The TraK protein is predicted to interact with the TraV and TraB proteins as part of the scaffold, which extends from the inner membrane, through the periplasm to the cell envelope and through which the F-type conjugative pilus passes. TraK is homologous to the P-type IV secretion system protein TrbG, the Ti-type prote...

[]

0

[ "NCBIFAM" ]

[ "TIGR02756" ]

[ "TraK_Ftype" ]

[ 905 ]

1

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[ "7oko", "7spb", "7spi" ]

3

[ "PUB00034396", "PUB00034401", "PUB00034402" ]

[ "16138100", "11722740", "12855161" ]

[ "Mobile genetic elements: the agents of open source evolution.", "Evidence that F-plasmid proteins TraV, TraK and TraB assemble into an envelope-spanning structure in Escherichia coli.", "F factor conjugation is a true type IV secretion system." ]

[ 2005, 2001, 2003 ]

3

[]

0

null

[ "Gammaproteobacteria", "Trichuris trichiura" ]

[ 904, 1 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type-F conjugative transfer system secretin TraK

TraK_Ftype

1

IPR014127

14,127

Conserved hypothetical protein CHP02757

CHP02757

Family

3,340

false

Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09674", "TIGR02757" ]

[ "DUF2400", "" ]

[ 3340, 3218 ]

2

[]

0

[]

0

[]

0

[]

0

null

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

[ 6, 3263, 2, 5, 64 ]

5

[]

0

true

Family

Conserved hypothetical protein CHP02757

CHP02757

7

IPR014128

14,128

Type IV secretion system coupling protein TraD

TraD

Family

1,436

false

The plasmid conjugative coupling protein TraD (also known as TrwB) is an integral inner membrane protein that binds nucleoside triphosphates. It serves as the structural prototype for type IV secretion system coupling proteins, a family essential for macromolecular transport between cells [ ]. TrwB assembles as a hexam...

[]

0

[ "NCBIFAM" ]

[ "TIGR02759" ]

[ "TraD_Ftype" ]

[ 1436 ]

1

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[]

0

[ "PUB00028411", "PUB00034396", "PUB00034403", "PUB00044522" ]

[ "11214325", "16138100", "15466052", "11748238" ]

[ "The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase.", "Mobile genetic elements: the agents of open source evolution.", "Thirty-eight C-terminal amino acids of the coupling protein TraD of the F-like conjugative resistance plasmid R1 are required and sufficient to confer binding to th...

[ 2001, 2005, 2004, 2002 ]

4

[]

0

null

[ "Ecdysozoa", "Pseudomonadati", "human gut metagenome" ]

[ 3, 1432, 1 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Type IV secretion system coupling protein TraD

TraD

8

IPR014129

14,129

Conjugative transfer relaxase protein TraI

Conjug_relaxase_TraI

Family

1,231

false

This entry represents TraI, which is a component of the relaxosome complex. In the process of conjugative plasmid transfer the relaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) o...

[]

0

[ "NCBIFAM" ]

[ "TIGR02760" ]

[ "TraI_TIGR" ]

[ 1231 ]

1

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

[ "5.6.2.-", "5.6.2.3", "GenProp0484" ]

[ "EC:5.6.2.-", "EC:5.6.2.3", "GP:GenProp0484" ]

3

[ "5n8o", "9f0x", "9f0y", "9f0z", "9f10", "9f11", "9f12" ]

7

[ "PUB00034404", "PUB00091215" ]

[ "15629940", "28457609" ]

[ "The F-plasmid TraI protein contains three functional domains required for conjugative DNA strand transfer.", "Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation." ]

[ 2005, 2017 ]

2

[]

0

null

[ "Ecdysozoa", "Gammaproteobacteria", "human gut metagenome" ]

[ 3, 1227, 1 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Conjugative transfer relaxase protein TraI

Conjug_relaxase_TraI

6

IPR014131

14,131

Chlamydia phage, Vp3, scaffold

Chlamydia_phage_Vp3

Family

355

false

This entry represents homologues of the Internal scaffolding protein VP3 found mainly in Microviridae. Some members of this entry are encoded by genes in chlamydiaphage such as Vp3. These viruses have around eight genes and infect obligately intracellular bacterial pathogens of the genus Chlamydia. This protein is anno...

[]

0

[ "PFAM" ]

[ "PF09675" ]

[ "Chlamy_scaf" ]

[ 355 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Ecdysozoa", "Microviridae" ]

[ 16, 8, 331 ]

3

[]

0

true

Family

Chlamydia phage, Vp3, scaffold

Chlamydia_phage_Vp3

4

IPR014132

14,132

Sporulation polysaccharide deacetylase PdaB-like

PdaB-like

Family

1,618

false

This entry describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reduced sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in spor...

[]

0

[ "NCBIFAM" ]

[ "TIGR02764" ]

[ "spore_ybaN_pdaB" ]

[ 1618 ]

1

[]

0

[ "4m1b", "7fbw", "7y51" ]

3

[ "PUB00034547", "PUB00093393" ]

[ "15598884", "15961396" ]

[ "Characterization of a polysaccharide deacetylase gene homologue (pdaB) on sporulation of Bacillus subtilis.", "Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus, highly conserved proteins in Bacillus anthracis." ]

[ 2004, 2005 ]

2

[ "IPR050248" ]

[]

1

0

1

[ "Bacillota", "Phytophthora kernoviae 00238/432", "ecological metagenomes" ]

[ 1614, 1, 3 ]

3

[]

0

true

Family

Sporulation polysaccharide deacetylase PdaB-like

PdaB-like

9

IPR014133

14,133

Cryptochrome DASH

Cry_DASH

Family

4,234

false

The cryptochrome and photolyase families consist of structurally related flavin adenine dinucleotide (FAD) proteins that use the absorption of blue light to accomplish different tasks. The photolyasess use the blue light for light-driven electron transfer to repair UV-damaged DNA, while the cryptochromes are blue-light...

[ "GO:0003913", "GO:0006281" ]

[ "DNA photolyase activity", "DNA repair" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02765" ]

[ "crypto_DASH" ]

[ 4234 ]

1

[]

0

[ "1np7", "2ijg", "2j4d", "2vtb", "6kii" ]

5

[ "PUB00076728", "PUB00076729", "PUB00076730" ]

[ "17062752", "25910181", "26352435" ]

[ "A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity.", "Binding of Substrate Locks the Electrochemistry of CRY-DASH into DNA Repair.", "Evolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes." ]

[ 2006, 2015, 2015 ]

3

[ "IPR002081" ]

[]

1

0

1

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

[ 2086, 2035, 104, 9 ]

4

[ "Arabidopsis thaliana", "Danio rerio", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Zea mays" ]

[ 4, 2, 1, 5, 4 ]

5

true

Family

Cryptochrome DASH

Cry_DASH

3

IPR014134

14,134

Cryptochrome, plant

Cryptochrome_pln

Family

1,863

false

The cryptochrome and photolyase families consist of structurally related flavin adenine dinucleotide (FAD) proteins that use the absorption of blue light to accomplish different tasks. The photolyasess use the blue light for light-driven electron transfer to repair UV-damaged DNA, while the cryptochromes are blue-light...

[ "GO:0009882", "GO:0009785" ]

[ "blue light photoreceptor activity", "blue light signaling pathway" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02766" ]

[ "crypt_chrom_pln" ]

[ 1863 ]

1

[]

0

[ "1u3c", "1u3d", "6k8i", "6k8k", "6lz3", "6lz7", "6m79", "6x24", "7x0x", "7x0y", "9lpg" ]

11

[ "PUB00076729", "PUB00076730", "PUB00076731", "PUB00076732", "PUB00076733" ]

[ "25910181", "26352435", "16703358", "20133010", "18988809" ]

[ "Binding of Substrate Locks the Electrochemistry of CRY-DASH into DNA Repair.", "Evolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes.", "Cryptochrome photoreceptors cry1 and cry2 antagonistically regulate primary root elongation in Arabidopsis thaliana.", "Arabidopsis cryptochrome-1 ...

[ 2015, 2015, 2006, 2010, 2008 ]

5

[ "IPR002081" ]

[]

1

0

1

[ "Viridiplantae" ]

[ 1863 ]

1

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

[ 22, 12, 23 ]

3

true

Family

Cryptochrome, plant

Cryptochrome_pln

4

IPR014135

14,135

Conjugal transfer protein TraG-like

Ti-typ_conjug_TS_TraG-like

Family

651

false

This entry contains the Agrobacterium tumefaciens Ti-plasmid TraG, it is responsible for conjugative transfer of the entire plasmid among Agrobacterium strains [ ]. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems. Also in th...

[]

0

[ "NCBIFAM" ]

[ "TIGR02767" ]

[ "TraG-Ti" ]

[ 651 ]

1

[ "GP" ]

[ "GenProp0490" ]

[ "GP:GenProp0490" ]

1

[]

0

[ "PUB00012375", "PUB00060321" ]

[ "8763953", "15642951" ]

[ "The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F.", "A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells." ]

[ 1996, 2005 ]

2

[ "IPR003688" ]

[]

1

0

1

[ "Alphaproteobacteria" ]

[ 651 ]

1

[]

0

true

Family

Conjugal transfer protein TraG-like

Ti-typ_conjug_TS_TraG-like

5

IPR014136

14,136

Ti-type conjugative transfer relaxase TraA

TraA_Ti

Family

1,626

false

This entry represents the Ti-type conjugative transfer relaxase TraA. TraA contains domains distinctive of a single strand exonuclease (N terminus, MobA/MobL, ) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, ). This protein likely fills the same role as...

[]

0

[ "NCBIFAM" ]

[ "TIGR02768" ]

[ "TraA_Ti" ]

[ 1626 ]

1

[ "GP" ]

[ "GenProp0490" ]

[ "GP:GenProp0490" ]

1

[]

0

[ "PUB00012375" ]

[ "8763953" ]

[ "The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F." ]

[ 1996 ]

1

[]

0

null

[ "Eukaryota", "Pseudomonadati", "unclassified sequences" ]

[ 3, 1618, 5 ]

3

[]

0

true

Family

Ti-type conjugative transfer relaxase TraA

TraA_Ti

8

IPR014137

14,137

Nickel import ATP-binding protein NikE

Nickel_NikE

Family

632

false

ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found o...

[ "GO:0015413", "GO:0016151", "GO:0015675", "GO:0005886" ]

[ "ABC-type nickel transporter activity", "nickel cation binding", "nickel cation transport", "plasma membrane" ]

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

4

[ "NCBIFAM" ]

[ "TIGR02769" ]

[ "nickel_nikE" ]

[ 632 ]

1

[ "EC", "GP" ]

[ "7.2.2.11", "GenProp0494" ]

[ "EC:7.2.2.11", "GP:GenProp0494" ]

2

[]

0

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

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

[ "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 ]

11

[ "IPR050319" ]

[]

1

0

1

[ "Bacteria" ]

[ 632 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Nickel import ATP-binding protein NikE

Nickel_NikE

3

IPR014138

14,138

Nickel import ATP-binding protein NikD

Nickel_NikD

Family

455

false

This entry represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are related families. ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which us...

[ "GO:0015413", "GO:0016151", "GO:0015675", "GO:0005886" ]

[ "ABC-type nickel transporter activity", "nickel cation binding", "nickel cation transport", "plasma membrane" ]

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

4

[ "NCBIFAM" ]

[ "TIGR02770" ]

[ "nickel_nikD" ]

[ 455 ]

1

[ "EC", "GP" ]

[ "7.2.2.11", "GenProp0494" ]

[ "EC:7.2.2.11", "GP:GenProp0494" ]

2

[]

0

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

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

[ "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 ]

11

[]

0

null

[ "Bacteria", "Methanosarcina" ]

[ 447, 8 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Nickel import ATP-binding protein NikD

Nickel_NikD

1

IPR014139

14,139

Peptidase S26C, conjugative transfer signal peptidase TraF

Peptidase_S26C_TraF

Family

923

false

This entry contains the conjugative transfer signal peptidase (TraF), which belongs to MEROPS peptidase family S26, subfamily S26C (TraF signal peptidase, clan SF). It is found in operons that encode elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases su...

[ "GO:0042597" ]

[ "periplasmic space" ]

[ "cellular_component" ]

1

[ "NCBIFAM" ]

[ "TIGR02771" ]

[ "TraF_Ti" ]

[ 923 ]

1

[ "GP" ]

[ "GenProp0490" ]

[ "GP:GenProp0490" ]

1

[]

0

[ "PUB00034405" ]

[ "1400217" ]

[ "Mutational analysis of essential IncP alpha plasmid transfer genes traF and traG and involvement of traF in phage sensitivity." ]

[ 1992 ]

1

[]

0

null

[ "Bacteria", "Gibberella intermedia", "ecological metagenomes", "plasmids" ]

[ 911, 1, 4, 7 ]

4

[]

0

true

Family

Peptidase S26C, conjugative transfer signal peptidase TraF

Peptidase_S26C_TraF

6

IPR014140

14,140

ATP-dependent helicase/deoxyribonuclease AddB

AddB

Family

2,565

false

DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in others. AddA is conserved between the firmicutes and the alphaproteobacteria, while its partner protein (RexB) is no...

[ "GO:0016788", "GO:0000724" ]

[ "hydrolase activity, acting on ester bonds", "double-strand break repair via homologous recombination" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_01452", "TIGR02773" ]

[ "AddB_type1", "addB_Gpos" ]

[ 2037, 2551 ]

2

[ "GP" ]

[ "GenProp0493" ]

[ "GP:GenProp0493" ]

1

[ "3u44", "3u4q", "4ceh", "4cei", "4cej" ]

5

[]

0

[]

0

null

[ "Bacillati", "metagenomes" ]

[ 2560, 5 ]

2

[]

0

true

Family

ATP-dependent helicase/deoxyribonuclease AddB

AddB

2

IPR014142

14,142

P-type conjugative transfer protein TrbG

TrbG_Ti

Family

3,164

false

The TrbG protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer [ ]. TrbG is a homologue of the F-type TraK protein (which is believed to be an outer membrane pore-forming secretin, ) as well as the vir system VirB9 protein [ ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02775" ]

[ "TrbG_Ti" ]

[ 3164 ]

1

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[]

0

[ "PUB00012375", "PUB00034401", "PUB00034402" ]

[ "8763953", "11722740", "12855161" ]

[ "The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F.", "Evidence that F-plasmid proteins TraV, TraK and TraB assemble into an envelope-spanning structure in Escherichia coli.", "F factor conjugation is a true type IV secretion system....

[ 1996, 2001, 2003 ]

3

[ "IPR010258" ]

[]

1

0

1

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

[ 3131, 6, 18, 9 ]

4

[]

0

true

Family

P-type conjugative transfer protein TrbG

TrbG_Ti

4

IPR014143

14,143

DNA ligase D

NHEJ_ligase_prk

Domain

5,860

false

Members of this entry are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NheJ). The system of the bacterial Ku protein ( ) plus this DNA ligase is seen in about 20% of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This entry describes a cen...

[]

0

[ "NCBIFAM" ]

[ "TIGR02776" ]

[ "NHEJ_ligase_prk" ]

[ 5860 ]

1

[]

0

[ "2fao", "2faq", "2far" ]

3

[]

0

[]

0

null

[ "Bacteria", "Candidatus Nitrosocosmicus", "Eukaryota", "metagenomes" ]

[ 5837, 2, 3, 18 ]

4

[]

0

true

Domain

DNA ligase D

NHEJ_ligase_prk

2

IPR014144

14,144

DNA ligase D, 3'-phosphoesterase domain

LigD_PE_domain

Domain

9,376

false

This entry represents a 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, which is involved along with bacterial Ku protein in non-homologous end joining [ ]- the less common of two general mechanisms of repairing double-stranded breaks in DNA sequences. LigD is variable in architecture, as ...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF13298", "TIGR02777" ]

[ "LigD_N", "LigD_PE_dom" ]

[ 9376, 8114 ]

2

[ "EC", "GP" ]

[ "6.5.1.1", "GenProp0492" ]

[ "EC:6.5.1.1", "GP:GenProp0492" ]

2

[ "2lj6", "3n9b", "3n9d", "3p43", "3p4h", "3ta5", "3ta7", "5dmp" ]

8

[ "PUB00034551" ]

[ "16046407" ]

[ "Essential constituents of the 3'-phosphoesterase domain of bacterial DNA ligase D, a nonhomologous end-joining enzyme." ]

[ 2005 ]

1

[]

0

null

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

[ 139, 8513, 675, 49 ]

4

[]

0

true

Domain

DNA ligase D, 3'-phosphoesterase domain

LigD_PE_domain

4

IPR014145

14,145

DNA ligase D, polymerase domain

LigD_pol_dom

Domain

18,199

false

DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see ), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria t...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF21686", "TIGR02778" ]

[ "LigD_Prim-Pol", "ligD_pol" ]

[ 18199, 15610 ]

2

[ "EC", "GP" ]

[ "6.5.1.1", "GenProp0492" ]

[ "EC:6.5.1.1", "GP:GenProp0492" ]

2

[ "2fao", "2faq", "2far", "2iru", "2irx", "2iry", "2r9l", "3pky", "4mky", "5dmu", "5op0", "6sa0", "6sa1" ]

13

[ "PUB00049296", "PUB00106908" ]

[ "17947582", "29089537" ]

[ "Structure of a NHEJ polymerase-mediated DNA synaptic complex.", "DNA Ligase C and Prim-PolC participate in base excision repair in mycobacteria." ]

[ 2007, 2017 ]

2

[]

[ "IPR033649", "IPR033651", "IPR033652" ]

0

3

0

[ "Archaea", "Bacteria", "Eukaryota", "Methanophagales virus PBV082", "metagenomes" ]

[ 16, 18099, 17, 1, 66 ]

5

[]

0

true

Domain

DNA ligase D, polymerase domain

LigD_pol_dom

1

IPR014146

14,146

DNA ligase D, ligase domain

LigD_ligase_dom

Domain

10,224

false

DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see ), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria t...

[]

0

[ "NCBIFAM" ]

[ "TIGR02779" ]

[ "NHEJ_ligase_lig" ]

[ 10224 ]

1

[ "EC", "GP" ]

[ "6.5.1.1", "GenProp0492" ]

[ "EC:6.5.1.1", "GP:GenProp0492" ]

2

[ "1vs0", "6nhx", "6nhz" ]

3

[ "PUB00037987" ]

[ "16476729" ]

[ "Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D." ]

[ 2006 ]

1

[]

0

null

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

[ 16, 10173, 5, 30 ]

4

[]

0

true

Domain

DNA ligase D, ligase domain

LigD_ligase_dom

3

IPR014147

14,147

Type IV conjugative transfer protein TrbJ

T4SS_TrbJ

Family

3,493

false

The TrbJ protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer [ , ]. TrbJ is a homologue of the F-type TraE protein (which is believed to be an inner membrane pore-forming protein ( ), as well as the vir system VirB5 protein...

[]

0

[ "NCBIFAM" ]

[ "TIGR02780" ]

[ "TrbJ_Ti" ]

[ 3493 ]

1

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[]

0

[ "PUB00012375", "PUB00019242", "PUB00034402" ]

[ "8763953", "10438776", "12855161" ]

[ "The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F.", "Essential components of the Ti plasmid trb system, a type IV macromolecular transporter.", "F factor conjugation is a true type IV secretion system." ]

[ 1996, 1999, 2003 ]

3

[]

0

null

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

[ 3451, 9, 25, 8 ]

4

[]

0

true

Family

Type IV conjugative transfer protein TrbJ

T4SS_TrbJ

1

IPR014149

14,149

Conjugative transfer, TrbB

Conjug-transfer_TrbB

Family

3,254

false

This entry represents TrbB, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer [ ]. TrbB is a homologue of the vir system VirB11 ATPase [ ], and the Flp pilus system ATPase TadA [ ].

[ "GO:0005524", "GO:0005737" ]

[ "ATP binding", "cytoplasm" ]

[ "molecular_function", "cellular_component" ]

2

[ "NCBIFAM" ]

[ "TIGR02782" ]

[ "TrbB_P" ]

[ 3254 ]

1

[ "GP" ]

[ "GenProp0490" ]

[ "GP:GenProp0490" ]

1

[]

0

[ "PUB00012375", "PUB00034407", "PUB00034408" ]

[ "8763953", "15554962", "11566992" ]

[ "The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F.", "Energetic components VirD4, VirB11 and VirB4 mediate early DNA transfer reactions required for bacterial type IV secretion.", "Nonspecific adherence and fibril biogenesis by Acti...

[ 1996, 2004, 2001 ]

3

[]

0

null

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

[ 3211, 8, 25, 10 ]

4

[]

0

true

Family

Conjugative transfer, TrbB

Conjug-transfer_TrbB

8

IPR014150

14,150

Conjugal transfer, TrbL

Conjugal_tfr_TrbL

Family

3,616

false

This entry represents TrbL, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer [ , ]. TrbL is a homologue of the F-type TraG protein (which is believed to be a mating pair stabilisation pore-forming protein, ) a...

[]

0

[ "NCBIFAM" ]

[ "TIGR02783" ]

[ "TrbL_P" ]

[ 3616 ]

1

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[]

0

[ "PUB00012375", "PUB00019242", "PUB00034402" ]

[ "8763953", "10438776", "12855161" ]

[ "The tra region of the nopaline-type Ti plasmid is a chimera with elements related to the transfer systems of RSF1010, RP4, and F.", "Essential components of the Ti plasmid trb system, a type IV macromolecular transporter.", "F factor conjugation is a true type IV secretion system." ]

[ 1996, 1999, 2003 ]

3

[ "IPR007688" ]

[]

1

0

1

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

[ 3585, 6, 17, 8 ]

4

[]

0

true

Family

Conjugal transfer, TrbL

Conjugal_tfr_TrbL

7

IPR014151

14,151

DNA helicase, AddA type

DNA_helicase_AddA

Family

2,876

false

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination [ ]. The term AddAB is used broadly, with AddA homologues between the alphaproteobacteri...

[]

0

[ "NCBIFAM" ]

[ "TIGR02784" ]

[ "addA_alphas" ]

[ 2876 ]

1

[ "GP" ]

[ "GenProp0493" ]

[ "GP:GenProp0493" ]

1

[]

0

[ "PUB00034450" ]

[ "15547262" ]

[ "The recombination genes addAB are not restricted to gram-positive bacteria: genetic analysis of the recombination initiation enzymes RecF and AddAB in Rhizobium etli." ]

[ 2004 ]

1

[ "IPR000212" ]

[]

1

0

1

[ "Bacteria", "Durusdinium trenchii", "metagenomes" ]

[ 2856, 2, 18 ]

3

[]

0

true

Family

DNA helicase, AddA type

DNA_helicase_AddA

1

IPR014152

14,152

ATP-dependent helicase/nuclease subunit A

AddA

Family

4,854

false

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the firmicutes and the alp...

[ "GO:0003678", "GO:0006302" ]

[ "DNA helicase activity", "double-strand break repair" ]

[ "molecular_function", "biological_process" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_01451", "TIGR02785" ]

[ "AddA", "addA_Gpos" ]

[ 4307, 4717 ]

2

[ "EC", "GP" ]

[ "5.6.2.4", "GenProp0493" ]

[ "EC:5.6.2.4", "GP:GenProp0493" ]

2

[ "3u44", "3u4q", "4ceh", "4cei", "4cej" ]

5

[ "PUB00034450" ]

[ "15547262" ]

[ "The recombination genes addAB are not restricted to gram-positive bacteria: genetic analysis of the recombination initiation enzymes RecF and AddAB in Rhizobium etli." ]

[ 2004 ]

1

[ "IPR000212" ]

[]

1

0

1

[ "Bacteria", "metagenomes" ]

[ 4845, 9 ]

2

[]

0

true

Family

ATP-dependent helicase/nuclease subunit A

AddA

6

IPR014153

14,153

Double-strand break repair protein AddB

Ds_break_AddB

Family

2,754

false

AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage [ ]. More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This...

[]

0

[ "NCBIFAM" ]

[ "TIGR02786" ]

[ "addB_alphas" ]

[ 2754 ]

1

[ "GP" ]

[ "GenProp0493" ]

[ "GP:GenProp0493" ]

1

[]

0

[ "PUB00034450" ]

[ "15547262" ]

[ "The recombination genes addAB are not restricted to gram-positive bacteria: genetic analysis of the recombination initiation enzymes RecF and AddAB in Rhizobium etli." ]

[ 2004 ]

1

[]

0

null

[ "Bacteria", "Durusdinium trenchii", "metagenomes" ]

[ 2735, 1, 18 ]

3

[]

0

true

Family

Double-strand break repair protein AddB

Ds_break_AddB

7

IPR014154

14,154

Global transcriptional regulator CodY

CodY

Family

3,329

false

This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. CodY is a DNA-binding protein that represses the expression of many genes that are induced as cells make the transitio...

[ "GO:0003677", "GO:0003700", "GO:0005525", "GO:0045892" ]

[ "DNA binding", "DNA-binding transcription factor activity", "GTP binding", "negative regulation of DNA-templated transcription" ]

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

4

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

[ "MF_00621", "PIRSF011572", "PTHR40062", "TIGR02787" ]

[ "HTH_type_CodY", "GTP_sensing_CodY", "", "codY_Gpos" ]

[ 3233, 3223, 3327, 2985 ]

4

[]

0

[ "2b0l", "2b18", "2gx5", "2hgv", "5ey0", "5ey1", "5ey2", "5lnh", "5loe", "5loj", "5loo", "5n0l", "8c7o", "8c7s", "8c7t", "8c7u" ]

16

[ "PUB00054248", "PUB00054249" ]

[ "8830686", "11331605" ]

[ "CodY is required for nutritional repression of Bacillus subtilis genetic competence.", "Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels." ]

[ 1996, 2001 ]

2

[]

0

null

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

[ 3309, 2, 18 ]

3

[]

0

true

Family

Global transcriptional regulator CodY

CodY

6

IPR014156

14,156

Nickel ABC transporter, permease subunit NikB

Nickel_NikB

Family

614

false

This entry includes NikB from E.coli and related sequences mainly from gammaprotebacteria and bacilli. This family consists of the NikB family of nickel ABC transporter permeases. The NikABCDE uptake system that contains this protein also contain a homologous permease subunit NikC [ ]. Based on sequence similarity, Nik...

[ "GO:0015099", "GO:0035444" ]

[ "nickel cation transmembrane transporter activity", "nickel cation transmembrane transport" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02789" ]

[ "nickel_nikB" ]

[ 614 ]

1

[ "GP" ]

[ "GenProp0494" ]

[ "GP:GenProp0494" ]

1

[]

0

[ "PUB00035598", "PUB00060987" ]

[ "7934931", "10648098" ]

[ "The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel.", "Nickel transport systems in microorganisms." ]

[ 1993, 2000 ]

2

[ "IPR050045" ]

[]

1

0

1

[ "Bacteria" ]

[ 614 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Nickel ABC transporter, permease subunit NikB

Nickel_NikB

6

IPR014158

14,158

Type IV secretion system protein VirB5-like

VirB5-like

Family

3,470

false

This entry contains VirB5, a protein that is involved in the type IV DNA secretion systems typified by the Agrobacterium Ti plasmid vir system where it interacts with several other proteins essential for proper pilus formation [ ]. VirB5 is homologous to the IncN (N-type) conjugation system protein TraC [ ] as well as ...

[]

0

[ "PFAM", "CDD" ]

[ "PF07996", "cd14262" ]

[ "T4SS", "VirB5_like" ]

[ 3469, 1534 ]

2

[ "GP" ]

[ "GenProp0485" ]

[ "GP:GenProp0485" ]

1

[ "1r8i", "7o3v", "8rt9", "8rtd" ]

4

[ "PUB00020399", "PUB00034402", "PUB00034409", "PUB00133871", "PUB00133872", "PUB00133873", "PUB00133874", "PUB00133875", "PUB00163255", "PUB00163256" ]

[ "14673074", "12855161", "15901731", "18165307", "17975085", "15155952", "10510235", "10482495", "35732732", "38886579" ]

[ "Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101.", "F factor conjugation is a true type IV secretion system.", "Identification of the VirB4-VirB8-VirB5-VirB2 pilus assembly sequence of type IV secretion systems.", "Th...

[ 2003, 2003, 2005, 2008, 2007, 2004, 1999, 1999, 2022, 2024 ]

10

[]

[ "IPR061293" ]

0

1

0

[ "Bacteria", "Eukaryota", "Sym plasmid", "metagenomes" ]

[ 3439, 15, 2, 14 ]

4

[]

0

true

Family

Type IV secretion system protein VirB5-like

VirB5-like

5

IPR014159

14,159

Protocatechuate 4,5-dioxygenase, alpha subunit

PCA_LigA

Family

829

false

Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways [ , ]. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. It is composed of A and B subunits that form a tet...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02792", "cd07924" ]

[ "PCA_ligA", "PCA_45_Doxase_A" ]

[ 829, 572 ]

2

[]

0

[ "1b4u", "1bou" ]

2

[ "PUB00011779", "PUB00081196", "PUB00081197", "PUB00081198" ]

[ "10467151", "15650824", "15357311", "2280721" ]

[ "Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.", "Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases.", "Characterizatio...

[ 1999, 2005, 2004, 1990 ]

4

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 819, 10 ]

2

[]

0

true

Family

Protocatechuate 4,5-dioxygenase, alpha subunit

PCA_LigA

7

IPR014160

14,160

Nickel-responsive transcriptional regulator NikR, proteobacteria

Nickel_NikR_proteobac

Family

917

false

The members of this entry from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterised nickel-binding and DNA-binding domains, act as nickel-resp...

[ "GO:0016151", "GO:0010045" ]

[ "nickel cation binding", "response to nickel cation" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02793" ]

[ "nikR" ]

[ 917 ]

1

[ "GP" ]

[ "GenProp0494" ]

[ "GP:GenProp0494" ]

1

[ "1q5v", "2hza", "2hzv", "3od2" ]

4

[ "PUB00062383", "PUB00062384" ]

[ "10595554", "9882686" ]

[ "NikR is a ribbon-helix-helix DNA-binding protein.", "Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli." ]

[ 1999, 1999 ]

2

[ "IPR022988" ]

[]

1

0

1

[ "Protostomia", "Pseudomonadota", "ecological metagenomes" ]

[ 2, 913, 2 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Nickel-responsive transcriptional regulator NikR, proteobacteria

Nickel_NikR_proteobac

5

IPR014161

14,161

Tol-Pal system, TolA

Tol-Pal_TolA

Family

8,002

false

Tol proteins are involved in the translocation of group A colicins. Colicins are bacterial protein toxins, which are active against Escherichia coli and other related species. TolA is anchored to the cytoplasmic membrane by a single membrane spanning segment near the N terminus, leaving most of the protein exposed to t...

[ "GO:0019534", "GO:0043213", "GO:0016020" ]

[ "toxin transmembrane transporter activity", "bacteriocin transport", "membrane" ]

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

3

[ "PFAM", "NCBIFAM" ]

[ "PF06519", "TIGR02794" ]

[ "TolA", "tolA_full" ]

[ 3745, 7577 ]

2

[ "GP" ]

[ "GenProp0542" ]

[ "GP:GenProp0542" ]

1

[ "1lr0", "1s62", "1tol", "2x9a", "3qdp", "3qdr", "4g7x", "6fw4", "6s3w", "9ddm", "9ddn", "9hcj", "9k49", "9kch" ]

14

[ "PUB00012639", "PUB00106716" ]

[ "12423782", "21252278" ]

[ "The Tol proteins of Escherichia coli and their involvement in the translocation of group A colicins.", "TolA mediates the differential detergent resistance pattern between the Salmonella enterica subsp. enterica serovars Typhi and Typhimurium." ]

[ 2002, 2011 ]

2

[]

0

null

[ "Bacteria", "Eukaryota", "Siphoviridae sp. ctekV29", "unclassified sequences" ]

[ 7911, 31, 1, 59 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Tol-Pal system, TolA

Tol-Pal_TolA

5

IPR014162

14,162

Cell division coordinator CpoB, C-terminal

CpoB_C

Domain

8,271

false

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF, which is then rename...

[]

0

[ "NCBIFAM" ]

[ "TIGR02795" ]

[ "tol_pal_ybgF" ]

[ 8271 ]

1

[ "GP" ]

[ "GenProp0542" ]

[ "GP:GenProp0542" ]

1

[ "2xev", "6g5s" ]

2

[ "PUB00034410", "PUB00084209" ]

[ "16207916", "25951518" ]

[ "Tol-Pal proteins are critical cell envelope components of Erwinia chrysanthemi affecting cell morphology and virulence.", "Coordination of peptidoglycan synthesis and outer membrane constriction during Escherichia coli cell division." ]

[ 2005, 2015 ]

2

[]

0

null

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

[ 8128, 13, 130 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Domain

Cell division coordinator CpoB, C-terminal

CpoB_C

3

IPR014163

14,163

Tol-Pal system, TolQ

Tol-Pal_TolQ

Family

9,174

false

TolQ is one of the essential components of the Tol-Pal system. Together with TolR, it harnesses proton motive force to energize TolA, which spans the periplasm to reach the complex of TolB and Pal at the outer member. The tol-pal system proves to be important for maintaining outer membrane integrity [ ]. Gene pairs sim...

[ "GO:0043213", "GO:0016020" ]

[ "bacteriocin transport", "membrane" ]

[ "biological_process", "cellular_component" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_02202", "TIGR02796" ]

[ "TolQ", "tolQ" ]

[ 8079, 9173 ]

2

[ "GP" ]

[ "GenProp0542" ]

[ "GP:GenProp0542" ]

1

[ "8odt", "8vlw", "9avi", "9ddm", "9ddn", "9k49", "9kch" ]

7

[ "PUB00009507", "PUB00067438", "PUB00088407", "PUB00088408" ]

[ "3294803", "10940016", "2651401", "27622343" ]

[ "Nucleotide sequence of a gene cluster involved in entry of E colicins and single-stranded DNA of infecting filamentous bacteriophages into Escherichia coli.", "Mutations in each of the tol genes of Pseudomonas putida reveal that they are critical for maintenance of outer membrane stability.", "Localization and...

[ 1987, 2000, 1989, 2016 ]

4

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified sequences", "uncultured marine group II/III euryarchaeote KM3_86_F07" ]

[ 9037, 15, 121, 1 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Tol-Pal system, TolQ

Tol-Pal_TolQ

5

IPR014164

14,164

TonB-system energizer ExbB type-1

TonB_ExbB_1

Family

3,483

false

This entry describes ExbB proteins, part of the MotA/TolQ/ExbB protein family. The paired proteins MotA and MotB, TolQ and TolR, and ExbB and ExbD harness the proton-motive force to drive the flagellar motor, energize the Tol-Pal system, or energize TonB, respectively. Tol-Pal and TonB are both active at the outer memb...

[ "GO:0022857", "GO:0055085", "GO:0016020" ]

[ "transmembrane transporter activity", "transmembrane transport", "membrane" ]

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

3

[ "NCBIFAM" ]

[ "TIGR02797" ]

[ "exbB" ]

[ 3483 ]

1

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

[ "GenProp0543", "GenProp1157", "R-HSA-9638334", "R-HSA-9638482", "R-HSA-9927020" ]

[ "GP:GenProp0543", "GP:GenProp1157", "REACTOME:R-HSA-9638334", "REACTOME:R-HSA-9638482", "REACTOME:R-HSA-9927020" ]

5

[ "5sv0", "5sv1", "5zfp", "5zfu", "5zfv", "6tyi", "6ye4", "7ajq", "9ddo", "9ddp", "9ddq" ]

11

[ "PUB00071891" ]

[ "8449962" ]

[ "Topology of the ExbB protein in the cytoplasmic membrane of Escherichia coli." ]

[ 1993 ]

1

[]

0

null

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

[ 3473, 3, 7 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

TonB-system energizer ExbB type-1

TonB_ExbB_1

6

IPR014166

14,166

Tol-Pal system-associated acyl-CoA thioesterase

Tol-Pal_acyl-CoA_thioesterase

Family

7,241

false

The tol-pal system consists of five critical genes. Inner membrane proteins TolQ and TolR convert proton motive force to energy that is transduced through TolA to an outer membrane complex of TolB and Pal. The system is known to be required to maintain outer membrane integrity. In a system with several homologous parts...

[ "GO:0016790" ]

[ "thiolester hydrolase activity" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR02799" ]

[ "thio_ybgC" ]

[ 7241 ]

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", "...

[ "3.1.2.-", "GenProp0542", "PWY-3602", "PWY-5109", "PWY-6322", "PWY-6585", "PWY-6917", "PWY-6948", "PWY-6995", "PWY-6997", "PWY-7007", "PWY-7216", "PWY-7292", "PWY-7401", "PWY-7402", "PWY-7471", "PWY-7690", "PWY-7706", "PWY-7733", "PWY-7734", "PWY-7738", "PWY-7740", "PWY-7...

[ "EC:3.1.2.-", "GP:GenProp0542", "METACYC:PWY-3602", "METACYC:PWY-5109", "METACYC:PWY-6322", "METACYC:PWY-6585", "METACYC:PWY-6917", "METACYC:PWY-6948", "METACYC:PWY-6995", "METACYC:PWY-6997", "METACYC:PWY-7007", "METACYC:PWY-7216", "METACYC:PWY-7292", "METACYC:PWY-7401", "METACYC:PWY-740...

35

[ "1s5u", "3hm0", "5kl9", "5t06", "5t07", "5v10" ]

6

[ "PUB00034410" ]

[ "16207916" ]

[ "Tol-Pal proteins are critical cell envelope components of Erwinia chrysanthemi affecting cell morphology and virulence." ]

[ 2005 ]

1

[ "IPR006684" ]

[]

1

0

1

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

[ 7160, 4, 77 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Tol-Pal system-associated acyl-CoA thioesterase

Tol-Pal_acyl-CoA_thioesterase

7

IPR014167

14,167

Tol-Pal system protein TolB

Tol-Pal_TolB

Family

9,634

false

Members of this protein family are the TolB periplasmic protein of Gram-negative bacteria. TolB is part of the Tol-Pal (peptidoglycan-associated lipoprotein) multiprotein complex, comprising five envelope proteins, TolQ, TolR, TolA, TolB and Pal, which form two complexes. The TolQ, TolR and TolA inner-membrane proteins...

[ "GO:0017038", "GO:0042597" ]

[ "protein import", "periplasmic space" ]

[ "biological_process", "cellular_component" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_00671", "TIGR02800" ]

[ "TolB", "propeller_TolB" ]

[ 9437, 9404 ]

2

[ "GP" ]

[ "GenProp0542" ]

[ "GP:GenProp0542" ]

1

[ "1c5k", "1crz", "2hqs", "2ivz", "2w8b", "3iax", "4jml", "4pwz", "4r40", "6pnv", "7mx5", "7nst", "7nsu" ]

13

[]

0

[]

0

null

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

[ 9498, 19, 117 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Tol-Pal system protein TolB

Tol-Pal_TolB

2

IPR014168

14,168

Tol-Pal system protein TolR

Tol-Pal_TolR

Family

7,830

false

This entry describes the inner membrane protein TolR, part of the TolR/TolQ complex that transduces energy from the proton-motive force, through TolA, to an outer membrane complex made up of TolB and Pal (peptidoglycan-associated lipoprotein). The complex is recruited to cell division sites and is required to maintain ...

[ "GO:0015031", "GO:0016020" ]

[ "protein transport", "membrane" ]

[ "biological_process", "cellular_component" ]

2

[ "HAMAP", "NCBIFAM" ]

[ "MF_02203", "TIGR02801" ]

[ "TolR", "tolR" ]

[ 4585, 7354 ]

2

[ "GP" ]

[ "GenProp0542" ]

[ "GP:GenProp0542" ]

1

[ "8odt", "9ddm", "9ddn", "9k49", "9kch" ]

5

[ "PUB00088398" ]

[ "26354441" ]

[ "Structure and function of the Escherichia coli Tol-Pal stator protein TolR." ]

[ 2015 ]

1

[ "IPR003400" ]

[]

1

0

1

[ "Bacteria", "Opisthokonta", "unclassified sequences", "uncultured marine group II/III euryarchaeote KM3_86_F07" ]

[ 7714, 10, 105, 1 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Tol-Pal system protein TolR

Tol-Pal_TolR

9

IPR014169

14,169

Peptidoglycan-associated lipoprotein, C-terminal

Pal_lipo_C

Domain

9,372

false

This entry represents the C-terminal domain of peptidoglycan-associated lipoprotein (Pal or OprL) of the Tol-Pal system. The system appears to be involved both in the maintenance of outer membrane integrity and in the import of certain organic molecules as nutrients [ ]. Pal contains a hydrodrophobic lipoprotein signal...

[ "GO:0009279" ]

[ "cell outer membrane" ]

[ "cellular_component" ]

1

[ "NCBIFAM" ]

[ "TIGR02802" ]

[ "Pal_lipo" ]

[ 9372 ]

1

[ "GP" ]

[ "GenProp0542" ]

[ "GP:GenProp0542" ]

1

[ "1oap", "2aiz", "2hqs", "2w8b", "4b5c", "4g4v", "4g4w", "4g4x", "4pwt", "4r40", "5lkw", "5n2c" ]

12

[ "PUB00088654" ]

[ "17233825" ]

[ "The trans-envelope Tol-Pal complex is part of the cell division machinery and required for proper outer-membrane invagination during cell constriction in E. coli." ]

[ 2007 ]

1

[ "IPR006665" ]

[]

1

0

1

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

[ 9200, 24, 148 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Domain

Peptidoglycan-associated lipoprotein, C-terminal

Pal_lipo_C

9

IPR014170

14,170

TonB system transport protein ExbD type-1

TonB_ExbD_1

Family

3,044

false

Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR . Members are always found next to a protein designated ExbB ( ), which is related to the TolQ family ( ). ExbD and ExbB together form a proton channel through which they can harness the proton-mot...

[ "GO:0055085", "GO:0016020" ]

[ "transmembrane transport", "membrane" ]

[ "biological_process", "cellular_component" ]

2

[ "NCBIFAM" ]

[ "TIGR02803" ]

[ "ExbD_1" ]

[ 3044 ]

1

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

[ "GenProp0543", "GenProp1157", "R-HSA-9638334", "R-HSA-9638482", "R-HSA-9927020" ]

[ "GP:GenProp0543", "GP:GenProp1157", "REACTOME:R-HSA-9638334", "REACTOME:R-HSA-9638482", "REACTOME:R-HSA-9927020" ]

5

[ "2pfu", "6tyi", "7ajq", "9ddo", "9ddp", "9ddq" ]

6

[]

0

[ "IPR003400" ]

[]

1

0

1

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

[ 3034, 4, 6 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

TonB system transport protein ExbD type-1

TonB_ExbD_1

3

IPR014171

14,171

TonB system transport protein ExbD type-2

TonB_ExbD_2

Family

545

false

Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR ( ). Members are always encoded next to a protein designated ExbB ( ), which is related to the TolQ ( ). ExbD and ExbB together form a proton channel through which they can harness the proton-motiv...

[ "GO:0055085", "GO:0016020" ]

[ "transmembrane transport", "membrane" ]

[ "biological_process", "cellular_component" ]

2

[ "NCBIFAM" ]

[ "TIGR02804" ]

[ "ExbD_2" ]

[ 545 ]

1

[ "GP", "GP" ]

[ "GenProp0543", "GenProp1157" ]

[ "GP:GenProp0543", "GP:GenProp1157" ]

2

[]

0

[]

0

[ "IPR003400" ]

[]

1

0

1

[ "Pseudomonadati", "ecological metagenomes" ]

[ 542, 3 ]

2

[]

0

true

Family

TonB system transport protein ExbD type-2

TonB_ExbD_2

1

IPR014172

14,172

TonB-system energizer ExbB type-2

TonB_ExbB_2

Family

911

false

Members of this protein family appear to be the ExbB protein of an ExbBD proton-transporting membrane complex that, by means of TonB, energizes transport by TonB-dependent receptors. Note that this family represents one of at least two distinct groups TolQ homologues designated ExbB - see also . Each group associates w...

[ "GO:0055085", "GO:0016020" ]

[ "transmembrane transport", "membrane" ]

[ "biological_process", "cellular_component" ]

2

[ "NCBIFAM" ]

[ "TIGR02805" ]

[ "exbB2" ]

[ 911 ]

1

[ "GP", "GP" ]

[ "GenProp0543", "GenProp1157" ]

[ "GP:GenProp0543", "GP:GenProp1157" ]

2

[]

0

[]

0

[]

0

null

[ "Bacteria", "Cyprideis torosa", "ecological metagenomes" ]

[ 893, 1, 17 ]

3

[]

0

true

Family

TonB-system energizer ExbB type-2

TonB_ExbB_2

7

IPR014173

14,173

Peptidase C11, Clostripain Clostridium species

Pept_C11_CLOspp

Family

83

false

Clostripain is a cysteine protease characterised from Clostridium histolyticum, and also known from Clostridium perfringens. It is a heterodimer processed from a single precursor polypeptide, using a specific Arg-|-Xaa cleavage. The older term alpha-clostripain refers to the most active, most reduced form, rather than ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02806" ]

[ "clostrip" ]

[ 83 ]

1

[]

0

[ "9cip" ]

1

[ "PUB00011704", "PUB00020025", "PUB00030423", "PUB00076953" ]

[ "11517925", "9891971", "14725770", "7044372" ]

[ "Evolutionary lines of cysteine peptidases.", "Identification of the active site of legumain links it to caspases, clostripain and gingipains in a new clan of cysteine endopeptidases.", "The structure of sortase B, a cysteine transpeptidase that tethers surface protein to the Staphylococcus aureus cell wall.", ...

[ 2001, 1998, 2004, 1982 ]

4

[ "IPR005077" ]

[]

1

0

1

[ "Clostridia" ]

[ 83 ]

1

[]

0

true

Family

Peptidase C11, Clostripain Clostridium species

Pept_C11_CLOspp

5

IPR014174

14,174

CRISPR-associated protein Cas6/Cmx6

CRISPR-assoc_prot_Cas6/Cmx6

Family

373

false

Members of this entry are designated type I-MYXAN CRISPR-associated protein Cas6/Cmx6 and resemble the Cas6 proteins described by in having a C-terminal motif GXGXXXXXGXG, where the single X of each GXG is hydrophobic and the spacer XXXXX has at least one Lys or Arg. Examples are found in cas gene operons of CRISPR reg...

[]

0

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

[ "PF09559", "TIGR02807", "cd09703" ]

[ "Cas6", "cas6_cmx6", "Cas6-I-III" ]

[ 373, 336, 30 ]

3

[ "GP" ]

[ "GenProp0922" ]

[ "GP:GenProp0922" ]

1

[ "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", "ecological metagenomes" ]

[ 343, 30 ]

2

[]

0

true

Family

CRISPR-associated protein Cas6/Cmx6

CRISPR-assoc_prot_Cas6/Cmx6

7

IPR014175

14,175

Conserved hypothetical protein CHP02808

CHP02808

Family

290

false

This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09574", "TIGR02808" ]

[ "DUF2374", "short_TIGR02808" ]

[ 290, 286 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria" ]

[ 290 ]

1

[]

0

true

Family

Conserved hypothetical protein CHP02808

CHP02808

3

IPR014176

14,176

Phasin, subfamily 3

Phasin_subfam-3

Family

586

false

Phasins (or granule-associate proteins) are surface proteins found covering Polyhydroxyalkanoate (PHA) storage granules in bacteria. Polyhydroxyalkanoates are linear polyesters produced by bacterial fermentation of sugar or lipids for the purpose of storing carbon and energy, and are accumulated as intracellular granul...

[]

0

[ "PIRSF", "NCBIFAM" ]

[ "PIRSF028226", "TIGR02809" ]

[ "Phasin_3", "phasin_3" ]

[ 132, 586 ]

2

[ "GP" ]

[ "GenProp0055" ]

[ "GP:GenProp0055" ]

1

[ "5ip0" ]

1

[ "PUB00045301", "PUB00045302", "PUB00045303" ]

[ "17965215", "18223073", "15256572" ]

[ "Effects of granule-associated protein PhaP on glycerol-dependent growth and polymer production in poly(3-hydroxybutyrate)-producing Escherichia coli.", "Binding of the major phasin, PhaP1, from Ralstonia eutropha H16 to poly(3-hydroxybutyrate) granules.", "The complex structure of polyhydroxybutyrate (PHB) gra...

[ 2007, 2008, 2004 ]

3

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 584, 2 ]

2

[]

0

true

Family

Phasin, subfamily 3

Phasin_subfam-3

4

IPR014177

14,177

Putative formate dehydrogenase, TAT signal-containing

Formate_DH_TAT-contain

Family

1,433

false

Members of this uncharacterised protein family are all small, extending 70 or fewer residues from their respective likely start codon. All have the twin-arginine-dependent transport (TAT) signal sequence at the N terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[...

[]

0

[ "PIRSF", "NCBIFAM" ]

[ "PIRSF036704", "TIGR02811" ]

[ "UCP036704", "formate_TAT" ]

[ 1291, 1035 ]

2

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 1423, 10 ]

2

[]

0

true

Family

Putative formate dehydrogenase, TAT signal-containing

Formate_DH_TAT-contain

2

IPR014178

14,178

Fatty acid response transcription factor FadR

FA-response_TF_FadR

Family

2,048

false

Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gamma proteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-te...

[ "GO:0000062", "GO:0003677", "GO:0003700", "GO:0019217" ]

[ "fatty-acyl-CoA binding", "DNA binding", "DNA-binding transcription factor activity", "regulation of fatty acid metabolic process" ]

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

4

[ "HAMAP", "NCBIFAM" ]

[ "MF_00696", "TIGR02812" ]

[ "HTH_FadR", "fadR_gamma" ]

[ 2016, 2048 ]

2

[]

0

[ "1e2x", "1h9g", "1h9t", "1hw1", "1hw2", "4p96", "4p9u", "4pdk", "5dv5", "5xgf", "8y3z", "8y41", "9wfi" ]

13

[]

0

[]

0

null

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

[ 2044, 2, 2 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Fatty acid response transcription factor FadR

FA-response_TF_FadR

4

IPR014179

14,179

PfaD-like, TIM-barrel domain

PfaD-like_TIM-barrel

Domain

1,716

false

The protein PfaD is part of a four-gene locus, similar to polyketide biosynthesis systems, which is responsible for omega-3 polyunsaturated fatty acid biosynthesis in several high pressure and/or cold-adapted bacteria. Several other members of the entry are found in loci presumed to act in polyketide biosynthesis per s...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02814", "cd04742" ]

[ "pfaD_fam", "NPD_FabD" ]

[ 1716, 1118 ]

2

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

[ "2.3.1.39", "PWY-4381", "PWY-6799", "PWY-8012", "PWY-8047", "PWY-8049", "PWY-8438" ]

[ "EC:2.3.1.39", "METACYC:PWY-4381", "METACYC:PWY-6799", "METACYC:PWY-8012", "METACYC:PWY-8047", "METACYC:PWY-8049", "METACYC:PWY-8438" ]

7

[ "4cw5", "4yx6", "4z38", "4z9r", "6lkc" ]

5

[ "PUB00097880", "PUB00097881", "PUB00097936", "PUB00101897" ]

[ "20853892", "17234808", "16707694", "27527703" ]

[ "Induced biosynthesis of cryptic polyketide metabolites in a Burkholderia thailandensis quorum sensing mutant.", "The identification of bacillaene, the product of the PksX megacomplex in Bacillus subtilis.", "Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amylo...

[ 2010, 2007, 2006, 2016 ]

4

[]

0

null

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

[ 1676, 31, 9 ]

3

[]

0

true

Domain

PfaD-like, TIM-barrel domain

PfaD-like_TIM-barrel

7

IPR014180

14,180

Sugar isomerase, AgaS

Sugar_isomerase_AgaS

Family

686

false

Some members of this protein family are found in genic regions associated with N-acetyl-galactosamine and galactosamine utilisation and are suggested to be isomerases [ ]. Proteins in this entry include Escherichia coli AgaS, which is suggested to be a Gam-6-P deaminase/isomerase in the Aga/Gam pathway [ ].

[ "GO:0016853" ]

[ "isomerase activity" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR02815" ]

[ "agaS_fam" ]

[ 686 ]

1

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

[ "3.5.99.-", "PWY-2942", "PWY-7006", "PWY-7077", "PWY-7357", "PWY-7395", "PWY-7512", "PWY-7621", "PWY-7770", "PWY-8037" ]

[ "EC:3.5.99.-", "METACYC:PWY-2942", "METACYC:PWY-7006", "METACYC:PWY-7077", "METACYC:PWY-7357", "METACYC:PWY-7395", "METACYC:PWY-7512", "METACYC:PWY-7621", "METACYC:PWY-7770", "METACYC:PWY-8037" ]

10

[ "3c3j" ]

1

[ "PUB00014682", "PUB00086892" ]

[ "10931310", "23634833" ]

[ "Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli.", "Genetic analysis of the roles of agaA, agaI, and agaS genes in the N-acetyl-D-galactosamine and D-galactosamine catabolic pathways in Escherichia coli strains O157:H7 and C." ]

[ 2000, 2013 ]

2

[]

0

null

[ "Bacteria", "invertebrate metagenome" ]

[ 685, 1 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Sugar isomerase, AgaS

Sugar_isomerase_AgaS

3

IPR014181

14,181

Omega-3 polyunsaturated fatty acid synthase-like

Omega3_polyunsat_FA_synth-like

Domain

381

false

This entry represents a group of proteins based on a PfaB protein family. The protein PfaB family is part of a four-gene locus, which is similar to polyketide biosynthesis systems, responsible for omega-3 polyunsaturated fatty acid biosynthesis in several high pressure and/or cold-adapted bacteria. The fairly permissiv...

[]

0

[ "NCBIFAM" ]

[ "TIGR02816" ]

[ "pfaB_fam" ]

[ 381 ]

1

[]

0

[]

0

[]

0

[ "IPR014043" ]

[]

1

0

1

[ "Bacteria", "hydrothermal vent metagenome" ]

[ 380, 1 ]

2

[]

0

true

Domain

Omega-3 polyunsaturated fatty acid synthase-like

Omega3_polyunsat_FA_synth-like

4

IPR014182

14,182

Alcohol dehydrogenase, zinc-binding type 1

ADH_Zn_typ-1

Family

8,210

false

Members of this entry form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases. Some current members of this entry carry designations as putative alginate lyase, however none have been characterised as such.

[ "GO:0008270" ]

[ "zinc ion binding" ]

[ "molecular_function" ]

1

[ "NCBIFAM", "CDD" ]

[ "TIGR02817", "cd08252" ]

[ "adh_fam_1", "AL_MDR" ]

[ 7829, 8168 ]

2

[]

0

[ "3fbg", "4dvj" ]

2

[]

0

[]

0

null

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

[ 7709, 471, 30 ]

3

[]

0

true

Family

Alcohol dehydrogenase, zinc-binding type 1

ADH_Zn_typ-1

3

IPR014183

14,183

Alcohol dehydrogenase class III

ADH_3

Family

14,598

false

Class III alcohol dehydrogenases (ADH3) ( ) tend to show poor activity for ethanol among their various substrate alcohols. They catalyze the oxidation and reduction of a wide variety of substrates that include S-(hydroxymethyl)glutathione (HMGSH), S-nitrosoglutathione, and long chain primary alcohols and aldehydes [ ]....

[ "GO:0008270", "GO:0051903", "GO:0046294" ]

[ "zinc ion binding", "S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity", "formaldehyde catabolic process" ]

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

3

[ "NCBIFAM", "CDD" ]

[ "TIGR02818", "cd08300" ]

[ "adh_III_F_hyde", "alcohol_DH_class_III" ]

[ 14245, 14494 ]

2

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

[ "1.1.1.-", "1.1.1.1", "1.1.1.284", "GenProp0562", "GenProp1292", "GenProp1328", "GenProp1334", "GenProp1467", "GenProp1655", "GenProp1698", "PWY-1121", "PWY-1186", "PWY-1801", "PWY-2541", "PWY-2601", "PWY-3162", "PWY-321", "PWY-3261", "PWY-3722", "PWY-5057", "PWY-5076", "PW...

[ "EC:1.1.1.-", "EC:1.1.1.1", "EC:1.1.1.284", "GP:GenProp0562", "GP:GenProp1292", "GP:GenProp1328", "GP:GenProp1334", "GP:GenProp1467", "GP:GenProp1655", "GP:GenProp1698", "METACYC:PWY-1121", "METACYC:PWY-1186", "METACYC:PWY-1801", "METACYC:PWY-2541", "METACYC:PWY-2601", "METACYC:PWY-316...

193

[ "1m6h", "1m6w", "1ma0", "1mc5", "1mp0", "1teh", "2fze", "2fzw", "3qj5", "3uko", "4dl9", "4dla", "4dlb", "4gl4", "4jji", "4l0q", "7aas", "7aau", "7av7", "8co4", "8gv3" ]

21

[ "PUB00027294", "PUB00080657", "PUB00080658", "PUB00080659" ]

[ "12484756", "1872853", "9059641", "7484406" ]

[ "Human glutathione-dependent formaldehyde dehydrogenase. Structural changes associated with ternary complex formation.", "Human liver class III alcohol and glutathione dependent formaldehyde dehydrogenase are the same enzyme.", "Expression of formaldehyde dehydrogenase and S-formylglutathione hydrolase activiti...

[ 2002, 1991, 1997, 1995 ]

4

[]

0

null

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

[ 9842, 4697, 59 ]

3

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

[ 4, 1, 1, 1, 1, 5, 2, 1, 1, 4, 1, 2, 6 ]

13

true

Family

Alcohol dehydrogenase class III

ADH_3

8

IPR014184

14,184

Formaldehyde dehydrogenase, glutathione-independent

HCHO_DH_non_GSH

Family

3,016

false

Members of this entry represent a distinct clade within the larger family of zinc-dependent dehydrogenases of medium chain alcohols. This entry includes the so-called glutathione-dependent formaldehyde dehydrogenase. Members of this entry have a tightly bound NAD that can act as a true cofactor, rather than a co-substr...

[ "GO:0016491" ]

[ "oxidoreductase activity" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR02819" ]

[ "fdhA_non_GSH" ]

[ 3016 ]

1

[ "EC", "METACYC" ]

[ "1.2.1.46", "PWY-7616" ]

[ "EC:1.2.1.46", "METACYC:PWY-7616" ]

2

[ "1kol", "4jlw" ]

2

[]

0

[]

0

null

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

[ 2995, 17, 4 ]

3

[]

0

true

Family

Formaldehyde dehydrogenase, glutathione-independent

HCHO_DH_non_GSH

9

IPR014185

14,185

Glutathione-dependent formaldehyde-activating enzyme

Formald_GSH

Family

1,713

false

This entry represents glutathione-dependent formaldehyde-activating enzyme, also known as S-(hydroxymethyl)glutathione synthase, an enzyme that converts glutathione and formaldehyde into S-(hydroxymethyl)glutathione. The reaction of glutathione and formaldehyde to form S-(hydroxymethyl)glutathione occurs naturally, but...

[ "GO:0008270", "GO:0051907", "GO:0046294" ]

[ "zinc ion binding", "S-(hydroxymethyl)glutathione synthase activity", "formaldehyde catabolic process" ]

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

3

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

[ "MF_00723", "PIRSF033318", "TIGR02820" ]

[ "Formald_GSH", "Formald_GSH", "formald_GSH" ]

[ 1695, 1619, 1713 ]

3

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

[ "4.4.1.22", "GenProp0562", "PWY-1801" ]

[ "EC:4.4.1.22", "GP:GenProp0562", "METACYC:PWY-1801" ]

3

[ "1x6m", "1xa8" ]

2

[ "PUB00034559" ]

[ "11741920" ]

[ "A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two-dimensional proton exchange NMR spectroscopy." ]

[ 2002 ]

1

[]

0

null

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

[ 1101, 610, 2 ]

3

[]

0

true

Family

Glutathione-dependent formaldehyde-activating enzyme

Formald_GSH

3

IPR014186

14,186

S-formylglutathione hydrolase

S-formylglutathione_hydrol

Family

14,508

false

This entry describes proteins from bacteria, yeast, and human, with a conserved critical role in formaldehyde detoxification as S-formylglutathione hydrolase ( ). Eukaryotic members, particularly the human protein, are better known as esterase D ( ), an enzyme with broad specificity, although S-formylglutathione hydrol...

[ "GO:0018738", "GO:0046294" ]

[ "S-formylglutathione hydrolase activity", "formaldehyde catabolic process" ]

[ "molecular_function", "biological_process" ]

2

[ "PANTHER", "NCBIFAM" ]

[ "PTHR10061", "TIGR02821" ]

[ "", "fghA_ester_D" ]

[ 14412, 13299 ]

2

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

[ "3.1.2.12", "GenProp0562", "GenProp1578", "PWY-1801", "R-BTA-156590", "R-HSA-156590", "R-MMU-156590", "R-RNO-156590", "R-SCE-156590", "R-SSC-156590" ]

[ "EC:3.1.2.12", "GP:GenProp0562", "GP:GenProp1578", "METACYC:PWY-1801", "REACTOME:R-BTA-156590", "REACTOME:R-HSA-156590", "REACTOME:R-MMU-156590", "REACTOME:R-RNO-156590", "REACTOME:R-SCE-156590", "REACTOME:R-SSC-156590" ]

10

[ "1pv1", "3c6b", "3e4d", "3fcx", "3i6y", "3ls2", "3s8y", "4b6g", "4flm", "4fol", "6jzl", "6vh9", "6vhd", "6vhe", "6wcx", "7l0a", "7yvt", "8ilj" ]

18

[]

0

[ "IPR000801" ]

[]

1

0

1

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

[ 47, 9786, 4602, 73 ]

4

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

[ 3, 1, 1, 3, 2, 5, 8, 1, 5, 8, 1, 12 ]

12

true

Family

S-formylglutathione hydrolase

S-formylglutathione_hydrol

2

IPR014187

14,187

Alcohol dehydrogenase, zinc-binding type 2

ADH_Zn_typ-2

Family

3,959

false

Members of this entry form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases. The gene neighbourhood of members of this family is not conserved and it appears that no members are characterised. Sequence alignments reveal 6 invariant ...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02822", "cd08298" ]

[ "adh_fam_2", "CAD2" ]

[ 3809, 3786 ]

2

[]

0

[]

0

[]

0

[]

0

null

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

[ 54, 3867, 13, 25 ]

4

[]

0

true

Family

Alcohol dehydrogenase, zinc-binding type 2

ADH_Zn_typ-2

3

IPR014188

14,188

Acrylyl-CoA reductase AcuI

Acrylyl-CoA_reductase_AcuI

Family

10,202

false

This entry represents acrylyl-CoA reductase AcuI, a subfamily of zinc-containing alcohol dehydrogenase. Acrylyl-CoA reductase AcuI catalyses the NADPH-dependent reduction of acrylyl-CoA to propanoyl-CoA [ , , ]. This entry also includes quinone oxidoreductase, YhdH from Escherichia coli [ ] and YhfP from Bacillus subti...

[]

0

[ "NCBIFAM" ]

[ "TIGR02823" ]

[ "oxido_YhdH" ]

[ 10202 ]

1

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

[ "1.3.1.84", "PWY-5743", "PWY-5744", "PWY-5789", "PWY-8180" ]

[ "EC:1.3.1.84", "METACYC:PWY-5743", "METACYC:PWY-5744", "METACYC:PWY-5789", "METACYC:PWY-8180" ]

5

[ "1o89", "1o8c", "1tt7", "1xa0", "1y9e", "3nx4", "4jxk", "5gxe", "5gxf" ]

9

[ "PUB00029345", "PUB00070193", "PUB00106218", "PUB00106911" ]

[ "15388933", "22563425", "19429610", "22056933" ]

[ "Structure of Escherichia coli YhdH, a putative quinone oxidoreductase.", "The Ruegeria pomeroyi acuI gene has a role in DMSP catabolism and resembles yhdH of E. coli and other bacteria in conferring resistance to acrylate.", "3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes ...

[ 2004, 2012, 2009, 2012 ]

4

[]

0

null

[ "Bacteria", "Eukaryota", "candidate division MSBL1 archaeon SCGC-AAA382M17", "unclassified sequences" ]

[ 10056, 54, 1, 91 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Acrylyl-CoA reductase AcuI

Acrylyl-CoA_reductase_AcuI

1

IPR014189

14,189

Quinone oxidoreductase PIG3

Quinone_OxRdtase_PIG3

Family

16,642

false

Members of this family include putative quinone oxidoreductases that belong to the broader superfamily of zinc-dependent alcohol (of medium chain length) dehydrogenases. A member of this family is human quinone oxidoreductase PIG3, which is induced by p53 and may be involved in the generation of reactive oxygen species...

[]

0

[ "NCBIFAM", "CDD" ]

[ "TIGR02824", "cd05276" ]

[ "quinone_pig3", "p53_inducible_oxidoreductase" ]

[ 16225, 16495 ]

2

[ "REACTOME" ]

[ "R-HSA-6803205" ]

[ "REACTOME:R-HSA-6803205" ]

1

[ "2j8z", "2oby", "4dup" ]

3

[ "PUB00047827" ]

[ "19349281" ]

[ "Three-dimensional Structure and Enzymatic Function of Proapoptotic Human p53-inducible Quinone Oxidoreductase PIG3." ]

[ 2009 ]

1

[]

0

null

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

[ 12886, 3542, 66, 148 ]

4

[ "Arabidopsis thaliana", "Danio rerio", "Homo sapiens", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Zea mays" ]

[ 6, 6, 1, 1, 2, 8 ]

6

true

Family

Quinone oxidoreductase PIG3

Quinone_OxRdtase_PIG3

6

IPR014190

14,190

Leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase

PTGR1

Family

2,068

false

Leukotriene B4 12-hydroxydehydrogenase is an NADP-dependent enzyme of arachidonic acid metabolism, responsible for converting leukotriene B4 to the much less active metabolite 12-oxo-leukotriene B4. The BRENDA database lists leukotriene B4 12-hydroxydehydrogenase as one of the synonyms of 2-alkenal reductase ( ), while...

[ "GO:0032440", "GO:0047522", "GO:0005737" ]

[ "2-alkenal reductase [NAD(P)H] activity", "15-oxoprostaglandin 13-reductase [NAD(P)+] activity", "cytoplasm" ]

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

3

[ "NCBIFAM", "CDD" ]

[ "TIGR02825", "cd08294" ]

[ "B4_12hDH", "leukotriene_B4_DH_like" ]

[ 198, 2068 ]

2

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

[ "1.3.1.48", "1.3.1.74", "GenProp1277", "PWY-8396", "PWY-8397", "PWY-8399", "R-HSA-2142691", "R-HSA-2142700" ]

[ "EC:1.3.1.48", "EC:1.3.1.74", "GP:GenProp1277", "METACYC:PWY-8396", "METACYC:PWY-8397", "METACYC:PWY-8399", "REACTOME:R-HSA-2142691", "REACTOME:R-HSA-2142700" ]

8

[ "1v3t", "1v3u", "1v3v", "1zsv", "2dm6", "2y05", "9d6w", "9d6x", "9d6y", "9d6z", "9d71" ]

11

[]

0

[ "IPR045010" ]

[]

1

0

1

[ "Metazoa" ]

[ 2068 ]

1

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

[ 3, 2, 2, 2 ]

4

true

Family

Leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase

PTGR1

8

IPR014191

14,191

Anaerobic ribonucleoside-triphosphate reductase activator

Anaer_RNR_activator

Family

457

false

Members of this entry represent a set of proteins related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR, see ). Members of this entry are found paired with members of a similarly divergent set of anaerobic r...

[]

0

[ "NCBIFAM" ]

[ "TIGR02826" ]

[ "RNR_activ_nrdG3" ]

[ 457 ]

1

[ "GP" ]

[ "GenProp0291" ]

[ "GP:GenProp0291" ]

1

[]

0

[ "PUB00020982" ]

[ "15949864" ]

[ "Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling." ]

[ 2005 ]

1

[]

0

null

[ "Bacteria", "metagenomes", "unclassified Caudoviricetes" ]

[ 450, 5, 2 ]

3

[]

0

true

Family

Anaerobic ribonucleoside-triphosphate reductase activator

Anaer_RNR_activator

9

IPR014193

14,193

Uncharacterised domain CHP02828, putative membrane fusion protein

CHP02828_mem_fusion

Domain

23

false

Members of this entry show similarity to those in , the membrane fusion protein (MFP) cluster 2 family, which is linked to RND transport systems.

[]

0

[ "NCBIFAM" ]

[ "TIGR02828" ]

[ "" ]

[ 23 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Clostridia" ]

[ 23 ]

1

[]

0

true

Domain

Uncharacterised domain CHP02828, putative membrane fusion protein

CHP02828_mem_fusion

8

IPR014194

14,194

Sporulation stage III, protein AE

Spore_III_AE

Family

2,764

false

This entry represents the stage III sporulation protein AE, which is encoded in a spore formation operon spoIIIAABCDEFGH under the control of sigma G [ ]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09546", "TIGR02829" ]

[ "Spore_III_AE", "spore_III_AE" ]

[ 2764, 1857 ]

2

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00012907" ]

[ "12662922" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis." ]

[ 2003 ]

1

[]

0

null

[ "Bacteria", "Phytophthora kernoviae 00238/432", "metagenomes" ]

[ 2742, 1, 21 ]

3

[]

0

true

Family

Sporulation stage III, protein AE

Spore_III_AE

8

IPR014195

14,195

Stage III sporulation protein AG

SpoIIIAG

Family

1,561

false

This entry represents the stage III sporulation protein AG, which is encoded in a spore formation operon: spoIIIAABCDEFGH under the control of sigma G [ ]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02830" ]

[ "spore_III_AG" ]

[ 1561 ]

1

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[ "5wc3" ]

1

[ "PUB00012907", "PUB00162512", "PUB00162513" ]

[ "12662922", "28784753", "29288127" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis.", "Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in <i>Bacillus subtilis</i>.", "Structural characterization of SpoIIIAB sporula...

[ 2003, 2017, 2018 ]

3

[]

0

null

[ "Bacillota", "bioreactor metagenome" ]

[ 1558, 3 ]

2

[]

0

true

Family

Stage III sporulation protein AG

SpoIIIAG

5

IPR014196

14,196

Stage II sporulation protein M

SpoIIM

Family

1,791

false

This entry represents the stage II sporulation protein M, which is encoded in a spore formation operon [ ]. SpoIIM is one of the three genes (spoIID, spoIIM and spoIIP, [ , , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are...

[]

0

[ "PIRSF", "NCBIFAM" ]

[ "PIRSF038973", "TIGR02831" ]

[ "SpoIIM", "spo_II_M" ]

[ 1784, 1738 ]

2

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00012907", "PUB00034447", "PUB00034448", "PUB00034449" ]

[ "12662922", "8501064", "7836306", "3011962" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis.", "Physical and functional characterization of the Bacillus subtilis spoIIM gene.", "Identification and characterization of the Bacillus subtilis spoIIP locus.", "spoIID operon of Bacillus subtilis: cloning and se...

[ 2003, 1993, 1995, 1986 ]

4

[ "IPR002798" ]

[]

1

0

1

[ "Bacillati", "ecological metagenomes" ]

[ 1786, 5 ]

2

[]

0

true

Family

Stage II sporulation protein M

SpoIIM

4

IPR014197

14,197

Sporulation protein YunB

Sporulation_prot_YunB

Family

2,272

false

This entry represents the sporulation protein YunB. In Bacillus subtilis its expression is controlled by sigmaE. The gene yunB seems to code for a protein involved, at least indirectly, in the pathway leading to the activation of sigmaK. Inactivation of yunB delays sigmaK activation and results in reduced sporulation e...

[]

0

[ "PFAM", "PIRSF", "NCBIFAM" ]

[ "PF09560", "PIRSF021383", "TIGR02832" ]

[ "Spore_YunB", "YunB", "spo_yunB" ]

[ 2272, 1811, 2168 ]

3

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00012907" ]

[ "12662922" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis." ]

[ 2003 ]

1

[]

0

null

[ "Bacteria", "Rhizophagus irregularis", "unclassified sequences" ]

[ 2250, 2, 20 ]

3

[]

0

true

Family

Sporulation protein YunB

Sporulation_prot_YunB

1

IPR014198

14,198

Stage III sporulation protein AB

Spore_III_AB

Family

2,469

false

This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation [ ]. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming speci...

[]

0

[ "PFAM", "PIRSF", "NCBIFAM" ]

[ "PF09548", "PIRSF021435", "TIGR02833" ]

[ "Spore_III_AB", "SpoIIIAB", "spore_III_AB" ]

[ 2469, 2091, 1589 ]

3

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[ "6bs9" ]

1

[ "PUB00012907" ]

[ "12662922" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis." ]

[ 2003 ]

1

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 2457, 12 ]

2

[]

0

true

Family

Stage III sporulation protein AB

Spore_III_AB

9

IPR014199

14,199

Sporulation protein YtxC

Spore_YtxC

Family

1,842

false

This uncharacterised protein is one of a number of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and it is not found in non-endospore forming species. It is uniformly distributed in the mother cell cytoplasm in Bacillus subtili...

[]

0

[ "PFAM", "PIRSF", "NCBIFAM" ]

[ "PF08812", "PIRSF012563", "TIGR02834" ]

[ "YtxC", "YtxC", "spo_ytxC" ]

[ 1842, 364, 836 ]

3

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00012907" ]

[ "12662922" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis." ]

[ 2003 ]

1

[]

0

null

[ "Bacillus phage G", "Bacteria", "Physcomitrium patens", "metagenomes" ]

[ 1, 1830, 1, 10 ]

4

[]

0

true

Family

Sporulation protein YtxC

Spore_YtxC

2

IPR014200

14,200

RNA polymerase sigma-E type

RNA_pol_sigma-E

Family

2,257

false

Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids [ ]. The bacter...

[ "GO:0003677", "GO:0003700", "GO:0016987", "GO:0006352", "GO:0006355" ]

[ "DNA binding", "DNA-binding transcription factor activity", "sigma factor activity", "DNA-templated transcription initiation", "regulation of DNA-templated transcription" ]

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

5

[ "NCBIFAM" ]

[ "TIGR02835" ]

[ "spore_sigmaE" ]

[ 2257 ]

1

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00000061", "PUB00002181", "PUB00004340", "PUB00034411", "PUB00088319" ]

[ "3052291", "1597408", "3092189", "3104904", "25596450" ]

[ "Structure and function of bacterial sigma factors.", "The sigma 70 family: sequence conservation and evolutionary relationships.", "Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins.", "Sporulation-specific sigma factor sigma 29 of Bacillus subtilis is synthesized from...

[ 1988, 1992, 1986, 1987, 2015 ]

5

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 2247, 10 ]

2

[]

0

true

Family

RNA polymerase sigma-E type

RNA_pol_sigma-E

8

IPR014202

14,202

Sporulation stage II, protein R

Spore_II_R

Family

2,757

false

This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF09551", "TIGR02837" ]

[ "Spore_II_R", "spore_II_R" ]

[ 2757, 2243 ]

2

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00012907", "PUB00034446" ]

[ "12662922", "7892217" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis.", "Identification of a gene, spoIIR, that links the activation of sigma E to the transcriptional activity of sigma F during sporulation in Bacillus subtilis." ]

[ 2003, 1995 ]

2

[]

0

null

[ "Bacteria", "Daphniidae", "metagenomes" ]

[ 2715, 16, 26 ]

3

[]

0

true

Family

Sporulation stage II, protein R

Spore_II_R

9

IPR014203

14,203

Sporulation stage V, protein AC

Spore_V_AC

Family

2,817

false

This entry describes stage V sporulation protein AC; a paralog of stage V sporulation protein AE. Both are proteins found to be present in a species, if and only if, that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans...

[]

0

[ "NCBIFAM" ]

[ "TIGR02838" ]

[ "spore_V_AC" ]

[ 2817 ]

1

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[]

0

[ "IPR005562" ]

[]

1

0

1

[ "Bacteria", "metagenomes" ]

[ 2799, 18 ]

2

[]

0

true

Family

Sporulation stage V, protein AC

Spore_V_AC

1

IPR014204

14,204

Sporulation stage V, protein AE

Spore_V_AE

Family

2,841

false

This entry describes stage V sporulation protein AE; a paralog of stage V sporulation protein AC. Both are proteins found to be present in a species, if and only if, that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans...

[]

0

[ "NCBIFAM" ]

[ "TIGR02839" ]

[ "spore_V_AE" ]

[ 2841 ]

1

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[]

0

[ "IPR005562" ]

[]

1

0

1

[ "Bacteria", "Phytophthora kernoviae 00238/432", "metagenomes" ]

[ 2820, 1, 20 ]

3

[]

0

true

Family

Sporulation stage V, protein AE

Spore_V_AE

2

IPR014205

14,205

Sporulation protein YtaF

Spore_YtaF

Family

1,814

false

This entry represents YtaF, which represents a protein family identified, at the time of the publication of the Carboxydothermus hydrogenoformans genome [ ]. The phylogenetic profile of the members matches the subset of the Firmicutes capable of forming endospores. These species include Bacillus anthracis, Clostridium ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02840" ]

[ "spore_YtaF" ]

[ 1814 ]

1

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00034421" ]

[ "16311624" ]

[ "Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901." ]

[ 2005 ]

1

[ "IPR003810" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 1807, 7 ]

2

[]

0

true

Family

Sporulation protein YtaF

Spore_YtaF

5

IPR014206

14,206

Cytochrome o ubiquinol oxidase, subunit III

Cyt_c_ubiqinol_oxidase_su3

Family

6,100

false

This entry represents subunit 3 (CyoC) of the cytochrome o terminal oxidase complex, which is a component of the aerobic respiratory chain that reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidas...

[ "GO:0009486", "GO:0019646" ]

[ "cytochrome bo3 ubiquinol oxidase activity", "aerobic electron transport chain" ]

[ "molecular_function", "biological_process" ]

2

[ "NCBIFAM" ]

[ "TIGR02842" ]

[ "CyoC" ]

[ 6100 ]

1

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

[ "GenProp0618", "GenProp1164", "GenProp1256", "GenProp1367", "GenProp1401", "GenProp1493", "GenProp1563", "GenProp1641", "GenProp1751" ]

[ "GP:GenProp0618", "GP:GenProp1164", "GP:GenProp1256", "GP:GenProp1367", "GP:GenProp1401", "GP:GenProp1493", "GP:GenProp1563", "GP:GenProp1641", "GP:GenProp1751" ]

9

[ "1fft", "6wti", "7cub", "7cuq", "7cuw", "7n9z", "7xmc", "7xmd", "8f68", "8f6c", "8go3", "8qqk" ]

12

[]

0

[ "IPR024791" ]

[]

1

0

1

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

[ 6082, 5, 13 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Cytochrome o ubiquinol oxidase, subunit III

Cyt_c_ubiqinol_oxidase_su3

7

IPR014208

14,208

Sporulation stage III, transcriptional regulator SpoIIID

Spore_III_D

Family

2,572

false

Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [ ].

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF12116", "TIGR02844" ]

[ "SpoIIID", "spore_III_D" ]

[ 2572, 2149 ]

2

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[ "2l0k" ]

1

[ "PUB00012907" ]

[ "12662922" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis." ]

[ 2003 ]

1

[]

0

null

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

[ 2529, 2, 8, 33 ]

4

[]

0

true

Family

Sporulation stage III, transcriptional regulator SpoIIID

Spore_III_D

6

IPR014209

14,209

RNA polymerase sigma-K type

RNA_pol_sigma-K

Family

1,685

false

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with th...

[ "GO:0003677", "GO:0003700", "GO:0016987", "GO:0006352", "GO:0006355" ]

[ "DNA binding", "DNA-binding transcription factor activity", "sigma factor activity", "DNA-templated transcription initiation", "regulation of DNA-templated transcription" ]

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

5

[ "NCBIFAM" ]

[ "TIGR02846" ]

[ "spore_sigmaK" ]

[ 1685 ]

1

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00000061", "PUB00002181", "PUB00004340", "PUB00034451", "PUB00088319" ]

[ "3052291", "1597408", "3092189", "2163341", "25596450" ]

[ "Structure and function of bacterial sigma factors.", "The sigma 70 family: sequence conservation and evolutionary relationships.", "Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins.", "The Bacillus subtilis gene for the development transcription factor sigma K is gene...

[ 1988, 1992, 1986, 1990, 2015 ]

5

[]

0

null

[ "Bacillati", "Phytophthora kernoviae 00238/432", "ecological metagenomes" ]

[ 1677, 1, 7 ]

3

[]

0

true

Family

RNA polymerase sigma-K type

RNA_pol_sigma-K

9

IPR014210

14,210

Cytochrome o ubiquinol oxidase subunit IV

Cyt_o_ubiqinol_oxidase_su4

Family

6,256

false

This entry represents subunit 4 (CyoD) of cytochrome o terminal oxidase complex, which is a component of the aerobic respiratory chain that reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase co...

[ "GO:0009486", "GO:0015990", "GO:0016020" ]

[ "cytochrome bo3 ubiquinol oxidase activity", "electron transport coupled proton transport", "membrane" ]

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

3

[ "NCBIFAM" ]

[ "TIGR02847" ]

[ "CyoD" ]

[ 6256 ]

1

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

[ "GenProp0618", "GenProp1164", "GenProp1256", "GenProp1367", "GenProp1401", "GenProp1493", "GenProp1563", "GenProp1641", "GenProp1751" ]

[ "GP:GenProp0618", "GP:GenProp1164", "GP:GenProp1256", "GP:GenProp1367", "GP:GenProp1401", "GP:GenProp1493", "GP:GenProp1563", "GP:GenProp1641", "GP:GenProp1751" ]

9

[ "6wti", "7cub", "7cuq", "7cuw", "7n9z", "7xmc", "7xmd", "8f68", "8f6c", "8go3", "8qqk" ]

11

[]

0

[ "IPR005171" ]

[]

1

0

1

[ "Bacteria", "Fungi", "unclassified sequences" ]

[ 6233, 4, 19 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Cytochrome o ubiquinol oxidase subunit IV

Cyt_o_ubiqinol_oxidase_su4

4

IPR014211

14,211

Stage III sporulation protein AD

Spore_III_AD

Family

1,851

false

Members of this entry represent the uncharacterised protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. The operon is regulated by sigmaG [ ]. Note that the start sites of members of this family as annotated tend to be variable; ...

[]

0

[ "NCBIFAM" ]

[ "TIGR02849" ]

[ "spore_III_AD" ]

[ 1851 ]

1

[ "GP" ]

[ "GenProp0610" ]

[ "GP:GenProp0610" ]

1

[]

0

[ "PUB00012907" ]

[ "12662922" ]

[ "The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis." ]

[ 2003 ]

1

[ "IPR025664" ]

[]

1

0

1

[ "Bacillota", "ecological metagenomes" ]

[ 1841, 10 ]

2

[]

0

true

Family

Stage III sporulation protein AD

Spore_III_AD

8