SII-SWORD/CoKE huggingface dataset:
MobP3 relaxase (MobP3)
Type: Family

This entry represents a group of proteins mainly from firmicutes that belong to the MobP3 family of relaxases .
Exoglucanase CbhB (Exoglucan_CbhB)
Type: Family

This entry represents exoglucanase CbhB from Cellulomonas, which has low but detectable endoglucanase activity and it is the second exo-cellobiohydrolase found in this organism .
FGLLP motif-containing membrane domain (Cola_memb_dom)
Type: Domain

This entry represents the FGLLP motif-containing C-terminal hydrophobic domain on a group of bacterial uncharacterised proteins of about 700 amino acids in length.
Iron-sulfur cluster repair protein DnrN (FeS_repair_DnrN)
Type: Family

This entry includes the iron-sulfur cluster repair protein DnrN from Neisseria sp. . DnrN is a di-iron-containing protein involved in the repair of iron-sulfur clusters damaged by oxidative and nitrosative stress conditions. It is required to repair damage caused by nitric oxide to FNR and NsrR transcription factors.
Sigma-54 dependent transcriptional regulator PrdR-like (PrdR-like)
Type: Family

This entry represents the sigma-54 dependent transcriptional regulator PrdR and related proteins found in firmicutes. Members of this family are multidomain proteins containing (

), (

), (

) and (

).
YgjJ-like (YgjJ-like)
Type: Family

This entry represents a group of uncharacterised proteins from gammaproteobacteria, including YgjJ from Escherichia coli K-12. Its function is unknown.
CBO2463/CBO2479 domain (CBO2463_dom)
Type: Domain

This domain occurs in proteins encoded typically between known subunits of the selenocysteine-containing D-proline reductase complex, a key contributor to Stickland metabolism. In Stickland metabolism, amino acids proline or glycine, or other compounds such as betaine or sarcosine, can be reduced, enabling energy-generating oxidation of various substrates such as other amino acids. Some members of this protein family have two copies of this domain .
Ferredoxin, 2Fe-2S, Clostridium-type (Fdxn_Clost-type)
Type: Family

This is a small family of proteins mainly from Clostridia, including Ferredoxin, 2Fe-2S (2FeCpFd) from Clostridium pasteurianum (

) and similar sequences . 2FeCpFd interacts with the nitrogenase MoFe protein, which suggests that it might be involved in nitrogen fixation .
SA1362/YqhP-like (SA1362/YqhP-like)
Type: Family

Members of this family include SA1362 from Staphylococcus aureus (

) and the uncharacterised protein YqhP from Bacillus subtilis (

). The N-terminal 50 amino acid residues of these proteins are highly hydrophobic suggesting the presence of two transmembrane α-helical regions. The C-terminal region is rich in basic residues, variable in number, and often repetitive. The members of this family are found in Gram-positive bacteria.
Ferredoxin 2Fe-2S, Azotobacter-type (Fdxn_Azotob-type)
Type: Family

This small entry represents Ferredoxin 2Fe-2s from Azotobacter vinelandii (also known as 2FeAvFdI) and similar proteins . It is homologous to 2FeCpFd (

) from Clostridium pasteurianum. The occurrence of 2FeAvFdI-encoding gene in the nif gene cluster, and the interaction between the 2FeCpFd and the nitrogenase MoFe protein, suggest that both proteins might be involved in nitrogen fixation, with possibly similar roles.
Iron oxidase (Feoxidase_Iro)
Type: Family

This family includes iron oxidase from Acidithiobacillus ferrooxidans (

) and similar proteins restricted to acidithiobacillus. It catalyses the oxidation of Fe2 to Fe3 coupled to cytochrome c552 reduction.
Flagellum-secreted protein A (FspA)
Type: Family

This entry represents FspA family. FspA-like proteins are a group of flagellum-secreted proteins from Campylobacter .
Type II secretion system protein GspC-like, Synergistales (T2SS_C_SYNERG)
Type: Family

This entry represents the GspC subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homologue of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain.
Type II secretion system protein GspL-like, Synergistales (T2SS_GspL_synerg)
Type: Family

This entry describes the GspL subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homologue of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain.
Type II secretion system protein GspM-like, Synergistales (T2SS_GspM_synerg)
Type: Family

This family describes the GspM subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homologue of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain.
Type II secretion system protein GspN-like, Synergistales (T2SS_GspN_synerg)
Type: Family

This entry represents the GspN subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homologue of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain.
Anti-phage protein KwaA (KwaA)
Type: Family

This entry represents the anti-phage protein KwaA, a component of the antiviral defense system Kiwa, which is composed of KwaA and KwaB. Its expression in E.coli (strain MG1655) confers resistance to phages lambda and SECphi18 .
Anti-phage protein KwaB (KwaB)
Type: Family

This family includes Kiwa protein KwaB from E.coli, a component of antiviral defense system Kiwa, composed of KwaA and KwaB. The expression of Kiwa in E.coli (strain MG1655) confers resistance to phages lambda and SECphi18 .
Site-specific integrase-like (Integrase-like)
Type: Family

This entry represents a group of uncharacterised proteins from proteobacteria. Members of this entry contain an integrase catalytic domain

.
Tannase subtype A (Tannase_A)
Type: Family

This entry represents tannin acyl hydrolases subtype A found in bacteria and archaea.

Tannin acyl hydrolases, also known as tannases, are critical for the transformation of tannins. Tannases catalyse the hydrolysis of ester and peptide bonds in varied substrates like gallotannins, gallic acid esters, epigallocatechin gallate, and epicatechin gallate leading to the release of gallic acid and glucose. The amino acid sequence analysis of bacterial, yeast, and fungal tannases showed that although the enzymes display rather divergent sequences, they share a common pentapeptide active site motif of Gly-X-Ser-X-Gly, a typical feature of the classical serine hydrolases .
O-unit flippase WZX-like (WZX-like)
Type: Family

This entry represents a group of bacterial proteins, including O-unit flippase-like protein from Yersinia pseudotuberculosis (Wzx,

) .
Na(+),Li(+),K(+)/H(+) antiporter subunit UmpB (NaLiK_antip_UmpB)
Type: Family

This entry includes Na(+), Li(+), K(+)/H(+) antiporter subunit B from Halomonas zhaodongensis (

), which is part of a two-component antiporter that catalyses the efflux of Na , Li and K in exchange for external protons. It shows a preference for Na , followed by K and Li .
Tannase subtype B (Tannase_B)
Type: Family

This entry represents tannin acyl hydrolases subtype B found in bacteria.

Tannin acyl hydrolases, also known as tannases, are critical for the transformation of tannins. Tannases catalyse the hydrolysis of ester and peptide bonds in varied substrates like gallotannins, gallic acid esters, epigallocatechin gallate, and epicatechin gallate leading to the release of gallic acid and glucose. The amino acid sequence analysis of bacterial, yeast, and fungal tannases showed that although the enzymes display rather divergent sequences, they share a common pentapeptide active site motif of Gly-X-Ser-X-Gly, a typical feature of the classical serine hydrolases .
Cyclic-di-AMP-binding protein CbpB (CBS_CbpB)
Type: Family

This entry includes CbpB (c-di-AMP-binding protein B) from bacteria which has two CBS (cystathionine beta synthase) domains. When levels of c-di-AMP are low, CbpB activates RelA, a bifunctional (p)ppGpp synthetase/hydrolase .
Toxin VasX (Toxin_VasX)
Type: Family

This entry represents toxinVasX (

) and related proteins that are found in proteobacteria. VasX is secreted by the type VI (T6SS) secretion system that acts on prokaryotic target cells. This toxin acts in conjunction with VasW, an accessory protein to VasX, to compromise the inner membrane of prokaryotic target cells .

Type VI protein secretion system (T6SS) is important for bacterial competition through contact-dependent killing of competitors. T6SS delivers effectors to neighboring cells and corresponding antagonistic proteins confer immunity against effectors that are delivered by sister cells. T6SS assembles as a molecular syringe that injects toxic protein effectors into cells .
Bacteriocin 51 precursor BacA (BacA)
Type: Family

This entry represents the bacteriocin 51 precursor protein BacA described in Enterococcus. Bacteriocin proteins are synthesised by diverse types of Gram-positive and Gram-negative bacteria. These proteins possess the ability to hinder the proliferation of bacteria that are closely related to the producing strain. Typically, bacteriocins display a limited range of effectiveness, targeting specific bacterial strains or species rather than a broad spectrum of microorganisms .
Isoafricanol/pristinol synthase (Isoafr/prist_syn)
Type: Family

This is a family of terpene cyclases from actinomycetes, including isoafricanol synthase (IAFRS) and pristinol synthase (PRISS).

IAFRS (

) catalyses the cyclization of farnesyl diphosphate (FPP) to isoafricanol, a sesquiterpene alcohol whose synthesis occur in Streptomyces violaceusniger and S.malaysiensis .

PRISS, isolated from Streptomyces pristinaespiralis (

), catalyses the conversion of (2E,6E)-farnesyl diphosphate (FPP) to yield a new 5-8 bicyclic (pristinane) sesquiterpenol (+)-(2S,3R,9R)-pristinol via a 1,11-cyclization, which requires the abstraction of the pyrophosphate from FPP to yield the humulyl cation. The only accepted substrate is farnesyl diphosphate (FPP) .
HrpD6-like (HrpD6-like)
Type: Family

This entry represents HrpD6 from Xanthomonas oryzae (

) and similar proteins specific to Xanthomonas. HrpD6 plays important roles in the regulation of the genes for hypersensitive response and pathogenicity (hrp), part of the type III secretion system (T3SS), and in the secretion of TAL effectors .
Type VI secretion system effector ExIF-like (T6SS_ExIF-like)
Type: Family

Members of this family are found typically in type VI secretion system (T6SS) regions of Burkholderia, Paraburkholderia, Acinetobacter, and related lineages, and may be effector proteins. The family is provisionally named ExIF after a motif well conserved across most family members.

Type VI protein secretion system (T6SS) is important for bacterial competition through contact-dependent killing of competitors. T6SS delivers effectors to neighboring cells and corresponding antagonistic proteins confer immunity against effectors that are delivered by sister cells. T6SS assembles as a molecular syringe that injects toxic protein effectors into cells .
HAEPLYID-like (HAEPLYID-like)
Type: Family

This family is named for start of a long and nearly invariant motif near the protein N-terminal found in bacteroidetes. Many members of this family previously carried an untraceable and probably incorrect annotation as phosphoribosylformylglycinamidine synthase.
KHG/KDPG aldolase/sugar kinase fusion protein (Trifunc_aldol)
Type: Family

This family represents a group of uncharacterised proteins mainly from spirochetes. The N-terminal region of its members resembles the bifunctional KHG/KDPG aldolase, while the C-terminal region resembles 2-dehydro-3-deoxygluconokinase and 2-dehydro-3 -deoxygalactonokinase.
Alkane oxidation protein activator PraA/PraB-like (PraA/PraB-like)
Type: Family

This entry represents alkane oxidation protein activator PraA and PraB, and related proteins found in gammaproteobacteria and actinomycetes .
MXAN_5187-like (MXAN_5187-like)
Type: Family

This entry represents a family of functionally uncharacterised proteins from Myxococcota.
Virulence-associated protein D-like (VapD-like)
Type: Family

This entry represents a group of bacterial sequences that are similar to Virulence-associated protein D from Campylobacter jejuni p11601MD (VapD) .
STM3941-like (STM3941-like)
Type: Family

This is a family of functionally uncharacterised proteins, widely distributed in bacteria.
HrpE-like (HrpE-like)
Type: Family

This entry represents a group of proteins specific to Xanthomonas, including Type III secretion pilin HrpE from Xanthomonas oryzae .
(-)-alpha-amorphene synthase (Amorph_synthase)
Type: Family

This entry represents the (-)-alpha-amorphene synthase, also known as terpene synthase or type I terpene cyclase. This enzyme catalyses the conversion of (2E,6E)-farnesyl diphosphate (FPP) to yield the bicyclic sesquiterpene (1R,6S,7S)-alpha-amorphene via cyclisation, which could involve the abstraction of the pyrophosphate from FPP to yield a (R)-bisabolyl cation . This enzyme only accepts (2E,6E)-farnesyl diphosphate (FPP) as substrate .
CiaI campylobacter virulence factor (CiaI)
Type: Family

The Campylobacter CiaI proteins are a family of proteins with an unknown function that are potentially associated with virulence in avian and human infections .
Phosphoribosylformylglycinamidine synthase-associated small membrane protein (FGAM_small_mem)
Type: Family

This entry represents a small protein that averages less than 40 amino acids, nearly all of which are hydrophobic and suggest integration into membrane. Members are regularly found encoded between or next to PurS and PurQ subunits of phosphoribosylformylglycinamidine synthase. The family appears to occur only in the Hyphomicrobiales, a branch of the alphaproteobacteria.
7-epi-alpha-eudesmol synthase (Eudesmol_syn)
Type: Family

This entry represents 7-epi-alpha-eudesmol synthase and related proteins found in Streptomyces. This enzyme catalyses the conversion of (2E,6E)-farnesyl diphosphate (FPP) to yield the bicyclic sesquiterpenol 7-epi-alpha-eudesmol via a 1,10-cyclization, which requires the abstraction of the pyrophosphate from FPP to yield the (E,E)-germacradienyl cation . This enzyme only accepts (2E,6E)0farnesyl diphosphate (FPP) as substrate .
RRQRL motif-containing zinc-binding protein (QRL_CxxC_CxxC)
Type: Family

Members of this family, found in actinomycetes, in multiple species of Streptomyces, contain a pair of CxxC motifs in the C-terminal region that are likely involved in Zn-binding. The family is named for a near-invariant QRL motif (usually RRQRL) closer to the N-terminal.
Selina-4(15),7(11)-diene synthase (Selin_dien_syn)
Type: Family

This entry represents selina-4(15),7(11)-diene synthase and related proteins found in actinomycetes. This enzyme catalyses the conversion of (2E,6E)-farnesyl diphosphate (FPP) to yield the bicyclic sesquiterpene selina-4(15),7(11)-diene via a cyclisation, which requires the abstraction of the pyrophosphate from FPP leading to a (E,E)-germacradienyl cation . It only accepts (2E,6E)-farnesyl diphosphate (FPP) as substrate .
YicS (YicS_fam)
Type: Family

This entry represents the YicS protein family, found in Escherichia coli and related species, which is in average 100 amino acids in size. It has a signal peptide and two widely spaced invariant Cys residues . It has been suggested that this protein may have a significant role in biofilm formation, motility, invasion of CEC-32 and Hep-2 cells and pathogenicity .
1,4-alpha-glucan branching enzyme TTHA1902 (TTHA1902)
Type: Family

This entry includes 1,4-alpha-glucan branching enzyme TTHA1902 (

) and related proteins found in Thermales. This enzyme belongs to GH family 57 and contains the five conserved family GH57 sequence motifs including the catalytic nucleophile glutamate and acid/base aspartate. It also possesses the D region thought to be typical for the GH57 glycogen branching enzyme (GBE) subfamily. TTHA1902 is involved in glycogen biosynthesis and catalyses the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position.

The structure of TTHA1902 is determined (

) and consists of two domains: a seven-stranded β/α-barrel and an α-helical C-terminal domain . Both N- and C-terminal domains are essential for catalysis and substrate binding.
RAxF-45-like (RAxF_45-like)
Type: Family

This entry represents a group of small proteins that are found broadly within the order Bacillales. The family is named for its best conserved motif, a nearly invariant RAxF motif, and its small size, about 45 amino acids in length.
CBO0543-like (CBO0543-like)
Type: Family

This family is named for an uncharacterised founding protein from Clostridium botulinum (

). The family is rather hydrophobic, about 165 amino acids in length, and found in Firmicutes. The function is unknown.
PA4780 RIO1-like protein kinase (Prot_kin_PA4780)
Type: Family

Members of this family are putative serine/threonine-protein kinases, closely related to founding member PA4780 (

) from Pseudomonas aeruginosa PAO1, which was shown to be upregulated by and important for the biodegradation of phenanthrene and naphthalene. Members of this entry belong more generally to the RIO1 atypical kinase family .
YjaA (YjaA)
Type: Family

YjaA is a protein with an unknown function that is utilised as a marker for phylogenetic clustering in Escherichia coli. Its folding has been predicted to be similar to that of the ribosomal protein family S11 .
Spore coat protein CotA-like (Spore_exo_CotA-like)
Type: Family

This entry represents the CotA family of proteins. CotA, found in Clostridium difficile (

), is a spore coat protein that has been detected in the exosporium . Similar proteins with homology to CotA can be identified in several closely related endospore-forming bacteria.
Ribosomal RNA small subunit methyltransferase F (RsmF)
Type: Family

This entry represents rRNA methyltransferase RsmF (

) and related proteins found inThermales. RsmF is responsible for 5-methylcytidine (m(5)C) modifications in 16S rRNA. RsmF modifies three positions in three residues that are clustered near the decoding site of the ribosome, but situated in distinct structural contexts .

The structure of RsmF from T. thermophilus was determined (

) and consists of a central canonical class I methyltransferase catalytic domain with additional N-terminal and C-terminal domains .
AMED_5909-like (AMED_5909-like)
Type: Family

This entry represents a group of proteins from actinomycetes, including AMED_5909 from Amycolatopsis mediterranei (

).
Neutral ceramidase, Mycobacterium (Ceramidase_neut_Mycobact)
Type: Family

This family represents the neutral ceramidase from Mycobacterium, which catalyses the cleavage of the N-acyl linkage of the ceramides (Cers) to yield sphingosine (Sph) and free fatty acid. It also catalyses the synthesis of Cers from Sph and fatty acid. Cers containning C6-C24 fatty acids are well hydrolyzed, and Cers with mono unsaturated fatty acids are much more hydrolyzed than those with saturated fatty acids .
PA2816-like (PA2816-like)
Type: Family

This entry represents a group of proteins specific to Pseudomonas, including PA2816 from Pseudomonas aeruginosa (

). Members of this family average about 140 amino acids in length, with an N-terminal signal peptide. The last 100 amino acids are rich in glutamine. The function of these proteins is unknown.
Nodulation protein NodU (Nodul_NodU)
Type: Family

This family includes nodulation protein NodU from alpha and betaproteobacteria. These proteins are involved in 6-O-carbamoylation of Nod-factors .
PA2817-like (PA2817-like)
Type: Family

This entry represents a group of proteins specific to Pseudomonadales, including PA2817 from Pseudomonas aeruginosa (

). Many members of the family have been annotated previously with the name dehydrogenase, but there is no clear evidence supporting it.
Nudix hydrolase DR_1025-like (Nud_hyd_Dein)
Type: Family

This entry includes Nudix hydrolases from Deinococcus such as DR_1025 from Deinococcus radiodurans. DR_1025 can act as a nucleoside triphosphatase and a dinucleoside polyphosphate pyrophosphatase. The best substrates are 8-oxo-dGTP and 8-oxo-GTP. Other substrates include Ap4A, dGTP and GTP. It may be involved in protection from damage caused by radiation .
Formate dehydrogenase, actinomycetes (Formate_DH_Act)
Type: Family

This entry represents a group of formate dehydrogenases predominantly found in actinomycetes. Many are selenoproteins.
Acyltransferase PE (Acyl_transf_PE)
Type: Family

This entry represents the acyltransferase PE found in Mycobacteriaceae. This enzyme is involved in the biosynthesis of trehalose polyphleates (TPP) . It catalyses the transfer of phleic acids onto 2,3-diacyl trehalose (DAT) to form TPP.
Prenyl-diphosphate phosphatase (Prenyl-diphosphate_PPase)
Type: Family

This family represents prenyl-diphosphate phosphatases from archaea, including that from Methanosarcina mazei (also known as Nudix hydrolase MM_2582). It hydrolyzes homoallylic isopentenyl diphosphate (IPP), its allylic isomer dimethylallyl diphosphate (DMAPP) and short-chain prenyl diphosphates geranyl diphosphate (GPP) and farnesyl diphosphate (FPP) to their corresponding monophosphate forms with high activity. The preferred substrate is IPP. ADP, NADPH, Ap5A and thiamine diphosphate (TPP) are weakly hydrolyzed. It shows no hydrolysis with ATP, dNTPs, 8-OH-dGTP, NAD, FAD or acetyl-CoA. The likely physiological role of this enzyme is to provide a substrate dimethylallyl phosphate (DMAP) for prenylated flavin mononucleotide (prenyl-FMN) synthase MM_1871 involved in the biosynthesis of prenyl-FMN, a coenzyme required in the archaea-specific mevalonate pathway .
PA2928-like (PA2928-like)
Type: Family

This entry represents a group of bacterial proteins, including PA2928 from Pseudomonas aeruginosa (

).
O-GlcNAcase BT_4395-like (O-GlcNAcase_BT_4395-like)
Type: Family

This family represents a group of poorly characterised proteins from bacteroidetes, such as BT_4395, which can hydrolyze the glycosidic link of O-GlcNAcylated proteins. In vitro, it can use p-nitrophenyl-beta-GlcNAc and 4-methylumbelliferone-GlcNAc as substrates .
MM0924-like (MM0924_fam)
Type: Family

Members of this family occur in both archaea and bacteria, and share sequence and structural similarity with DUF2642 (

).
YjdP (YjdP-like)
Type: Family

Members of this family average 108 amino acids in length, with a signal peptide and with a highly charged C-terminal region of typically five tandem 7-mer repeats approximated by DDRRRQL. The family is named for founding member YjdP from Escherichia coli K-12 (

).