SII-SWORD/CoKE huggingface dataset:
Acetophenone carboxylase epsilon subunit (ApcE)
Type: Family

This entry represents Acetophenone carboxylase epsilon subunit from Aromatoleum aromaticum (ApcE) and similar sequences from proteobacteria. Acetophenone carboxylase catalyses the carboxylation of acetophenone to form 3-oxo-3-phenylpropanoate (benzoylacetate) in the anaerobic catabolism of ethylbenzene .
Acetophenone carboxylase delta subunit (ApcD)
Type: Family

This entry includes Acetophenone carboxylase delta subunit from Aromatoleum aromaticum (ApcD) and similar sequences from proteobacteria. Acetophenone carboxylase catalyses the carboxylation of acetophenone to form 3-oxo-3-phenylpropanoate (benzoylacetate) in the anaerobic catabolism of ethylbenzene .
Acetophenone carboxylase gamma subunit (ApcC)
Type: Family

This entry represents Acetophenone carboxylase gamma subunit from Aromatoleum aromaticum (ApcC) and similar sequences from proteobacteria. Acetophenone carboxylase catalyses the carboxylation of acetophenone to form 3-oxo-3-phenylpropanoate (benzoylacetate) in the anaerobic catabolism of ethylbenzene .
Acetophenone carboxylase beta subunit (ApcB)
Type: Family

This entry includes Acetophenone carboxylase beta subunit from Aromatoleum aromaticum (ApcB) and similar sequences from proteobacteria. Acetophenone carboxylase catalyses the carboxylation of acetophenone to form 3-oxo-3-phenylpropanoate (benzoylacetate) in the anaerobic catabolism of ethylbenzene .
Mycofactocin biosynthesis chaperone MftB-like (MftB-like)
Type: Family

This entry represents a group of proteins from halobacteria that are an alternate form of mycofactocin biosynthesis chaperone. Size and several motifs are similar to MftB (see

), but it is unclear if the two families are truly homologous.
HgcAB-like fusion protein (HgcAB-like)
Type: Family

This entry represents a family of prokaryotic proteins. Members of this family have a long N-terminal region that resembles HgcA, and a shorter C-terminal region that resembles HgcB, where HgcA and HcgB are a protein pair required for the methylation that converts inorganic mercury into the more toxic organic compound methylmercury, a neurotoxin in humans. The HgcAB-like fusion protein is not currently known to have this activity. Some members have an additional N-terminal methyltransferase domain, while others are encoded adjacent to an uncharacterised methyltransferase .
DNA-binding protein HMf-2-like (HmfB-like)
Type: Family

This entry includes DNA histones, which are involved in the compaction and organisation of archaeal genomes, including DNA-binding protein HMf-2 from Methanothermus fervidus (HmfB). HmfB binds and compacts DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils . Proteins of this family are homologues of human histone H4.
D-erythronate dehydrogenase (DenD)
Type: Family

This entry represents D-erythronate dehydrogenase from Haemophilus influenzae (DenD) and similar sequences, mainly found in proteobacteria, actinomycetes and fungi. DenD catalyses the oxidation of D-erythronate to 2-oxo-tetronate. It can use either NAD+ or NADP+ as cosubstrate, with a preference for NAD+ .
L-threonate dehydrogenase (LtnD)
Type: Family

This entry represents L-threonate dehydrogenase from Escherichia coli (LtnD) and similar protein sequences predominantly found in proteobacteria. LtnD catalyses oxidation of L-threonate to 2-oxo-tetronate. It can use either NAD+ or NADP+ as cosubstrate, with a preference for NAD+ .
3-oxo-tetronate kinase (OtnK)
Type: Family

This entry represents 3-oxo-tetronate kinase from Haemophilus influenzae (OtnK) and similar bacterial proteins. OtnK catalyses the ATP-dependent phosphorylation of 3-oxo-tetronate to 3-oxo-tetronate 4-phosphate . This protein is organised into two distinct domains,

and

.
MFS transporter MMSYN1_0478-like (MMSYN1_0478-like)
Type: Family

This entry represents a small family of MFS transporters from Mollicutes .
3-dehydroshikimate dehydratase QuiC (QuiC)
Type: Family

This entry represents the homologues of 3-dehydroshikimate dehydratase QuiC found mainly in Pseudomonas species. This enzyme catalyses the conversion of 3-dehydroshikimate to protocatechuate (3,4-dihydroxybenzoate), a common intermediate of quinate and shikimate degradation pathways. It is required for growth on either quinate or shikimate as a sole carbon source . The structure of a QuiC1 enzyme from P. putida revealed that the protein is a fusion of two distinct modules: an N-terminal sugar phosphate isomerase-like domain associated with dehydroshikimate dehydratase activity and a novel C-terminal hydroxyphenylpyruvate dioxygenase-like domain .
ETEC_3214-like domain (ETEC_3214_dom)
Type: Domain

This entry represents a domain found in a protein of unknown function encoded by ETEC_3214 in E.coli . This protein is strongly upregulated by CfaD, an AraC-like transcriptional regulator that plays a key role in virulence gene expression by enterotoxigenic Escherichia coli (ETEC).
2-oxoglutarate ferredoxin oxidoreductase subunit delta (OGOR_delta)
Type: Family

2-oxoglutarate ferredoxin oxidoreductases (OGOR) belong to the larger family of 2-oxoacid:ferredoxin oxidoreductases (KOR). These enzymes perform oxidative decarboxylations in amino acid catabolism. This entry represents the delta subunit of an OGOR, with distinctive architecture particular to the Thermococci .
Trans-4-hydroxy-L-proline dehydratase (Glycl_HYPD)
Type: Family

This entry represents Trans-4-hydroxy-L-proline dehydratase from Clostridioides difficile and related bacterial proteins.The trans-4-hydroxy-L-proline dehydratase HypD is a glycyl-radical enzyme that depends on an activator that is a radical SAM enzyme. It catalyses the dehydration of the non-proteinogenic amino acid trans-4-hydroxy-L-proline (Hyp), the most abundant modified residue in human proteins, to produce delta1-pyrroline-5-carboxylate (P5C), being involved in the anaerobic degradation of 4-hydroxyproline .
3-oxo-tetronate 4-phosphate decarboxylase (OtnC)
Type: Family

This entry represents 3-oxo-tetronate 4-phosphate decarboxylase from Escherichia coli (OtnC) and similar protein sequences from proteobacteria and some species of actinomycetes. OtnC catalyses the decarboxylation of 3-oxo-tetronate 4-phosphate to dihydroxyacetone phosphate (DHAP) and CO2 .
Trans-4-hydroxy-L-proline dehydratase activase (T4HPD_activ_SAM)
Type: Family

This family includes the trans-4-hydroxy-L-proline dehydratase activase PflE (also known as trans-4-hydroxy-L-proline dehydratase activating enzyme or glycyl-radical enzyme activating enzyme PflE) found in some gram-positive species. This enzyme catalyses the activation of the trans-4-hydroxy-L-proline dehydratase under anaerobic conditions by generation of an organic free radical on a glycine residue, via a homolytic cleavage of S-adenosyl-L-methionine (SAM). PflE is involved in the anaerobic degradation of 4-hydroxyproline .
3-oxo-isoapionate kinase OiaK (OiaK)
Type: Family

This entry represents 3-oxo-isoapionate kinase from Paraburkholderia graminis (OiaK) and similar proteins from proteobacteria. This enzyme is involved in catabolism of D-apiose. It catalyses the phosphorylation of 3-oxo-isoapionate to 3-oxo-isoapionate 4-phosphate .
Dot/Icm T4SS effector AnkX/LegA8 (T4SS_AnkX)
Type: Family

This entry represents a group of proteins from Legionellales, including the Dot/Icm type IV secretion system (T4SS) effector phosphocholine transferase AnkX from Legionella pneumophila. AnkX plays a role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). It functions as a phosphocholine transferase by mediating the addition of phosphocholine to Ser residues of host RAB1 (RAB1A, RAB1B or RAB1C) and RAB35, leading to displacement of GDP dissociation inhibitors (GDI) .
Dipeptide ABC transporter periplasmic-binding protein DppA (DppA_dipep)
Type: Family

This family includes the dipeptide-binding protein DppA from E.coli and related sequences from enterobacteria. DppA is part of the ABC transporter DppABCDF involved in dipeptide transport .

DppA binds dipeptides and accepts a wide range of side chains, including small neutral, bulky hydrophobic, and positively and negatively charged groups and controls the specificity of the Dpp transporter . Additionally, it plays a role in chemotaxis toward peptides via interaction with the chemotaxis protein Tap .
Dot/Icm T4SS effector AnkY/LegA9 (T4SS_AnkY)
Type: Family

This entry represents a group of proteins from Legionellales, including the Dot/Icm type IV secretion system (T4SS) effector AnkY/LegA9 from Legionella pneumophila (

,

].
Dot/Icm T4SS effector AnkQ/LegA10 (T4SS_AnkQ)
Type: Family

This entry represents a group of proteins from Legionellales, including the Dot/Icm type IV secretion system (T4SS) effector AnkQ/LegA10 from Legionella pneumophila (

,

].
Dimethylsulfoniopropionate lyase DddP (DddP)
Type: Family

This entry includes Dimethylsulfoniopropionate lyase DddP from Roseovarius nubinhibens and similar protein sequences from proteobacteria and some fungal species. DddP is capable of cleaving dimethylsulfonioproprionate (DMSP), releasing dimethyl sulfide (DMS), the principal form by which sulphur is transported from oceans to the atmosphere , although the real activity of the protein is yet unclear as the low activity with DMSP as substrate suggests that DMSP is not its native substrate . Interestingly, the structure of DddP from Roseobacter denitrificans revealed a metalloproteinase-like fold .
Dipeptide ABC transporter ATP-binding subunit DppF (DppF)
Type: Family

This entry represents Dipeptide transport ATP-binding protein DppF found mainly in Enterobacterales species. This protein is a part of the ABC transporter DppABCDF involved in dipeptide transport and it may be responsible for energy coupling to the transport system . When a foreign outer membrane heme receptor is expressed in E.coli, DppABCDF can also transport heme and its precursor, 5-aminolevulinic acid (ALA), from the periplasm into the cytoplasm.
Spermidine/putrescine ABC transporter MMSYN1_0195-like (MMSYN1_0195-like)
Type: Family

Proteins of this family consist of fused permease and substrate-binding domains of spermidine/putrescine ABC transporter .
Diglucosylglycerate octanoyltransferase (OctT)
Type: Family

This entry represents a group of proteins from actinomycetes, including diglucosylglycerate octanoyltransferase from Mycobacterium tuberculosis (OctT), a sugar octanoyltransferase likely involved in the biosynthesis of mycobacterial methylglucose lipopolysaccharide (MGLP) .
Spermidine/putrescine ABC transporter permease MMSYN1_0196-like (MMSYN1_0196-like)
Type: Family

This small family includes uncharacterised proteins from Mollicutes which are likely spermidine/putrescine ABC transporter permeases .
D-arabinitol 4-dehydrogenase (DalD)
Type: Family

This entry represents a group of proteins from proteobacteria, including D-arabinitol 4-dehydrogenase from Klebsiella pneumoniae (DalD), which is involved in D-arabinitol metabolism .
Polyhydroxyalkanoate granule regulatory protein PhaM, N-terminal domain (PHA_gran_PhaM_N)
Type: Domain

This entry represents PhaM and related proteins from betaproteobacteria. PhaM was identified in Ralstonia eutropha (also known as Cupriavidus necator) as a multifunctional protein, found as part of poly(3-hydroxybutyrate) granules, a type of polyhydroxyalkanoate (PHA) storage granule, able to bind the PHA synthase PhaC, but also shown to have DNA-binding activity. This domain occurs in PhaM, near the N terminus, and in additional homologs, some no longer than the domain itself .
Deaminated glutathione amidase, Morganellaceae-type (Nit1_Morganellaceae)
Type: Family

This entry represents a group of proteins from Morganellaceae, including Deaminated glutathione amidase from Yersinia enterocolitica (Nit1), which hydrolyses deaminated glutathione (dGSH, 2-oxoglutaramate) to alpha-ketoglutarate (alpha-KG) and cysteinylglycine. It may function as a metabolite repair enzyme .
Xanthine dehydrogenase subunit XdhA (XdhA_XDHase)
Type: Family

This family includes xanthine dehydrogenase molybdenum-binding subunit XdhA from E.coli, a xanthine dehydrogenase that participates in limited purine salvage (requires aspartate) but does not support aerobic growth on purines as the sole carbon source .
Acetylxylan esterase (AxeA1)
Type: Family

This entry represents a group of proteins from Bacteroidales, including acetylxylan esterase from Prevotella ruminicola (AxeA1), an acetyl esterase involved in the degradation of plant cell wall polysaccharides .
3-oxo-isoapionate-4-phosphate decarboxylase (OiaX)
Type: Family

This entry represents the homologues of 3-oxo-isoapionate-4-phosphate decarboxylase OiaX found mainly in alphaproteobacteria. This enzyme is involved in the catabolism of D-apiose. It catalyses the decarboxylation of 3-oxo-isoapionate 4-phosphate to L-erythrulose 1-phosphate .
Xanthine dehydrogenase subunit XdhB (XdhB_XDHase)
Type: Family

This family includes Xanthine dehydrogenase subunit XdhB from E.coli and related sequences. This is a dehydrogenase that participates in limited purine salvage (requires aspartate) but does not support aerobic growth on purines as the sole carbon source (purine catabolism) .
3-sulfinopropanoyl-CoA desulfinase (AcdA)
Type: Family

This entry represents the 3-sulfinopropanoyl-CoA desulfinase from Variovorax paradoxus (AcdA) and similar proteins mainly found in proteobacteria. This enzyme catalyses the conversion of 3-sulfinopropanoyl-CoA (3SP-CoA) to propanoyl-CoA by abstraction of sulfite . It does not possess a dehydrogenase activity.
Xanthine dehydrogenase subunit XdhC (XdhC_XDHase)
Type: Family

This family represents xanthine dehydrogenase subunit XdhC from E.coli and related sequences. Together with XdhA and XdhB, it participates in limited purine salvage (requires aspartate) but does not support aerobic growth on purines as the sole carbon source (purine catabolism) .
Oligopeptide ABC transporter substrate-binding protein Opp4A (Opp4A)
Type: Family

This entry represents the oligopeptide ABC transporter substrate-binding protein Opp4A from Bacilli species, including Bacillus cereus and Staphylococcus aureus .
Nickel ABC transporter substrate-binding protein NikA (NikA)
Type: Family

This entry includes NikA, a member of the ABC transporter complex NikABCDE (Opp2) involved in nickel import. It binds nickel and transfers it to the membrane-bound permease. This protein is required for full urease activity and plays a significant role in the virulence of S.aureus during urinary tract infection (UTI) . It may bind nickel via a nickel-chelator .
Metal-staphylopine import system permease protein CntB (CntB)
Type: Family

This family includes metal-staphylopine import system permease protein CntB (also Known as Opp1B) which is part of the ABC transporter complex CntABCDF (Opp1) involved in the uptake of metal in complex with the metallophore staphylopine (StP). This proteinn is involved in the import of divalent metals ions such as nickel, cobalt and zinc. It is probably responsible for the translocation of the substrate across the membrane . It plays a major role in nickel/cobalt import in zinc-depleted conditions. CntB also contributes to virulence. It is required for full urease activity in vitro .
Putative alpha/beta hydrolase CPn0927-like (CPn0927-like928-like)
Type: Family

This entry represents a family of proteins from Clamydiia, including CPn0927 from Chlamydia pneumoniae (

) . Members of this family have similarity to (

) and are predicted to adopt an α/β hydrolase fold.
ADP-polyphosphate phosphotransferase (PPK2)
Type: Family

This entry represents a group of bacterial proteins, mainly from proteobacteria, including ADP-polyphosphate phosphotransferase from Rhodopseudomonas palustris (PPK2), which uses inorganic polyphosphate (polyP) as a donor to convert ADP to ATP .
Putative transporter MAB_1171c-like (MAB_1171c-like)
Type: Family

This entry represents the homologues of Integral membrane protein from Mycobacterium abscessus (MAB_1171c,

), a putative integral membrane transporter protein . This protein is likely associated with the transport of biofilm constituents out of the cell. Proteins in this family are found mainly in Actinomycetes.
Acetylxylan esterase/glucomannan deacetylase (CE2A)
Type: Family

This entry includes acetylxylan esterase/glucomannan deacetylase from Cellvibrio japonicus (CE2A) and similar sequences from beta- and gammaproteobacteria. CE2A is involved in the degradation of plant cell wall polysaccharides. It catalyses the deacetylation of acetylated birchwood xylan and glucomannan, with equal efficiency, and of the synthetic substrate 4-nitrophenyl acetate (4-NPAc) .
Acryloyl-CoA reductase electron transfer subunit beta (ETF_beta)
Type: Family

This entry represents a group of proteins from firmicutes, including Acryloyl-CoA reductase electron transfer subunit beta from Anaerotignum propionicum (ETF_beta), which is part of the ETF-acryloyl-CoA reductase complex involved in the pathway of L-alanine fermentation. The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for acryloyl-CoA reductase .
Acryloyl-CoA reductase (AcrC)
Type: Family

This entry represents a group of proteins from firmicutes, including Acryloyl-CoA reductase (NADH) from Anaerotignum propionicum (AcrC), which is probably the catalytic subunit of the acryloyl-CoA reductase complex involved in the pathway of L-alanine fermentation .
IncP plasmid survival protein KfrC-like domain (KfrC-like_dom)
Type: Domain

This entry represents a domain found in KfrC from Pseudomonas aeruginosa (

), at the C-terminal of Protein TraN from Escherichia coli, and in similar proteins from proteobacteria. KfrC along with KfrA and KfrB is encoded in plasmid R751, and are all found to be essential for its survival . These proteins seem to form a complex KfrABC complex that may be an important component in the organisation and control of the plasmid clusters that seem to form the segregating unit in bacterial cells . Some members of this group have an additional phosphoribosyltransferase-like N-terminal domain (

).
Acryloyl-CoA reductase electron transfer subunit gamma (AcrB)
Type: Family

This entry represents a group of proteins from firmicutes, including Acryloyl-CoA reductase electron transfer subunit gamma from Anaerotignum propionicum (AcrB), part of the ETF-acryloyl-CoA reductase complex involved in the pathway of L-alanine fermentation. The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for acryloyl-CoA reductase .
Nickel import system permease protein NikB (Opp2B)
Type: Family

This entry includes nickel permeases NikB from bacteria and some archaeal species .

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, NikA is the periplasmic binding protein, NikB and NikC are the membrane components, and NikD and NikE are the ATP-binding components of the ABC transporter. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases. To avoid nickel toxicity, the synthesis of the Nik system is tightly controlled by the nickel-responsive repressor NikR .
MFS cation transporter, mollicutes (MSF_cation_mollicutes)
Type: Family

This entry represents a group of MFS cation transporters from mollicutes .
Disulfide reductase DsbH (DsbH)
Type: Family

This entry represents a group of proteins from Chlamydia, including disulfide bond reductase DsbH from Chlamydia pneumoniae, which catalyses the reduction of disulfide bonds . Members of this family show a thioredoxin-like fold.
Trans-2-enoyl-CoA reductase-like, NAD(P)H binding domain (FabV-like_NADH_b)
Type: Domain

This entry represents the N-terminal NAD(P)H binding domain of the enzyme trans-2-enoyl-CoA reductase,

. The activity of the enzyme was characterised in Euglena gracilis where an unusual fatty acid synthesis pathway in the mitochondria performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. The full enzyme catalyses the reduction of enoyl-CoA to acyl-CoA. The binding site is conserved as GA/CSpGYG, where p is any polar residue .
Dodecin, bacteria (Dodecin_bact)
Type: Family

This entry represents dodecin from Thermus thermophilus and similar bacterial sequences. This protein may function as storage protein that sequesters various flavins and other cofactors, thereby protecting the cell against undesirable reactions mediated by the free cofactors. It binds and sequesters FMN, FAD, lumiflavin and lumichrome, and can also bind coenzyme A .
Carboxynorspermidine synthase (CANSDH)
Type: Family

This entry represents a group of proteins from gammaproteobacteria, including Carboxynorspermidine synthase from Vibrio cholerae (also known as Carboxynorspermidine dehydrogenase, CANSDH), which is involved in norspermidine biosynthesis. It is essential for biofilm formation .
Type VII secretion system protein EccE domain (EccE_dom)
Type: Domain

This entry represents a domain of the Type VII secretion system protein EccE and similar proteins found in Actinobacteria, which are part of type VII secretion system (T7SS) .
ATP-dependent Clp protease ATP-binding subunit ClpX (ATP-dep_Clp_protease_ClpX)
Type: Family

The ClpX chaperone family includes ATP-dependent specificity components of the Clp protease complex. These proteins use cycles of ATP binding and hydrolysis to unfold and translocate specific protein substrates to the ClpP protease for degradation. They play a crucial role in various cellular processes by directing the Clp protease to degrade misfolded, damaged, or regulatory proteins. Some family members can perform chaperone functions independently of ClpP, aiding in the proper folding of proteins. They are involved in the regulation of DNA replication, stress responses, and the maintenance of mitochondrial nucleoid structure. The family also includes ATPase subunits of proteasome-like degradation complexes, essential for the unfolding of protein substrates before their hydrolysis by HslV.
ATPase alpha/beta chains (ATPase_alpha/beta_chains)
Type: Family

The ATPase alpha/beta chains family is characterized by its fundamental role in cellular energy metabolism. Members of this family are involved in the synthesis of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) utilizing a proton gradient across a membrane. This process is essential for a wide range of cellular activities, as ATP serves as a universal energy currency in living organisms. The family includes ATP synthase subunits that form the catalytic core of F-type ATPases, which are found in various cellular locations including mitochondria, chloroplasts, and bacterial plasma membranes. These ATPases consist of multiple subunits, with the alpha and beta subunits constituting the catalytic core where ATP synthesis is coupled to proton translocation through a rotary mechanism of the central stalk subunits.
Uracil phosphoribosyltransferase/Adenine phosphoribosyltransferase (UPRTase/APRTase)
Type: Family

The UPRTase family proteins are responsible for the salvage pathway of pyrimidine metabolism, which is a more energy-efficient alternative to de novo synthesis. They catalyze the conversion of uracil and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP and diphosphate. This reaction is crucial for the reuse of uracil, allowing the cell to efficiently maintain nucleotide pools. Members of this family are allosterically activated by GTP, indicating a regulatory mechanism that ensures the balance of pyrimidine nucleotides in response to cellular energy levels and GTP availability. The family also includes adenine phosphoribosyltransferase proteins, which catalyze a similar salvage reaction resulting in the formation of AMP from adenine and PRPP, further underscoring the importance of these enzymes in nucleotide salvage pathways.