SII-SWORD/CoKE huggingface dataset:
Cytochrome c551 (Cytochro_C551)
Type: Family

C-type cytochrome c551 (also known as CccB) differs from its close homologue CccA by having a lipoprotein signal peptide . Cytochrome c551 has been related to virulence in Bacillus species . Members of this protein family are specific to Bacillales.
HinT-interacting membrane complex lipoprotein P60-like (P60-like)
Type: Family

This entry represents a group of proteins from Mycoplasmatota, including lipoprotein P60 from Metamycoplasma hominis. This protein is part of a complex that interacts with HinT, a lineage-specific subgroup of the cytosolic histidine triad (HIT) family of proteins .
HpyAIV-type II restriction enzyme (HpyAIV-type_restriction_enz)
Type: Family

This entry represents a group of bacterial proteins, inluding HP1351 from Helicobacter pylori (

), designated HpyAIV by the restriction enzyme database REBASE. It is a type II restriction enzyme that recognises GANTC.
Type II restriction enzyme HinfI (HinfI)
Type: Family

This entry represents a group of bacterial type II restriction enzymes, including Type II restriction enzyme HinfI from Haemophilus influenzae, which recognises the double-stranded sequence 5'-GANTC-3' and cleaves after G-1 .
MYPU_1760-like (MYPU_1760-like)
Type: Family

This entry represents a group of proteins from Mycoplasmatota, including MYPU_1760 from Mycoplasmopsis pulmoni (

). Members of this family average over 600 amino acids in length, and contain a region similar to a region of the zinc metalloproteases from

, including the signature motif HEYxH.
TrlF AAA-like ATPase (TrlF_ATPase)
Type: Family

This entry represents TrlF from Photorhabdus laumondii (

) and similar bacterial sequences. TrlF was described as an 875-amino acid protein encoded in a small genomic island operon next to TrlG, whose mutation and loss of function restores an ability to grow at 36 degrees .
MSC_0620/UU052-like (MSC_0620_UU052-like)
Type: Family

This entry represents a group of proteins from Mycoplasmatota, including MSC_0620 from Mycoplasma mycoides (

) and UU052 from Ureaplasma parvum (

). Neighbouring proteins include paralogues to the alpha, beta, gamma, and epsilon subunits of the F1 ATPase, and are subunits of a related complex found only in the Mycoplasmatota. This subunit includes transmembrane domains and is designated X0 .
P97 adhesin, N-terminal domain (P97_adhes_N)
Type: Domain

This entry represents a region found at the N-terminal of a group of P97-like proteins mainly found in Mesomycoplasma species, including Mhp107 (

, ) and Mhp385 (

, ).
N-acetylmuramate alpha-1-phosphate uridylyltransferase (MurU)
Type: Family

This family includes N-acetylmuramate alpha-1-phosphate uridylyltransferase (MurU) from beta and gammaproteobacteria. It catalyses the formation of UDP-N-acetylmuramate (UDP-MurNAc), a crucial precursor of the bacterial peptidoglycan cell wall, from UTP and MurNAc-alpha-1P. It is involved in peptidoglycan recycling as part of a cell wall recycling pathway that bypasses de novo biosynthesis of the peptidoglycan precursor UDP-MurNAc . MurU also plays a role in intrinsic resistance to fosfomycin, which targets the de novo synthesis of UDP-MurNAc .
N-acetylmuramate/N-acetylglucosamine kinase (AmgK)
Type: Family

This entry includes N-acetylmuramate/N-acetylglucosamine kinase AmgK from Neisseriales, a sugar kinase that catalyses the ATP-dependent phosphorylation of N-acetylmuramate (MurNAc) and N-acetylglucosamine (GlcNAc) at its C1 hydroxyl group, leading to MurNAc alpha-1P and GlcNAc alpha-1P, respectively. It may be involved in peptidoglycan recycling as part of a cell wall recycling pathway that bypasses de novo biosynthesis of the peptidoglycan precursor UDP-MurNAc . AmgK is able to complement the fosfomycin sensitivity phenotype of a P.putida mutant lacking amgK .
HSGNP motif-containing (seleno)protein TsoX (TsoX)
Type: Family

This entry represents a small group of short bacterial selenoproteins with a UxxC selenocysteine-containing motif immediately preceded by a signature motif HSGNPX. Most members contain selenocysteine. At least five members are fusion proteins with a C-terminal thioredoxin-disulfide reductase region (

). Members of this family are given the gene symbol TsoX (Three Selenoprotein Operon protein X), as it occasionally occurs in the same operon as selenoproteins TsoA, TsoB, and TsoC.
HTH-type transcriptional regulator AlsR (AlsR)
Type: Family

This entry represents the HTH-type transcriptional regulator AlsR from Bacillus subtilis and similar proteins from Bacillales.

AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon . The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyses the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources .
Antitoxin TumA (TumA)
Type: Family

This family represents the antitoxin component TumA from the TumE-TumA toxin-antitoxin system .
Toxin TumE (TumE)
Type: Family

This entry represents a small group of bacterial sequences, recently described as the toxin component TumE from the novel toxin-antitoxin system TumE-TumA .
Gas vesicle protein GvpL (Gas_vesic_GvpL)
Type: Family

This entry includes gas vesicle protein L (GvpL) from archaea, mainly from halobacteria. A cluster of 12-14 gvp genes (gvpMLKJIHGFEDACNO) is responsible for gas vesicle synthesis in Halobacterium sp. . GvpL is essential for gas vesicle formation and displays sequence similarity to GvpF, both containing predicted coiled-coil domains that are often involved in self-oligomerisation. They are structural components of the vesicle .
Gas vesicle protein GvpG, halobacteria (Gas_vesic_GvpG_halobact)
Type: Family

Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea . They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light

,

]. This family represents Gas vesicle protein G from halobacteria.
AAA-like ATPase Spaf_1101-like (Spaf_1101-like)
Type: Family

This entry represents a family of AAA-like ATPases, including Spaf_1101 from Streptococcus parasanguinis (

), which was found at one end of a reported transposon. The high frequency of pseudogenes related to the intact members of this family, typical for genes with higher than average potential costs to the host species such as transposases, suggests a role in mobile element function .
Nicotine blue oxidoreductase (NboR)
Type: Family

This entry represents nicotine blue oxidoreductase from Paenarthrobacter nicotinovorans (NboR) and similar sequences from actinomycetes. NboR catalyses the reduction of nicotine blue to its hydroquinone form. Nicotine blue is the name given to the compound formed by the autocatalytic condensation of two molecules of 2,3,6-trihydroxypyridine, an intermediate in the nicotine degradation pathway . NboR may play a role in preventing the intracellular formation of nicotine blue semiquinone radicals, which by redox cycling would lead to the formation of toxic reactive oxygen species. Besides nicotine blue, several other quinones are reduced by this enzyme.
Nigerythrin (Nigrythrn)
Type: Family

This entry represents Nigerythrin from Nitratidesulfovibrio vulgaris, a member of the rubrerythrin (Rbr) family that has NADH peroxidase activity , and similar sequences from actinomycetota.
Styrene monooxygenase subunit StyA (StyMonoxStyA)
Type: Family

Styrene monooxygenase StyA catalyses the first step in the aerobic styrene degradation pathway by enantioselective epoxidation of the vinyl side chain. In a two-component system, StyB reductase utilizes NADH to reduce FAD, which is then transferred to the oxygenase; the electron transfer is proposed to occur via a diffusing flavin .
NADH-dependent flavin reductase StyB (StyMonoxStyB)
Type: Family

This entry includes NADH-dependent flavin reductase StyB, the reductase component of a two-component system that catalyses the first step in the aerobic styrene degradation pathway by enantioselective epoxidation of the vinyl side chain. It utilizes NADH to reduce FAD, which is then transferred to the styrene monooxygenase StyA .
Styrene-oxide isomerase StyC (StyOxIsoStyC)
Type: Family

This entry represents Styrene-oxide isomerase StyC, an epoxystyrene isomerase that catalyses the second step in the aerobic styrene degradation pathway by converting epoxystyrene to phenylacetaldehyde .
Rhodanese/DsbD fusion-like TsoB selenoprotein (TsoB)
Type: Family

This entry represents a group of bacterial selenoproteins with a double-selenocysteine motif, FYUAGLXUVR. The shorter N-terminal region contains a rhodanese-like domain (similar to

). The C-terminal region resembles the thiol-disulfide exchange protein DsbD (

).
Phenylacetaldehyde dehydrogenase (StyD)
Type: Family

This entry includes phenylacetaldehyde dehydrogenase StyD, which catalyses the last step in the aerobic styrene degradation pathway by mediating oxidation of phenylacetaldehyde to phenylacetic acid . Members of this group are mainly found in Betaproteobacteria.
NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon (PadH)
Type: Family

This entry includes NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon (PadH) from Aromatoleum evansii, which is involved in the anaerobic metabolism of phenylalanine and phenylacetate. The system catalyses the oxidative decarboxylation of phenylglyoxylate to benzoyl-CoA and CO2. It can also react slowly with 2-oxo-3-methylbutanoate and use different electron acceptors such as benzyl viologen, methyl viologen, FAD or FMN, but NAD seems to be the physiological electron acceptor. Also catalyzes an isotope exchange between CO2 and the carboxyl group which proves partial or complete reversibility of the oxidative decarboxylation .
NADH-dependent phenylglyoxylate dehydrogenase subunit alpha (PadG)
Type: Family

This family represents NADH-dependent phenylglyoxylate dehydrogenase subunit alpha (PadG), which is involved in the anaerobic metabolism of phenylalanine and phenylacetate. It catalyses the oxidative decarboxylation of phenylglyoxylate to benzoyl-CoA and CO2. It can also react slowly with 2-oxo-3-methylbutanoate and use different electron acceptors such as benzyl viologen, methyl viologen, FAD or FMN, but NAD seems to be the physiological electron acceptor. Also catalyses an isotope exchange between CO2 and the carboxyl group which proves partial or complete reversibility of the oxidative decarboxylation reaction .
NADH-dependent phenylglyoxylate dehydrogenase subunit beta (PadI)
Type: Family

This family represents NADH-dependent phenylglyoxylate dehydrogenase subunit beta (PadI), which is involved in the anaerobic metabolism of phenylalanine and phenylacetate. This system catalyses the oxidative decarboxylation of phenylglyoxylate to benzoyl-CoA and CO2. It can also react slowly with 2-oxo-3-methylbutanoate and use different electron acceptors such as benzyl viologen, methyl viologen, FAD or FMN, but NAD seems to be the physiological electron acceptor. It also catalyses an isotope exchange between CO2 and the carboxyl group which proves partial or complete reversibility of the oxidative decarboxylation reaction .
PilM-like pilus complex protein Amuc_1101-like (Amuc_1101-like)
Type: Family

This entry represents a group of proteins from Verrucomicrobiota, including Amuc_1101 from Akkermansia muciniphila
(

), a PilM-like protein from a variant type of IV-pilin complex.
Sulfate respiration complex iron-sulfur protein HmcF (HmcF)
Type: Family

This entry represents a group of proteins mainly from Thermodesulfobacteriota, including HmcF (also known as Protein DVU_0531 and ORF6) from Nitratidesulfovibrio vulgaris. HmcF is protein F of the high-molecular-weight cytochrome (Hmc) complex, which features the 16-heme protein HmcA. HmcF is predicted to bind two 4Fe-4S clusters. The complex is involved in sulfate respiration .
NADH-dependent phenylglyoxylate dehydrogenase subunit gamma (PadE)
Type: Family

This entry includes NADH-dependent phenylglyoxylate dehydrogenase subunit gamma (PadE) which is involved in the anaerobic metabolism of phenylalanine and phenylacetate. The system catalyzes the oxidative decarboxylation of phenylglyoxylate to benzoyl-CoA and CO2. It can also react slowly with 2-oxo-3-methylbutanoate and use different electron acceptors such as benzyl viologen, methyl viologen, FAD or FMN, but NAD seems to be the physiological electron acceptor. It also catalyses an isotope exchange between CO2 and the carboxyl group which proves partial or complete reversibility of the oxidative decarboxylation reaction .
NADH-dependent phenylglyoxylate dehydrogenase subunit delta (PadF)
Type: Family

This family includes NADH-dependent phenylglyoxylate dehydrogenase subunit delta (PadF), which is involved in the anaerobic metabolism of phenylalanine and phenylacetate. The pathway catalyses the oxidative decarboxylation of phenylglyoxylate to benzoyl-CoA and CO2. It can also react slowly with 2-oxo-3-methylbutanoate and use different electron acceptors such as benzyl viologen, methyl viologen, FAD or FMN, but NAD seems to be the physiological electron acceptor. It also catalyses an isotope exchange between CO2 and the carboxyl group which proves partial or complete reversibility of the oxidative decarboxylation reaction .
Sulfate respiration complex hexadecaheme cytochrome HmcA (HmcA)
Type: Family

This entry represents a group of proteins mainly from Thermodesulfobacteriota, including HmcA (high molecular weight cytochrome complex protein A or high molecular weight cytochrome c), a periplasmic protein typically with 16 intact CxxCH motifs typical of c-type cytochromes. HmcA is encoded in a six-gene operon well-conserved in sulfur-reducing bacteria .
Sulfate respiration complex iron-sulfur protein HmcB (HmcB)
Type: Family

This entry represents a group of proteins mainly from Thermodesulfobacteriota, including HmcB (also known as Protein DVU_0535 and ORF2) from Nitratidesulfovibrio vulgaris. Members of this family are the periplasmic 4Fe-4S cluster-binding protein, part of the sulfate respiration complex Hmc .
DVU0259-like (DVU0259-like)
Type: Family

This entry represents a group of proteins mainly from Thermodesulfobacteriota, including DVU0259 from Nitratidesulfovibrio vulgaris (

, also known as DivK), a response regulator receiver domain protein apparently with no DNA-binding domain. The architecture suggests that DivK acts through protein-protein interaction rather than DNA-binding. DivK is found only in sulfate-reducing bacteria, and generally is found next to the operon that the hexadecaheme cytochrome HmcA.
Mollicutes-type lipoprotein signal peptide region (Lipoprotein_mollicutes-type_CS)
Type: Conserved_site

This entry represents a lipoprotein signal peptide predominantly found in Mollicutes, including Spiralin from Spiroplasma citri.
Glycosylhydrolase F510_1955-like (Glycosyl_F510_1955-like)
Type: Family

This entry represents a group of bacterial predicted glycosylhydrolases. This family is after for F510_1955, a lipoprotein from the Gram-positive bacterium Anoxybacillus gonensis .
Variant surface antigen A, N-terminal region (VlpA_N)
Type: Domain

This entry represents the N-terminal region of the highly repetitive surface antigen VlpA (variant lipoprotein A) of Mycoplasma hyorhinis, a pig pathogen, and similar sequences.
Variant surface antigen C, N-terminal region (VlpC_N)
Type: Domain

This entry represents the N-terminal region of the highly repetitive surface antigen VlpC (variant lipoprotein C) of Mycoplasma hyorhinis, a pig pathogen.
MPN555 chaperone-like (MPN555-like)
Type: Family

This entry includes MNP55 from Mycoplasma pneumoniae, also known as MG377 homolog. According to structural homology, this protein may be involved in protein folding as a molecular chaperone .
Transcciptional activator PmfR (Trans_act_PmfR)
Type: Family

This family includes transcriptional activator PmfR, a transcriptional regulator involved in the activation of the purU-mabO-folD-nepA-nepB and mao-ORF55-nbr operons implicated in the nicotine catabolic pathway. The sequence GTTT-14 bp-AAAC seems to be the core binding site of the regulator upstream of the -35 promoter region of the operon .
Sulfate reduction electron transfer complex DsrMKJOP subunit DsrO-like (DsrO-like)
Type: Family

This family represents a group of prokaryotic members of the DsrMKJOP dissimilatory sulfate reduction complex that contain an iron-sulphur binding domain (

), including subunit DsrO from Desulfovibrio desulfuricans (

), a periplasmic FeS protein. This membrane-bound redox complex is involved in sulfate reduction in sulfate-reducing organisms (SROs) . HmeA (Hdr-like menaquinol oxidoreductase iron-sulfur subunit 1) also belongs to this family. This protein is a subunit of HmeACDE, which is found in the sulfate-reducing archaeon Archaeoglobus fulgidus .
Sulfate reduction electron transfer complex DsrMKJOP subunit DsrP-like (DsrP-like)
Type: Family

This family represents a group of prokaryotic proteins, including the DsrP subunit of the DsrMKJOP dissimilatory sulfate reduction complex from Desulfovibrio desulfuricans (

), a highly hydrophobic protein .
Gas vesicle protein GvpO-like, N-terminal domain (GvpO-like_N)
Type: Domain

This entry represents the N-terminal domain of gas vesicle protein GvpO sequences from halobacteria. It is around 35-amino acids long and has three invariant Cys residues.
Surface lipoprotein P68-like (P68-like)
Type: Family

This entry represents a group of proteins from Mycoplasmatota, including P68 from Mesomycoplasma hyopneumoniae (

, Mhp390, a membrane-associated lipoprotein). P68 plays an important role in binding to swine tracheal cilia. It contributes to the production of proinflammatory cytokines and could induce significant apoptosis of lymphocytes and monocytes, which might weaken the host immune response .
Thiol peroxidase Prx-SUH (Perox_SUH)
Type: Family

This entry represents a group of thiol peroxidases Prx from Epsilonproteobacteria in which the last six amino acids are typically CCGXCH or CCGSUH, where U is selenocysteine. The function if this C-terminal hexapeptide region is not yet well understood .
Thermosome subunit alpha (thermosome_alpha)
Type: Family

This entry represents members of the TCP-1 chaperonin family, which includes thermosome subunits and T-complex protein 1 (TCP1) subunits. These proteins function as molecular chaperones, assisting in the folding of proteins upon ATP hydrolysis. The thermosome subunits, found in archaea, bind unfolded polypeptides and have weak ATPase activity. The TCP1 subunits, found in eukaryotes, are components of the chaperonin-containing T-complex (TRiC), which mediates the folding of proteins such as actin and tubulin. The TRiC complex also plays roles in telomere maintenance and ciliogenesis by regulating the assembly of the BBSome complex.
Vitamin B12-binding protein (Vit_B12_bind_prot)
Type: Family

This entry represents the Vitamin B12-binding protein, also known as the Cobalamin-binding protein or BtuF family protein. These proteins are part of the ABC transporter complex BtuCDF involved in the import of vitamin B12 (cobalamin). They bind vitamin B12 and deliver it to the periplasmic surface of BtuC. The function of these proteins is crucial for the utilization of vitamin B12, which is an essential cofactor in various enzymatic reactions. Members of this family are found in a wide range of bacterial species, including Escherichia coli, Salmonella, Vibrio, and Yersinia. The proteins typically belong to the BtuF family and share significant sequence similarity.
Ferredoxin-1 (FdxA)
Type: Family

Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. These proteins are found in various bacterial species including Pseudomonas aeruginosa, Pseudomonas putida, Rickettsia prowazekii, Rickettsia bellii, Rhodobacter capsulatus, Azotobacter vinelandii, Stutzerimonas stutzeri, Caulobacter vibrioides, Afipia felis, and Rickettsia typhi. Ferredoxins play a crucial role in electron transfer processes and may be involved in regulating gene expression by interacting directly with DNA in some species. The ferredoxin family includes different types such as Ferredoxin-1 and Ferredoxin-2, which are distinguished based on their specific sequences and functions.
Ferredoxin (FdxA_Actino)
Type: Family

Ferredoxins are iron-sulfur proteins that play a crucial role in electron transfer across a variety of metabolic reactions. These proteins are characterized by their ability to transfer electrons, which is essential for numerous biochemical processes. The ferredoxins described here are found in various Actinobacteria, including Mycolicibacterium smegmatis, Mycobacterium tuberculosis, Saccharopolyspora erythraea, Streptomyces griseus, and Mycobacterium bovis. They are typically small proteins, ranging from 105 to 114 amino acids in length. The primary function of these ferredoxins is to facilitate electron transport, which is vital for the metabolic activities of the organisms in which they are found.
UPF0122 family protein (UPF0122_fam_protein)
Type: Family

The UPF0122 family proteins are a group of conserved proteins that are believed to be involved in the signal recognition particle (SRP) pathway. This inference is based on the conservation of their genetic proximity to ftsY/ffh genes, which are key components of the SRP pathway. The exact function of these proteins is not fully understood, but they may act as regulatory proteins within this pathway. Members of the UPF0122 family are found across a wide range of bacterial species, indicating a potentially important and conserved role in bacterial cellular processes.
Transposase IS91 family (transpos_IS91)
Type: Family

The IS91 family transposase is involved in the transposition of insertion sequence elements. Members of this family are found in various bacterial species, including Pseudomonas savastanoi pv. phaseolicola and Sinorhizobium fredii. These transposases belong to the transposase 32 family and play a crucial role in the mobility of genetic elements within the genome. The transposase catalyzes the cut-and-paste mechanism of transposition, facilitating the movement of insertion sequences to new genomic locations. This activity can contribute to genetic diversity and adaptation in bacterial populations.
Acetamidase/formamidase family (FormamaseFmdA)
Type: Family

This entry represents formamidases, which are enzymes that hydrolyze formamide to produce ammonia, which can be used as a nitrogen source for growth. These enzymes may also act on other amides such as acetamide, propanamide, and butanamide, albeit more slowly. Members of this family include the putative formamidase C869.04 from Schizosaccharomyces pombe, formamidase from Methylophilus methylotrophus, and acetamidase from Mycolicibacterium smegmatis. These enzymes belong to the acetamidase/formamidase family.
Small archaeal modifier protein 1/3 (SAMP1_3)
Type: Family

Small archaeal modifier proteins 1 and 3 (SAMP1 and SAMP3) from Haloferax volcanii function as protein modifiers covalently attached to lysine residues of substrate proteins. This modification process, termed sampylation, involves the formation of an isopeptide bond between the C-terminal glycine carboxylate of SAMP proteins and the epsilon-amino group of lysine residues on target proteins. SAMP1 also serves as a sulfur carrier in molybdenum cofactor (MoCo) biosynthesis and may act as a proteolytic signal targeting proteins for degradation by proteasomes. In contrast, SAMP3 can form polymeric chains with itself at specific lysine residues and may regulate MoCo biosynthesis by inhibiting the activity of MPT synthase MoaE under aerobic conditions.