SII-SWORD/CoKE huggingface dataset:
HP0729-like (HP0729-like)
Type: Family

This entry represents the HP0729 protein from Helicobacter pylori (

) and related proteins found in Campylobacterales. The function of these proteins is unknown. They are predicted to adopt globular structure consisting of two domains, an N-terminal open β-barrel domain and a C-terminal domain composed of α-helices.
Zinc finger protein HVO_2753-like, euryarchaeota (HVO_2753-like_euryarch)
Type: Family

This entry represents the small zinc finger protein HVO_2753 from Haloferax volcanii (

) and related proteins from Euryarchaeota. HVO_2753 (also known as Small CPxCG-related zinc finger protein) has four C(P)XCG motifs, two that form a zinc binding pocket and binds one zinc atom, and two that form form a four-Cys cluster that do not bind zinc, All of them are critical for protein stability, folding and functionality . Short proteins of this family are important for stress adaptation, biofilm formation, and swarming.
Ion-translocating oxidoreductase complex subunit RnfC, Methanosarcinaceae (Ion_transpt_RnfC_Methano)
Type: Family

This entry represents the Ion-translocating oxidoreductase complex subunit C (RnfC,

) from Methanosarcina acetivorans and related proteins foind in Methanosarcinaceae species. RnfC is part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. RnfC catalyses sodium transport, most probably coupled to electron transfer from reduced ferredoxin to methanophenazine and heterodisulfide reductase. It is involved in heterodisulfide reduction during methanogenesis from acetate .
Ion-translocating oxidoreductase complex subunit RnfD, Methanosarcinaceae (Ion_transpt_RnfD_Methano)
Type: Family

This entry represents the Ion-translocating oxidoreductase complex subunit D (RnfD,

) from Methanosarcina acetivorans and related proteins found in Methanosarcinaceae species. RnfD is part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. RnfD catalyses sodium transport, most probably coupled to electron transfer from reduced ferredoxin to methanophenazine and heterodisulfide reductase. It is involved in heterodisulfide reduction during methanogenesis from acetate .
Ion-translocating oxidoreductase complex subunit RnfG, Methanosarcinaceae (Ion_transpt_RnfG_Methano)
Type: Family

This entry represents the Ion-translocating oxidoreductase complex subunit G (RnfG,

) from Methanosarcina acetivorans and related proteins found in Methanosarcinaceae species. RnfG is part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. RnfG catalyses sodium transport, most probably coupled to electron transfer from reduced ferredoxin to methanophenazine and heterodisulfide reductase. It is involved in heterodisulfide reduction during methanogenesis from acetate .
DNA import protein CedA, archaea (CedA_arc)
Type: Family

This entry represents the DNA import protein CedA (

) from Sulfolobus acidocaldarius and related proteins from Sulfolobaceae species. CedA is part of the Ced system, which is involved in DNA import. In most of the species, carrying the gene encoding CedA, CedA gene is flanked by two small genes (cedA1 and cedA2) and together, these three genes form an operon. CedA protein forms a complex with CedA1 and CedA2 and this highly stable complex localises to the membrane .
DNA import protein CedA1, archaea (CedA1_arc)
Type: Family

This entry represents the DNA import protein CedA1 (

) from Sulfolobus acidocaldarius and related proteins found in Thermoprotei species. CedA1 is part of the Ced system, which is involved in DNA import. In most of the species, the gene encoding CedA1 is located in the same operon with cedA and cedA2 genes. CedA1 protein forms a complex with CedA and CedA2 and this highly stable complex localises to the membrane .
Daptide-type RiPP biosynthesis methyltransferase (Daptide_MTase)
Type: Family

The members of this family are the methyltransferase proteins in Actinomycetota-type daptide biosynthesis operons. Daptides are a class of ribosomally synthesised and post-translationally modified peptides (RiPPs) that feature a C terminus modified with (S)-N2,N2-dimethyl-1,2-propanediamine . These proteins contain a methyltransferase domain (

).
Daptide-type RiPP biosynthesis aminotransferase (Daptide_aminotransferase)
Type: Family

Members of this family are the aminotransferase, or D protein, of Actinomycetota-type daptide biosynthesis operons. Daptides are a class of ribosomally synthesised and post-translationally modified peptides (RiPPs) that feature a C-terminal modified with (S)-N2,N2-dimethyl-1,2-propanediamine .
Daptide-type RiPP biosynthesis dehydogenase (Daptide_DH)
Type: Family

Members of this family are dehydrogenases, or C proteins, of Actinomycetota-type daptide biosynthesis operons. Daptides are a class of ribosomally synthesised and post-translationally modified peptides (RiPPs) that feature a C terminus modified with (S)-N2,N2-dimethyl-1,2-propanediamine . These proteins contain an alcohol dehydrogenase (iron-type) domain (

).
Daptide biosynthesis RiPP recognition element containing protein (Daptide_RRE)
Type: Family

Members of this family are the B proteins of Actinomycetota-type daptide biosynthesis operons. The C-terminal region of these proteins contains a RiPP recognition element (RRE). Daptides are a class of ribosomally synthesised and post-translationally modified peptides (RiPPs) that feature a C terminus modified with (S)-N2,N2-dimethyl-1,2-propanediamine .
Daptide biosynthesis intramembrane metalloprotease (Daptide_HExxH)
Type: Family

Members of this family are intramembrane metalloendopeptidases with a typical HExxH motif, found in biosynthetic gene clusters for daptide-type RiPP peptide biosynthesis and probably performing export-related cleavage. Daptides are a class of ribosomally synthesised and post-translationally modified peptides (RiPPs) that feature a C terminus modified with (S)-N2,N2-dimethyl-1,2-propanediamine .
Zinc finger protein HVO_0416-like (HVO_0416-like)
Type: Family

This entry represents the zinc finger protein HVO_0416 from Haloferax volcanii (

) and related proteins from Halobacteria. Short proteins of this family are important for stress adaptation, biofilm formation, and swarming . These proteins are predicted to adopt a rubredoxin-like fold.
Zinc finger protein HVO_0649-like (HVO_0649-like)
Type: Family

This entry represents the zinc finger protein HVO_0649 from Haloferax volcanii (

) and related proteins from Halobacteria. Members of this family are microproteins (less than 100 residues long) that are important for stress adaptation, biofilm formation, and swarming . They are predicted to adopt rubredoxin-like fold.
Zinc finger mu-protein HVO_0758-like (HVO_0758-like)
Type: Family

This entry represents the HVO_0758 mu-protein from halophilic mesophile archaeon Haloferax volcanii (

) and related proteins from Halobacteria. HVO_0758 is a small protein of 56 amino acid residues, containing two highly conserved CXXC and CPXC sequence motifs. The structure of this protein has a typical Zinc ribbon fold consisting of a small N-terminal α-helix and two knuckles at the tip of two β-hairpins that contain the zinc coordinating residues . This protein plays an essential role in swarming behaviour and biofilm formation .
Teichoic acid glycerol-phosphate primase (TarB)
Type: Family

This protein family represents Teichoic acid glycerol-phosphate primase from Staphylococcus aureus (TarB) (

) and similar sequences from Staphylococcus species. TarB catalyses the addition of a single glycerol phosphate residue to the prenoldiphosphate-linked disaccharide .
Zinc finger protein HVO_2142-like (HVO_2142-like)
Type: Family

This entry represents the zinc finger protein HVO_2142 from Haloferax volcanii (

) and related sequences from Haloferacales species. Members of this family are short proteins, about 50-70 residues long, and are important for stress adaptation, biofilm formation, and swarming . These proteins are predicted to adopt a rubredoxin-like fold.
Teichoic acid glycerol-phosphate transferase (TarF)
Type: Family

This protein family represents Teichoic acid glycerol-phosphate transferase from Staphylococcus aureus (TarF) (

) and similar sequences from Staphylococcus species. TarF catalyses the addition of a second glycerol phosphate unit from CDP-glycerol to the prenolpyrophosphate-linked disaccharide, to complete the linkage unit .
Zinc finger protein HVO_2523-like (HVO_2523-like)
Type: Family

This entry represents the zinc finger protein HVO_2523 from Haloferax volcanii (

) and related proteins from Halobacteria. Members of this family are short proteins about 40-70 residues long and are important for stress adaptation, biofilm formation, and swarming . These proteins are predicted to adopt rubredoxin-like fold.
Teichoic acid ribitol-phosphate polymerase TarL (TarL)
Type: Family

This protein family represents Teichoic acid ribitol-phosphate polymerase TarL from Staphylococcus aureus (

) and similar sequences from Staphylococcus species. TarL is responsible for the polymerisation of the main chain of the major teichoic acid by sequential transfer of ribitol phosphate units from CDP-ribitol to the second glycerol phosphate attached to the disaccharide linkage unit. It synthesises polymers of more than 40 ribitol phosphate units in length .
Zinc finger protein HVO_2901-like (HVO_2901-like)
Type: Family

This entry represents the zinc finger protein HVO_2901 from Haloferax volcanii (

) and related proteins from Halobacteria. Members of this family are microproteins that are important for stress adaptation, biofilm formation, and swarming . This group includes proteins that are predicted to adopt two domain architecture composed of an N-terminal C2HC and a C-terminal rubredoxin-like zinc fingers.
Aminotransferases class-III pyridoxal-phosphate attachment site (Aminotrans_3_PPA_site)
Type: Conserved_site

This entry represents the class-III Aminotransferase pyridoxal-phosphate attachment site.

Aminotransferases share certain mechanistic features with other pyridoxalphosphate-dependent enzymes, such as the covalent binding of the pyridoxalphosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies . One of these, called class-III, includes:

Acetylornithine aminotransferase (

), which catalyses the transfer of an amino group from acetylornithine to alpha-ketoglutarate, yielding N-acetyl-glutamic-5-semi-aldehyde and glutamic acid ;

Ornithine aminotransferase (

), which catalyses the transfer of an amino group from ornithine to alpha-ketoglutarate, yielding glutamic-5-semi-aldehyde and glutamic acid ;

Omega-amino acid--pyruvate aminotransferase (

), which catalyses transamination between a variety of omega-amino acids, mono-and diamines, and pyruvate ;

4-aminobutyrate aminotransferase (

) (GABA transaminase), which catalyses the transfer of an amino group from GABA to alpha-ketoglutarate, yielding succinate semialdehyde and glutamic acid ;

DAPA aminotransferase (

), a bacterial enzyme (bioA), which catalyses an intermediate step in the biosynthesis of biotin, the transamination of 7-keto-8-aminopelargonic acid to form 7,8-diaminopelargonic acid ;

2,2-dialkylglycine decarboxylase (

), a Burkholderia cepacia (Pseudomonas cepacia) enzyme (dgdA) that catalyses the decarboxylating amino transfer of 2,2-dialkylglycine and pyruvate to dialkyl ketone, alanine and carbon dioxide ;

Glutamate-1-semialdehyde aminotransferase (

) (GSA) ;

Bacillus subtilis aminotransferases yhxA and yodT;

Haemophilus influenzae diaminobutyrate--2-oxoglutarate aminotransferase (HI0949) ;

Caenorhabditis elegans alanine--glyoxylate aminotransferase 2-like (T01B11.2).
Sensor histidine kinase VxrA-like (VxrA-like)
Type: Family

This family includes Sensor histidine kinase VxrA from Vibrio cholerae and similar sequences from Vibrionales. VxrA is a sensor histidine kinase that, together with response regulator VxrB, is responsible for virulence, the positive regulator of biofilm formation, and for regulation of the type VI secretion system (T6SS) . It contributes to the resistance to beta-lactam treatment .
PP0621-like (PP0621-like)
Type: Family

This entry represents PP0621 family protein from Halomonas sp. (

) and similar short bacterial sequences. Members of this family contain an N-terminal signal peptide and three invariant Cys residues, two of which are located within a CXXC sequence motif.
Isoniazid-inducible protein IniB-like, N-terminal domain (IniB-like_N)
Type: Domain

This entry represents a small domain found N-terminal in a number of low-complexity proteins from Actinomycetes that often bear little or no similarity to each other in a full length, including Isoniazid-induced protein IniB from Mycobacterium tuberculosis (

).
PA3371-like (PA3371-like)
Type: Family

This entry represents the uncharacterised protein PA3371 from Pseudomonas aeruginosa (

) and related short sequences from Pseudomonadales. Members of this family have a C-terminal extension with a nearly invariant motif GRRIKRDPVLR.
Polysaccharide export protein (Poly_export)
Type: Family

This entry represents a group of bacterial polysaccharide export proteins, including Wza from Escherichia coli (

), which is likely to be involved in the export of the extracellular polysaccharide colanic acid (CA) from the cell to medium and Capsule polysaccharide export outer membrane protein CtrA from Neisseria meningitidis, which may function as a membrane anchor for capsular polysaccharides.
Pr6Pr membrane protein-like (Pr6Pr-like)
Type: Family

Members of this prokaryotic family (Pr6Pr) have fairly uniform sizes and topologies with about 250 amino acid residues and 6 predicted transmembrane helices. Their function is unknown.
BB0208-like (BB0208-like)
Type: Family

This family is named for uncharacterised protein BB_0208 (

) from the Lyme disease spirochete Borrelia burgdorferi. Members average about 570 amino acids in length and are found in over twenty species of Borrelia and Borreliella.
Biofilm-surface layer hydrophobin BslB (BslB-like)
Type: Family

This entry represents the BslB-like family of proteins. BslB (biofilm-surface layer protein A), found in Bacillus subtillis (

) and in other Bacillus species, is a paralog of the better characterised BslA (

), which forms a hydrophobic surface on biofilms. Both are classified as hydrophobins, a bacterial counterpart to small amphiphilic proteins of filamentous fungi .
Galactofuranose ABC transporter YtfR (YtfR-like)
Type: Family

This entry represents the Galactofuranose transporter ATP-binding protein YtfR from E.coli (

) and related proteins from alpha- and gammaproteobacteria. YtfR has been identified as subunit of the YtfQRT-YjfF complex .
Acyl halogenase CylC-like (CylC-like)
Type: Family

This entry represents the homologues of CylC and related proteins mainly from cyanobacteria. CylC has been characterised as a halogenase involved in the biosynthesis of cylindrocyclophane . Another member of this family, cyanobacterial NocO, has recently been implicated in the biosynthesis of chlorosphaerolactylates and nocuolactylates . NocO had been suggested to play a role in the synthesis of natural oxadiazines such as nocuolin A (NoA, exhibits anti-proliferative activity against human cancer cell lines). Members of this family are also similar to cyanobacterial ColD and ColE, putative acyl halogenases involved in columbamide biosynthesis .
Brucella phage major capsid protein AKO59007-like (AKO59007-like)
Type: Family

A founding member of this family, (AKO59007,

) was identified as the major head protein in Brucella phage 02_19 during a comparison of Brucella phage genomes . The N-terminal half appears to the better conserved region with fewer insertions and deletions.
Type 4 apparatus protein DotZ-like (DotZ-like)
Type: Family

This entry represents the Type 4 apparatus protein DotZ (

) from Legionella pneumophila and related proteins fround in Legionella species. DotZ is a component of membrane-embedded T4 coupling complex (T4CC), which consists of the DotL ATPase, the DotM and DotN proteins, and DotY and DotZ. The DotLMNYZ hetero-pentamer plays an essential role in the recruitment and delivery of effectors to the Type IV secretion (T4S) machinery in Legionella pneumophila, a bacterial pathogen that uses a T4S system to inject effector proteins into human macrophages. DotZ is an integral part of the T4CC and plays a significant role in the translocation of effectors .
Translation elongation factor EF1B, beta/delta subunit (EF1B_bsu/dsu)
Type: Family

This family represents Elongation factor 1-beta/delta, which stimulate the exchange of GDP bound to EF-1-alpha to GTP, regenerating EF-1-alpha for another round of transfer of aminoacyl-tRNAs to the ribosome.

Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) .
Metallo-beta-lactamase VIM-1/2, metallo-hydrolase domain (VIM-1/2_MBL)
Type: Domain

This entry represents the metallo-hydrolase domain found in the metallo-beta-lactamases VIM-1 from Pseudomonas aeruginosa, VIM-2 from Escherichia coli, and similar VIM (Verona integron-encoded metallo-beta-lactamase)-type proteins from gammaproteobacteria. These proteins are class B beta-lactamases that confer resistance to the beta-lactam antibiotics, including penicillins, cephalosporins and carbapenems via hydrolysis of the beta-lactam ring .

VIM-type metallo-beta-lactamases (MBLs) are integron-associated and are widely distributed acquired MBLs. MBLs (class B of the Ambler beta-lactamase classification) have been divided into three subclasses B1, B2 and B3, based on their sequence and structural relationships, and on their substrates, with the B1 and B2 MBLs being most closely related to each other . This subgroup of VIM-type MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile .
Stressosome-associated protein Prli42 (Prli42-like)
Type: Family

This entry represents the family of Prli42, characterised in Listeria monocytogenes and found broadly in the Firmicutes . Prli42 is a membrane protein of very small size, essential to the function of the stressosome. In L. monocytogenes, this protein is capable of activating the stressosome via direct interaction with the non-haem binding domain of RsbR. Prli42 communicates with RsbR through its N-terminal domain, which may be responsible for sensing or transmission of stress signals from the extracellular environment . Prli42 family appears to be distantly related to DUF4044 (

).
BPSL0761 protein-like (BPSL0761-like)
Type: Domain

This entry represents a domain found N-terminal in the uncharacterised protein BPSL0761 (

) from Burkholderia pseudomallei and related proteins from proteobacteria. The function of this domain is unknown.
Trehalose monomycolate transport factor TtfA (Treh_trans_TtfA)
Type: Family

This family represents the trehalose monomycolate transport factor A (TtfA) which is required for the transport of trehalose monomycolate across the inner membrane, potentially by forming a complex with the atypical lipid transporter MmpL3. Trehalose monomycolate is a component of the mycobacterial envelope. The core domain of TtfA shows strong structural similarity to class I type III secretion system (T3SS) chaperones. It is also required for growth and cell elongation .
STM3845 retron effector protein (STM3845-like)
Type: Family

Members of this bacterial family, such as STM3845 from a retron in Salmonella enterica called St-85 (

), are found in the vicinity of reverse transcriptases (RNA-directed DNA polymerase) and retron structural RNA genes. This protein is not required for msDNA (Multicopy Single-Stranded DNA) biosynthesis, but instead is assigned an effector function .
Trehalose monomycolate transport factor A-like, core domain (TtfA-like_core)
Type: Domain

TtfA (trehalose monomycolate transport factor A) plays a role in the transport of trehalose monomycolate across the inner membrane, potentially by forming a complex with the atypical lipid transporter MmpL3. Trehalose monomycolate is a component of the mycobacterial envelope. The core domain of TtfA shows strong structural similarity to class I type III secretion system (T3SS) chaperones, and TtfA may play other roles besides assisting in mycolate transport, given its phylogenetic distribution .

This domain is only found in actinobacteria, in which the high sequence identity is found in homologues from mycobacteria. However, TtfA homologues are also found in other mycolic acid-producing bacteria such as corynebacteria, nocardia, or rhodococcus. Unexpectedly, although less conserved, TtfA homologues were also identified in non-producing mycolic acid bacteria, such as pseudonocardia or streptomyces .
ABC transporter permease subunit YbbP (YbbP)
Type: Family

This entry represents the ABC transporter permease YbbP from E.coli and related proteins mainly found in enterobacteriaceae. YbbP is associated with and presumed to form a complex with the putative ABC transporter ATP-binding protein YbbA. The exact function of this protein is unknown.
BA3454 stress response protein (BA3454-like)
Type: Family

This entry represents the family of BA3454 protein (

), a protein that is up-regulated strongly by SpxA2 during stress conditions . Members of this family are found in Bacillales.
Peptidoglycan endopeptidase RipB (RipB)
Type: Family

This entry represents the Peptidoglycan endopeptidase RipB from Mycobacterium tuberculosis and related proteins from mycobacteriales. RipB is a peptidoglycan endopeptidase that cleaves the bond between D-glutamate and meso-diaminopimelate . It binds high-molecular weight peptidoglycan, but does not degrade it. RipB is required for the normal separation of daughter cells after cell division and cell wall integrity .
SNF2/RAD5-like, C-terminal helicase domain (SNF2/RAD54-like_C)
Type: Domain

This entry represents the C-terminal helicase domain of yeast DNA repair and recombination protein RAD54 and similar sequences from all domains in life.

The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA .
LVIS_2131-like (LVIS_2131-like)
Type: Family

This entry represents a family of uncharacterised proteins, found mainly in Lactobacillales, including LVIS_2131 (

) from Levilactobacillus (Lactobacillus) brevis. The function of these proteins is unknown.
Smlt3025-like (Smlt3025-like)
Type: Family

This family includes Smlt3025 (

), an immunity protein of the type IV secretion system (T4SS) found in the multi-drug-resistant opportunistic pathogen Stenotrophomonas maltophilia. Experiments show that Smlt3025 counteracts Smlt3024, an effector protein transferred by the T4SS into target cells. The crystal structure of Smlt3025 reveals a topology similar to the iron-regulated protein FrpD from Neisseria meningitidis which has been shown to interact with the RTX protein FrpC, while its counterpart Smlt3024 is homologous to the N-terminal domain of large Ca2-binding RTX proteins .