SII-SWORD/CoKE huggingface dataset:
BCAM0308-like (BCAM0308-like)
Type: Family

This family includes BCAM0308 from Burkholderia cenocepacia (

) and similar bacterial proteins. BCAM0308 is one of several proteins in the lxa (low oxygen-activated) locus, whose proteins are induced upon low oxygen concentrations . Members of this family are ~170 amino acids long, and contain a conserved pair of CxxC motifs, suggesting metal-binding.

This family is predicted to share structural similarity to the central part of Nmd3 that consists of eL22-like α/β domain and a treble clef zinc finger.
Phenolic acid decarboxylase VdcD-like (VdcD-like)
Type: Family

This entry represents a family of bacterial enzymes that are involved in non-oxidative decarboxylation and detoxification of phenolic derivatives both aerobic and anaerobic conditions, such as Protein VdcD from Streptomyces sp. and Protein BsdD from Bacillus subtilis or under anaerobic conditions , such as Protein EcdD from Escherichia coli . It is not known if VdcD form a hetero-complex composed of VdcB, VdcC and VdcD. The term subunit here is used to refer to the operon, however, currently there is no experimental evidence for the existence of the complex .
CD1871A-like (CD1871A-like)
Type: Family

This entry represents a group of bacterial proteins, including CD1871A from Clostridium difficile . Members of this family typically are small proteins (often less than 50 amino acids in length) with a highly conserved C-terminal motif CLECxGIG that is predicted to feature a redox-active disulfide bond. The N-terminal portion is hydrophobic and resembles a transmembrane α-helix.
HpsJ-like (HpsJ-like)
Type: Family

This entry represents HpsJ (hormogornium polysaccharide J) and related proteins. HpsJ is thought to be a part of a secretion system, unique to filamentous cyanobacteria, and involved in the biosynthesis or secretion of an extracellular polysaccharide, essential for motility .
IS5-like transposase (Transpos_IS5-like)
Type: Family

This entry represents a group of bacterial IS5 transposases. Most members have as an N-terminal domain

.
Conjugated bile acid hydrolase (CBAH)
Type: Family

This entry represents conjugated bile acid hydrolase from Clostridium perfringens (CBAH) and similar sequences from firmicutes and actinomycetes. CBAH is a bile salt hydrolase that catalyses the deconjugation of glycine- and taurine-linked bile salts, which occurs naturally in the intestines of humans, releasing amino acid residues and deconjugated bile salts (bile acids). This enzyme can also hydrolyse the amide bond in major human bile salts, such as glycocholate (GCA), taurocholate (TCA) and taurodeoxycholate (TDCA). It shows a slight preference for taurine-conjugated bile acids as substrates .
FAD-dependent urate hydroxylase (HpxO)
Type: Family

This entry represents a FAD-dependent urate hydroxylase from Klebsiella pneumoniae (HpxO) and similar sequences mainly found in gammaproteobacteria and actinomycetes. HpxO is an FAD-dependent urate hydroxylase (

) that is responsible for the conversion of uric acid to 5-hydroxyisourate, which decomposes spontaneously to allantoin and CO2. It oxidises NADH to NAD(+), and produces H20 . This enzyme contains the GxGxxG(x)17E sequence motif and is a member of the well-studied flavin adenine dinucleotide (FAD)-dependent glutathione reductase superfamily . HpxO consists of two domains with the FAD-binding and active site located at the interface of these domains.
Uncharacterised cupin fold protein DHCW (DHCW_cupin)
Type: Family

This entry represents a group of uncharacterised bacterial proteins that resemble other cupin superfamily small barrel proteins and have a motif DHCW, for which the family is named.
Mks condensin complex protein MksF, putative (MksF_put-like)
Type: Family

This entry represents a small family of proteins found in gammaproteobacteria, including sequences related to the MksBEF complex, which primarily function in structural chromosome maintenance .
EboA domain (EboA_dom)
Type: Domain

This entry represents the bacterial EboA (eustigmatophyte/bacterial operon A) domain, which belongs to a broadly distributed system of six proteins. The ebo system in general appears to be involved in trafficking of certain natural product precursors whose biosynthesis requires export at least as far as the periplasm. Scytonemin is an example of one natural product whose biosynthesis requires an Ebo system .
Metabolite traffic protein EboA (EboA)
Type: Family

This entry represents a group of proteins specific to cyanobacteria that carry the EboA (eustigmatophyte/bacterial operon A) domain. Members of this family appear required for transport of certain secondary metabolite precursors to the periplasm, including (but not limited) to precursors of scytonemin. More than half members of this group belong to scytonemin producers .
CC-star protein (CC_star_Cory)
Type: Family

This entry represents a family of bacterial proteins that contain the CC-star motif (Cys-Cys-COOH), that is, a pair of Cys residues as the final two residues, including

from Corynebacterium pollutisoli. Members of this family are typically encoded next to an ArsA family ATPase, suggesting a role in heavy metal metabolism, and predicted carbon starvation protein A.
Anti-sigma factor RsbA-like (RsbA-like_anti_sig)
Type: Family

This entry represents a group of proteins specific to actinomycetes, including RsbA of Streptomyces coelicolor (

). RsbA was suggested as an anti-sigma factor by genomic location preceding sigB, by homology to RsbW of Bacillus subtilis, and by binding to SigmaB and effects on its activity . Members of this family have MEDS sensory domain in the N-terminal region and a histidine kinase-like ATPase domain in the C-terminal region. The proteins included in this group may perform different regulatory functions in different lineages such as PrsR from Streptomyces avermitilis (

), an important regulator of both avermectin production and stress responses .
SCO5918-like (SCO5918-like)
Type: Family

This entry represents a family of uncharacterised proteins found in Streptomyces, including SCO5918 (

).
Mks condensin complex protein MksB, putative (MksB_put-like)
Type: Family

This entry represents a small family of proteins found in gammaproteobacteria that are part of MksBEF complex, including MksB. This complex is involved in structural chromosome maintenance . MksB, together with SMC, is essential during ocular infections. Inactivation of MksB, whether in the presence or absence of SMC, impairs biofilm formation and facilitates planktonic growth . In addition, inactivation of MksB and SMC reduces the production of virulence factors.
DISARM protein DrmB (DrmB)
Type: Family

This entry represents a group of proteins found in bacteria and some archaeal species, including DISARM protein DrmB from Bacillus paralicheniformis. DrmB is a component of anti-phage defence system DISARM (defense island system associated with restriction-modification), probably a multi-gene restriction module. This subunit has an unknown function. Expression of DISARM in B.subtilis confers resistance to several phages. This system does not interfere with phage adsorption, but instead interferes with viral DNA replication early in its cycle, preventing replication, circularisation and lysogeny and probably causes phage DNA degradation . Many other members of this group show a MrfA-like Zn-binding domain (

) at the C-terminal end.
Uncharacterised protein STM4015-like (STM4015-like)
Type: Family

This entry represents a group of bacterial proteins of unknown function, regularly found in a conserved gene neighbourhood that also includes two uncharacterised radical SAM proteins. This protein family includes STM4015 from Salmonella typhimurium (

).
Mks condensin complex protein MksE, pseudomonadaceae (MksE_pseudomon-like)
Type: Family

This entry represents a small family of proteins found in gammaproteobacteria, including MksE. These proteins are part of MksBEF complex, which primarily function in structural chromosome maintenance . These are also integrated into the control of multiple genetic programs related to epigenetic and virulent behaviour.

The N-terminal part of MksE is remotely related to the chromosome partition protein MukE and most likely adopts the same structure that consists of two winged helix domains (WHD) .
Streptophobe SCO7274-like (Streptophobe)
Type: Family

This entry represents a group of uncharacterised proteins that are restricted almost entirely to the genus Streptomyces , including SCO7274 from Streptomyces coelicolor (

). Members are probably associated with membrane given its high hydrophobicity.
Transcriptional regulator AlgP, N-terminal domain (AlgP_N)
Type: Domain

This entry represents the conserved N-terminal domain of Transcriptional regulatory protein AlgP from Pseudomonas aeruginosa and similar proteins from pseudomonadales.

The insights into the AlgP function are rather controversial. It was suggested that AlgP is required for transcription of the key biosynthetic gene AlgD, which is necessary for production of the exopolysaccharide alginate causing mucoidy in P. aeruginosa . However, more recent studies counter this by providing evidence that alginate production is not greatly affected by AlgP .
Chaperone CsgH domain (CsgH_dom)
Type: Domain

This entry represents a domain found in CsgH homologues. The designation CsgH was given to a broad set of homologues, found outside the Enterobacteriales, of the curli amyloid fibre formation periplasmic chaperone CsgC from species such as Escherichia coli and Salmonella.

The homologous CsgH and CsgC proteins adopt the same fold with a typical Ig-like topology of the β-sandwich .
Uncharacterised protein Sce7725-like (Sce7725-like)
Type: Family

This entry represents a family of uncharacterised bacterial proteins, including Sce7725 from Sorangium cellulosum (

). It belongs to a gene pair found sporadically in genera as diverse as Enterococcus, Lactobacillus, Staphylococcus, Streptococcus, Acinetobacter, and Klebsiella. The partner in each gene pair is a member of the Sce7726 family (

).
Lipid droplet-associated protein (LipDrop-assoc)
Type: Family

This entry represents a family of lipid droplet-associated proteins from actinomycetes, including

from Rhodococcus jostii RHA1, which has been shown to associate specifically with lipid droplets , and it orthologue

from Mycobacterium tuberculosis. These lipid droplets consist of a neutral lipid core enveloped by a phospholipid monolayer and surface proteins. Lipid droplets of triacylglycerol can be especially prominent in proteins from the genus Rhodococcus, but occur also in Mycobacterium tuberculosis and can support dormancy of that pathogen.
Sce7726-like (Sce7726-like)
Type: Family

This entry represents a group of uncharacterised proteins, including Sce7726 from Sorangium cellulosum (

). It belongs a gene pair found sporadically in genera as diverse as Enterococcus, Lactobacillus, Staphylococcus, Streptococcus, Acinetobacter, and Klebsiella, or in tailed bacteriophages from those lineages. The partner in each gene pair is a member of the Sce7725 family (

).
ABZJ_00895-like (ABZJ_00895-like)
Type: Family

This entry represents a family of functionally uncharacterised proteins mainly found in proteobacteria that resemble transmembrane transporters in their extensive hydrophobicity, including ABZJ_00895 from Acinetobacter baumannii (

). The expression of this protein was shown to be reduced significantly in a colistin-resistant lpxC disruption mutant of Acinetobacter baumannii .
Zinc beta-ribbon finger, putative (Zinc_ribbon_put)
Type: Domain

This domain of unknown function is predominantly found in uncharacterised proteins from Bacteroidetes. This domain is about 60 amino acids in length and is found N-terminal to

that resembles DNA primase core domain. It has four nearly invariant Cys residues, two of which located in unusual motif VGRCxxxxxCGYH.

This domain has remote similarity to the zinc-ribbon domain of DNA primase (

)and it is predicted to adopt the same structure.
Inner membrane protein YedE-like (YedE-like)
Type: Family

This entry represents a group of proteins mainly found in proteobacteria, including inner membrane protein YedE from Escherichia coli and Cj1500 from Campylobacter jejuni (

, also known as FdhT), which was show to be essential for formate dehydrogenase (a selenocysteine-containing enzyme) expression and activity . Members of this family are predicted multiple membrane-spanning proteins, and therefore thought likely to be transporters . All proteins belonging to this group carry a sulphur transport domain (

). It appears that all species whose genomes encode a member of this family produce selenocysteine-containing enzymes, typically formate dehydrogenase. This family is related to (but distinct from) that of

, which is similarly restricted to species with pathways for selenium incorporation.
Thiosulfate transporter TsuA (TsuA-like)
Type: Family

This entry represents a group of proteins specific to enterobacteria, including thiosulfate transporter TsuA from Escherichia coli, also known as YeeE, is involved in thiosulfate utilisation .
GrdX-like (GrdX-like)
Type: Family

This entry represents a family of bacterial proteins, including GrdX. GrdX is a small protein, of unknown function, encoded in grd operons for selenocysteine-dependent glycine reductase systems . A small number of GrdX proteins appear to be encoded with a UGA-encoded selenocysteine residue appearing close to the N terminus, at sites that do not align with Cys residues in other members of the family. This arrangement suggests that the ability to complete translation of GrdX selenoproteins may have regulatory value, in addition to its molecular function.
Rodlin protein RdlA/B-like (RdlA/B-like)
Type: Family

This entry represents a group of proteins from actinomycetes, including Rodlin protein RdlA/B from Streptomyces coelicolor. Both proteins are required for rodlet formation and form part of the rodlet layer on the spore surface . Unlike RdlB, RdlA does not form amyloid fibrils in vitro .
Rz1-like lysis system protein LysC (LysC)
Type: Family

This entry represents a group of proteins from tailed bacteriophages and bacterial prophages mainly found in proteobacteria, including LysC from Burkholderia phage ST79 (Bacteriophage ST79) (

). LysC is an Rz1-like component of a phage lytic system, substantially overlapping although not fully embedded in the gene for the Rz-like LysB component. The phage lysis defect in the absence of a functional LysB/LysC system appears in the presence of high concentrations of divalent cations .
SAV_2336-like, N-terminal (SAV_2336-like_N)
Type: Domain

This entry describes an N-terminal domain shared by SAV_2336 from Streptomyces avermitilis (

) whose C-terminal region suggests restriction enzyme activity , and other proteins with unrelated C-terminal regions. A member protein was also identified in a kanamycin biosynthetic gene cluster , while N-terminal regions of two other member proteins were named Trypco1 in a bioinformatic study of predicted bacterial conflict systems. Members of this group are predominantly found in actinomycetes and cyanobacteria.
Growth-regulating ATPase SCO5717-like, N-terminal domain (SCO5717-like_N)
Type: Domain

This entry represents the short N-terminal domain of the tyrosine-phosphorylated protein SCO5717 from Streptomyces coelicolor (

) and similar sequences from actinomycetes. SCO5717 seems to be involved in the regulation of bacterial growth . Members of this unusual protein family usually have a long, low-complexity, typically Pro-rich region, then a AAA+ family ATPase domain, and then another region of low-complexity sequence.
SMEK domain (SMEK_dom)
Type: Domain

This entry represents the SMEK domain, which is found at the N-terminal end of a group of bacterial proteins. It is named for four genera in which multiple, diverse members of this group of bacterial proteins are found: Staphylococcus, Mycoplasma, Escherichia, and Klebsiella.

The SMEK domain is predicted to adopt an α/β fold that resembles the core of restriction endonuclease enzymes. It contains four scattered invariant residues (Glu, Asp, Gln, and Lys) that may be functionally relevant.
Uncharacterised protein DIP1984-like (DIP1984-like)
Type: Family

This entry represents a group of uncharacterised bacterial sequences, including DIP1984 from Corynebacterium diphtheriae (

), which has a solved crystal structure. Some members of this family previously have been annotated, incorrectly, as septolysin. However, septolysin O, and other members of the family of cholesterol-dependent cytolysins such as listeriolysin O, are unrelated.

DIP1984 protein adopt α-helical structure consisting of four α-helices arranged in L-shape that self-associate to form a hollow pumpkin-like particle

.
Uncharacterised protein PA4642-like (PA4642-like)
Type: Family

This family represents small (about 95 amino acids), uncharacterised proteins apparently restricted to gammaproteobacteria, including PA4642 from Pseudomonas aeruginosa (

).
Membrane protein YnhF-like (YnhF-like)
Type: Family

This entry represents a group of proteins from gammaproteobacteria, including YnhF from Escherichia coli, which was shown to have an intact fMet residue at the N terminus and to be chloroform-soluble . Members of this protein family, are small membrane proteins, about 29 amino acids in length. These proteins are predicted to fold into a single transmembrane helix.
Membrane protein YmiA, putative-like (YmiA_put-like)
Type: Family

This entry represents a small family of uncharacterised proteins found in Gammaproteobacteria. They are predicted to fold into a single transmembrane helix.
Autotransporter-associated protein SinI-like (SinI-like)
Type: Family

Members of this family, including SinI from Salmonella enterica LT2, are putative passenger proteins of a variant-type type V secretion system (T5SS) . In this system, SinH or a homologue is an inverse autotransporter that transports a member of this family as well as its own passenger domain.

These proteins are predicted to have two similar domains with Ig-like topology.
Cell wall amidase Dae2/Tae2-like (Dae2/Tae2-like)
Type: Family

This entry represents cell wall amidases, including domesticated amidase effector 2 (Dae2) from ticks and type VI amidase effector 2 (Tae2, also known as BTH_I0068

) from bacteria .
Dae2 has been horizontally acquired from bacteria and has structurally and biochemically diverged from its ancestral bacterial counterparts, leading to broadened antimicrobial specificity .

Dae2 is a gut and saliva antibacterial peptide that directly antagonizes host skin commensals which enter the ticks during feeding . It acts as a cell wall hydrolase that cleaves the bond between gamma-D-glutamate-meso-diaminopimelate of a peptide stem and D-alanine of another peptide stem in peptidoglycans .

These proteins are predicted to fold into an open β-barrel with SH3-like topology.
Zinc ABC transporter ATP-binding protein AztA-like (AztA-like)
Type: Family

This entry represents a group of proteins mainly from proteobacteria and actinomycetes, including

from Paracoccus denitrificans . Members of this family show an AAA ATPase domain (

).
Pathogenicity island replication protein STY4528-like (STY4528-like)
Type: Family

This entry represents a group of proteins mainly found in gamma/betaproteobacteria, including STY4528 from Salmonella pathogenicity island 7 (SPI-7) of Salmonella typhi (

), which belongs to the core set of proteins of SPI-7-related conjugative elements, and is assigned to the replication region . Members include a protein designated Api5 from the Yersinia pseudotuberculosis adhesion pathogenicity island (YAPI) .
Uncharacterized protein YdjY-like (YdjY-like)
Type: Family

The founding member of this family is the poorly characterised protein YdjY, an apparent lipoprotein, of Escherichia coli K-12. Many members are lipoproteins. YdjY and other members of its branch of the broader family have an invariant GCxxCxxxC motif.
Plasmid mobilization protein MobA-like (MobA-like)
Type: Family

This entry represents a small family of MobA homologues, including mobilisation protein NikA. These proteins are involved in mobilisation and replication functions of plasmids . They are distantly related to accessory factor PcfF and most likely adopt the same homo-dimeric structure consisting of N-terminal DNA binding ribbon-helix-helix (RHH) domain and a C-terminal stalk domain.
PBP2a activator MacP (MacP)
Type: Family

This entry represents the penicillin-binding protein 2a activator MacP protein. MacP is a membrane-anchored cofactor of penicillin-binding protein (PBP2a) that belongs to a major family of peptidoglycan synthases involved in building the cell wall matrix . MacP was characterised in Streptococcus pneumoniae where it forms a complex with PBP2a and required for its synthase activity.
Membrane protein YtzI-like (YtzI-like)
Type: Family

This entry represents YtzI from Bacillus subtilis and its homologues widely distributed in firmicutes. The pattern of sequence conservation suggests the presence of conserved hydrophobic stretch near N terminus. This region is predicted as a single transmembrane helix.
T3SS inner rod subunit SctI-like (T3SS_SctI-like)
Type: Family

This entry represents SctI (Secretion and Cellular Translocation I) protein and its homologues. SctI is an inner rod protein in the basal body of the type III secretion system (T3SS) and is found in many pathogenic bacteria. SctI has some sequence similarity to the needle filament protein SctF. Lineage-specific names for SctI in various bacteria include BsaK, PrgJ, and MxiI .
AKP thiolase subunit OrtA (OrtA)
Type: Family

This entry represents 2-amino-4-ketopentanoate thiolase (also known as AKP thiolase) subunit OrtA. OrtA is a subunit of a PLP-dependent enzyme that catalyses the thiolytic cleavage with coenzyme A (CoA) to form acetyl-CoA and alanine .

OrtA is predicted to adopt a β-barrel structurally similar to Tudor/PWWP/MBT superfamily.
IcmT-like (IcmT-like)
Type: Family

This entry represents IcmT family of bacterial proteins . IcmT is essential for pore formation-mediated lysis of mammalian and protozoan cells and the subsequent bacterial egress. Residues at the C terminus of IcmT are essential for both pore formation and bacterial egress .
Gamma-butyrolactone biosynthesis protein AfsA-like (AfsA-like)
Type: Family

This entry represents a group of gamma-butyrolactone biosynthesis proteins mostly found in actinomycetes, including 2-oxo-3-(phosphooxy)propyl 3-oxoalkanoate synthase from Streptomyces coelicolor (ScbA). Members of this family initiate the biosynthesis of gamma-butyrolactone autoregulators, a class of compound that include A-factor in (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) . Through its receptor, a member of the TetR/AcrR family of transcriptional regulators, gamma-butyrolactones can control various processes such as antibiotic biosynthesis.
Di-heme-cytochrome C peroxidase (CytoC_perox)
Type: Family

This entry represents a group of proteins predominantly from proteobacteria, including

from Pseudomonas aeruginosa .
Antiholin LysA-like (LysA-like)
Type: Family

This entry represents antiholin LysA from Bacteriophage P2 and related proteins. LysA is involved in lysis inhibition, which interacts with and inhibits holin thereby delaying the host cell lysis timing . Members of this protein family are predicted to be membrane proteins, and in bacteria are found encoded within prophage regions.