SII-SWORD/CoKE huggingface dataset:
Bluetail putative surface-anchoring domain (Bluetail_dom)
Type: Domain

This entry represents a short domain named Bluetail that is found primarily in Cyanobacteria (blue), at the extreme C terminus of proteins (tail), that otherwise may differ in length and domain content. This pattern of occurrence suggests a role in anchoring proteins on the cell surface, although bluetail does not have the tripartide structure of signature motif, then transmembrane α-helix, then cluster of Arg residues like the sorting domains PEP-CTERM, Gly-Gly-CTERM and MYXO-CTERM. S-layer protein from Synechocystis sp., which has been seen to play a supportive but not a critical role in the function of the cyanobacterium .
VVA0879-like (VVA0879-like)
Type: Family

Members of this family average about 120 amino acids in length, including an apparent redox-active disulfide motif CxxC and two other invariant Cys residues. The family is named after VVA0879 from Vibrio vulnificus (

) but it includes proteins also from Gram-positive species such as Streptococcus suis (

).
AQJ64_40280-like (AQJ64_40280-like)
Type: Family

Members of this family are found almost exclusively in Streptomyces. Their function is unknown. Some members, such as AQJ64_40280 (

) for which the family was named, previously were annotated as amine oxidase, but this annotation could not be confirmed.
Flexitail putative surface-anchoring domain (Flexitail_dom)
Type: Domain

This entry represents the Flexitail domain, which is found in several hundred proteins from metagenome-assembled genomes (MAGs) of Chloroflexi bacteria. Usually, the Flexitail domain, which averages about 110 amino acids in length, is located at the protein C terminus, and is separated from other recognisable domains by stretches of low complexity sequences. This resembles the pattens seen for short, tripartite, C-terminal protein-sorting signals for surface-anchored proteins, such as PEP-CTERM, GlyGly-CTERM, or MYXO-CTERM, or longer C-terminal sorting signals such as type IX secretion system (T9SS) signals. The Flexitail domain may represent an adaptation to a lifestyle that has not been conducive to isolation in culture conditions known so far.
DNA damage-induced SOS-independent cell division inhibitor A-like (DidA-like)
Type: Family

This entry represents a group of proteins found in Caulobacter that are homologous to the cell division inhibitor A (DidA). DidA is a cell division inhibitor that is induced by DNA damage, but in an SOS-independent manner . DidA does not disrupt assembly of the division machinery and instead binds the essential division protein FtsN to block cytokinesis.
DNA damage-induced cell division inhibitor SosA-like (SosA-like)
Type: Family

This entry represents a group of proteins, found in Bacillales, that are homologous to SosA. SosA is a cell division inhibitor that blocks cell division in response to DNA damage . SosA is a small, predicted membrane protein with an extracellular C-terminal domain in which the conserved residues are essential for the inhibitory activity. SosA halts cell division and synchronises the cell population at a stage where division proteins such as FtsZ and EzrA are localised at midcell, and the septum formation is initiated but unable to progress to closure .
Cell division-associated protein YmgF (YmgF)
Type: Family

This entry represents a group of proteins, found in enterobacteria, that are homologous to YmgF (

). YmgF is a small, about 72 amino acid residues long, integral membrane protein that participate in the stabilisation of the cell divisome under specific conditions .
Serine endopeptidase HhoA/HhoB/HtrA-like (HhoA_HhoB_HtrA-like)
Type: Family

This entry represents a family of cyanobacterial proteins that include the paralogous serine proteases HhoA, HhoB, and HtrA of the model cyanobacterial isolate Synechocystis sp. PCC 6803. They resemble the paralogous trio of serine proteases DegQ, DegP, and DegS of Escherichia coli .
Sll0314-like (Sll0314-like)
Type: Family

This entry represents Sll0314 from Synechocystis sp. (

) and similar cyanobacterial sequences. Sll0314 was found to be upregulated as part of the iron deprivation stress regulon . Members of this family have signal peptides and are called periplasmic. The central part of these proteins contain regions with similarity to tetratricopeptide repeats (TPR).
O-antigen biosynthesis glycosyltransferase WbnI-like (WbnI-like)
Type: Family

This entry represents O-antigen biosynthesis glycosyltransferase WbnI from Escherichia coli and similar bacterial proteins. WbnI is involved in the assembly of the O-repeating unit during O-antigen biosynthesis .
CD1290-like (CD1290-like)
Type: Family

This family represents homologs of CD1290. CD1290 (or CD630_12900

) from Clostridioides difficile 630 is the founding member of a group of small acid-soluble spore proteins (SASP). Members of this family are related to the alpha/beta family

, but are shorter on average and typically score below thresholds for that model. Sequences that resemble germination protease GPR cleavage motifs are EIAx[D/E] and [E/D]IIEN .
TrbC, F-type conjugative transfer protein (TrbC)
Type: Family

This entry represents TrbC homologs found in Gammaproteobacteria. TrbC is a protein that plays a crucial role in the process of conjugation, which is the horizontal transfer of genetic material between bacterial cells. As a component of the Type IV secretion system (T4SS), TrbC is involved in the assembly and function of the conjugative pilus. The conjugative pilus acts as a bridge between the donor and recipient cells, facilitating the transfer of plasmids or other mobile genetic elements. TrbC is responsible for the formation and elongation of the pilus structure, allowing for efficient contact and DNA transfer between the bacterial cells .
MobP1 relaxase-like (MobP1_relaxase-like)
Type: Family

This entry represents the MobP1 family (also known as TaxC or nickase) of bacterial relaxases .
Anti-adapter protein SpxO-like (SpxO-like)
Type: Family

This entry represents the Anti-adapter protein SpxO from Bacillus subtilis and similar sequences from Bacillus species. SpxO is an inhibitor of Spx proteolytic control, while Spx is a global regulator of the oxidative stress response . SpxO acts by interacting with SpxH/YjbH, which disrupts interaction between SpxH and Spx, and inhibits SpxH-enhanced proteolysis of Spx by ClpXP . It is required for the stabilisation of Spx and activation of Spx-regulated genes in response to cell wall stress .
Toxin PezT (PezT)
Type: Family

This entry represents toxin PezT, found mainly in lactobacillales. PezT is the toxic component of a type II toxin-antitoxin (TA) system in which PezA is the cognate antitoxin. In this system, PezA functions as a transcriptional repressor with PezT as a corepressor. PezT interacts with PezA and forms a tight complex.

PezAT TA system is a PezA2PezT2 heterotetramer, which has a dumbbell-shaped arrangement with an internal 2-fold symmetry . The PezAT core is formed by a stack of two PezA antitoxin polypeptide chains that are sandwiched between two PezT toxin molecules whose dyad axis lies parallel to the PezA homodimer interface (

).
Antitoxin PezA (PezA)
Type: Family

This entry represents antitoxin PezA, found mainly in lactobacillales. PezA is the antitoxin component of a type II toxin-antitoxin (TA) system in which PezT is the cognate toxin. In this system, PezA functions as a transcriptional repressor with PezT as a corepressor. PezT interacts with PezA and forms a tight complex .

PezAT TA system is a PezA2PezT2 heterotetramer, which has a dumbbell-shaped arrangement with an internal 2-fold symmetry . The PezAT core is formed by a stack of two PezA antitoxin polypeptide chains that are sandwiched between two PezT toxin molecules whose dyad axis lies parallel to the PezA homodimer interface (

).
Malolactic enzyme (Malolactic_enz)
Type: Family

This entry includes malolactic enzyme, mainly from Firmicutes. Malolactic enzyme converts L-malate anaerobically to L-lactate and carbon dioxide . The malolactic enzyme from Lactobacillus plantarum (

) is involved in the malolactic fermentation of wine, which results in a natural decrease in acidity and favorable changes in wine flavors .
GlnX-like (GlnX-like)
Type: Family

This entry represents group of proteins from mycobacteriales, including a transmembrane protein named GlnX. It has been suggested that GlnX, GlnH, and PknG are part of a signal transduction cascade in which GlnH serves as an extracellular sensor, presumably for amino acids, whereas GlnX transmits the ligandation status of GlnH to PknG to control its kinase activity .
Type 8 capsular polysaccharide synthesis protein Cap8I-like (Cap8I-like)
Type: Family

This entry represents a group of proteins from Staphylococcus species that includes the type 8 capsular polysaccharide synthesis protein Cap8I, which is potentially involved in the biosynthesis of type 8 capsule (CP8) . Its structural predictions exhibit similarity to the bacterial WzyE family, which is implicated in the polymerisation of enterobacterial common antigen (ECA) trisaccharide repeat units.
Anti-sigma E factor RseA-like (Anti_sigE_RseA-like)
Type: Family

This entry represents Anti-sigma-E factor RseA from Mycobacterium tuberculosis and similar proteins from mycobacteriales. RseA plays a crucial role in regulating the sigma E-dependent stress response in bacteria. It functions as a negative regulator, inhibiting the activity of sigma E and preventing its interaction with RNA polymerase. This regulatory mechanism allows bacteria to tightly control the expression of genes involved in the stress response, ensuring a timely and appropriate cellular response to external stresses .
General secretion pathway protein N-like (XpsN-like)
Type: Family

This entry represents a group of proteins from Xanthomonas species, including General secretion pathway protein N from Xanthomonas campestris (XspN,

), which is implicated in the general secretion pathway (GSP) for the efficient export of proteins .
YmfL-like (YmfL-like)
Type: Family

This entry represents a group of proteins from tailed bacteriophages and proteobacterial prophages, including the uncharacterised protein YmfL from Escherichia coli. Members of this family are homologues of the e14 prophage region protein YmfL from E. coli. Distant homology to phage regulatory protein CII, as described by

, suggests a similar function.
Type I toxin DinQ-like (DinQ-like)
Type: Family

This entry represents a group of proteins from enterobacterales, including DinQ from Escherichia coli. DinQ, a transmembrane peptide, is a membrane-depolarising type I toxin that provokes reactive oxygen species formation under oxidative stress and has a putative regulatory role in modulating membrane-dependent activities in bacteria .
YkgR-like (YkgR-like)
Type: Family

This entry represents a family of stress response membrane proteins, including YkgR from Escherichia coli. YkgR expression is induced by the cyclic AMP response protein (CRP), and the expressed protein is inserted into the inner membrane .
YoaI-like (YoaI-like)
Type: Family

This entry represents a group of proteins from enterobacterales, including YoaI, a small membrane protein shown to be regulated as part of the phosphate regulon . Members of this group average about 34 amino acids in length.
YldA-like (YldA-like)
Type: Family

This family of small membrane proteins, averaging about 29 amino acids in length, is named for YldA of Escherichia coli but is found in multiple members of enterobacterales. Members of this group appear to be homologous to YoaI, also found in E.coli (

) .
YnaM/YnfT (YnaM_YnfT)
Type: Family

This uncharacterised protein family from enterobacterales includes two identical proteins found in prophage regions of Escherichia coli K-12, YnaM (Rac prophage) and YnfT (Qin prophage) .
Small, acid-soluble spore protein M (SspM)
Type: Family

This entry represents a group of proteins from Bacillus species, including Small, acid-soluble spore protein M from Bacillus subtilis (SspM), a small protein of unknown function that is only transcribed in the forespore compartment of the sporulating cell .
Outer membrane protein OmpB, Rickettsia (OmpB_ricketsia)
Type: Family

This family represents the outer membrane protein B from Rickettsia (rOmpB), a surface-exposed major structural protein which is involved in adhesion and invasion of host cells, playing a role as a rickettsial virulence factor and immunogen during infection, as it serves as a protective envelope . These proteins contain two structural segments, an N-terminal long β-peptide that may serve as an adhesin and a C-terminal β-barrel, an autotransporter domain (

).
Ornithine lipid N-methyltransferase (Ornithlipidmtase_OlsG)
Type: Family

This entry represents the ornithine lipid N-methyltransferase OlsG (

) from planctomycetes, which catalyses the 3-fold methylation of ornithine lipids. It forms ornithine lipids that are mono-, di-, and trimethylated on the delta-nitrogen of the ornithine head group .
Papain inhibitor (Papain_inhib)
Type: Family

Streptomyces papain inhibitor (SPI) adopts a rigid, thermo-resistant double-psi-β-barrel (DPBB) fold that is stabilized by two cysteine bridges. SPI serves as a glutamine and lysine donor substrate for microbial transglutaminase (MTG,

) from Streptomycetes, that is used to covalently and specifically link functional amines to glutamine donor sites of therapeutic proteins. SPI is a stress protein produced under hyperthermal stress conditions, and is able to inhibit the cysteine proteases, papain and bromelain, as well as the bovine serine protease trypsin .
Sporulation membrane protein YtrI (YtrI)
Type: Family

This entry represents a group of proteins mainly found in Bacillus species, including Sporulation membrane protein YtrI from Bacillus subtilis. YtrI is a protein involved in sporulation, the process by which certain bacteria form spores for survival .
Stage II sporulation protein SB-like (SpoIISB-like)
Type: Family

This entry represents a group of proteins from Bacillus species, including Stage II sporulation protein SB from Bacillus cereus. SpoIISB is an antitoxin component of a type II toxin-antitoxin (TA) system. SpoIISB antitoxin binds toxin SpoIISA and neutralises its toxic activity .
HrpD5-like (HrpD5-like)
Type: Family

This entry represents the HrpD5 protein from Xanthomonas (

) and similar sequences from proteobacteria that are encoded by the hypersensitive response and pathogenicity (hrp) gene cluster of the Type III secretion system (T3SS) .
Hpa3-like (Hpa3-like)
Type: Family

This entry represents a group of sequences mainly found in Xanthomonas, including Hpa3, a type III secretion system protein .
SCO1860-like (SCO1860-like)
Type: Family

This entry represents SCO1860 from Streptomyces coelicolor (

) and similar proteins found in actinomycetes. SCO1860 is a surface protein whose C-terminal domain (

) contain a variant type sortase recognition and cleavage sorting signal. The sorting signal motif, LAETG, is compatible with processing by a SrtE family sortase enzyme .
Spore maturation protein CgeC-like (CgeC-like)
Type: Family

This entry represents the spore maturation protein CgeC from Bacillus subtilis and similar proteins found in Bacillus species. CgeC is involved in sporulation, the process by which certain bacteria form spores for survival. Its transcription is dependent on GerE, a DNA binding protein and the latest-acting regulatory protein during sporulation in this bacteria .
Oxoglutarate dehydrogenase inhibitor (OxygluDhInhib_OdhI)
Type: Family

This entry includes the oxoglutarate dehydrogenase inhibitor (Odhl) from corynebacterium, which is a key regulator of the TCA cycle in Corynebacterium glutamicuman and an essential component of the protein kinase PknG signaling pathway . When this protein is unphosphorylated, it inhibits the activity of 2-oxoglutarate dehydrogenase (OdhA), while when it is phosphorylated it does not inhibit OdhA .
Phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase (Cycl_ph_dihydrol)
Type: Family

This family represents a group of proteins found in Eggerthellaceae, which includes the phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase (PhnPP) from Eggerthella lenta. It is involved in degradation of methylphosphonate as it catalyses the hydrolysis of the phosphate ester at carbon-1 of 5-phospho-D-ribose 1,2-cyclic phosphate to form ribose 2,5-bisphosphate. This intermediate is then hydrolyzed to ribose-5-phosphate and inorganic phosphate .
HrpV-like (HrpV-like)
Type: Family

This entry represents HrpV from Erwinia amylovora (

) and similar proteins from the type III secretion system protein (T3SS) found in enterobacterales .
HrpT-like (HprT-like)
Type: Family

This entry represents a group of sequences mainly found in gammaproteobacteria, including HrpT, a type III secretion system protein .
Capsular polysaccharide synthesis, CpsB (Caps_polysacc_synth_CpsB)
Type: Family

This entry represents the metal-dependent Tyrosine-protein phosphatase CpsB from Streptococcus pneumoniae and similar sequences from Streptococcus species. CpsB is involved in the regulation of capsular polysaccharide biosynthesis.

Capsular polysaccharide biosynthesis proteins are critical for the production of a mature capsule in vitro. Members of Streptococcus pneumoniae have variable capsules, with about 90 known capsular serotypes that all have their own polysaccharide structure. cps14B to cps14H products are similar to other proteins involved in bacterial polysaccharide biosynthesis in both Gram-negative and -positive bacteria . CpsA to cpsD are common to most serotypes. CpsD is an autophosphorylating protein-tyrosine kinase. CpsC is required for CpsD tyrosine-phosphorylation, and CpsB is required for dephosphorylation of CpsD. CpsB is a novel manganese-dependent phosphotyrosine-protein phosphatase that belongs to the PHP (polymerase and histidinol phosphatase) family of phosphoesterases . Phosphorylation of proteins on hydroxyl amino acids (serine, threonine, tyrosine) occurs at different stages of pathenogenesis, including cell-cell interaction and adherence, translocation of bacterial effectors into host cells, and changes in host cellular structure and function induced by infection . CpsB, CpsC, CpsD, and ATP form a stable complex that enhances capsule synthesis and acts to regulate it .
YmiC-like (YmiC-like)
Type: Family

This entry represents a group of proteins from enterobacterales, including YmiC from Escherichia coli, an uncharacterised predicted protein about 32 amino acids long predicted to be a membrane protein based on conservation across multiple gammaproteobacteria with constant length and hydrophobic character. Expression was verified for a construct with an added C-terminal epitope. Homologues tend to show a pattern of conservative amino acid substitutions. A usual feature is three perfectly invariant Trp residues, and a highly conserved fourth, in a stretch of 19 residues . They are predicted to adopt an α-helical configuration.
Transcriptional regulator TagK-like (TagK-like)
Type: Family

This entry represents the AraC-type transcription factor TagK and similar proteins found in Xanthomonas. TagK promotes expression of type 6 secretion system (T6SS) proteins in response to a protozoan predator .
Cytoskeleton protein RodZ-like (RodZ-like)
Type: Family

This entry represents a group of proteins from Streptococcus species, including Cytoskeleton protein RodZ from Streptococcus pneumoniae, which acts as a scaffolding protein required for elongasome assembly and function, and plays a role in elongasome regulation and possibly peripheral PG synthesis .
Pyrroloquinoline quinone transporter (PqqU)
Type: Family

This entry represents Pyrroloquinoline quinone transporter from Escherichia coli (PqqU) and similar proteins found in enterobacterales. PqqU, also known as TonB-dependent receptor PqqU, mediates the high affinity transport across the outer membrane of pyrroloquinoline quinone (PQQ), a redox cofactor required for the activity of Gcd and Asd dehydrogenases .
Exosortase-dependent surface-anchored protein 1-like (EDSA_1-like)
Type: Family

This entry represents a family of proteins from proteobacteria named EDSA-1 (exosortase-dependent surface-anchored protein 1). Most members of this group have an N-terminal signal peptide and a C-terminal PEP-CTERM region (

) for recognition and processing by an exosortase.
XopA/Hpa1-like (XopA_Hpa1-like)
Type: Family

This entry represents a group of type III secretion system proteins found in Xanthomonas, including Xop A and Hpa1, .
Manganese-oxidizing multicopper oxidase MnxG-like (MnxG-like)
Type: Family

This entry represents Manganese-oxidizing multicopper oxidase MnxG from Pseudomonas sp. and similar proteins predominantly found in Pseudomonas species. Member of this family contain cupredoxin-like domains
Sigma-O factor regulatory protein RsoA (RsoA-like)
Type: Family

This entry represents a group of proteins from Bacillus species, including Sigma-O factor regulatory protein RsoA from Bacillus subtilis (

). Together with RNA polymerase sigma factor SigO, RsoA positively regulates the expression of at least three operons, including oxdC-yvrL, sigO-rsoA and yvrJ. This protein is also required for the acid stress-dependent induction of the oxalate decarboxylase OxdC .
RING-type E3 ubiquitin transferase BIG BROTHER, RING finger, H2 subclass (BB-like_RING-H2)
Type: Domain

E3 ubiquitin-protein ligase BIG BROTHER BB (also known as protein ENHANCER OF DA1-1 or EOD1) is an E3 ubiquitin-protein ligase that limits organ size, and possibly seed size, in a dose-dependent manner. It negatively regulates the duration of cell proliferation in leaves and petals independently of the major phytohormones (e.g. auxin, cytokinin, gibberellin, brassinosteroids, ethylene, abscisic acid, jasmonic acid), probably by targeting growth stimulators for degradation. It limits the proliferation of root meristematic cells . BB activate the latent peptidases DA1, DAR1 and DAR2 by monoubiquitination in multiple sites . It is involved in the promotion of leaf senescence, in addition to its function in restricting plant growth. BB-related is an E3 ubiquitin-ligase probably involved in organ size regulation.

This entry represents the C3H2C3-type RING-H2 finger.
Terminal beta-(1->2)-arabinofuranosyltransferase-like, mycobacteriaceae (AftB-like_mycobacteriaceae)
Type: Family

This entry represents Terminal beta-(1->2)-arabinofuranosyltransferase from Mycobacterium tuberculosis (AftB) and similar sequences specific to mycobacteriaceae. AftB is involved in the biosynthesis of the arabinogalactan (AG) region of the mycolylarabinogalactan-peptidoglycan (mAGP) complex, an essential component of the mycobacterial cell wall. It catalyses the transfer of arabinofuranosyl (Araf) residues from the sugar donor decaprenyl-phospho-arabinose (DPA) to the arabinan domain to form terminal beta-(1->2)-linked Araf residues, which marks the end point for AG arabinan biosynthesis before decoration with mycolic acids .