SII-SWORD/CoKE huggingface dataset:
OmpL47-like, Ig-like domain (Ig-like_OmpL47-like)
Type: Domain

This entry represents an Ig-like domain in Leptospira surface-exposed protein OmpL47 and related proteins, usually annotated as Ig-like domain-containing proteins or as carbohydrate-active enzymes. This domain can be found as tandem copies from 3 to 12 repetitions.
Psb35-like (Psb35-like)
Type: Family

This undescribed putative photosystem II protein is related to Psb35

and is restricted to species that have photosystem II, primarily derived from cyanobacteria .
Sensor histidine protein kinase/phosphatase WalK-like (WalK-like)
Type: Family

This protein family includes Sensor histidine protein kinase/phosphatase WalK from Streptococcus pneumoniae, the histidine kinase SMU_1516 from Streptococcus mutans (CovS,

) and similar proteins mainly found in Lactobacillales.

WalK functions as a sensor protein kinase which is autophosphorylated at a histidine residue and transfers its phosphate group to WalR , the other member of the two-component regulatory system WalK/WalR that regulates genes involved in cell wall metabolism. CovS plays a role in the regulation of acid production and tolerance conducive to dental caries, including proton expulsion. This protein has one transmembrane domain before a HAMP signal transducer domain (

), a PAS sensor domain (

), a DHp domain (

) and a CA domain (

).
PatX (PatX)
Type: Family

PatX is a small protein found in heterocyst-forming cyanobacteria. It contributes to the maintenance of a vegetative state by opposing the differentiation of cells into heterocysts. PatX contains a motif near its C-terminal, RG(S/T)GR, similar to the RGSGR found in both PatS and HetN .
BRANT-like (BRANT-like)
Type: Family

This entry represents putative uncharacterised bacterial proteins mainly from genera Bradyrhizobium, Rhodopseudomonas, Afipia, Nitrobacter, and Tardiphaga (BRANT). It has an N-terminal probable signal-anchor domain and a His-rich C-terminal region.
XAC0095-like domain (T3SS_XAC0095_dom)
Type: Domain

This entry represents a domain found standalone in XAC0095

from the plant pathogen Xanthomonas axonopodis pv. citri. XAC0095 was shown to interact with HrpG, a response regulator transcription factor responsible for type III secretion system (T3SS) hrp gene expression . The interaction between XAC0095 and HrpG could modulate HrpG's activity, possibly stabilising its phosphorylated or dephosphorylated state, or influencing its interactions with other regulators and promoters involved in virulence gene expression . Homologues of XAC0095 include both proteins of similar lengths and substantially longer proteins that contain additional domains.
Secretion system apparatus protein SsaO (SsaO)
Type: Family

This entry represents the homologues of Salmonella pathogenicity island 2 protein SsaO which is a member of a type III secretion system involved in the survival and replication of Salmonella in a host cell .
Salmonella pathogenicity island 2 protein C (SipC)
Type: Family

This entry represents the Salmonella pathogenicity island 2 protein C (spiC) and related proteins. SipC is a virulence protein that plays a central role in mammalian macrophage infection, by inhibiting phagosome-lysosome fusion and cellular trafficking, including trafficking of organelles that are devoid of Salmonella .
Transcriptional regulator peptide PatS (PatS)
Type: Family

This entry represents Transcriptional regulator peptide PatS. PatS occurs in a subset of HetR-containing, heterocyst-forming species .

PatS inhibits heterocyst differentiation; a peptide corresponding to the last 5-6 amino acids blocks heterocyst formation when added exogenously in culture. It controls heterocyst pattern formation through intercellular signaling mechanisms. In Nostoc filaments, approximately every 10th vegetative cell terminally differentiates into a heterocyst specialised for nitrogen fixation. It seems to inhibit the formation of adjacent heterocysts .

The C-terminal peptide binds HetR, inhibits hetR transcription and blocks the DNA-binding of HetR. Peptide binding to HetR alters its conformation, probably leading to dissociation of the HetR-DNA complex and cessation of transcription . Two PatS peptides bind to the lateral clefts of HetR Hood domain, and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary α-helix and eventually release of HetR from the DNA major grove

.
SPI-1 type 3 secretion system stator protein (SCTL1)
Type: Family

This entry represents the SPI-1 type 3 secretion system stator protein (SCTL1) from Salmonella typhimurium, also known as Oxygen-regulated invasion protein OrgB, and related proteins. SCTL1 is found in the Salmonella pathogenicity island 1 (SPI-1), a component of the SPI-1 type III secretion system (T3SS). It is homologous to counterparts such as MxiN in Shigella. In Salmonella enterica, it is one of the several genes required for invasion and secretion
Type III secretion system chaperone SseA (SseA)
Type: Family

This entry represents the type III secretion system chaperone SseA and related proteins. SseA functions as a type III secretion system (T3SS) chaperone, which is required for SseB and SseD accumulation and secretion . It may have a direct role in secretion of SseB and SseD, or may facilitate their correct folding, for efficient secretion and function. It is required for survival and replication within epithelial cells and macrophages. SseA is required for translocation of Salmonella pathogenicity island-2 effectors into host cells .
Secretion system apparatus protein SsaP (SsaP)
Type: Family

This entry represents the Secretion system apparatus protein SsaP and related proteins. SsaP is a component of the type III secretion system from Salmonella pathogenicity island 2 (SPI2), involved in the survival and replication of Salmonella in a host cell . SsaP along with ssaL and ssaM do not have significant similarity to products of other type III secretion systems, and might be important for the specific function of the SPI2 type III secretion system.
Slr1339 (Slr1339)
Type: Family

This entry represents Slr1339 and related proteins, strictly found in cyanobacteria. Slr1339 is one of several genes (along with sll1734, ssr3402, and ssr1853) found to be significantly induced after a 3-day salt stress in Synechocystis. Knockout mutants of these genes, including slr1339, were notably salt-sensitive, indicating that Slr1339 plays a role in long-term salt stress acclimation .
CptlN-like (CptIN-like)
Type: Family

This entry represents CptN-like toxin component of a type III toxin-antitoxin (TA) system, which consists of a ribonuclease (RNase) toxin that processes its structured and specific cognate RNA antitoxin, which in turn then directly inhibits the toxin. TA systems have been associated with many important phenotypes, like phage resistance, maintenance of genomic islands, and formation of bacterial persister cells .

CptIN-like toxins are widely found in numerous bacteria and archaea .
FlcA, C-terminal (FlcA_C)
Type: Domain

This entry represents the C-terminal domain in FlcA. This domain contains TPR repeats.

In spirochetes, flagella are located within the periplasm. FlcA is one of several structural proteins involved in the formation of the flagellar collar. The conserved N-terminal domain of about 40 amino acids and the C-terminal region domain of about 650 amino acids are separated by a long and variable-length stretch of low-complexity sequence .
GCG_CRPN domain (GCG_CRPN_dom)
Type: Domain

This entry represents a conserved domain with a core region featuring two invariant Cys residues in the consensus sequence GCGPGFHRGPWGGCRPN. This domain is usually followed by repetitive, low-complexity (reduced alphabet) sequence to the C-terminal.
RcgR-like (RcgR-like)
Type: Family

RcgA (Rhizobial Conjugative Gene A), from a Rhizobium favelukesii plasmid, plays an essential role in a quorum-sensing-dependent conjugative transfer system. It is thought to be a transporter that allows uptake of a quorum-signalling lactone. Its partner protein, RgcR, with an α/β hydrolase domain, inhibits the transfer, probably by inactivating the signalling molecule.

This entry represents RcgR and similar proteins in gram-negative bacteria.
CD3337/EF1877-like (CD3337_EF1877-like)
Type: Family

Members of this family regularly are found in mobile elements. Only the N-terminal 450 amino acids are well-conserved. That portion is strongly hydrophobic and the proteins are predicted to embed in the membrane. Members of this family appear to distantly related to TrbL/VirB6 family conjugal transfer proteins

.
Tryptophan biosynthesis modulator TrpM (TrpM_modulator)
Type: Family

TrpM (tryptophan biosynthesis modulator) is a predicted small protein encoded between trpC and trpB in many Streptomyces genomes . This entry represents its homologues found mainly in Streptomyces.
RcgA-like (RcgA-like)
Type: Family

RcgA (Rhizobial Conjugative Gene A), from a Rhizobium favelukesii plasmid, plays an essential role in a quorum-sensing-dependent conjugative transfer system. It is thought to be a transporter that allows uptake of a quorum-signalling lactone. Its partner protein, RgcR, with an α/β hydrolase domain, inhibits the transfer and may catabolise the signalling molecule.
Lmo0673 (Lmo0673)
Type: Family

In Listeria monocytogenes, lmo0673 is encoded immediately downstream of mogR in a bicistronic operon encoded divergently from flagellar genes. MogR is a transcriptional repressor essential for temperature-dependent transcription of flagellar genes. The gene lmo0673 is therefore considered the end gene of a large flagellar biosynthesis and motility region from lmo0673 to lmo0718. Lmo0673 is commonly cited as a biofilm formation-associated protein . This entry represents its homologues.
SA0570-like (SA0570-like)
Type: Family

The founding member of this mainly staphylococcal protein family, SA0570 Staphylococcus aureus, was listed as part of the core secretome of Staphylococcus aureus, that is, as a secreted protein found in more than 80% of strains. Being both secreted and well-conserved suggests SA0570 proteins may be virulence proteins .
BV97_02767-like (BV97_02767-like)
Type: Family

This entry represents uncharacterised bacterial proteins. They are predicted to contain transmembrane helices. Members of this family are probably distantly related to

.
Telomere-protecting terminal protein Tpg (Tpg)
Type: Family

Tpg (terminal protein gene) and Tap (telomere-associated protein) together act to maintain the linear topology and telomere regions of the linear chromosome, and some linear plasmids, in Streptomyces and a few related bacteria. These proteins are covalently bound to the 5' ends of the DNA and the threonine in a motif TD[DQ] defines the site of DNA attachment to protein. In addition, the presence of helix-turn-helix (HTH) domain is important for functionality .
SCO0607-like (SCO0607-like)
Type: Family

This entry represents the homologues of SCO0607 lipoprotein. The lipoprotein SCO0607 of Streptomyces coelicolor (

), along with a number of morphogenic membrane proteins, is regulated by the response regulator transcription factor MarR (SCO2120)

. Related lipoproteins are found in a large number of Streptomyces species .
Methylation-associated defense system protein MAD7 (MADS7)
Type: Family

This entry represents the methylation-associated defense system protein MAD7 and related proteins. The methylation-associated defense system (MADS) is distributed across gram-positive and gram-negative bacteria. MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages. MADS comprises eight genes .

MAD7 and MAD8 components of MADS are related to the subunits of the ATP-dependent nuclease effector of phosphorothioate (PT)-dependent restriction systems which target unmodified DNA . MAD7 probably plays a role in distinguishing unmethylated non-self DNA for loading into the MAD8 motor nuclease.
Exodeoxyribonuclease WalJ/YycJ (WalJ/YycJ)
Type: Family

This entry represents Exodeoxyribonuclease WalJ/YycJ from Streptococcus pneumoniae and similar 5'->3' double-stranded DNA exonucleases predominantly found in bacilli. Members of this family are involved in the WalK/WalR signal transduction pathway and may contribute to mutation mismatch repair (MMR) . They play a crucial role in ensuring the coordination of cell division with DNA replication and are potentially involved in cell wall metabolism . Most members of this family contain the metallo-beta-lactamase domain (

), indicating a shared structural framework and potential catalytic mechanism involving metal ions.
Transcriptional regulatory protein CpxR (CpxR)
Type: Family

This entry represents Transcriptional regulatory protein CpxR from Klebsiella pneumoniae and similar proteins from enterobacterales.

CpxR is a member of the two-component regulatory system CpxA/CpxR which responds to envelope stress response by activating or, in some cases, repressing expression of downstream genes .
FlcA, N-terminal (FlcA_N)
Type: Domain

This entry represents the N-terminal region in FlcA.

In spirochetes, flagella are located within the periplasm. FlcA is one of several structural proteins involved in the formation of the flagellar collar. The conserved N-terminal domain of about 40 amino acids and the C-terminal region domain of about 650 amino acids are separated by a long and variable-length stretch of low-complexity sequence .
CpxR-like, receiver domain (CpxR-like_REC)
Type: Domain

This entry represents the N-terminal receiver (REC) domain of Transcriptional regulatory protein CpxR from Klebsiella pneumoniae and similar proteins mainly from gammaproteobacteria. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays .

CpxR is a member of the two-component regulatory system CpxA/CpxR which responds to envelope stress response by activating or, in some cases, repressing expression of downstream genes .
Sensor histidine kinase CpxA (CpxA)
Type: Family

This entry represents Sensor histidine kinase CpxA from Vibrio parahaemolyticus , Klebsiella pneumoniae , and similar proteins from gammaproteobacteria.

The Cpx system is one of extracytoplasmic stress response systems (ESR) found in Gram-negative bacteria. ESRs are operated by a two-component signalling system which consists of a sensory histidine kinase (HK) and a response regulator (RR) as basal elements. In the Cpx system, CpxA is the inner membrane-spanning, sensory HK .
Sensor histidine kinase CpxA, ATPase domain (CpxA-like_HATPase)
Type: Domain

This entry represents the histidine kinase-like ATPase (HATPase) domain of Sensor histidine kinase CpxA from Vibrio parahaemolyticus , Klebsiella pneumoniae , Escherichia coli and similar proteins mainly from gammaproteobacteria. These proteins may function in acid stress and in cell wall stability. Proteins having this HATPase domain often contain as well a periplasmic domain (

), an histidine kinase dimerisation and phosphoacceptor domain (HisKA,

) and a HAMP sensor domain (

); some also contain a CpxA family periplasmic domain .

The Cpx system is one of extracytoplasmic stress response systems (ESR) found in Gram-negative bacteria. ESRs are operated by a two-component signalling system which consists of a sensory histidine kinase (HK) and a response regulator (RR) as basal elements. In the Cpx system, CpxA is the inner membrane-spanning, sensory HK .
DedA (DedA)
Type: Family

This entry represents the DedA family protein from Klebsiella pneumoniae and similar bacterial sequences. DedA may be involved in undecaprenyl phosphate (UndP) transport and recycling . It is involved in biosynthesis of LPS lipid A and in the maintenance of membrane potential and plays a role in virulence, probably by allowing bacteria to resist the host immune response .
Phosphatidylethanolamine transferase Mcr-1 (Mcr1)
Type: Family

This entry represents Phosphatidylethanolamine transferase Mcr-1 from Escherichia coli (Mcr1) and similar sequences from gammaproteobacteria. Mcr-1 is thought to catalyse the addition of a phosphoethanolamine moiety to lipid A . The phosphoethanolamine modification of lipid A was found to confer polymyxin resistance .
Phosphatidylethanolamine transferase Mcr-2 (Mcr2)
Type: Family

This entry represents Phosphatidylethanolamine transferase Mcr-2 from Escherichia coli (Mcr2) and similar sequences from bacteria. Mcr-2 is thought to catalyse the addition of a phosphoethanolamine moiety to lipid A . It was found that it confers resistance to polymyxin-type antibiotics such as colistin .