SII-SWORD/CoKE huggingface dataset:
Sigma-54 interaction domain, ATP-binding site 2 (Sigma_54_int_dom_ATP-bd_2)
Type: Binding_site

Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section.

The domain involved in interaction with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction . The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B.

This entry represents a conserved site corresponding to the second ATP-binding motif located in the N-terminal section of the sigma-54 interaction domain.
Sigma-54 interaction domain, conserved site (Sigma_54_int_dom_CS)
Type: Conserved_site

Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section.

The domain involved in interaction with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction . The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B.

This entry represents a conserved site found in the C-terminal section of the sigma-54 interaction domain.
DHHW protein (DHHW)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 366 and 404 amino acids in length. There is a conserved DHHW motif.
CABIT domain (CABIT_dom)
Type: Domain

The CABIT domain (for 'cysteine-containing, all- in Themis') is found twice in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik). These proteins function downstream of tyrosine kinase signalling and interact with GRB2. In addition to their CABIT domains, the proteins also share a highly conserved proline-rich region . In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians (including the insect Serrano proteins), have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded β-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function.
HTH-like domain (HTH-like_dom)
Type: Domain

This domain contains a predicted helix-turn-helix, suggesting a DNA-binding function.
PapC-like, C-terminal domain (PapC-like_C)
Type: Domain

The PapC C-terminal domain is a structural domain found at the C terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the C-terminal domain from PapC and its homologues. This domain has a β-sandwich structure similar to the plug domain of PapC .
GXWXG domain (GXWXG_dom)
Type: Domain

This domain is found in bacterial and eukaryotic sequences, and is approximately 60 amino acids in length. There is a conserved GXWXG motif.
R3H-associated N-terminal domain (R3H-assoc_dom)
Type: Domain

This domain is sometimes found towards the N terminus of R3H domain-containing proteins. Its function is not known.
Putative coat protein YlbD (YlbD_coat)
Type: Family

This is a family of putative bacterial coat proteins . Proteins in this family are approximately 140 amino acids in length.
DBC1/CARP1, catalytically inactive NUDIX hydrolase domain (DBC1/CARP1_inactive_NUDIX)
Type: Domain

This entry represents the central conserved globular domain present in DBC1 and homologues and is a catalytically inactive version of the Nudix hydrolase (MutT) domain . It may have a role in binding NAD metabolites, such as ADP-ribose.

Cell cycle and apoptosis regulator protein 2 (CCAR2, also known as DBC-1) regulates biological processes such as transcription, heterochromatin formation, metabolism, mRNA splicing, apoptosis, and cell proliferation . It is a core component of the DBIRD complex, which affects local transcript elongation rates and alternative splicing of a large set of exons embedded in (A + T)-rich DNA regions . It binds to SIRT1 and is a negative regulator of SIRT1 . DBC-1 has been implicated in tumorigenesis .

Cell division cycle and apoptosis regulator protein 1 (CCAR1) associates with components of the Mediator and p160 coactivator complexes that play a role as intermediaries transducing regulatory signals from upstream transcriptional activator proteins to basal transcription machinery. CCAR1 also functions as a p53 coactivator and regulates expression of key proliferation-inducing genes .

This entry also includes protein SHORT ROOT IN SALT MEDIUM 1 (RSA1, also known as EMB1579) from Arabidopsis. It regulates the transcription of several genes involved in the detoxification of reactive oxygen species generated by salt stress and the SOS1 gene that encodes a plasma membrane Na(+)/H(+) antiporter essential for salt tolerance . RSA1 is localised to the nucleus and the loss of function of RSA1 affects global transcription and mRNA splicing .
Type-IV secretion system protein TraC/Conjugative transfer ATPase (TraC/Conjuga_ATPase)
Type: Family

This family of TraC-related proteins is conserved in Proteobacteria. TraC is a cytoplasmic, peripheral membrane protein and is one of the proteins encoded by the F transfer region of the conjugative plasmid that is required for the assembly of F pilin into the mature F pilus structure. F pili are filamentous appendages that help establish the physical contact between donor and recipient cells involved in the conjugation process . This family also includes predicted ATPases associated with DNA conjugal transfer. These are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons.
Cytoplasmic dynein 1 intermediate chain 1/2 (DYNC1I1/DYNC1I2)
Type: Family

In mammals, cytoplasmic dynein 1 is comprised of a dimer of heavy chain subunits (DYNC1H1), which associate with two copies of an intermediate chain (DYNC1I1 or DYNC1I2, depending on the tissue type), two copies of light intermediate chains (DYNC1LI1 or DYNC1LI2) and a number of light chain subunits (including the dynein light chain (DYNLL1), roadblock (DYNLRB1 and DYNLRB2) and Tctex families (DYNLT1, DYNLT3)) .

This entry includes the mammalian intermediate chain 1 and 2 (DYNC1I1 and DYNC1I2) and their homologues. Mammalian cytoplasmic dynein-1 complexes contain two copies of the same intermediate chain (typically DYNC1I2 in most cells, DYNC1I1 in neurons) and same light intermediate chain. DYNC1I1 and DYNC1I2 interact with the dynein light chains and the p150 subunit of dynactin at the N terminus and with the heavy chains through WD40 repeats at the intermediate chain C terminus. Both DYNC1I1 and DYNC1I2 are expressed in multiple splice isoforms, the expression of different isoforms may play an important part in dynein complex function and cargo specificity .
Cysteine-rich KTR (Cys_rich_KTR)
Type: Family

This family of proteins is functionally uncharacterised. Family members are found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length. There are 4 conserved cysteines and a conserved KTR sequence motif.
SID1 transmembrane family (SID1_TM_fam)
Type: Family

This is a family of proteins that are transmembrane dsRNA-gated channels. They passively transport dsRNA into cells and do not act as ATP-dependent pumps . They are required for systemic RNA interference .

This entry also includes CHUP-1 from C. elegans. CHUP-1 is the SID-1 paralog. However, it does not transport dsRNA . Instead, it is involved in dietary cholesterol uptake .
Winged helix-turn helix domain (Winged_HTH_dom)
Type: Domain

This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
Reverse transcriptase, N-terminal domain (RVT_N)
Type: Domain

This domain is found at the N terminus of bacterial reverse transcriptases.
Heavy-metal resistance protein (Metal_resist)
Type: Family

This is a family of metal-binding proteins which are involved in resistance to heavy-metal ions . These proteins form a four-helix hooked hairpin, consisting of two long α helices each flanked by a shorter α helix. They bind a metal ion in a type-2 like centre and contain two copies of an LTXXQ motif.

This family includes Signaling pathway modulator ZraP which is Is the main zinc containing protein under zinc stress conditions and is a component of the Zra signaling pathway, an envelope stress response (ESR) system composed of the periplasmic accessory protein ZraP, the histidine kinase ZraS and the transcriptional regulator ZraR . Another members of this family are the Nickel and cobalt resistance proteins CnrR and NccX which are responsible for the linked resistance to nickel and cobalt .
SdpI/YhfL protein family (SdpI/YhfL)
Type: Family

This family of proteins includes the SdpI and YhfL proteins from Bacillus subtilis. The SdpI protein is a multipass integral membrane protein that protects toxin-producing cells from being killed. Killing is mediated by the exported toxic protein SdpC an extracellular protein that induces the synthesis of an immunity protein .
FlgD Tudor-like domain (FLgD_Tudor)
Type: Domain

This domain consists of a tudor-like β barrel fold. It is found in FlgD, a flagellar-hook capping protein. The structure for this domain shows that it contains a nested Ig-like domain within it . However, in some firmicute proteins this inserted domain is absent, such as Q67K21.
GGGtGRT protein (GGGtGRT)
Type: Family

This family of proteins is functionally uncharacterised. Family members are found in bacteria. Proteins in this family are approximately 330 amino acids in length and contain many highly conserved residues including a GGGtGRT motif.
FlgD/Vpr, Ig-like domain (FlgD/Vpr_Ig-like)
Type: Domain

This domain has an immunoglobulin-like β-sandwich fold. It is found in the FlgD protein, a flagellar hook-capping protein and in the minor extracellular protease Vpr from Bacillus subtilis, a serine protease involved in the production of the competence and sporulation stimulating factor CSF . The structure for this domain shows that it is inserted within a Tudor-like β-barrel domain .
Oligopeptide transport permease C-like, N-terminal domain (OppC_N)
Type: Domain

Oligopeptide permeases (Opp) have been identified in numerous Gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation. This N-terminal domain appears to be the first TM domain of the molecule .
YwqJ-like deaminase (YwqJ_deaminase)
Type: Family

Members of this family are present in a wide phyletic range of bacteria and represent nucleic acid/nucleotide deaminase superfamily members prototyped by Bacillus YwqJ . Members of this family function as toxins in bacterial polymorphic toxin systems , such as YenC2 from Yersinia entomophaga .
Abscisic acid G-protein coupled receptor-like domain (ABA_GPCR_dom)
Type: Domain

This domain is found in eukaryotes, and is typically between 177 and 216 amino acids in length. It is found in the abscisic acid (ABA) G-protein coupled receptor . ABA is a stress hormone in plants. It is also found proteins identified as Golgi pH regulators .
SusE outer membrane protein (SusE)
Type: Domain

Proteins containing this domain include the SusE outer membrane protein from Bacteroides thetaiotaomicron,

. This protein has a role in starch utilisation, but is not essential for growth on starch .
LppP/LprE lipoprotein (LppP/LprE)
Type: Family

The family includes putative lipoproteins LppP and LprE from species of Mycobacterium and related proteins. LppP is required for optimal growth of M. tuberculosis .
Beta-galactosidase, domain 3 (BetaGal_dom3)
Type: Domain

This is the third domain of the five-domain beta-galactosidase enzyme that altogether catalyses the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides, as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain has an Ig-like fold .
Cysteine-rich VLP domain (Cys_rich_VLP_dom)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in bacterial sequences and is approximately 60 amino acids in length. It contains 6 conserved cysteines and a conserved VLP sequence motif.
Mif2/CENP-C cupin domain (Mif2/CENP-C_cupin)
Type: Domain

This entry represents a C-terminal domain found in Mif2 and CENP-C.

CENP-C is the inner-kinetochore centromere (CEN) binding protein. In the budding-yeast, Mif2, the yeast homologue, binds in the CDEIII region of the centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins . Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerisation domain of a bacterial transcription factor . The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast . This C-terminal domain is the region via which CENP-C localises to centromeres throughout the cell cycle .
Polysaccharide lyase (Polysacc_lyase)
Type: Family

This family includes heparin lyase I (

). Heparin lyase I depolymerises heparin by cleaving the glycosidic linkage next to an iduronic acid moiety . The structure of heparin lyase I consists of a β-jelly roll domain with a long, deep substrate-binding groove and an unusual thumb domain containing many basic residues extending from the main body of the enzyme . This family also includes glucuronan lyase, (

) . The structure glucuronan lyase is a β-jelly roll .
Nuclear condensin complex subunit 3, C-terminal domain (Cnd3_C)
Type: Domain

The Cnd1-3 proteins are the three non-SMC (structural maintenance of chromosomes) proteins that go to make up the mitotic condensation complex along with the two SMC protein families, XCAP-C and XCAP-E, (or in the case of fission yeast, Cut3 and Cut14) . The five-member complex seems to be conserved from yeasts to vertebrates. This domain is the C-terminal, cysteine-rich domain of Cnd3. The complex shuttles between the nucleus, during mitosis, and the cytoplasm during the rest of the cycle. Thus this family is made up of the C-termini of XCAP-Gs, Ycg1 and Ycs5 members.
ChrR-like cupin domain (ChrR-like_cupin_dom)
Type: Domain

This entry represents the cupin domain found in transcriptional activator ChrR and other proteins.
ATP-sulfurylase PUA-like domain (ATP-Sase_PUA-like_dom)
Type: Domain

This PUA-like domain is found at the N terminus of ATP-sulfurylase enzymes.
Ribosomal RNA aminoglycoside-resistance methyltransferase (rRNA_MeTrfase)
Type: Family

This family consists of several bacterial ribosomal RNA methyltransferase (aminoglycoside-resistance methyltransferase) proteins . They specifically methylate the N7 position of guanine 1405 in 16S rRNA and confer resistance to various aminoglycosides, including gentamicin, kanamycin and sisomicin .
Superinfection exclusion protein B (SieB)
Type: Family

This family includes superinfection exclusion proteins. These proteins prevent the growth of superinfecting phage which are insensitive to repression. It aborts lytic development of superinfecting phage .
Cysteine-rich CPCC domain (Cys_rich_CPCC)
Type: Domain

This domain is functionally uncharacterised. It is found in bacteria, archaea, eukaryotes and viruses. It contains six conserved cysteines and a conserved CPCC sequence motif.
dCTP pyrophosphatase 1 (DCTPP)
Type: Family

RS21-C6 proteins (also known as dCTP pyrophosphatases 1, DCTPP1) are NTP pyrophosphatases that structurally belong to the group of all-α NTP pyrophosphatases . They show significant sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins . However, unlike typical tandem-domain MazG proteins, RS21-C6 contains a single MazG-like domain and functions as a tetramer (a dimer of dimers) with a typical four-helical bundle. Divalent ions, such as Mg2+, are required for its pyrophosphatase activity . Human dCTP pyrophosphatase 1 has been shown to be involved in nucleotide homoeostasis, contributing to detoxification of deoxycytidine triphosphate derivatives .
YnbE (YnbE)
Type: Family

This family includes E. coli YnbE and similar lipoproteins. The N-terminal contains a lipid attachment site.

YnbE is involved in maintaining outer membrane lipid homeostasis . It interacts with the inner membrane protein YdbH to form a functional protein bridge that connects the inner and outer membranes of the cell. Its presence is essential for YdbH's function and may facilitate the transport of phospholipids across the periplasm.
RNA-polymerase II-associated protein 3-like, C-terminal domain (RPAP3-like_C)
Type: Domain

This domain is found at the C terminus of the RNA-polymerase II-associated protein 3 (RPAP3). RPAP3 binds to Monad and is involved in regulating apoptosis . This domain represents the potential Monad-binding region of RPAP3. RPAP3 contains TPR-repeats towards the N terminus. This domain is also found in other proteins with TPR-repeats at the N terminus, like sperm-associated antigen 1 , and in proteins without TPR-repeats.
GW domain (GW_dom)
Type: Domain

The GW domain or cell wall targeting (CWT) signal is a module of about 80-90 amino acids named for a conserved Gly-Trp (GW) dipeptide. GW domains have only been identified in Gram-positive bacteria and form a small protein family. They are divergent members of the SH3 family. However, GW domains are unlikely to mimic SH3 domains functionally, as their potential peptide-binding sites are destroyed or blocked. GW domains constitute a motif for cell-surface anchoring in Listeria and other Gram-positive bacteria . The GW domains bind polyanions, including lipoteichoic acid (LTA), on the bacterial surface and heparan sulfate of host cell surface heparan sulfate proteoglycans (HSPGs); binding to the latter enhances human receptor tyrosine kinase MET activation through the internalin domain .

The GW domain is composed of seven β-strands, five of which are organized into an open barrel conformation like the SH3 domains one. The eponymous GW dipeptide, located in the fourth β-strand, is more conserved in GW domains than in SH3 domains. Both the glycine and tryptophan are buried in GW proteins, while the equivalent residues in SH3 proteins are surface accessible, perhaps explaining the greater conservation in GW proteins .
YWFCY domain (YWFCY_dom)
Type: Domain

This domain is found in bacteria, and is approximately 60 amino acids in length. It contains a conserved YWFCY motif.
Virulence factor domain (Virulence_F_dom)
Type: Domain

This domain is found in conserved virulence factors . It is often found in association with

and

.
Cysteine-rich CPXCG protein (Cys_rich_CPXCG)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There are 5 conserved cysteines which occur in a CPXCG motif and a DCXXCCXP motif.
Chemoreceptor zinc-binding domain (Chemoreceptor_zinc-bind_dom)
Type: Domain

The chemoreceptor zinc-binding domain (CZB) is found in bacterial signal transduction proteins - most frequently receptors involved in chemotaxis and motility, but also in c-di-GMP signalling and nitrate/nitrite-sensing. Originally discovered in the cytoplasmic chemoreceptor TlpD from Helicobacter pylori, it is often found C-terminal to the MCPsignal domain in cytoplasmic chemoreceptor proteins. The CZB domain contains a core sequence motif, Hxx[WFYL]x21-28Cx[LFMVI]Gx[WFLVI]x18-27HxxxH. The highly-conserved H-C-H-H residues of this motif are believed to coordinate zinc; mutating the latter two histidines of the motif to alanines abolishes Zn binding. This domain binds zinc with high affinity, with a Kd in the femtomolar range. This domain has been shown in E. coli to be a zinc sensor that regulates the catalytic activity of the GGDEF domain (

) . This domain also binds the chemoattractant HOCl at a site very close to that of zinc. It has been shown that zinc participates in HOCl sensing by forming a redox 'Cys-Zn switch' that reacts towards HOCl .
Haem-binding domain (Haem-bd)
Type: Domain

This domain contains a potential haem-binding motif, CXXCH and it is often found in association with

and

.
Ceramide glucosyltransferase (Ceramide_glucosylTrfase)
Type: Family

This is a family of ceramide beta-glucosyltransferases (

), which catalyse the transfer of glucose to ceramide, the first glycosylation step in glycosphingolipid biosynthesis . They belong to the glycosyl transferase family 21.
BRCA1, serine-rich domain (BRCA1_serine_dom)
Type: Domain

This serine-rich domain is found on BRCA1 proteins.
RNA binding activity-knot of a chromodomain (Tudor-knot)
Type: Domain

This is a novel knotted tudor domain which is required for binding to RNA. The knot influences the loop conformation of the helical turn Ht2 (residues 61-63) that is located at the side opposite the knot in the tudor domain-chromo domain; stabilisation of Ht2 is essential for RNA binding .
HTH-type transcriptional regulator MT1864/Rv1816-like, C-terminal domain (MT1864/Rv1816-like_C)
Type: Domain

This domain is around 80 amino acids in length and it is found to the C terminus of a DNA-binding helix-turn-helix domain from a group of bacterial sequences, including the HTH-type transcriptional regulator MT1864 and Rv1816 from Mycobacterium tuberculosis. MT1864 and Rv1816 may participate in the regulatory network that controls the expression of MmpL lipid transporters . Rv1816 binds to intragenic and/or promoter regions of rv1816, mmpL3, rv0204, mmpL11, mmpL7, kasA and mmpS3 . This is a regulatory domain whose natural ligands may be fatty acids that allow a transcriptional regulation response .
Periplasmic binding protein (SBP_2_dom)
Type: Domain

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .

On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped into eight family clusters , which generally correlate with the nature of the solute bound. This entry represents the family 2 .

This entry represents a domain found in a variety of bacterial periplasmic binding proteins belonging mainly to family 2 which can recognise fructose .