SII-SWORD/CoKE huggingface dataset:
Bacterial DNA polymerase III, alpha subunit, NTPase domain (DNA_pol3_alpha_NTPase_dom)
Type: Domain

This is a conserved region found in the the DNA polymerase III alpha subunit, (

). DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase .
DEAD-box helicase, OB fold (DEAD-box_helicase_OB_fold)
Type: Domain

This domain is found towards the C terminus of the DEAD-box helicases (

). In these helicases it is apparently always found in association with

. There do seem to be a couple of instances where it occurs by itself - e.g.

. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins .
Coatomer beta subunit, C-terminal (Coatomer_bsu_C)
Type: Domain

This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal

domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway .

Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer . While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins . For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi . Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes . COPI coated vesicle assembly is initiated by recruitment of the small GTPase Arf1 which recruits the coatomer protein complex from the cytoplasm and anchors it at the membrane. Then, Arf1 is activated by a guanine exchange factor and hydrolyses GTP to mediate uncoating of the vesicle which subsequently fuses with its target membrane . As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits, and can be subdivided into an outer-coat and an adaptor subcomplex .
GntR, C-terminal (GntR_C)
Type: Domain

Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon . In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (

), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (

), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA .

This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in

and

that are regulators of sugar biosynthesis operons.
Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain (Sig_transdc_His_kin_sub3_dim/P)
Type: Domain

This entry represents the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with

and

.

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions . Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk . These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more . Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) . The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response .

Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms . Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation , and CheA, which plays a central role in the chemotaxis system . Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water . The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily.
Leucine-rich repeat 3 (Leu-rich_rpt_3)
Type: Repeat

Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape . LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions .Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response .

Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel β sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the β-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins.
3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with α-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions . Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20-to 30-residue repeats .

This entry includes some LRRs that fail to be detected by the

model.
Seven residue repeat (Seve_residue_repeat)
Type: Repeat

This repeat is found in some Plasmodium and Theileria proteins.
Tyrosine aminotransferase ubiquitination region (Tyr_aminoTrfase_ubiquitination)
Type: Conserved_site

This region contains a probable site of ubiquitination that ensures rapid degradation of tyrosine aminotransferase in rats. The half life of the enzyme
in vivo
is about 2-4 hours. The enzyme contains at least 2 phosphorylation sites including CAPK at Ser29 and, at the other end of the protein, a casein kinase II site at S*QEECDK. This region of TAT is probably primarily related to regulatory events. Most other transaminases are much more stable and are not phosphorylated.
Tetratricopeptide TPR-3 (TPR-3)
Type: Repeat

This entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones .
Tetratricopeptide TPR-4 (TPR-4)
Type: Repeat

This entry includes tetratricopeptide-like repeats not detected by the

,

and

models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) .
Glutamate--cysteine ligase GshA (GshA)
Type: Family

This entry represents a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria . It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.
Conserved hypothetical protein CHP02058 (CHP02058)
Type: Family

This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Thr operon leader peptide (Thr_lead_pept)
Type: Family

This family consists of examples of the threonine biosynthesis (Thr) operon leader peptide, also called the Thr operon attenuator. The small gene for this peptide is often missed in genome annotation. It should be looked for in genomes of the proteobacteria, immediately upstream of genes for threonine biosynthesis, typically aspartokinase I/homoserine dehydrogenase, homoserine kinase, and threonine synthase. Transcription of the rest of the Thr operon is attenuated (mostly turned off) unless the ribosome pauses during a stretch of the leader sequence rich in both Ile (made from Thr) and in Thr itself because of the scarcity of those amino acids at the time. The leader peptide itself, once made, may have no role other than to be degraded. Similar systems exist for some other amino acid biosynthetic operons, such as Trp.
Conserved hypothetical protein CHP02096 (CHP02096)
Type: Family

This entry represents proteins, which are about 135 amino acids in length and largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes .
Hemimethylated DNA-binding domain (Hemimethylated_DNA-bd_dom)
Type: Domain

Heat shock protein HspQ, also known as YccV, is an Escherichia coli hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression .

This entry represents a YccV-like hemimethylated DNA binding domain that can also be found in longer eukaryotic proteins, such as F-box only protein 21 from mammals and ClpF from Arabidopsis.
Zinc finger/thioredoxin putative (Znf/thioredoxin_put)
Type: Domain

This entry represents a region, which contains a CXXCX(19)CXXC motif, is usually found at the N terminus of prokaryotic proteins. One partially characterised gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility . This domain is predicted to adopt a fold typical for zinc beta-ribbon domains

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Cyd operon protein YbgT (Cyd_oper_YbgT)
Type: Family

This entry describes a very small (as short as 33 amino acids) protein of unknown function, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase . It begins with an aromatic motif MWYFXW and appears to contain a membrane-spanning helix. This protein appears to be restricted to the Proteobacteria and exist in a single copy only. We suggest it may be a membrane subunit of the terminal oxidase. The family is named after the Escherichia coli member YbgT (

). This model excludes the apparently related protein YccB (

).
Coenzyme PQQ biosynthesis protein A (PQQ_synth_PqqA)
Type: Family

This entry describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product .
K+ transporting P-type ATPase, F subunit (KdpF)
Type: Family

This entry represents the F subunit (KdpF) of a P-type K+ translocating ATPase (Kdp) in archaea and bacteria. KdpF is a very small integral membrane peptide. The kdpABC operon of Escherichia coli codes for the high affinity K+ translocating Kdp complex . KdpF is found upstream of the KdpA subunit (

). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation.Though KdpF is not essential in vivo it is part of the complex and functions as a stabilising element in vitro .

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
Conserved hypothetical protein CHP02117 (CHP02117)
Type: Family

This conserved hypothetical protein of unknown function is predominantly found in proteobacteria. Its function is unknown and its genome context is not well-conserved. It is found amid urease genes in at least one species.
Polyhydroxyalkanoic acid inclusion protein PhaP (PhaP_Bmeg)
Type: Family

This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage .
Polyhydroxyalkanoic acid synthase, PhaR subunit (PhaR_Bmeg_synth)
Type: Family

This entry describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit .
Mycoplasma virulence, signal domain (Mycoplasma_virulence_signal)
Type: Domain

This entry represents the N-terminal region of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum. It includes a probable signal sequence or signal anchor, which, in most instances, has four consecutive Lys residues before the hydrophobic stretch.
Conserved hypothetical CHP02185, integral membrane (CHP02185_IM)
Type: Family

This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
WlaTC/HtrL glycosyltransferase (WlaTC/HtrL_glycosyltransf)
Type: Family

This family includes HtrL (also known as YibB) in Escherichia coli, where its gene is found in a region of LPS core biosynthesis genes . Homologues are found in Shigella flexneri, Campylobacter jejuni, and some eukaryotic species, such as Caenorhabditis elegans. WlaTC from Campylobacter jejuni, is involved in lipooligosaccharide synthesis (LOS) together with WlaRG, and WlaTB. WlaTC showed great similarity to HtrL and it has been described as the glycosyltransferase .
Ehrlichia tandem repeat (Ehrlichia_tandem_rpt)
Type: Repeat

This entry represents 77 residues of an 80 amino acid (240 nucleotide) tandem repeat, found in a variable number of copies in an immunodominant outer membrane protein of Ehrlichia chaffeensis, a tick-borne obligate intracellular pathogen .
Conserved hypothetical protein CHP02206, TP0381 (CHP02206_TP0381)
Type: Family

This entry represents a family of hydrophobic proteins with seven predicted transmembrane α helices. Members are found in Bacillus subtilis (ywaF), TP0381 from Treponema pallidum (TP0381), Streptococcus pyogenes, Rhodococcus erythropolis, etc.
Phage conserved hypothetical protein (Phage_CHP)
Type: Family

This entry describes a putative DNA packaging protein from bacteriophage 16-3, related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) , including ORFg6 (RCAP_rcc01688) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in

].
Gene transfer agent, rcc01693 (GTA_rcc01693)
Type: Family

This entry represents gene transfer agents (GTAs), which are involved in a novel mechanism for bacterial gene transfer. They resemble small, tailed bacteriophages in ultrastructure and act like generalized transducing prophages. In contrast to functional prophages, GTAs package random fragments of bacterial genomes and incomplete copies of their own genomes. The packaged DNA content is characteristic of the GTA and ranges in size from 4.4 to 13.6kb. GTAs have been reported in species of Brachyspira, Methanococcus, Desulfovibrio, and Rhodobacter. The best studied GTAs are VSH-1 of the anaerobic, pathogenic spirochete Brachyspira hyodysenteriae and RcGTA of the nonsulfur, purple, photosynthetic bacterium Rhodobacter capsulatus. VSH-1 and RcGTA have likely contributed to the ecology and evolution of these bacteria. The existence of GTAs in phylogenetically diverse bacteria suggests GTAs may be more common in nature than is now appreciated .

In Rhodobacter capsulatus, cultures that enter the stationary phase of growth, release particles of the gene transfer agent (RcGTA). The morphology of RcGTA resembles that of a small, tailed bacteriophage, with a protein capsid surrounding a ~4 kb linear, double-stranded fragment of DNA. However, the DNA present consists of random segments of the R. capsulatus genome, which may be transferred to another strain of R. capsulatus. The recipient in RcGTA-mediated gene transduction may acquire new alleles and thus express a new phenotype. The genes encoding the structural proteins of the RcGTA are clustered on the R. capsulatus chromosome, whereas genes that encode proteins that regulate the production of RcGTA are scattered around the chromosome .

This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in

]. The function is not known.
Domain of unknown function DUF2460 (DUF2460)
Type: Domain

The entry represents a domain found in a number of conserved hypothetical proteins. Their genes are often, though not always, encoded in apparent phage-derived regions of bacterial chromosomes. The Rhodobacter capsulatus sequence is apparently part of the gene transfer agent [see Fig.1, in

].
Phage conserved hypothetical protein, C-terminal (Phg_2220_C)
Type: Domain

This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
CRISPR-associated protein, TM1812 (CRISPR-assoc_prot_TM1812)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents a family of Cas proteins, including TM1812 from Thermotoga maritima and MJ1674 from Methanocaldococcus jannaschii. Family members are also found in Vibrio vulnificus (strain YJ016), Nitrosomonas europaea (strain ATCC 19718), a large plasmid of Synechocystis sp.(strain PCC 6803), and Fibrobacter succinogenes subsp. succinogenes S85.
Caa(3)-type oxidase, subunit IV (Caa3_sub_IV)
Type: Family

This entry represents a small set of proteins with weak similarity to the sequences in Pfam family

, which describes the cytochrome C oxidase subunit IV .
F0F1-ATPase subunit, putative (ATPase_gene1)
Type: Family

This entry represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme .