SII-SWORD/CoKE huggingface dataset:
Arginyl tRNA synthetase N-terminal domain (Arg-tRNA-synth_N)
Type: Domain

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .

This domain is found at the N terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested to be involved in tRNA recognition .
Transcription regulator PadR, N-terminal (Tscrpt_reg_PadR_N)
Type: Domain

Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response .
Cellulose synthase (Cellulose_synth)
Type: Family

Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium spp. More correctly designated as "cellulose synthase catalytic subunits", plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity .
Tail specific protease (Tail-specific_protease)
Type: Domain

This entry represents a domain found in the tail-specific proteases, such as retinol-binding protein 3 (also known as IRBP) from animals, C-terminal processing peptidases from algae and tricorn proteases from archaea. This domain share structural similarity with the crotonase fold that is formed from repeated β/β/α units, which comprises two perpendicular β-sheet surrounded by α-helices.
Lipase, secreted (Lipase_secreted)
Type: Family

This entry represents a family of secreted lipases. Family members include the LIP lipases from Candida albicans, which are expressed and secreted during the infection cycle of these pathogens .

This entry also includes trichothecene C-3 esterase (also known as Tri8) from Fusarium sporotrichioides. It is part of the core gene cluster that mediates the biosynthesis of trichothecenes, a very large family of chemically related bicyclic sesquiterpene compounds acting as mycotoxins, including T2-toxin . Also included in this family is lactone esterase (also known as lipase-like enzyme SBLE), which is responsible for the lactonization of acidic sophorolipids .
MbtH-like domain (MbtH-like_dom)
Type: Domain

This domain is found in the MbtH protein

as well as at the N terminus of the antibiotic synthesis protein NIKP1. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues. Many of the members of this family are found in known antibiotic synthesis gene clusters.
Alpha glucuronidase, N-terminal (Glyco_hydro_67_aGlcAse_N)
Type: Domain

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

This represents a family of alpha-glucuronidases (

). Deletion mutants have indicated that the central region is responsible for the catalytic activity. Within this central domain, the invariant Glu and Asp (residues 391 and 364 respectively from Bacillus stearothermophilus (Geobacillus stearothermophilus)) are thought to from the the catalytic centre .
UPF0113, PUA domain (UPF0113_PUA)
Type: Domain

This entry represents the PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain found in 60S ribosome subunit biogenesis protein NIP7, some UPF0113 family members, such as KD93, and similar proteins found in eukaryotes and some archaeal species . PUA domains are predicted to bind RNA molecules with complex folded structures . NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.

Nip7 orthologues share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. Structural analyses of the RNA-interacting surfaces of the orthologues from Saccharomyces cerevisiae and Pyrococcus abyssi Nip7 indicate that, in the archaeal PUA domain, C-terminal positively charged residues (arginines and lysines) are involved in RNA interaction while equivalent positions in eukaryotic orthologues are occupied by mostly hydrophobic residues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis .
Bacterial transcriptional activator domain (BTAD)
Type: Domain

Found in the DNRI/REDD/AFSR family of regulators, this domain of AFSR (

) along with the C-terminal region is capable of independently directing actinorhodin production. AFSR is important for the formation of secondary metabolites .
WCCH motif (WCCH)
Type: Domain

The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif .
Ku70/Ku80 C-terminal arm (Ku_C)
Type: Domain

The Ku heterodimer (composed of Ku70

and Ku80

) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C-terminal arm. This α helical region embraces the β-barrel domain

of the opposite subunit .
Ku70/Ku80, N-terminal alpha/beta (Ku_N)
Type: Domain

The Ku heterodimer (composed of Ku70

and Ku80

) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the N-terminal α/β domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded β sheet of the Rossman fold .
Retrotransposon gag domain (Retrotrans_gag_dom)
Type: Domain

Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins, including Retrotransposon-derived protein PEG10 from Mus musculus, which binds its own mRNA and self-assembles into virion-like capsids . There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved .
YiiM-like, triple helical domain (Tri_helical_YiiM-like)
Type: Domain

This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C-terminal of proteins related to the YiiM protein (

) from Escherichia coli .
Allantoicase (Allantoicase)
Type: Family

Allantoicase (also known as allantoate amidinohydrolase) is involved in purine degradation, facilitating the utilization of purines as secondary nitrogen sources under nitrogen-limiting conditions. While purine degradation converges to uric acid in all vertebrates, its further degradation varies from species to species. Uric acid is excreted by birds, reptiles, and some mammals that do not have a functional uricase gene, whereas other mammals produce allantoin. Amphibians and microorganisms produce ammonia and carbon dioxide using the uricolytic pathway. Allantoicase performs the second step in this pathway catalyzing the conversion of allantoate into ureidoglycolate and urea.

allantoate + H(2)0 = (S)-ureidoglycolate + urea

The structure of allantoicase is best described as being composed of two repeats (the allantoicase repeats: AR1 and AR2), which are connected by a flexible linker. The crystal structure, resolved at 2.4A resolution, reveals that AR1 has a very similar fold to AR2, both repeats being jelly-roll motifs, composed of four-stranded and five-stranded antiparallel β-sheets . Each jelly-roll motif has two conserved surface patches that probably constitute the active site .

The mammalian proteins matched by this entry are thought to be non-functional as mammals do not appear to possess allantoicase activity .
Anthrax toxin, edema factor, central (Anthrax_toxin_edema_cen)
Type: Domain

Anthrax toxin is a plasmid-encoded toxin complex produced by the Gram-positive, spore-forming bacteria, Bacillus anthracis. The toxin consists of three non-toxic proteins: the protective antigen (PA), the lethal factor (LF) and the edema factor (EF) . These component proteins self-assemble at the surface of host cell receptors, yielding a series of toxic complexes that can produce shock-like symptoms and death. Anthrax toxin is one of a large group of Bacillus and Clostridium exotoxins referred to as binary toxins, forming independent enzymatic (A moiety) and binding (B moiety) components. The LF and EF proteins are the enzymes (A moiety) that act on cytosolic substrates, while PA is a multi-functional protein (B moiety) that binds to cell surface receptors, mediates the assembly and internalisation of the complexes, and delivers them to the host cell endosome . Once PA is attached to the host receptor , it must then be cleaved by a host cell surface (furin family) protease before it is able to bind EF and LF. The cleavage of the N terminus of PA enables the C-terminal fragment to self-associate into a ring-shaped heptameric complex (prepore) that can bind LF or EF competitively. The PA-LF/EF complex is then internalised by endocytosis, and delivered to the endosome, where PA forms a pore in the endosomal membrane in order to translocate LF and EF to the cytosol. LF is a Zn-dependent metalloprotease that cleaves and inactivates mitogen-activated protein (MAP) kinases, kills macrophages, and causes death of the host by inhibiting cell proliferation . EF is a calcium-and calmodulin-dependent adenylyl cyclase that can cause edema (fluid-filled swelling) when associated with PA. EF is not toxic by itself, and is required for the survival of germinated Bacillus spores within macrophages at the early stages of infection. EF dramatically elevates the level of host intracellular cAMP, a ubiquitous messenger that integrates many processes of the cell; increases in cAMP can interfere with host intracellular signalling .

This entry represents a central domain in the edema factor adenylyl cyclase protein of anthrax toxin, as well as in adenylyl cylcases from other bacterial toxins.
Rous sarcoma virus, Gp95, envelope protein (RSV_p95_env)
Type: Family

A family of a vain specific viral glycoproteins that forms a receptor-binding Gp95 polypeptide that is linked through disulphide to a membrane-spanning gp37 spike. Gp95 confers a high degree of subgroup specificity for interaction with distinct cell receptors .
Bunyavirus glycoprotein G1 (Bunya_G1)
Type: Domain

Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 (also known as Gc) and G2 (also known as G2), and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G1 glycoprotein, which is the viral attachment protein . It interacts with the G2 polyprotein (

).
Bunyavirus glycoprotein G2 (Bunya_G2)
Type: Domain

Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the

G1 glycoprotein .
CagA exotoxin, phosphopeptide substrate mimic region (CagA_C)
Type: Domain

Helicobacter pylori is the most common world-wide infection and plays an important role in pathogenesis of peptic ulcers. The CagA (cytotoxin-associated gene A) protein is a cell-surface antigen which may play a role in determining the relative virulence of the viral strains. This entry represents the phosphopeptide substrate mimic region of CagA. This region mimics substrates of human kinase PAR1b/MARK2, resembling eukaryotic protein kinase inhibitors .
Transporter-associated domain (Transptr-assoc_dom)
Type: Domain

This small domain is found in a family of proteins with the CBS

domain and two CBS domains with this domain found at the C-terminal of the proteins, the domain is also found at the C-terminal of some Na
+
/H
+
antiporters . This domain is also found in CorC that is involved in Magnesium and cobalt efflux . The function of this domain is uncertain but might be involved in modulating transport of ion substrates.
Cytochrome C oxidase subunit IV, prokaryotes (Cyt_c_oxidase_su4_prok)
Type: Family

Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyses the final step of electron transfer through the respiratory chain on the mitochondrial inner membrane. Bacterial cytochrome c oxidases generally consist of four different subunits, I to IV. This family is composed of cytochrome c oxidase subunit IV from prokaryotes, which is present in a cleft formed by subunits I and III. Subunit IV assists the a copper ion, CuB, binding to subunit I during biosynthesis or assembly of the oxidase complex .
CRC domain (CRC)
Type: Domain

The following proteins of the tesmin/TSO1 family contain two cysteines-rich repeats with the consensus C-X-C-X(4)-C-X(3)-Y-C-X-C-X(6)-C-X(3)-C-X-C-X(2)-C separated by a region of variable length containing the short conserved sequence R-N-P-X-A-F-X-P-K:

Animal tesmin or MTL5, originally identified by its specific expression in testes, but subsequently it was also detected at specific stages of ovary development.

Animal tesmin-like (tesl) or LIN54.

Drosophila melanogaster tombola (tomb), a meiotic arrest protein which is expressed specifically in testis.

Arabidopsis thaliana TSO1, 'tso' means 'ugly' in Chinese and refers to the appearance of tso1 mutant flowers.

Arabidopsis thaliana TSO1-like 1 and 2 (SOL1 and SOL2).

Legume Cysteine-rich Polycomb-like Protein 1 (CPP1), a DNA-binding protein acting as a negative regulator of the leghemoglobin gene.

This domain has been named the CRC domain (C1-RNPXAFXPK-C2). It binds zinc and is able to bind DNA .

The CRC domain shows some similarity to the CXC domain found in the E(z)-type of Polycomb group proteins . However, a clear distinction can be made, since the CXC domain lacks the RNPXAFXPK motif.
DMRTA motif (DMA)
Type: Domain

This entry represents the DMA domain found to the C terminus of the DM DNA-binding domain [

] in Doublesex- and mab-3-related transcription factors (Dmrt proteins) from eukaryotes. These proteins are involved in sexual development . The function of the region DMA, conserved in Dmrt3, Dmrt4, and Dmrt5 (also known as Dmrt2), is still unknown .
KIB1-4, beta-propeller (KIB1-4_b-propeller)
Type: Domain

This entry, previously known as DUF295, represents the β-propeller domain found in F-box proteins KIB1-4, from Arabidopsis thaliana, and similar plant proteins. This domain adopts a β-propeller structure with 6 blades and is often found in association with F-box domain (

). KIB1-4 are ubiquitin ligases that act as essential positive regulators in brassinosteroid signalling, mediating the ubiquitination, substrate interaction and degradation of GSK3 kinase BIN2 .

This domain is also found in Protein UNUSUAL FLORAL ORGANS (UFO), likely a meristem identity factor required for normal growth of the young floral meristem . It acts together with LEAFY to positively regulate the B class floral homeotic genes APETALA3 and PISTILLATA .

Protein PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 also contain this domain. This protein regulates growth and development adaptation to the ambient environment by controlling negatively phytochrome B (phyB) dark reversion, a temperature-dependent thermal relaxation process during which phyB reverts from the active to the inactive state .
PPC domain (PPC_dom)
Type: Domain

The Plants and Prokaryotes Conserved (PPC) domain contains a hydrophobic region in the C-terminal, and in the case of plants, is often found in several proteins with the AT-hook motif. Proteins with PPC domains are found in Bacteria, Archaea and the plant kingdom .

The PPC domain has a single α-helix packed against an antiparallel β-sheet, which is formed by five β-strands. Three conserved histidine residues appear to form a zinc-binding site, and the domain has been observed to form homotrimers. The domain co-occurs with a thioredoxin-like domain in uncharacterised cyanobacterial proteins .
Potentiating neddylation domain (PONY_dom)
Type: Domain

This domain is found in the eukaryotic family defective in cullin neddylation, which includes DCN1 and DCN1-like proteins. Proteins of the DCN family may contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes, which are multi-protein complexes required for polyubiquitination and subsequent degradation of target proteins by the 26S proteasome .

The structure of this domain is composed entirely of α helices . It has been referred to as potentiating neddylation domain (PONY) and can be found in association with an N-terminal UBA domain. The PONY domain contains a cullin-binding surface within its C-terminal region and is sufficient to promote neddylation .
Bifunctional kinase-pyrophosphorylase (Kinase-pyrophosphorylase)
Type: Family

This family of regulatory proteins has ADP-dependent kinase and inorganic phosphate-dependent pyrophosphorylase activity .
Organic solute transporter subunit alpha/Transmembrane protein 184 (Ostalpha/TMEM184C)
Type: Family

This entry includes Organic solute transporter subunit alpha (OSTalpha, also known as SLC51A), an essential component of the Ost-alpha/Ost-beta complex, a heterodimer that acts as the intestinal basolateral transporter responsible for bile acid export from enterocytes into portal blood , the transmembrane protein 184 (TMEM184) and the homologue from yeast, HFL1, a vacuole membrane protein that recruits ATG8 to facilitate the degradation of vacuolar integral membrane proteins during early-stationary vacuole turnover (EVT) when cells enter stationary phase .
Domain of unknown function DUF302 (DUF302)
Type: Domain

This domain is found in poorly characterised set of proteins, including the putative fluoride ion transporter CrcB 1 and CrcB 2 (also known as FluC 1 and FluC 2) from Brucella sp. It normally occurs uniquely within a sequence, but is found as a tandem repeat (

). It has an interesting phylogenetic distribution with the majority of examples in bacteria and archaea, but it is also found in some fungal proteins. The hypothetical protein TT1751 from Thermus thermophilus has a β-α-β(4)-α structural fold .
Sialate O-acetylesterase domain (SASA)
Type: Domain

This entry represents a domain found in eukaryotic sialic acid acetylesterases (SIAEs). The catalytic triad of this esterase enzyme comprises residues Ser127, His403 and Asp391 in mouse SIAE . Proteins containing this domain also include some uncharacterised bacterial proteins.
YdbS-like, PH domain (YdbS-like_PH)
Type: Domain

This domain is found in an uncharacterised family of membrane proteins mainly found in prokaryotes, including	UPF0699 transmembrane protein YdbS from Bacillus subtilis. Members of this group contain 1-3 copies of this domain, with each copy flanked by transmembrane helices. It has a PH domain-like structure (

) .
Domain of unknown function DUF305, CopM-like (DUF305_CopM-like)
Type: Domain

This entry represents a domain found in CopM from Synechocystis sp. (also known as Slr6039) and similar uncharacterised bacterial proteins. CopM is a cyanobacterial metallochaperone that shows a simple four-helical fold . This domain is also found in Uncharacterized protein L153 from Acanthamoeba polyphaga mimivirus. It is short and found in one or two copies.
Domain of unknown function DUF306, Meta/HslJ (DUF306_Meta_HslJ)
Type: Domain

This entry represents a domain found in proteins of unknown function , some of which are described as heat shock protein (HslJ). In Helicobacter pylori (Campylobacter pylori) the protein is secreted e.g. (

) and implicated in motility. In Leishmania spp. it is described as an essential protein, over-expression of which, in Leishmania amazonensis increases virulence (

). In E. coli, hslJ is not induced by heat shock. It encodes a putative outer-membrane protein that is CysB-regulated and is involved in displaying novobiocin resistance .

A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond.
Inner membrane component domain (YccF)
Type: Domain

This domain occurs as one or more copies in bacterial and eukaryotic proteins. These are membrane proteins of four TM regions, two appearing in each of the two copies when both are present. Many of the latter members also carry the sodium/calcium exchanger membrane region (

), which have multipass membrane regions .
FlaG protein (FlaG)
Type: Family

This entry includes protein FlaG (encoded from the flagellin locus) and an uncharacterised protein, YvyC, whose structure has been solved . In Aeromonas caviae, mutation of FlaG does not affect motility but does significantly reduce the level of its adherence to HEp-2 cells .