SII-SWORD/CoKE huggingface dataset:
Bifunctional protein PutA (Bifunct_PutA)
Type: Family

This entry represents PutA, which is a bifunctional enzyme with proline dehydrogenase (PDH) and delta 1-pyrroline-5-carboxylate dehydrogenase (P5CDH) activities . PutA also acts as a transcriptional repressor of proline utilisation (put) genes .
E3 ubiquitin ligase UBR4, C-terminal (E3_Ub_ligase_UBR4_C)
Type: Domain

Proteins containing this domain includes E3 ubiquitin ligase UBR4 from animals, auxin transport protein BIG from plants and protein purity of essence from fruit flies.

UBR4, also known as p600, is a member of the N-recognin family, which contains proven and predicted E3 ligases that recognize and degrade proteins containing destabilizing N termini . It is involved in anoikis, viral transformation and protein degradation . It also has roles in neurogenesis, neuronal migration, neuronal signaling and survival in mammalian brains .

BIG is required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development) . Auxin transport protein is also involved in the elongation of the pedicels and stem internodes through auxin action, the expression/modulation of light-regulated genes, repression of CAB1 and CAB3 genes in etiolated seedlings, etc .

Protein purity of essence, found in Drosophila melanogaster, has a role in growth of the perineurial glial layer of the larval peripheral nerve and it may have a role in male fertility and eye development or function .
Beta-hexosaminidase (Beta_hexosaminidase_sua/sub)
Type: Family

This entry represents beta-hexosaminidase (

). There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor.

Beta-hexosaminidase belongs to the glycoside hydrolase family 20 (

).
Endo-alpha-N-acetylgalactosaminidase (Endoa_GalNAc)
Type: Domain

Virulence of pathogenic organisms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolise the resultant carbohydrates.
Predicted DNA-binding protein with PD1-like DNA-binding motif (DNA_bp_PD1)
Type: Family

This entry represents a predicted DNA-binding protein with PD1-like DNA-binding motif.
Heat shock protein 15 (HSP15)
Type: Family

This entry represents heat shock protein 15 (Hsp15), an abundant nucleic acid-binding protein whose RNA synthesis is induced upon temperature upshift . The protein contains an RNA-binding motif . The in vivo target of Hsp15 appears to be the free 50S ribosomal subunit - it does not bind it when it is part of the 70S ribosome . Hsp15 may be involved in the recycling of free 50S subunits that still carry a nascent chain .
Leucyl-tRNA synthetase, editing domain (Leu_tRNA-synth_edit)
Type: Domain

This entry represents the editing domain (known as CP1 domain) of Leucyl-tRNA synthetase (

), which hydrolyses mischarged tRNALeu. In the case of Leucyl-tRNA synthetase, the β-strands that link the CP1 domain to the aminoacylation core of the protein are also required for editing activity .
L-cysteine S-thiosulfotransferase subunit SoxA (SoxA)
Type: Family

SoxA protein is a c-type cytochrome with a CxxCH motif. It is part of the SoxAX cytochrome complex that contributes to thiosulfate oxidation to sulfate .
PepSY domain (PepSY)
Type: Domain

This domain is likely to have a protease inhibitory function. The name is derived from peptidase (M4) and YpeB of Bacillus subtilis .

This domain is found in the propeptide of members of the MEROPS peptidase family M4 (clan MA(E)), which contains the thermostable thermolysins (

), and related thermolabile neutral proteases (bacillolysins) (

) from various species of Bacillus. It is also in many non-peptidase proteins, including Bacillus subtilis YpeB protein -a regulator of SleB spore cortex lytic enzyme -and a large number of eubacterial and archaeal cell wall-associated and secreted proteins which are mostly annotated as 'hypothetical protein'.
Nucleoporin Nup54, alpha-helical domain (Nup54_alpha-helical_dom)
Type: Domain

This entry represents the α-helical domain of human Nup54. Nup54 interacts with Nup58 via the C-terminal part of this domain and Nup62 via the N-terminal part to form the nucleoporin complex . Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them . In yeast, Nup54 is known as Nup57.
Motility protein B-like, N-terminal domain (MotB-like_N_dom)
Type: Domain

This domain is found in MotB, a component of the Escherichia coli MotA/MotB proton-channel complex that forms the stator of the bacterial membrane flagellar motor. Key residues in MotB act as a plug to prevent premature proton flow. The plug is in the periplasm just C-terminal to the MotB TM (transmembrane helix), consisting of an amphipathic α-helix flanked by Pro-52 and Pro-65, eg in

. In addition to the Pro residues, Ile-58, Tyr-61, and Phe 62 are also essential for plug function .

This domain is also found in ZorB, a distant homologue of MotB. ZorB is a component of the antiviral defense system Zorya type I, composed of ZorA, ZorB, ZorC and ZorD. ZorA and ZorB may assemble in the cell inner membrane .
Methyltransferase domain (Methyltranfer_dom)
Type: Domain

This domain appears to be a methyltransferase domain.
Chromatin target of PRMT1 protein, C-terminal (FoP_C)
Type: Domain

This LDXXLDAYM region (where X is any amino acid) is duplicated in the C terminus of chromatin target of PRMT1 protein (also known as Fop), which are chromatin-associated proteins that co-localise with facultative heterochromatin and are critical for oestrogen-dependent gene activation . The region also occurs in other proteins, including THO complex subunit 4 (

) and RNA and export factor-binding protein 2 (

).
Post-transcriptional regulator (Post-transcriptional_regulator)
Type: Family

This entry includes post-transcriptional regulators such as YrzD, which is renamed to ComN. The comN gene is a regulatory factor in competence development that functions through the 5'-UTR of the comE operon .
Histone deacetylase complex subunit SAP30 zinc-finger (SAP30_zn-finger)
Type: Domain

SAP30 is a subunit of the histone deacetylase complex, and this domain is a zinc-finger. Solution of the structure shows a novel fold comprising two β-strands and two α-helices with the zinc organising centre showing remote resemblance to the treble clef motif. In silico analysis of the structure reveals a highly conserved surface dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 Zn-finger motif indicate a strong preference for nucleic acid substrates. The zinc-finger of SAP30 probably functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 co-repressor complex .
Histone deacetylase complex subunit SAP30, Sin3 binding domain (SAP30_Sin3-bd)
Type: Domain

This C-terminal domain of the SAP30 proteins appears to be the binding region for Sin3 .
Myelin gene regulatory factor C-terminal domain 2 (MYRF_C2)
Type: Domain

Myelin regulatory factor (Myrf) is a transcription regulator required in vertebrates for expression of central nervous system (CNS) myelin genes such as Mbp and Mog, thereby playing a central role in oligodendrocyte maturation and CNS myelination . It is also required for the maintenance of expression of myelin genes and the mature oligodendrocytes identity in the adult CNS . A Caenorhabditis elegans orthologue, pqn-47, may function as a regulator of molting , while a Dictyostelium orthologue has been described to regulate prestalk differentiation .

This domain is found at the C terminus of myelin regulatory factor. The function of the domain is not known.
ECF transporter, Riboflavin transporter RibU (RibU)
Type: Family

This entry represents the riboflavin ECF transporter S component RibU which mediates riboflavin uptake and may also transport FMN and roseoflavin . The crystal structure of RibU from Staphylococcus aureus (

) has been solved, revealing the protein to possess six transmembrane segments and to adopt a previously unreported transporter fold . RibU belongs to the prokaryotic riboflavin transporter family which is a member of the bile/arsenite/riboflavin transporter superfamily . For more information, please refer to the Transporter Classification Database (http://www.tcdb.org/search/result.php?tc=2.A.87).

Energy-coupling factor (ECF) transporters consist of a substrate-specific component (known as the S component), and an energy-coupling module . The substrate-binding component is a small integral membrane protein which captures specific substrates and forms an active transporter in the presence of the energy-coupling AT module. The energy coupling module is composed of an ATPase typical of the ATP binding cassette (ABC) superfamily (A component) and a characteristic transmembrane protein (T component). Unlike the ABC transporters, an energy coupling module can be shared between multiple different substrate-binding components.
Exosome complex component, N-terminal domain (Exosome_cplx_N_dom)
Type: Domain

This entry represents a domain found in the N-terminal region of some exosome complex components, including ribosomal RNA-processing protein 4 (RRP4) and CSL4. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.
Bacterial transcriptional repressor TetR (TetR)
Type: Family

This family of bacterial transcriptional repressors is characterised by the short approximately 50 amino acid stretch of residues constituting the helix-turn-helix DNA binding motif, around the YRFhY motif. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The regulatory network in which TetR itself is involved is in being released in the presence of tetracycline, binding to the target operator, and repressing tetA transcription .
ArsA/GET3, Anion-transporting ATPase-like domain (ArsA/GET3_ATPase-like)
Type: Domain

This entry represents a conserved domain in ArsA/GET3 proteins . This entry also matches some sequences from the Mrp/NBP35 ATP-binding proteins family and related ATPases.

Active extrusion is a common mechanism for the detoxification of heavy metals, drugs and antibiotics in bacteria, protozoa and mammals. This is particularly important for arsenic extrusion because of its prevalence in the environment and its potential to cause health and environmental problems. In prokaryotes, arsenic detoxification is accomplished by chromosomal and plasmid-borne operon-encoded efflux systems. ArsA from Escherichia coli is the catalytic subunit of the ArsAB extrusion pump, providing resistance to arsenite and antimonite. This pump consists of a soluble ATPase (ArsA) and a membrane channel (ArsB). Maintenance of a low intracellular concentration of oxidation produces resistance to the toxic agents. A third protein, ArsC, expands the substrate specificity to allow for arsenate resistance. ArsC reduces arsenate to arsenite, which is subsequently pumped out of the cell . ArsA contains two nucleotide-binding sites (NBSs) and a binding site for arsenic or antimony. Binding of metalloids to the pump stimulates the ATPase activity .

Homologues of the bacterial ArsA ATPase are found in eukaryotes, where they have several recognised functions unrelated to arsenic resistance . Caenorhabditis elegans homologue Asna-1 is required for defence against arsenite and antimonite toxicity , and may be also involved in insulin signaling . The homologue in yeast, GET3/Arr4, is part of the GET complex and not only is involved in stress tolerance to metals and heat , but also specifically recognises transmenbrane domains of tail-anchored (TA) proteins destined for the secretory pathway . Archaeal GET3 homologues have also been discovered, suggesting that that archaea may possess a TA protein targeting pathway similar to that in eukaryotes .
GAG-pre-integrase domain (GAG-pre-integrase_dom)
Type: Domain

This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.
E3 ubiquitin-protein ligase SopA-like, catalytic domain (SopA-like_cat)
Type: Domain

This domain is found in the Escherichia coli Type III secretion effector proteins SopA and NleL . These proteins have been shown to act as E3 ubiquitin ligase enzymes. This domain contains the active site cysteine residue.
E3 ubiquitin ligase SopA-like central domain (SopA-like_central)
Type: Domain

This domain is found in the E. coli Type III secretion effector proteins SopA and NleL . These proteins have been shown to act as E3 ubiquitin ligase enzymes.
YbfN-like lipoprotein (YbfN-like)
Type: Family

This family of proteins is functionally uncharacterised and is found in bacteria. Members of this family are lipoproteins of approximately 110 amino acids in length.
YsaB-like lipoprotein (YsaB-like)
Type: Family

This family of proteins is functionally uncharacterised. These proteins are related to Escherichia coli YsaB (

). This family of proteins is found in bacteria. Proteins in this family are lipoproteins and they are approximately 100 amino acids in length.
MsyB protein (MsyB)
Type: Family

The MsyB protein has been found to be able to restore protein export defects caused by a temperature-sensitive secY or secA mutation . Its exact molecular function is still unknown, but it may play a role in protein export. Proteins in this family are approximately 120 amino acids in length and are found in bacteria.
Biofilm regulator BssS (Biofilm_BssS)
Type: Family

The BssS protein family is a group of proteins that are involved in regulation of biofilm formation . Proteins in this family are approximately 80 amino acids in length.
YecR-like lipoprotein (YecR-like)
Type: Family

The YecR-like family of lipoproteins includes the YecR protein from Escherichia coli (

). This family of proteins is found in bacteria and viruses and is functionally uncharacterised. Proteins in this family are approximately 110 amino acids in length.
MarB protein (MarB)
Type: Family

The MarB protein is found in the multiple antibiotic resistance (mar) locus in Escherichia coli . The MarB protein is functionally uncharacterised. Proteins in this family are approximately 70 amino acids in length and contain a conserved GSDKSD sequence motif.
Purple acid phosphatase, C-terminal domain (PAPs_C)
Type: Domain

This domain is found at the C-terminal of purple acid phosphatase proteins (PAPs) and related acid phosphatase proteins. It acquires a fold consisting of two sandwiched β-sheets flanked by α-helical segments .

Purple acid phosphatases (PAPs) (

) are a family of binuclear metallohydrolases that break down phosphate esters and anhydrides in acidic conditions; they have been identified in plants, animals, and fungi. The best-characterised enzyme is from kidney bean, and that enzyme binds Fe
3+
and Zn
2+
ions. The metals bound differ according to source species; for example, the enzyme from sweet potato binds iron and manganese . The structure of the kidney bean enzyme has been solved and shows a disulfide-linked homodimer, with each monomer having a two-domain structure . Human acid phosphatase type 7 is also known as purple acid phosphatase long form. It is associated with bone resorption and microbial killing through its phosphatase activity and hydroxyl radical production . While most of the PAPs are active on a wide range of substrates, some PAPs display higher activity on phytate or 2-phosphoenolpyruvate (PEP) .
EspG family (EspG)
Type: Family

This entry includes the EspG1, EspG2, EspG3 and EspG5 proteins from Mycobacterium tuberculosis. These proteins are involved in the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis which is important for virulence and intercellular spread .
RIP homotypic interaction motif (RHIM)
Type: Binding_site

This entry represents the RHIM (RIP homotypic interaction motif) binding site found in receptor-interacting serine/threonine-protein kinases or cell death proteins , including human Z-DNA-binding protein 1 (ZBP1, also known as DAI) is involved in virus recognition. This motif is necessary for the recruitment of RIP and RIP3. Both RIP kinases contribute to DAI-induced NF-kappaB activation. RIP3 undergoes auto phosphorylation on binding to DAI .

RHIM is also located at the C terminus of TIR-domain-containing adapter-inducing IFN-beta (TRIF). It is essential for TRIF-induced apoptosis, and has been shown to contribute to TRIF-induced NF-kappaB activation .
PucR C-terminal helix-turn-helix domain (PucR_C-HTH_dom)
Type: Domain

This helix-turn-helix domain is often found at the C terminus of PucR-like transcriptional regulators, such as

, and is likely to be DNA-binding .
Functional amyloid transporter FapF (FApF)
Type: Family

This family includes the functional amyloid transporter FapF from Pseudomonas aeruginosa and similar bacterial proteins. FapF transports fibril components across the outer membrane . Many sequences in this family are classified by TCDB as belonging to the putative β-barrel porin/alpha amylase or MetA-pathway of phenol degradation superfamily, including

from Pseudomonas putida (

).
Aerotolerance-related protein BatD (BatD)
Type: Family

This family of proteins carries up to three membrane spanning regions and is involved in tolerance to oxygen in in Bacteroides species .
Centrosome-associated, FAM110, N-terminal domain (FAM110_N)
Type: Domain

This entry represents the N terminus of a family of proteins that colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis .
FAM110 (FAM110)
Type: Family

This entry represents FAM110 which consists of members A, B, C and D. These proteins colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis .
Centrosome-associated, FAM110, C-terminal domain (FAM110_C)
Type: Domain

This entry represents the C terminus of a family of proteins that colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis .
Cleavage stimulation factor subunit 2, hinge domain (CSTF2_hinge)
Type: Domain

The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localisation. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex .
Type VI secretion system component TssM1, N-terminal domain (TssM1_N)
Type: Domain

This domain is found at the N-terminal of the Type VI secretion component TssM1 from Pseudomonas aeruginosa, which plays a role in the release of toxins targeting both eukaryotic and prokaryotic species, plays an essential role in stabilization of assembled TssK1 structure at a fixed perimembrane site and forms part of the tip complex . This domain is also found in bacterial IcmF (intracellular multiplication and human macrophage-killing) proteins and is usually found N-terminal to

.
Ribosomally synthesised peptide in Streptomyces (Rbsml_synth_pep_Strp)
Type: Family

This family consists of ribosomally synthesised peptides from Streptomyces species and related to microviridin and marinostatin. They are usually in the gene neighbourhood of one or more RimK-like ATP-grasp. The gene-context suggests that it is further modified by the ATP-grasp. The peptide is predicted to function in a defensive or developmental role, or as an antibiotic .
Restriction system protein Mrr-like N-terminal domain (Mrr-like_N_dom)
Type: Domain

This domain is found N-terminal to the catalytic domain in Mrr restriction endonucleases . It is also found in other proteins, including predicted methyltransferases and ATPases. Fold recognition analysis predicts that it is a diverged member of the winged helix variant of helix turn helix proteins. It may play a role in DNA sequence recognition .
Type 4 fimbrial biogenesis protein PilX, N-terminal domain (PilX_N_dom)
Type: Domain

This domain is found at the N terminus of the PilX prepilin-like proteins, which are involved in type 4 fimbrial biogenesis .
ThiC-associated domain (ThiC-associated_dom)
Type: Domain

This domain is frequently found at the N terminus of the ThiC family of proteins . Its function is not known.
PrcB C-terminal domain (PrcB_C_dom)
Type: Domain

This domain is found at the C terminus of Treponema denticola PrcB (

). PrcB interacts with the PrtP protease (dentilisin) and is required for the stability of the protease complex . Dentilisin has been suggested to be an important virulence factor of T. denticola with a role in epithelial cell layer penetration .
Sphingomyelin synthase-like domain (Sphingomyelin_synth-like_dom)
Type: Domain

This domain is found in sphingomyelin synthase (also known as phosphatidylcholine:ceramide cholinephosphotransferase), and other proteins. Sphingomyelin synthase is a bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa . This domain is closely related to the C-terminal a region of phosphatidic acid phosphatase type 2 (PAP2).
DPF1-3, N-terminal domain (DPF1-3_N)
Type: Domain

This putative domain has been detected on requiem/DPF family proteins. It was identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodeling factor .
RsbT co-antagonist protein RsbRD, N-terminal domain (RsbRD_N_dom)
Type: Domain

This domain is found at the N terminus of a number of anti-sigma-factor antagonist proteins including Bacillus subtilis RsbRD (

). These proteins are negative regulators of the general stress transcription factor sigma(B) .
High pH protein family (HPH_family)
Type: Family

This is a family of closely related high pH (HPH) proteins that are integral endoplasmic reticulum (ER) membrane proteins required for yeast survival under environmental stress conditions . They interact with several subunits of the Sec63/Sec62 complex that mediates post-translational translocation of proteins into the ER . Cells with mutant Hph1 and Hph2 proteins reveal phenotypes resembling those of mutants defective for vacuolar proton ATPase (V-ATPase) activity. The yeast V-ATPase is a multisubunit complex whose function, structure, and assembly have been well characterised. Cells with impaired V-ATPase activity fail to acidify the vacuole, cannot grow at alkaline pH, and are sensitive to high concentrations of extracellular calcium.
AAA-type ATPase, N-terminal domain (AAA_N_dom)
Type: Domain

This domain is found in association with the ATPase AAA-type domain (

).