SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF4734 (DUF4734)
Type: Domain

This domain is found in species of Drosophila, and is approximately 90 amino acids in length.
Protein of unknown function DUF4735 (DUF4735)
Type: Family

This family of proteins is found in eukaryotes and includes human C16orf89, which is thyroid-specific . Proteins in this family are typically between 288 and 410 amino acids in length. There are two completely conserved C residues that may be functionally important.
Herpes viral adaptor, REF-binding domain (HHV-1_REF-bd)
Type: Domain

This entry represents the short region of the Herpes simplex 1 virus' specific signature adaptor protein that binds to the cellular mRNA export factor, such as mouse REF .
Stomagen (Stomagen)
Type: Family

Stomagen (epidermal patterning factor-like protein 9) is a defensin-like secretory epidermal patterning factor (EPF) peptide hormones which acts as a positive regulator of stomatal development .
Protein of unknown function DUF4736 (DUF4736)
Type: Family

This family of functionally uncharacterised proteins is found in insects. Proteins in this family are typically between 186 and 228 amino acids in length.
Peptidase inhibitor I66 (Inhibitor_I66)
Type: Family

This family of serine protease inhibitors has a β-trefoil fold and inhibits trypsin and chymotrypsin .
Beta-1,3-glucan-binding protein, N-terminal (BGBP_N)
Type: Domain

This domain, also known as the recognition domain, is found at the N terminus of beta-1,3-glucan-binding proteins. It has an immunoglobulin-like β-sandwich fold composed of two antiparallel β-sheets containing three and five β-strands .

Beta 1,3-glucan recognition proteins (GRP, also called Gram-negative bacteria binding proteins or GNBPs) have specific affinity for beta 1,3-glucan, a component on the surface of fungi and bacteria. Beta-GRP (beta-1,3-glucan recognition protein) is one of several pattern recognition receptors (PRRs), also referred to as biosensor proteins, that complexes with pathogen-associated beta-1,3-glucans and then transduces signals necessary for activation of an appropriate innate immune response. They are present in insects and lack all catalytic residues .
Lgt1, glycosyltransferase domain (Lgt1_Glycosyltransf)
Type: Domain

This is the glycosyltransferase domain of type A glycosyltransferases found in Legionella. L. pneumophila glucosyltransferase, also known as Lgt1, belongs to Glycosyltransferase Family 88 and acts as a virulence factor by the glucosylation of EF1A (elongation factor 1A) thereby blocking protein synthesis in the host cell .
Putative substrate of the Dot/Icm secretion system (SoDot-IcmSS)
Type: Family

This is a family of putative substrates of the Dot/Icm type IVA secretion system from Legionella species.
Effector protein HopAB, BAK1-binding domain (HopAB_BAK-bd)
Type: Domain

HopAB family members are type III effector proteins that are secreted by the plant pathogen Pseudomonas syringae into the host plant to inhibit its immune system and facilitate the spread of the pathogen . AvrPtoB, also called HopAB3, is the best studied member of the family. It suppresses host basal defenses by interfering with PAMP (pathogen-associated molecular signature)-triggered immunity (PTI) through binding and inhibiting BAK1, a kinase which serves to activate defense signaling . It also recognizes the kinase Pto to activate effector-triggered immunity (ETI) .

AvrPtoB contains an N-terminal region that contains two kinase-interacting domains (KID) and a C-terminal E3 ligase domain. The first KID recognizes the PTI-associated kinase Bti9 as well as Pto, and is referred to as the Pto-binding domain (PID). The second KID interacts with BAK1 and FLS2, which are leucine-rich repeat-containing receptor-like kinases, and is called the BAK1-interacting domain (BID)
. The family member HopPmaL is shorter and lacks the C-terminal E3 ligase domain .

This entry represents the second KID of AvrPtoB that binds to BAK1 thereby preventing its kinase activity after the perception of flagellin .
Centromere DNA-binding protein complex CBF3 subunit B, C-terminal (Cep3_C)
Type: Domain

This entry represents the C-terminal domain of Cep3, one of the major components of the CBF3. The Cep3 dimer forms a large central channel that is large enough to accommodate duplex B-form DNA. The dimerisation region is followed by a linker to the zinc-finger domain at the C terminus. The CBF3 complex is an essential core component of the budding yeast kinetochore and is required for the centromeric localisation of all other kinetochore proteins. Cep3 is the only component with DNA-binding properties .
Folded gastrulation, N-terminal domain (FOG_N)
Type: Domain

This is the N-terminal domain of the folded gastrulation protein. Folded gastrulation is required for morphogenic movements during gastrulation and nervous system development. It may act as a secreted signal and activate the G protein alpha subunit. This domain may be the G protein-coupled receptor ligand .
Protein of unknown function DUF4738 (DUF4738)
Type: Family

This family of uncharacterised proteins is found in Bacteroidetes, mostly from Bacteroides and Prevotella genera present in human gut and oral cavity, respectively. The experimentally determined structure (JCSG target SP13584B,

) consists of two WD40-like β sheet repeats forming a β sandwich.
Dinitrogenase iron-molybdenum cofactor, N-terminal (NafY_N)
Type: Domain

This entry represents the N-terminal domain of the gamma (Y) subunit of nitrogenase, also known as nitrogenase accessory factor Y, NafY. This region is negatively charged and appears to be necessary for recognising and interacting with the apo state of dinitrogenase. The full-length NafY protein facilitates the transfer of iron-molybdenum cofactor (FeMo-co) into apodinitrogenase by binding to both. The C-terminal region (

), is the part that binds to the cofactor, and the N terminus binds to apodinitrogenase. Nitrogenase is the bacterial enzyme responsible for nitrogen fixation by catalysing the reduction of nitrogen gas (N2) to ammonium in an ATP-dependent manner. It has two components, dinitrogenase and dinitrogenase reductase .
Domain of unknown function DUF4739 (DUF4739)
Type: Domain

This presumed domain is functionally uncharacterised. This domain is found in insect proteins, and is typically between 138 and 167 amino acids in length.
Mdy2, Get4 binding domain (Mdy2_get4-bd)
Type: Domain

This entry represents the binding domain at the N terminus of Mdy2 (also known as Get5) that binds to Get4. Together with Get3, this tripartite complex is involved in the insertion of tail-anchored proteins in the ER membrane .
Occluded RNA-recognition motif (RRM_occluded)
Type: Domain

This is an unusual, frequently C-terminal, RNA-recognition motif found in fungi. In yeast it is the fourth RRM domain on the essential splicing factor Prp24. Structurally, it has a non-canonical RRM fold with the expected β-α-β-β-α-β RRM-fold is flanked by N- and C-terminal α-helices. These two additional flanking α-helices occlude the β-sheet face. The electropositive surface thereby presented is an alternative RNA-binding surface that allows both binding and unwinding of the U6 small nuclear RNA's internal stem loop, at least in vitro .

Prp24 is an RNA-binding protein with four well conserved RNA recognition motifs (RRMs). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly . Prp24 specifically binds free U6 RNA primarily with RRM 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases .
Inhibitor of glucose uptake transporter SgrT (SgrT)
Type: Family

SgrT is a small regulatory polypeptide that inhibits glucose transport activity by a yet unknown mechanism. It is part of a posttranscriptional regulation system in E. coli which consists of a small regulatory RNA (SgrS) and SgrT. During accumulation of glucose-6-phosphate or fructose-6-phosphate, SgrS is involved in downregulation of ptsG mRNA stability, whereas SgrT inhibits glucose transport .
Carbohydrate binding module, xylan-binding domain (CBM60_xylan-bd)
Type: Domain

This entry represents the xylan-binding domain found in the CBM60 (carbohydrate binding module 60) family members.

CBM60 is a family of xylan-binding modules found in conjunction with xylanase enzymes in many bacterial species that attack plant cell walls. Xylan is the major hemicellulose component of most plant cell walls, and is one of the most complex carbohydrates targeted by CBMs. CBM60 modules are evolutionarily related to CBM36 domains as both show circular permutation in the β-barrel folds. CBM60 targets xylan but is also able to bind cellulose and galactan and thus contribute towards breakdown of the plant cell wall. Recognition of the ligand is conferred primarily through the polar interactions of O2 (oxygen) and O3 of a single sugar with a protein-bound calcium ion .
Actin-like protein 7A, N-terminal (ACTL7A_N)
Type: Domain

This entry represents the N terminus of actin-like protein 7A. This domain interacts and forms a heterodimer with TES, a putative human tumor suppressor. This heterodimer then interacts with ENAH to form a heterotrimer .
Antibacterial factor-related peptide (Abf-1/2)
Type: Family

This family of antimicrobial peptides is found in nematodes. It includes ABF-1 and ABF-2 proteins from C. elegans. Recombinant ABF-2 has been shown to possess potent microbicidal activity against Gram-positive and Gram-negative bacteria, and yeasts .
CAAX box protein 1 (CAAX_1)
Type: Family

CAAX box protein 1 (CAAX1, FAM127A) is found in primates. CAAX refers to the highly characteristic C-terminal residues, a cysteine and two aliphatic residues followed by any residue, a C-terminal tetrapeptide recognition motif called the Ca1a2X box . This motif on substrates is recognised by prenyltransferases that then attach an isoprenoid lipid (a process termed prenylation), one of the many post-translational modifications that occur in cells . The function of the prenylated protein is not known.
Tail knob protein gp9, N-terminal (Gp9_N)
Type: Domain

This is the N-terminal domain of Tail knob protein gp9 from Bacillus phage phi29 and similar proteins from tailed bacteriophages and prokaryotic prophages. This protein blocks the end of the tube before DNA ejection while forming a channel perforating the host membrane in the process by adopting a hexameric tube structure with six flexible hydrophobic loops .
Protein of unknown function DUF4741 (DUF4741)
Type: Family

Proteins in this family are also known as FAM231. Their function is not known.
SF3A3 domain (SF3A3_dom)
Type: Domain

This entry represents a domain found in the SF3A3 protein, which is s component of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). This domain can also be found in SF3A3 yeast homologues, Prp9 and Sap61.

In budding yeasts, SF3a complex shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). Prp9 and Prp21 were not thought to interact with each other but the alpha1 helix of Prp9 does make important contacts with the SURP2 domain of Prp21, thus the two do interact via a bidentate-binding mode. Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA .
cGMP-dependent protein kinase, interacting domain (PRKG1_interact)
Type: Domain

This domain is found at the C terminus of protein phosphatase 1 regulatory subunits 12A (PPP1R12A), 12B and 12C. In PPP1R12A it has been found to bind to cGMP-dependent protein kinase 1 via a leucine zipper motif located at the C terminus of this domain .
Sortilin, C-terminal (Sortilin_C)
Type: Domain

This domain is the C-terminal cytoplasmic tail of sortilin, a Vps10p domain-containing family of proteins . Most sortilin is expressed within intracellular compartments, where it chaperones diverse ligands, including proBDNF and acid hydrolases. The sortilin cytoplasmic tail is homologous to mannose 6-phosphate receptor and is required for the intracellular trafficking of cargo proteins via interactions with distinct adaptor molecules . In addition to mediating lysosomal targeting of specific acid hydrolases, the sortilin cytoplasmic tail also directs trafficking of BDNF to the secretory pathway in neurons, where it can be released in response to depolarisation to modulate cell survival and synaptic plasticity .
Sortilin, N-terminal (Sortilin_N)
Type: Domain

Sortilin, also known in mammals as neurotensin receptor-3, is the archetypical member of the vacuolar protein sorting 10 protein domain (Vps10-D) receptor family that binds neurotrophic factors and neuropeptides . This entry represents a domain that constitutes the entire luminal part of Sortilin and is activated in the trans-Golgi network by enzymatic propeptide cleavage . The structure of the domain has been determined as a ten-bladed propeller, with up to 9 BNR or β-hairpin turns in it . The mature receptor binds various ligands, including its own propeptide (Sort-pro), neurotensin, the pro-forms of nerve growth factor-beta (NGF)-6 and brain-derived neurotrophic factor (BDNF)-7, lipoprotein lipase (LpL), apo lipoprotein AV14 and the receptor-associated protein (RAP)1 .
Shu complex, component Psy3 (Psy3)
Type: Family

Psy3 is a component of the Shu complex (also known as PCSS complex) involved in the error-free DNA post-replication repair (PRR) . Psy3 forms a complex first with Cms2, and their L2 loops confer the DNA-binding activity to the Shu complex . The Shu complex binds to recombination sites and is required for Rad51 assembly and function during meiosis. Psy3-Csm2 constitutes a core sub-complex that can stabilise the Rad51-single-stranded DNA complex independently of nucleotide cofactor .
FAM65, N-terminal (FAM65_N)
Type: Domain

This entry represents the N-terminal domain of proteins of the FAM65 family (FAM65A, B and C). PL48 (FAM65B, C6orf32) is associated with cytotrophoblast and lineage-specific HL-60 cell differentiation . The N-terminal part of FAM65B was found to induce the formation of filopodia .
SF3A2 domain (SF3A2_dom)
Type: Domain

This entry represents a domain found in the SF3A2 protein, which is a component of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). This domain can also be found in SF3A2 yeast homologues, Prp11 and Sap62.

In budding yeasts, SF3a complex shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1) .
LKB1 serine/threonine kinase interacting protein 1, N-terminal (LIP1_N)
Type: Domain

This domain represents the N terminus of LIP1, a leucine-rich-repeat protein that interacts with kinase LKB1/STK11, implicated in Peutz-Jeghers syndrome. LIP1 (LKB1 serine/threonine kinase interacting protein 1), also known as STK11IP, interacts with the TGF-beta-regulated transcription factor SMAD4 to form a LKB1-LIP1-SMAD4 ternary complex. Mutations in SMAD4 lead to juvenile polyposis, suggesting a mechanistic link between these two diseases .
Chromosome segregation in meiosis protein 2 (Csm2)
Type: Family

Csm2 (chromosome segregation in meiosis protein 2) is a component of the Shu complex (also known as PCSS complex) involved in the error-free DNA post-replication repair (PRR) . Psy3 forms a complex first with Cms2, and their L2 loops confer the DNA-binding activity to the Shu complex . The Shu complex binds to recombination sites and is required for Rad51 assembly and function during meiosis. Psy3-Csm2 constitutes a core sub-complex that can stabilise the Rad51-single-stranded DNA complex independently of nucleotide cofactor .
Krueppel-like factor 1, transactivation domain 2 (EKLF_TAD2)
Type: Domain

This is the first part of the minimal transactivation (TAD) domain of krueppel-like factor 1 (also known as EKLF), a transcription regulator of erythrocyte development that probably serves as a general switch factor during erythropoiesis. At the first 90 residues at the N terminus EKLF carries a minimal TAD domain that is highly acidic. This minimal TAD of EKLF can be further subdivided into two independent domains, TAD1 (residues 1-40) and TAD2 (residues 51-90), that are both capable of independently activating transcription. Both TAD1 and TAD2 are highly acidic and carry a PEST (sequence rich in proline, glutamic acid, serine, and threonine) region. Deletion of either PEST domain significantly slows down degradation of EKLF by ubiquitin. The minimal TAD has an overlapping activation/degradation function that is critical for the role of EKLF in red blood cell development .
Krueppel-like factor 1, transactivation domain 1 (EKLF_TAD1)
Type: Domain

This is the first part of the minimal transactivation (TAD) domain of of krueppel-like factor 1 (also known as EKLF), a transcription regulator of erythrocyte development that probably serves as a general switch factor during erythropoiesis. At the first 90 residues at the N terminus, EKLF carries a minimal TAD domain that is highly acidic. This minimal TAD of EKLF can be further subdivided into two independent domains, TAD1 (residues 1-40) and TAD2 (residues 51-90), that are both capable of independently activating transcription. TAD1 is able to form a non-covalent interaction with ubiquitin. Both TAD1 and TAd2 are highly acidic and carry a PEST (sequence rich in proline, glutamic acid, serine, and threonine) region. Deletion of either PEST domain significantly slows down degradation of EKLF by ubiquitin. The minimal TAD has an overlapping activation/degradation function that is critical for the role of EKLF in red blood cell development .
CS6 fimbrial subunit A/B (CssA/B)
Type: Family

This is a family of CS6 pilins from E.coli, including both subunits A (CssA) and B (CssB). They act as colonisation factors for the enterotoxigenic species of E.coli to mediate bacterial attachment to the small intestinal epithelium. Both subunits in the fibre bind to receptors on epithelial cells. CssB, but not CssA, specifically recognises the extracellular matrix protein fibronectin .
NBD94 domain (NBD94)
Type: Domain

This entry represents a domain found in one of the reticulocyte binding protein homologue family members or RH proteins expressed by the malaria parasite merozoite. RH proteins recognise erythrocytes and are important in virulence. This domain has been shown to exhibit selective binding to ATP and ADP. Binding of ATP or ADP induces nucleotide-dependent structural changes in the C-terminal hinge-region of NBD94 that directly impact on the ability of the RH to bind to the red blood cells .
Nitric oxide synthase-interacting protein, zinc-finger (Znf-NOSIP)
Type: Domain

This entry represents a zinc-finger in nitric oxide synthase-interacting protein (NOSIP) . NOSIP may modulate nitric oxide homeostasis in physiological and pathological pain conditions .
Avirulence protein ATR13 (ATR13)
Type: Family

The avirulence protein ATR13 is expressed by the plant pathogen oomycete Hyaloperonospora. Such phytopathogenic oomycetes like the one that infects Arabidopsis, Hyaloperonospora arabidopsidis (Hpa), grow intercellularly, forming parasitic structures called haustoria. Haustoria play a role in feeding and suppression of host defence systems. A whole range of pathogen proteins, called effectors, are secreted across this haustorial membrane, a subset of which are further translocated across the plant plasma membrane by an unknown mechanism that is present in both plants and animals. ATR13 is an RxLR effector from the downy mildew oomycete, and is a very dynamic protein. It contains two surface-exposed patches of polymorphism, one of which is involved in the specific recognition by host R-genes. The R-gene-products detect the presence of the infection by recognising the effector proteins. Once detected, the host R-genes trigger apoptosis of the host cell. The R-gene-products carry a specific motif, RxLR, that is recognises the effector proteins .
Surface antigen, GAG-binding domain (GAG_BD)
Type: Domain

This entry represents a domain found in the surface antigen protein from the swine pathogen Streptococcus suis and related species. This domain expresses three clusters of basic residues, largely lysines, that are critical for heparin-binding and cell adhesion during bacterium-host cell adhesion. This domain binds to the host cell surface glycosaminoglycans or GAGs of the Streptococcus .
Integrin-alpha FG-GAP repeat-containing protein 2 (KICSTOR_ITFG2)
Type: Family

Integrin-alpha FG-GAP repeat-containing protein 2 (ITFG2) may play a critical role in B cell differentiation and development of autoimmunity . It is a component of protein complex KICSTOR, also composed of KPTN, C12orf66 and SZT2, which is required for inhibition of mTORC1 as a result of amino acid or glucose deprivation .
Hyaluronan-mediated motility receptor, C-terminal (HMMR_C)
Type: Domain

This domain corresponds to the C-terminal region of eukaryotic hyaluronan-mediated motility receptor protein (RHAMM), and may be involved in centrosome targeting . This domain is also found C-terminal in kinesin-like protein KIF15 .
Putative zinc-finger containing protein (Zf-HC3)
Type: Family

This is a family of putative zinc-finger containing proteins from Actinobacteria.
Protein of unknown function DUF5076 (DUF5076)
Type: Family

This entry represents a group of uncharacterised bacterial proteins.
IGP family C-type lectin domain (DUF5075)
Type: Family

This C-type lectin domain is present in the IGP 'invariant glycoprotein' family of proteins from Trypanosoma and Leishmania .
Alginate biosynthesis protein AlgX, C-terminal carbohydrate-binding module (AlgX_C)
Type: Domain

This entry represents the C-terminal domain of the alginate biosynthesis protein AlgX. This domain is a bacterial carbohydrate-binding module (CBM) frequently found at the C terminus of enzymes. The combination is not unusual as the CBMs function to bring the relevant polysaccharide into close proximity to the active site .
C2H2-type zinc ribbon (Znf-C2H2_ribbon)
Type: Domain

This domain consists of three zinc-fingers in tandem.
Cyclic di-GMP receptor, atypical PilZ domain (PilZ_atypical)
Type: Domain

This entry represents an atypical PilZ domain, which has the same structure as canonical PilZ domains with the exception of a short N-terminal α-helix and an insert that forms two additional α-helices . This domain is found in the cyclic di-GMP receptors XCC6012 from the plant pathogen Xanthomonas campestris pv. campestris (Xcc). XCC6012 forms a tetramer that adopts a novel 'house-like' construct, with a central pillar domain of the four vertical alpha3 helices, a roof-top domain made up of the eight inclined alpha2 and alpha4 helices, and four corner-stone domains making up the PilZ domain, referred to as tetrameric PilZ domain (tPliZ) .
Virilizer, N-terminal (VIR_N)
Type: Domain

This entry represents the N-terminal domain of the protein virilizer, necessary for male and female viability and required for the production of eggs capable of embryonic development .
FAM193, C-terminal (FAM193_C)
Type: Domain

This C-terminal region of uncharacterised protein family FAM193 carries the most conserved residues.
Bacterioopsin transcriptional activator, GAF and HTH associated domain (BAT_GAF/HTH-assoc)
Type: Domain

This domain is found between GAF (

) and HTH (

) domains on bacterio-opsin activator proteins . The exact function is not known.
Domain of unknown function DUF4743 (DUF4743)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in bacteria and eukaryotes, and is approximately 150 amino acids in length.