SII-SWORD/CoKE huggingface dataset:
Ndc10, domain 2 (NDC10_II)
Type: Domain

This entry represents the second of five domains on the Kluyveromyces lactis Ndc10 protein . Each subunit of the Ndc10 dimer binds a separate fragment of DNA, suggesting that Ndc10 stabilises a DNA loop at the centromere. Proteins containing this domain also include Cbf2 from S. cerevisiae. S. cerevisiae Ndc10 (also known as Cbf2) is a component of the centromere DNA-binding protein complex CBF3, which is essential for chromosome segregation and movement of centromeres along microtubules . The structure of the protein shows that it can be divided in the two α-helical N- and C-lobes. The N-lobe consists of an antiparallel four-helix bundle with a central β-sheet which is involved in DNA binding .
Adult cuticle protein 1 (Cuticle_Acp1)
Type: Family

Adult cuticle protein 1 (Acp1) from Drosophila may be involved in some specialised function such as thickening of the adult cuticle .
Recombination enhancement, RecA-dependent nuclease (RecA_dep_nuc)
Type: Family

This is a family of P1-like phage RecA-dependent nucleases. It does not appear to act as a positive RecA regulator. It is a new kind of enzyme, a RecA-dependent nuclease .
Protein of unknown function DUF4760 (DUF4760)
Type: Family

This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 147 and 190 amino acids in length. There is a single completely conserved residue R that may be functionally important.
Metal-binding protein SmbP (SmbP)
Type: Family

SmbP (small metal-binding protein) is a histidine-rich protein that capable of binding multiple equivalents of a variety of divalent and trivalent metals, including Cu2+ and Fe3+ but also Mn2+, Ni2+, Mg2+ and Zn2+. This protein is found to bind up to six Cu(II) atoms. It may have a role in cellular copper management in the ammonia-oxidizing bacterium N. europaea .
Commissureless (Commissureless)
Type: Family

Commissureless (Comm) functions in neurons to regulate the intracellular trafficking and surface levels of Roundabout (Robo) receptors and, as a result, regulates axon guidance across the Drosophila embryo midline .
Fanconi anemia group M protein, MHF binding domain (FANCM-MHF-bd)
Type: Domain

This entry represents a structured region found in the Fanconi anemia group M protein (FANCM) that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin .
Protein of unknown function DUF4761 (DUF4761)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
Protein of unknown function DUF4762 (DUF4762)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved TTC sequence motif.
Protein of unknown function DUF4763 (DUF4763)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are typically between 237 and 332 amino acids in length. There are two completely conserved residues (C and R) that may be functionally important.
Nucleotide exchange factor Sil1, fungi (Sil1_fungi)
Type: Family

This entry represent Sil1 from fungi. Sil1 is a nucleotide-exchange factor protein that interacts with Hsp70 chaperone Kar2 . It is required for protein translocation and folding in the endoplasmic reticulum (ER) . The structure of Sil1 has been solved .
Domain of unknown function DUF4764 (DUF4764)
Type: Domain

This domain is found in eukaryotes. Its function is not known.
Domain of unknown function DUF4765 (DUF4765)
Type: Domain

This domain family is found in bacteria, and is approximately 90 amino acids in length.
Serologically defined colon cancer antigen 8 (SDCCAG8)
Type: Family

Serologically defined colon cancer antigen 8 (SDCCAG8), also known as CCCAP (centrosomal colon cancer autoantigen protein), is a family of proteins found in eukaryotes. Mutations of SDCCAG8 are associated with nephronophthisis and Bardet-Biedl syndrome , as well as schizophrenia. SDCCAG8 is associated with the centrosome and interacts with pericentriolar material 1 (PCM1), a centriolar satellite protein crucial for targeting proteins to the centrosome. It regulates centrosomal accumulation of pericentriolar material and neuronal polarisation and migration in the developing mouse cortex .

SDCCAG8 is localized at both centrioles and interacts directly with OFD1 (oral-facial-digital syndrome 1), which is linked to an autosomal recessive cystic kidney disease, NPHP-RC (nephronophthisis-related ciliopathies). Depletion of SDCCAG8 causes kidney cysts and a body axis defect in zebrafish .
Protein of unknown function DUF5068 (DUF5068)
Type: Family

This family is expressed by Firmicutes. The function is not known.
AIMP2, lysyl-tRNA synthetase binding domain (AIMP2_LysRS-bd)
Type: Domain

This entry represents the lysyl-tRNA synthetase (LysRS) binding domain of AIMP2 (aminoacyl tRNA synthase complex-interacting multifunctional protein 2). LysRS can serve as a transcription regulator that can be released from the cytoplasmic multi-tRNA synthetase complex (MSC) to activate the transcription factor MITF in stimulated mast cells. In quiescent cells, LysRS is held in the MSC via its interactions with AIMP2 .
F-box only protein 30/40 (Fbxo30/Fbxo40)
Type: Family

This entry includes F-box only protein 30 (Fbxo30) and F-box only protein 40 (Fbxo40) . Fbxo30 is a ubiquitin ligase required for muscle loss, hence it is also known as muscle ubiquitin ligase of the SCF complex in atrophy-1 (MUSA1) . Fbxo40 id an E3 ubiquitin ligase that induces IRS1 ubiquitination and breakdown specifically in skeletal muscle cells and only upon IGF1 (insulin-like growth factor 1) stimulation .
DNA-mimic protein DMP12 (DMP12)
Type: Family

DMP12 is a DNA-mimic protein from Neisseria species. In its monomeric form DMP12 interacts with the Neisseria dimeric form of the bacterial histone-like protein HU. HU proteins promote the assembly of higher-order DNA-protein structures. The interaction between DMP12 and HU may be instrumental in controlling the stability of the nucleoid in Neisseria, as DMP12 prevents Neisseria HU protein from being digested by trypsin .
Abi component, membrane-anchored ion channel RexB (RexB)
Type: Family

RexB is a family of anti-lambda phage inner-membrane ion-channels with four transmembrane domains . On infection by phage, a phage protein-DNA complex is produced as a replication or recombination intermediate which activates RexA. RexA is an intracellular sensor that activates the membrane-anchored RexB. At least two RexA proteins are needed to activate one RexB protein. Activation opens the ion-channel leading to a drop in membrane potential, the outcome of which is the death of the host cell but also the cessation or abortion of the phage infection. RexA-RexB is one of the most well characterised bacterial abortive infection systems, or Abis .
Phage tail assembly chaperone-like domain (Phage_tail_APC)
Type: Domain

This entry represents a domain found in general phage tail assembly chaperone proteins from double-stranded DNA viruses with no RNA stage, many of which are unclassified. This entry also includes bacterial proteins, suggesting prophage matches
Abi component, intracellular sensor of Lambda phage RexA (RexA)
Type: Family

RexA is a family of bacterial anti-phage proteins. It forms one partner in the two-component abortive infection system, Abi, of E. coli in partnership with RexB, a membrane-anchored ion- channel . Two RexA are needed to activate one RexB, and activation causes opening of the channel, the efflux of cations, a drop in cellular levels of ATP and subsequent death of the host cell and abortion of the phage infecting process which requires ATP.
RHH transcriptional regulator CopG (RHH_CopG)
Type: Family

This entry represents a ribbon-helix-helix protein family expressed by Helicobacter species. These proteins bind to specific DNA sequences with high affinity and usually act as repressors. Many are putatively named CopG .
INPP5B, PH domain (INPP5B_PH_dom)
Type: Domain

This entry represents the PH domain found in the N terminus of type II inositol 1,4,5-trisphosphate 5-phosphatase (INPP5B). The structure of this domain has been revealed . INPP5B hydrolyses phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signalling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signalling events .

INPP5B contains a PH domain, a 5-phosphatase domain, an ASH domain and a Rho-GAP domain. It shares ~45% sequence identity with OCRL1 (not included in this entry) and has the same domain organization. However, a loop in the Rho GAP domain contains a second clathrin box which is absent in INPP5B. INPP5B shares most interacting partners with OCRL, except for clathrin and the endocytic clathrin adaptor AP-2 .
DolP-mannose mannosyltransferase AglS (AglS)
Type: Family

AglS is a is a dolichol phosphate-mannose mannosyltransferase that catalyses the transfer of mannose from dolichol phosphate (DolP)-mannose to the N-linked tetrasaccharide bound to the S-layer glycoprotein to form a pentasaccharide .
Lytic exoenzyme, target recognition domain (ZoocinA_TRD)
Type: Domain

This entry represents a domain found downstream the catalytic domain of various lytic enzymes, such as peptidase M23 and phage lysins. The domain is composed of strands of antiparallel β sheet with one short α helix at the C-terminal end .
Distal tail protein, N-terminal domain (Dit_N)
Type: Domain

This domain is found at the N-terminal end of Distal tail protein from Lactococcus phage p2 (Dit) and similar sequences predominantly found in tailed bacteriophagues and bacterial prophages.

Distal tail protein (Dit) has a structural role and forms the distal part of the tail. It is organised into two domains, a ring domain that shows a split barrel-like fold and a C-terminal galectin domain. Consecutive Dit N-terminal domains form a tight ring with two layers of β-strands. This ring frames a channel sufficiently large for dsDNA passage . This protein is involved in the process of viral genome ejection through the host cell envelope using a long flexible tail mechanism. The distal tail protein forms the distal part of the tail structure and plays a role in DNA ejection. It self-associates as two rings that are arranged back to back, creating a central channel through which the DNA is ejected into the host cell. Additionally, it interacts with the receptor binding protein, facilitating the attachment of the phage to the host cell. At the structural level, the distal tail protein is composed of homohexameric subunits.
Lactococcus phage single-stranded DNA binding protein (Phage_SSB)
Type: Family

This single-stranded DNA binding protein (SSB) is found in Lactococcus phage. It can stimulate RecA-mediated homologous recombination. Its structure is a variation of the typical oligonucleotide/oligosaccharide binding-fold of single-stranded DNA binding proteins .
Unpaired protein (Unpaired)
Type: Family

Unpaired (Upd) protein activates the JAK/STAT (Janus kinase/signal transducer and activator of transcription) pathway, an evolutionarily conserved signalling system that plays essential roles in numerous biological processes in vertebrates and invertebrates, including immunity, hematopoiesis and proliferation . In Drosophila, the unpaired family (Upd1-3) is the only class of ligands associated with JAK stimulation .
Telomeric repeat-binding factor 2, Rap1-binding domain (TERF2_RBM)
Type: Domain

This domain, found in mammalian telomeric repeat-binding factor 2 (TERF2, also known as TRF2) and fission yeast Taz1, binds to the C terminus of repressor activator protein 1 (RAP1) (telomeric repeat-binding factor 2-interacting protein 1) . Through this interaction, RAP1 is targeted to chromosome ends for telomere protection .
Domain of unknown function DUF4766 (DUF4766)
Type: Domain

This presumed domain is functionally uncharacterised. It is found in eukaryotes, and is typically between 106 and 128 amino acids in length. There is a conserved KVI sequence motif.
Cadherin, C-terminal catenin-binding domain (Cadherin_CBD)
Type: Domain

This is the cytoplasmic catenin-binding domain found at the C terminus of cadherin . This domain binds to the ARM domain of beta-catenin, a catenin that plays a crucial role in the regulation of cell-cell adhesion at adherens junctions (AJs) .
Flotillin, C-terminal domain (Flotillin_C)
Type: Domain

Flotillin is a family of lipid-membrane-associated proteins found in bacteria, archaea and eukaryotes. Flotillins in vertebrates are associated with sphingolipids and cholesterol-enriched membrane microdomains, known as lipid-rafts . These rafts, along with other membrane components, are important in cell-signalling. This entry includes flotillin-1 (also known as reggie-2), flotillin-2 (also known as reggie-1) and their homologues. They play a role in various cellular processes such as insulin signaling, T cell activation, membrane trafficking, phagocytosis, and epidermal growth factor receptor signaling . Flotillins in other organisms have roles in viral pathogenesis, endocytosis, and membrane shaping . In bacteria, these proteins are found in membrane microdomains that may be equivalent to eukaryotic membrane rafts . Similarly to eukaryotic flotillin proteins, flotillins in bacteria play an essential role in organizing and maintaining the correct architecture of the functional membrane microdomains .
Regulator of Ty1 transposition protein 107, BRCT domain (RTT107_BRCT_6)
Type: Domain

This is the sixth BRCT domain of regulator of Ty1 transposition protein 107 (Rtt107). It is involved in binding phosphorylated histone H2A .
Germinal-centre associated nuclear protein, MCM3AP domain (MCM3AP_GANP)
Type: Domain

This entry represents the C-terminal MCM3AP domain of germinal-centre associated nuclear protein (GANP) from higher eukaryotes. GANP is involved in the nuclear export of poly(A)-containing mRNAs by acting as a scaffold for the TREX-2 complex. The localisation of the TREX-2 complex to nuclear pore complexes requires the MCM3AP domain of GANP .
Germinal-centre associated nuclear protein, nucleoporin homology domain (NupH_GANP)
Type: Domain

This entry represents the nucleoporin-homology domain at the N terminus of human GANP or germinal-centre associated nuclear proteins (GANP). GANP is involved in the nuclear export of poly(A)-containing mRNAs by acting as a scaffold for the TREX-2 complex. This domain binds to export factor NXF1. Through this interaction, GANP facilitates the transfer of NXF1-containing mRNPs (messenger ribonucleoproteins) to nuclear pore complexes .
Alginate biosynthesis sensor protein KinB, sensor domain (KinB_sensor_dom)
Type: Domain

This entry reprsents the N-terminal sensor domain of histidine kinase from Pseudomonas species. The domain is the extracellular sensing domain with four helical bundle . It recognises inorganic phosphate .
Germinal-centre associated nuclear protein, CID domain (GANP_CID_dom)
Type: Domain

CID is a domain found in higher eukaryotic germinal-cent associated nuclear protein (GANP) that binds to the transcription and mRNA export factor ENY2. The complex of these two proteins forms part of the TREX-2 complex that links transcription with nuclear messenger RNA export .
Pesticin immunity protein (Pim)
Type: Family

Pim is the immunity protein produced by Yersinia pestis and other Gammaproteobacteria to protect themselves against the bacteriostatic activity of the toxin pesticin (

) .
Sharpin, PH domain (Sharpin_PH)
Type: Domain

This PH domain is found at the N terminus of sharpin and is involved in dimerisation. Sharpin is part of the LUBAC complex, a large multi-protein E3 ubiquitin ligase complex that catalyses the formation of linear ubiquitin chains and regulates immune and apoptopic signalling pathways .
Spidroin, N-terminal (Spidroin_N)
Type: Domain

Spidroin is produced by a number of arachnids. Spidrions are made up of repetitive segments flanked by conserved non-repetitive domains, and this domain is the conserved non-repetitive region. Aggregation to form the rigid silk occurs due to association at the repetitive regions, and the N-terminal domain is necessary to prevent premature aggregation during storage before extrusion. This N-terminal region inhibits precocious aggregation and then accelerates and directs self-assembly as the pH is lowered along the extrusion duct .
XACb0070, ribbon-helix-helix domain (XACb0070_RHH_dom)
Type: Domain

This ribbon-helix-helix domain can be found in the XACb0070 protein from Xanthomonas axonopodis pv. citri. It binds to DNA and may be a part of a toxin-antitoxin system .
Cryptic loci regulator 2, N-terminal (Clr2_N)
Type: Domain

This entry represents a domain carrying the first and second of three regions on Clr2 that are necessary for transcriptional silencing by the protein . Clr2 is part of the SHREC complex, an effector complex for heterochromatic transcriptional silencing .
DNA ligase 3, BRCT domain (LIG3_BRCT)
Type: Domain

The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerisation .
Pilus assembly protein, C-terminal domain (Pilus_assem_C)
Type: Domain

This is a highly conserved C-terminal domain on fimbrial outer membrane usher proteins like TcfC or CooC or PapC . CooC is required for CS1 pilus formation .
Herpesvirus membrane glycoprotein UL141 (UL141)
Type: Family

UL141 is a a glycoprotein from herpesvirus species. Its N-terminal Ig-like β-sandwich domain binds to the cysteine-rich region of TRAIL-R2, a family of tumour necrosis factor receptor proteins. UL141 is both necessary and sufficient to retain TRAIL receptors in the ER, thereby preventing their cell surface expression and it is also necessary and sufficient to inhibit cell surface expression of CD155 .
Alpha-L-fucosidase, C-terminal (Fucosidase_C)
Type: Domain

The C-terminal domain of alpha-L-fucosidase consists of eight anti-parallel-strands packed into two-sheets of five and three strands, respectively, forming a two-layer-sandwich containing a Greek key motif .
Partner and localiser of BRCA2, WD40 domain (PALB2_WD40)
Type: Domain

This domain is found at the C terminus of partner and localiser of BRCA2 (PALB2). It is a seven-bladed WD40-type β-propeller. It binds to the N terminus of BRCA2 .
Pesticin, C-terminal (Pesticin_C)
Type: Domain

This entry represents the C-terminal activator domain of pesticin.

Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. It is referred to as a bacteriocin and it leads to the hydrolysis of peptidoglycan. Its immunity protein is Pim. Pesticin carries an elongated N-terminal translocation domain, an intermediate receptor binding domain, and a C-terminal activity domain with structural analogy to lysozyme homologues. The full-length protein is toxic to bacteria when taken up to the target site via the outer or the inner membrane .

Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides. .
Helicobacter TNF-alpha-inducing protein (Tipalpha)
Type: Family

TNF-alpha-inducing protein (Tipalpha) is secreted from Helicobacter pylori as dimers and enters the gastric cells. It binds to DNA via the positively charged surface-patch formed between the two monomers of the crystal structure by the loop between helices alpha1 and alpha2. Each monomer consists of a helical domain and a mixed domain .
Glycosyl hydrolase family 115 (GH115)
Type: Family

Glycosyl hydrolase family 115 (GH115) members are alpha-glucuronidases that catalyses the cleavage of 4-O-methyl D-glucuronic acid side chains from native xylan polysaccharides (

) . Family GH115 appears to be restricted to Archaea,
Bacteria, and Fungi . This entry includes Schizophyllum commune Agu1 protein (

) and SpGlcA115A (

) from Streptomyces pristinaespiralis .
Tubulin-specific chaperone C, N-terminal (TBCC_N)
Type: Domain

Tubulin binding cofactor C (TBCC) is a post-chaperonin involved in folding pathways that lead to the final release of alpha beta native heterodimers incorporated in microtubules. TBCC is organised into three different domains: N-terminal, CARP and C-terminal .

This entry represents the N-terminal domain of TBCC. The N-terminal comprises a structured coiled coil and a highly dynamic N-terminal region which concentrates 80% of charged and polar residues and is believed to be important in interaction with tubulin . Overall, the N-terminal domain of TBCC is responsible for its interaction with components of the centrosome by its N-terminal domain.
Transmembrane protein 135, N-terminal domain (TMEM135_N)
Type: Domain

This domain is found in putative peroxisomal membrane proteins from eukaryotes. It represents the highly conserved N-terminal region that has several highly conserved cysteine residues.
Domain of unknown function DUF4767 (DUF4767)
Type: Domain

This domain is found in bacteria, and is approximately 140 amino acids in length. There is a single completely conserved residue Q that may be functionally important.
Anti-sigma-D factor RsdA, sigma factor binding region (RsdA_SigD-bd)
Type: Domain

This entry represents a domain found in the N terminus of anti-sigma-D factor RsdA proteins. It binds to the -35 promoter binding domain of sigma-D. The complex formed regulates the transcriptional expression of the bacterium .
Bacterial collagen-like protein, middle domain (CLP_mid)
Type: Domain

This domain is the conserved central region of bacterial collagen-like proteins (CLPs). Similar to animal collagens, bacterial CLPs contain the G-X-Y repeat motifs . They are involved in pathogenicity, immune response elicitation and host-parasite interactions, possibly evolving as mimics of host proteins containing G-X-Y motifs .
Two-component histidine kinase, sensor domain (HK_sensor)
Type: Domain

This entry represents the sensor domain found at the N terminus of integral membrane two-component system sensor histidine kinases, such as PfeS from Pseudomonas aeruginosa .
Protein of unknown function DUF4768 (DUF4768)
Type: Family

This family of proteins from Drosophila is functionally uncharacterised. Proteins are typically between 116 and 180 amino acids in length. There is a conserved FFFGQY sequence motif.
Arterivirus nonstructural protein 7 alpha (Arteri_nsp7a)
Type: Family

Translation of the arterivirus genome results in two large precursor polyproteins, pp1a and the C-terminally extended frameshift product pp1ab. These proteins are cleaved by up to four virus-encoded proteases to yield at least 13 nonstructural proteins (nsps) (nsp1 to nsp12, including nsp7) plus a substantial number of processing intermediates of unknown function. Nsp7 can be internally cleaved by the nsp4 protease, yielding small amounts of nsp7alpha and nsp7beta. This entry represents nsp7alpha, which is likely to have a role in viral RNA synthesis .
UPF0767 family (UPF0767)
Type: Family

This family of uncharacterised proteins is found in eukaryotes. Proteins in this family are described as small integral membrane protein 12. There are two conserved sequence motifs: IGYN and SPSL.
Protein of unknown function DUF4769 (DUF4769)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in insects. Proteins in this family are typically between 291 and 501 amino acids in length.