SII-SWORD/CoKE huggingface dataset:
CST complex subunit Ten1, fungal (Ten1_fungal)
Type: Family

Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length . Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex . These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution . Ten1 is one of the three components of the CST complex, which, in conjunction with the Shelterin complex helps protect telomeres from attack by DNA-repair mechanisms .

This entry represent Ten1 from fungi.
DENND6 (DENND6)
Type: Family

The DENND6 family of proteins includes DENND6A and B. They act as guanine nucleotide exchange factors (GEF) for RAB14 .
Cyclic-AMP phosphodiesterase class-II, conserved site (cAMP-PdiesteraseII_CS)
Type: Conserved_site

Cyclic-AMP phosphodiesterase (

) (PDE) catalyses the hydrolysis of cAMP to the corresponding nucleoside 5' monophosphate. On the basis of sequence similarity, most PDEs can be grouped together , but some enzymes lie apart from the main family and represent a second distinct class that includes PDEs from Dictyostelium and yeast. In the central part of these enzymes there is a highly conserved site which contains three histidines. This entry represents that conserved site.
Protein of unknown function DUF3795 (DUF3795)
Type: Family

This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Regulatory protein NPR, central domain (NPR_central_dom)
Type: Domain

This domain can be found in the plant NPR proteins. Arabidopsis NPR1 is a key regulator of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway . Its paralogs, NPR3, and NPR4, bind SA and control the proteasome-mediated degradation of NPR1 through their interaction with NPR1 .
Protein of unknown function DUF3781 (DUF3781)
Type: Family

This family of functionally uncharacterised proteins is found in bacteria and archaea. These proteins are typically between 82 and 98 amino acids in length and have two conserved sequence motifs: GKNWY and ITA.
GspL, cytoplasmic actin-ATPase-like domain (GspL_cyto_dom)
Type: Domain

The general secretion pathway of Gram-negative bacteria is responsible for extracellular secretion of a number of different proteins, including proteases and toxins. This pathway supports secretion of proteins across the cell envelope in two distinct steps, in which the second step, involving translocation through the outer membrane, is assisted by at least 13 different gene products. GspL is predicted to contain a large cytoplasmic domain and has been shown to interact with the autophosphorylating cytoplasmic membrane protein GspE. It is thought that the tri-molecular complex of GspL, GspE and GspM might be involved in regulating the opening and closing of the secretion pore and/or transducing energy to the site of outer membrane translocation .

This N-terminal domain is found in general secretion pathway protein L sequences from several Gram-negative bacteria. It is a cytoplasmic domain that shows structural homology with the superfamily of actin-like ATPases. However, it is entirely missing domains 1B and 2B of the actin-like ATPases. As domain 2B of the actin-like superfamily is critically important for binding the adenosine part of ATP and absent altogether in cyto-EpsL, it is therefore unlikely that EpsL is an ATP-binding protein .
Poly(A) polymerase, nucleotidyltransferase domain, Poxvirus (PolyA_pol_nucTrfase_Poxvir)
Type: Domain

Poly(A) polymerase (

) catalyses template-independent extension of the 3'-end of a DNA or RNA strand by one nucleotide at a time. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer of a catalytic and a regulatory subunit. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer composed of a catalytic (VP55, also known as PAP-L) and a regulatory subunit (VP39). VP55 comprises three domains: the N-terminal or N domain, the central or catalytic domain, and the C-terminal or C domain, all three domains having distinct topologies. The core comprises a mixed nine-stranded twisted β sheet, with the first seven strands being folded from one long (118 residue) polypeptide segment that follows the N domain and the last two strands originating from the extreme C-terminal-most 15 residues of the entire polypeptide chain. Of the four α-helices in the catalytic domain, the two longest (J and L) near the surface pack against one side of the β-sheet in a nearly parallel orientation to the β-strands .
Stage III sporulation protein AH-like (SpoIIIAH)
Type: Family

Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling . This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.
Protein of unknown function DUF3801 (DUF3801)
Type: Family

This functionally uncharacterised protein family is found in bacteria. Proteins found in this family are typically between 158 and 187 amino acids in length and include the PcfB protein.
Serine/threonine-protein kinase 40 (Ser/Thr_kinase_40)
Type: Family

This entry represents serine/threonine-protein kinase 40 (STK40), also known as SINK-homologous inhibitory kinase (SHIK), which acts as a negative regulator of NF-kappa-B and p53-mediated gene transcription . It It was identified as a protein related to SINK, a p65-interacting protein that inhibits p65 phosphorylation by the catalytic subunit of PKA, thereby inhibiting transcriptional competence of NF-kappaB.
VirE1 (VirE1)
Type: Family

The VirE1 family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length and contain a conserved IELE sequence motif.

VirE1 is an acidic chaperone protein which binds to VirE2, a ssDNA binding protein . These proteins are virulence factors of the plant pathogen Agrobacterium tumefaciens.
Initiator binding protein 39kDa, C-terminal (IBP39_C)
Type: Domain

This entry represents the C-terminal domain in IBP39 proteins.

Initiator binding protein 39kDa (IBP39) recognises the initiator (Inr), which in Trichomonas vaginalis is solely responsible for transcription start site selection. IBP39 consists of an N-terminal Inr binding domain, a flexible linker, and a C-terminal domain. The C-terminal domain interacts with the RNAP II large subunit C-terminal domain. Binding of IBP39 to Inr recruits RNAP II and initiates transcription .
Exopolysaccharide production repressor (SyrA)
Type: Family

SyrA is a small protein located in the cytoplasmic membrane that lacks an apparent DNA binding domain. SyrA mediates the transcriptional up-regulation of exo genes involved in the biosynthesis of the symbiotic exopolysaccharide succinoglycan. It does this through a mechanism which requires a two component system .
Alpha-N-acetylglucosaminidase, N-terminal (NAGLU_N)
Type: Domain

Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate . Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations . The structure shows that the enzyme is composed of three domains.

This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an α-β fold .
Non-classical export protein 1 (NCE101)
Type: Family

This entry represents the non classical export protein 1 family. Family members are Involved in a novel pathway of export of proteins that lack a cleavable signal sequence .
Protein of unknown function DUF2537 (DUF2537)
Type: Family

This bacterial family of proteins has no known function.
Cell wall synthesis protein CwsA (CwsA)
Type: Family

Cell wall synthesis protein CwsA is required for cell division, cell wall synthesis and cell shape maintenance .
Protein of unknown function DUF2674 (DUF2674)
Type: Family

This family of proteins with unknown function appears to be restricted to Rickettsia spp.
Protein of unknown function DUF2673 (DUF2673)
Type: Family

This family of proteins with unknown function appears to be restricted to Rickettsiae spp.
Protein of unknown function DUF2695 (DUF2695)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF2761 (DUF2761)
Type: Family

Members of this family of proteins are annotated as KleF . Their function is known.
Protein of unknown function DUF2711 (DUF2711)
Type: Family

Some members in this family of proteins are annotated as ywbB. The function of these proteins is unknown.
Membrane protein, Torovirus (M_Torovirus)
Type: Family

This is a family of potential membrane proteins that may be components of the viral envelope.
Protein of unknown function DUF2528 (DUF2528)
Type: Family

Some sequences in this family are annotated as ea10. However the function of this protein family is unknown.
Phosducin, thioredoxin-like domain (Phosducin_thioredoxin-like_dom)
Type: Domain

The outer and inner segments of vertebrate rod photoreceptor cells contain phosducin, a soluble phosphoprotein that complexes with the beta/gamma-subunits of the GTP-binding protein, transducin. Light-induced changes in cyclic nucleotide levels modulate the phosphorylation of phosducin by protein kinase A . The protein is thought to participate in the regulation of visual phototransduction or in the integration of photo-receptor metabolism. Similar proteins have been isolated from the pineal gland and it is believed that the functional role of the protein is the same in both retina and pineal gland .

This entry represents a domain found in members of the phosducin family. This domain has a thioredoxin-like fold .
MJ0366-like (MJ0366-like)
Type: Family

This family of proteins, previously known as DUF2540, includes Uncharacterized protein MJ0366 from Methanocaldococcus jannaschii and similar proteins predominantly found in Methanococci. This protein adopts the 3-1 trefoil knot conformation .
Spore germination GerPB (GerPB)
Type: Family

Members of this family are required for formation of functionally normal spores. They may be involved in the establishment of spore coat structure or permeability .
Domain of unknown function DUF3797 (DUF3797)
Type: Domain

This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Protein of unknown function DUF3796 (DUF3796)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.
Protein of unknown function DUF3798 (DUF3798)
Type: Family

This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.
Alkylmercury lyase, helix-turn-helix domain (MerB_HTH_dom)
Type: Domain

Alkylmercury lyase (

) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.
Vacuolar segregation subunit 7 (Vac7)
Type: Family

Vac7 is localised at the vacuole membrane, a location which is consistent with its involvement in vacuole morphology and inheritance . Vac7 has been shown to function as an upstream regulator of the Fab1 lipid kinase pathway . The Fab1 lipid pathway is important for correct regulation of membrane trafficking events. It has been identified as a LEA-2 homologue together with TMEM106B from humans and Tag1 in yeast, all predicted to be lipid transfer proteins .
RNA binding protein She2 (RNA-bd_She2)
Type: Domain

This entry represents the main structural domain of She2.

She2 is a RNA binding protein which binds to RNA via a helical hairpin. The protein is required for the actin dependent transport of ASH1 mRNA in yeast, a form of mRNP translocation . She2 contains a globular domain consisting of a bundle of five α-helices .
Stn1, C-terminal, fungi (Stn1_C_fungi)
Type: Domain

Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex . These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast. Two separate protein complexes are required for chromosome end protection in fission yeast while a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution .

This entry represents the C-terminal domain of Stn1 and consists of tandem winged helix-turn-helix motifs .
Domain of unknown function DUF3786 (DUF3786)
Type: Domain

This presumed domain is functionally uncharacterised and is found in bacteria. Proteins containing this domain are typically between 201 and 257 amino acids in length. Some proteins also contains an iron-sulphur cluster.
Protein of unknown function DUF3788 (DUF3788)
Type: Family

This family of functionally uncharacterised proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 149 amino acids in length and may be distantly related to RelE proteins.
Domain of unknown function DUF3806 (DUF3806)
Type: Domain

This entry represents a domain found at the C terminus of a family of bacterial proteins, whose function is unknown. In two related Bacteroides species the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase.
Domain of unknown function DUF4878 (DUF4878)
Type: Domain

This is a domain found in a group of sequences from bacteria. Proteins containing this domain are probably related to the NTF2-like transpeptidase family.
rRNA methyltransferase AviRa (AviRa)
Type: Family

This family of proteins includes the methyltransferase AviRa from Streptomyces viridochromogenes. This protein mediates the resistance to the antibiotic avilamycin. AviRa methylates a specific guanine base within the peptidyl-transferase loop of the 23S ribosomal RNA .
Protein of unknown function DUF3791 (DUF3791)
Type: Family

This entry represents proteins of unknown function.
Urocortin II/III (Urocortin_II/III)
Type: Family

This entry represents urocortin II and III, which are members of the corticotropin-releasing factor (CRF) family of neuropeptides. Urocortin II and III are secreted peptides and bind with high affinity to CRF receptors 2-alpha and 2-beta. They are involved in the suppression of food intake, the delay of gastric emptying, and may represent endogenous ligands for maintaining homeostasis after stress. Their backbone is mainly α-helical, but contains a helix-loop-helix motif .
Protein of unknown function DUF3782 (DUF3782)
Type: Family

This functionally uncharacterised family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length.
MAFF2-related (MAFF-rel)
Type: Family

This family of short membrane proteins are related to the protein Maff2. Maff2 lies just outside the direct repeats of a tetracycline resistance transposable element. This protein family may contain transmembrane helices.
Anaphase-promoting complex, subunit 9 (APC9)
Type: Family

The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis, such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome .

All APC subunits are members of the cullin family proteins, which bind to a ring-finger subunit via a conserved cullin domain .The APC can be divided in four parts, the third of which is a tetratricopeptide repeat arm (TPR) that contains multiple subunits, including Apc9 .

This entry represents Apc9, one of the subunits of the anaphase-promoting complex.
Crustacean cardioactive peptide (CCAP)
Type: Family

Crustacean cardioactive peptide (CCAP), also known as cardioacceleratory peptide 2a, exerts a reversible and dose-dependent cardio-stimulatory effect on the semi-isolated heart of experimental beetles. CCAP also increases free hemolymph sugar concentration in young larvae and adults of the meal-worm beetle .
Domain of unknown function DUF3821 (DUF3821)
Type: Domain

This is a domain largely confined to sequences from Methanomicrobiales. It is found in putative lipases but the function is unknown.
DUF3823, N-terminal (DUF3823_N)
Type: Domain

This domain has a β-sandwich prealbumin-like fold.
Paramyxovirinae protein V, zinc-binding domain (Paramyx_V_Zn-bd)
Type: Domain

The paramyxoviruses, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT .

The P mRNA encodes a variety of proteins beyond P. Protein V consists of PNT fused to a C-terminal zinc-binding region. This conserved region consists of the two-zinc-binding section sandwiched between β sheets 6 and 7 of the overall V protein. It is the binding of this core domain of V protein with the DDB1 protein (part of the ubiquitin-ligase complex) of eukaryotes which represents the key element of the virus-host protein interaction . In the Henipavirus family, which includes Nipah and Hendra viruses, the V protein is able to block IFN (interferon) signalling by preventing IFN-induced STAT phosphorylation and nuclear translocation .
FAM167 (FAM167)
Type: Family

This entry describes a eukaryotic protein family of unknown function designated FAM167.
Bacteriophage T7-like virion assembly protein (Phage_T7-like_viron_assmbl)
Type: Family

This family of proteins represents the gene product 7.3 from T7 bacteriophage and T7-like phages. The protein is localised to the tail and is thought to be important in virion assembly. Particles assembled in the absence of the protein fail to adsorb to cells .
Domain of unknown function DUF3376 (DUF3376)
Type: Domain

This domain is found in a family of bacterial proteins of unknown function that contain an N-terminal patatin domain.
Translocase of chloroplast 159/132, membrane anchor domain (TOC159_MAD)
Type: Domain

This is the membrane-anchor domain of translocase of chloroplast 159, TOC159/132. This domain is present in plants at the C terminus of the GTPase, AIG1, and anchors the GTPase region to the outer membrane of the chloroplast. The domain may carry a very C-terminal sequence motif that resembles a transit peptide .
Protein of unknown function DUF3826 (DUF3826)
Type: Family

This is a putative sugar-binding family.
Schizont-infected cell agglutination, extracellular beta domain (SICA_extracell_b)
Type: Domain

The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain .

This entry represents the extracellular SICA-beta domain.
Domain of unknown function DUF3700 (DUF3700)
Type: Domain

This entry represents a domain found in plant proteins that is approximately 120 amino acids in length. There are two conserved sequence motifs: YGL and LRDR.
Schizont-infected cell agglutination, C-terminal domain (SICA_C)
Type: Domain

The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain .

The conserved C-terminal domain is thought to remain within the cytoplasm of the infected erythrocyte.
Domain of unknown function DUF3828 (DUF3828)
Type: Domain

This entry represents a domain found covering the whole length of Putative periplasmic protein Rpic12D_3261 from Ralstonia pickettii (

, Tai3), a cognate immunity protein from the type VI secretion system (T6SS) that shows four helices and five strands . This domain is also found in uncharacterised bacterial proteins such as YbjP and YqhG from Escherichia coli. Its specific function is currently unknown.
Schizont-infected cell agglutination, extracellular alpha domain (SICA_extracell_a)
Type: Domain

The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain .

This entry represents the extracellular SICA-alpha domain.
Protein of unknown function DUF3829 (DUF3829)
Type: Family

This is a small family of proteins from several bacterial species, whose function is not known. It may, however, be related to the GvpL/GvpF family of gas vesicle synthesis proteins (

).
Nodavirus capsid (Nodavirus_capsid)
Type: Family

The capsid or coat protein of this family is expressed in Nodaviridae, that are ssRNA positive-strand viruses, with no DNA stage. These viruses are the causative agents of viral nervous necrosis in marine fish .