SII-SWORD/CoKE huggingface dataset:
Pfam PF23168: CUL7/CUL9, N-terminal beta-barrel domain (domain)
This domain is found N-terminal in the homologues of human Cullin-7 (CUL7) and Cullin-9 (CUL9). It adopts a beta-barrel structure with some similarity to chromodomains and is known as a small beta-domain (SBD). In both CUL7 and CUL9, this domain is usually followed by an ARM-like domain.
Pfam PF20465: MmeI, helicase spacer domain (domain)
Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues  301-320) via a multi-helical spacer (residues 156-300).  These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The endonuclease cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage. This domain corresponds to the multi-helical spacer. It is thought to play a key role in positioning the endonuclease cleavage domain correctly.
Pfam PF23857: Phage tail chaperone protein (domain)
This entry represents a family of phage tail chaperone proteins found in viruses and cyanobacteria. Based on a structure prediction of family members, they are similar to other phage tail chaperone proteins. The family contains proteins between 50-164 amino acids in length.  Phage tail chaperone proteins play a role in the assembly of the phage tail apparatus.
Pfam PF02625: XdhC and CoxI family (domain)
This domain is often found in association with an NAD-binding region, related to TrkA-N ([pfam:PF02254]; personal obs:C. Yeats). XdhC is  believed to be involved in the attachment of molybdenum to Xanthine Dehydrogenase ().
Pfam PF03708: Avian retrovirus envelope protein, gp85 (family)
Family of a vain specific viral glycoproteins that forms a receptor-binding gp85 polypeptide that is linked through disulfide  to a membrane-spanning gp37 spike.  Gp85 confers a high degree of subgroup  specificity for interaction with distinct cell receptors.
Pfam PF08255: Trp-operon Leader Peptide (family)
The tryptophan operon regulatory region of C. freundii's (leader transcript) encodes a 14-residue peptide containing characteristic tandem tryptophan residues. It is about 10 nucleotides shorter than those of E. coli and S. typhimurium.
Pfam PF11122: Inner spore coat protein D (family)
This family is conserved in the Enterobacteriaceae family. CotD is an inner spore coat protein that is expressed in the middle phase of mother cell gene expression. Along with CotD, CotH, CotS and CotT it is assumed to assemble into the loose skeleton of the matrix, between the shells of SpoIVA and CotE. Coat proteins do not share much sequence similarity between species, but this does not imply they do not share secondary, tertiary, or quaternary features.
Pfam PF17848: Acetyl-CoA carboxylase zinc finger domain (domain)
Acetyl-CoA carboxylase (ACC) is a central metabolic enzyme that catalyzes the committed step in fatty acid biosynthesis: biotin- dependent conversion of acetyl-CoA to malonyl-CoA. In bacteria this protein contains a small zinc finger domain.
Pfam PF08114: ATPase proteolipid family (family)
This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast with no modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear.
Pfam PF16010: Cytochrome domain of cellobiose dehydrogenase (family)
CDH-cyt is the cytochrome domain, at the N-terminus, of cellobiose dehydrogenase. CDH-cyt folds as a beta sandwich with the topology of the antibody Fab V(H) domain and binds iron. The haem iron is ligated by Met83 and His181 in UniProtKB:Q01738.
Pfam PF16469: Nematode polyprotein allergen ABA-1 (domain)
The nematode polyprotein allergen ABA-1 is a lipid-binding protein comprising multiple tandem repeats of this domain.
Pfam PF23071: Domain of unknown function (DUF7044) (domain)
This domain is found in a group of uncharacterised metazoan proteins. It is predicted to adopt a globular structure with lipocalin fold. It also contains several highly conserved cysteine residues that are likely involved in the formation of intra-domain disulfide bridges.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00967: Barwin family (domain)
Barwin is a basic protein isolated from aqueous extracts of barley seeds. It is 125 amino acids in length, and contains six cysteine residues that combine to form three disulphide bridges . Comparative analysis shows the sequence to be highly similar to a 122 amino acid stretch in the C-terminal of the products of two wound-induced genes (win1 and win2) from potato, the product of the hevein gene of rubber trees, and pathogenesis-related protein 4 from tobacco. The high levels of similarity to these proteins, and their ability to bind saccharides, suggest that the barwin domain may be involved in a common defence mechanism in plants.
Wikipedia: In molecular biology, the barwin domain is a protein domain found in barwin, a basic protein isolated from aqueous extracts of barley seeds. Barwin is 125 amino acids in length, and contains six cysteine residues that combine to form three disulphide bridges. In the pathogenesis-related protein nomenclature, it is PR-4. This domain is found in a 122 amino acid stretch in the C-terminal of the products of two wound-induced genes from potato, the product of the Pro-hevein gene of rubber trees, and pathogenesis-related protein 4 from tobacco. The high levels of similarity among these proteins, and their ability to bind saccharides, suggest that the barwin domain may be involved in a common defence mechanism in plants.
Pfam PF08014: Microtubule-associated tyrosine carboxypeptidase (domain)
This entry includes microtubule-associated tyrosine carboxypeptidases, proteins that remove the C-terminal tyrosine residue of alpha-tubulin, thereby regulating microtubule dynamics and function. They are also able to remove the C-terminal phenylalanine residue of alpha-tubulin TUBA8. These proteins recognise adjacent tubulin dimers along the same protofilament.
Wikipedia: KIAA0895 is a protein that in Homo sapiens is encoded by the KIAA0895 gene. The gene encodes a protein commonly known as the KIAA0895 protein. Its aliases include hypothetical protein LOC23366, OTTHUMP00000206979, OTTHUMP00000206980, 9530077C05Rik, and 1110003N12Rik. It is located at 7p14.2.
Pfam PF23933: Family of unknown function (DUF7269) (family)
This entry represents uncharacterised proteins found mainly in Halobacteria. They are likely composed mainly of alpha-helices. These proteins contain a semi-conserved GxWTDDxxAA sequence motif toward their C terminus.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF06305: Lipopolysaccharide assembly protein A domain (family)
This family includes a domain found in lipopolysaccharide assembly protein A (LapA). LapA functions along with LapB in the assembly of lipopolysaccharide (LPS). Domains in this family are also found in some uncharacterised bacterial proteins.
Pfam PF22662: Csa3 CRISPR-associated Rossmann-like domain (domain)
This domain is found N-terminal in CRISPR-associated protein Csa3 and related proteins. Csa3 consists of two domains. The N-terminal domain is a unique variation on the dinucleotide binding domain and it is responsible for dimer formation. In addition, it utilizes two conserved sequence motifs T(h)GF(N/D)E(x)4R and L(x)2G(h)R to form a 2-fold symmetric pocket on the dimer axis. This pocket is likely to represent a regulatory ligand-binding site.
Pfam PF03101: FAR1 DNA-binding domain (domain)
This domain contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Pfam PF13798: Protein of unknown function with PCYCGC motif (family)
This domain contains a PCYCGC motif and four other conserved cysteines. Its function is unknown.
Pfam PF17969: L,D-transpeptidase C-terminal domain (domain)
This is the C-terminal domain found in d-transpeptidases (Ldt) homologues from E.coli. Three of these enzymes (YbiS, ErfK, YcfS) have been shown to cross-link Braun's lipoprotein to the peptidoglycan (PG), while the other two (YnhG, YcbB) form direct meso-diaminopimelate (DAP-DAP, or 3-3) cross-links within the PG. Family members include erfK (ldtA), ybiS (ldtB), ycfS (ldtC), and ynhG (ldtE).
Pfam PF03735: ENT domain (family)
This presumed domain is named after Emsy N Terminus (ENT). Emsy is a protein that is amplified in breast cancer and interacts with BRCA2. The N terminus of this protein is found to be similar to other vertebrate and plant proteins of unknown function.  This domain has a completely conserved histidine residue that may be functionally important.
Pfam PF14862: Big defensin (domain)
Big defensins are antimicrobial peptides. They consist of a hydrophobic N-terminal half, which is active against Gram-positive bacteria, and a cationic C-terminal half, which is active against Gram-negative bacteria. The C-terminal half adopts a beta-defensin-like structure.
Pfam PF12211: Low molecular weight S layer protein N terminal (domain)
This family of proteins is found in bacteria. Proteins in this family are typically between 328 and 381 amino acids in length. There is a conserved LGDG sequence motif. Clostridial species have a layer of surface proteins surrounding their membrane. This layer is comprised of a high molecular weight protein and a low molecular weight protein. This domain is the N terminal domain of the low molecular weight protein. It is a structural domain.
Pfam PF12853: C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit (domain)
This family is the C-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi.
Pfam PF19355: Family of unknown function (DUF5932) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in Bacteroidetes, and is approximately 110 amino acids in length. The family is found in association with [pfam:PF00072]. There is a conserved PIL sequence motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF05645: RNA polymerase III subunit RPC82 (family)
This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa.
Pfam PF00641: Zn-finger in Ran binding protein and others (domain)
This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import . RanBP2 contains multiple zinc fingers which mediate binding to RanGDP .
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Pfam PF22753: Peptidoglycan O-acetylesterase, N-terminal (domain)
This domain is found at the N-terminal end of the peptidoglycan O-acetylesterase N875_00620 from Neisseria meningitidis (Ape1) and similar sequences mainly found in proteobacteria. Ape1, which occurs in bacteria that O-acetylate their peptidoglycan, has an SGNH catalytic domain ([pfam:PF13472]) at the C-terminal end. This entry represents the N-terminal canonical beta-sandwich that consists of two antiparallel beta-sheets. It is likely to interact with a specific carbohydrate moiety.
Pfam PF16139: Domain of unknown function (DUF4847) (domain)
This uncharacterized domain has a lipocalin fold.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14978: Mitochondrial ribosome protein 63 (family)
This family of proteins is present in the intact 55S subunit of the mitochondrial ribosome. It is not known if it belongs to the 28S or to the 39S subunit.
Pfam PF05803: Chordopoxvirus L2 protein (family)
This family consists of several Chordopoxvirus L2 proteins.
Pfam PF00040: Fibronectin type II domain (domain)
Fibronectin is a multi-domain glycoprotein, found in a soluble form in plasma, and in an insoluble form in loose connective tissue and basement membranes, that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin. Fibronectins are involved in a number of important functions e.g., wound healing; cell adhesion; blood coagulation; cell differentiation and migration; maintenance of the cellular cytoskeleton; and tumour metastasis .

The major part of the sequence of fibronectin consists of the repetition of three types of domains, which are called type I, II, and III (also called FN1, FN2 and FN3 respectively). In fibronectin the type II domain is duplicated. Type II domain is approximately forty residues long, contains four conserved cysteines involved in disulphide bonds and is part of the collagen-binding region of fibronectin. Type II domains have also been found in a range of proteins including blood coagulation factor XII; bovine seminal plasma proteins PDC-109 (BSP-A1/A2) and BSP-A3 ; cation-independent mannose-6-phosphate receptor ; mannose receptor of macrophages ; 180 Kd secretory phospholipase A2 receptor . DEC-205 receptor ; 72 Kd and 92 Kd type IV collagenase (3.4.24.24) ; and hepatocyte growth factor activator .
Wikipedia: Fibronectin type II domain  is a collagen-binding protein domain. Fibronectin is a multi-domain glycoprotein, found in a soluble form in plasma, and in an insoluble form in loose connective tissue and basement membranes, that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin. Fibronectins are involved in a number of important functions e.g., wound healing; cell adhesion; blood coagulation; cell differentiation and migration; maintenance of the cellular cytoskeleton; and tumour metastasis. The major part of the sequence of fibronectin consists of the repetition of three types of domains, which are called type I, II, and III.
Pfam PF11322: Protein of unknown function (DUF3124) (family)
This bacterial family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07027: Protein of unknown function (DUF1318) (family)
This family consists of several bacterial proteins of around 100 residues in length and is often known as YdbL. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17419: Methylamine utilization protein MauJ (family)
This domain family is found in MauJ proteins. The exact function of the MauJ proteins is unknown but thought to be involved in methylamine utilization. MauJ is predicted to be a cytoplasmic protein. MauJ itself is inactive HEPN, other members are active HEPN.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF18230: Glycosyl hydrolases family 38 C-terminal sub-domain (domain)
This is a subdomain found in the C-terminal region of golgi alpha-mannosidase II present in Drosophila melanogaster. These proteins are important in glycoprotein processing and are thought to cleave mannosidic bonds through a double displacement mechanism involving a reaction intermediate.This subdomain is found at the C-terminal of Glycosyl hydrolases family 38 C-terminal domain.
Pfam PF08505: Mitochondrial Myo2 receptor-related protein (family)
Myo2p, a class V myosin, is essential for mitochondrial distribution, class V being vital for organelle distribution in S. cerevisiae. It is the myosin essential for mitochondrial distribution. The established mechanism for distribution of cellular components by class V myosins is that they interact with the cargo at the C-terminal tail domain and transport it along the actin cytoskeleton using the N-terminal motor domain. Cargo-specific myosin receptors act as the link between the myosin tail and cargo. Myo2 binds with MMR1 (mitochondrial Myo2p receptor-related 1), the receptor on cargo, via the C-terminal domain.
Pfam PF06071: Protein of unknown function (DUF933) (domain)
This domain is found at the C terminus of the YchF GTP-binding protein ([swissprot:O13998]) and is possibly related to the ubiquitin-like and MoaD/ThiS superfamilies.
Wikipedia: In molecular biology, this protein domain is found at the C terminus of the GTP-binding protein, YchF-GTPase found in both prokaryotes and eukaryotes.
Pfam PF15546: Domain of unknown function (DUF4653) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 229 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17465: Chemokine-like protein, HHV-6 U83 gene product (family)
Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. HHV6 A/B encode two putative chemokine receptors and a chemokine-like protein. The HHV6 U83 gene encodes a CC chemokine, which functions as a highly selective and efficacious agonist for the human CCR2 receptor both in respect of signal transduction and the ability to induce chemotaxis. Homologues of the U83 gene products are found in Human cytomegalovirus encoded chemokines vCXC1 and vCXC2. HHV-6 CCL4 contains a region with the CC/CX3C chemokine motif and a glycosaminoglycan (GAG)-binding epitope, BBXB (B being a basic residue), found right before the third Cys residue, which very likely forms a disulfide bridge back to the first Cys of the protein. This gene is the only HHV-6A/B divergent gene that is specific for these viruses. The U83 chemokine gene is distinct between HHV-6A and HHV-6B strains, encoding up to 13 % amino acid differences. The HHV-6A (U83A) and HHV-6B (U83B) chemokines have distinct specificities which determine chemoattraction or diversion of different leukocyte subsets for infection or immune evasion, thus an early component of cellular tropism as well as mediator of innate immunity. U83 also has a varied gene structure, with N-terminal length variation determining production of the encoded mature secreted chemokine, coupled with control by cell-directed splicing which truncates the chemokine gene early in replication to encode an antagonist. The 'long' active form of U83A has a unique broad specificity for receptors CCR1, CCR4, CCR5, CCR6 and CCR8 present on plasmacytoid and myeloid dendritic and monocyte/macrophage antigen presenting cells, as well as both TH1 and TH2 skin homing lymphocytes and NK cells; it is also amongst the highest affinity ligands for CCR5 and inhibits HIV-1 binding at this coreceptor. U83A can both block and divert human chemokine action while occupying the human chemokine receptors.