SII-SWORD/CoKE huggingface dataset:
Pfam PF16058: Mucin-like (disordered)
This region is found repeated at the C-terminus (C-tail) of bile salt-activated lipase, where is O-glycosylated. This region is composed of biased amino acid composition that is likely to be disordered. The region contains many repeats of an approximately 11 residue degenerate repeat.
Pfam PF06697: Protein of unknown function (DUF1191) (family)
This family contains hypothetical plant proteins of unknown 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 PF08854: Domain of unknown function (DUF1824) (domain)
This uncharacterised family of proteins are principally found in cyanobacteria.
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 PF00567: Tudor domain (domain)
The drosophila Tudor protein, the founder of the Tudor domain family, is encoded by a 'posterior group' gene, which when mutated disrupt normal abdominal segmentation and pole cell formation. Another drosophila gene, homeless, is required for RNA localization during oogenesis. The tudor protein contains multiple repeats of a domain which is also found in homeless .

The tudor domain is found in many proteins that colocalise with ribonucleoprotein or single-strand DNA-associated complexes in the nucleus, in the mitochondrial membrane, or at kinetochores. At first it was not clear if the domain binds directly to RNA and ssDNA, or controls interactions with the nucleoprotein complexes but it is now known that this domain recognises and binds to methyl-arginine-lysine residues, playing important roles in diverse epigenetics, gene expression and the regulation of various small RNAs . The tudor-containing protein homeless, also contains a zinc finger typical of RNA-binding proteins .

This domain has been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. One example is the Tudor domain of Survival of Motor Neuron (SMN), linked to spinal muscular atrophy, which binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The resolution of the solution structure of the Tudor domain of human SMN revealed that the Tudor domain forms a strongly bent antiparallel Î²-sheet with five strands forming a barrel-like fold. The structure exhibits a conserved negatively charged surface that interacts with the C-terminal Arg and Gly-rich tails of the spliceosomal Sm D1 and D3 proteins .
Wikipedia: In molecular biology, a Tudor domain is a conserved protein structural domain originally identified in the Tudor protein encoded in Drosophila. The Tudor gene was found in a Drosophila screen for maternal factors that regulate embryonic development or fertility. Mutations here are lethal for offspring, inspiring the name Tudor, as a reference to the Tudor King Henry VIII and the several miscarriages experienced by his wives.
Pfam PF18278: Receptor activator of the NF-KB cysteine-rich repeat domain 2 (domain)
This domain is found in the receptor activator of the NF-KB (RANK) present in Mus musculus. RANK and its cognate ligand RANKL play a role in bone remodelling, immune function and mammary gland development in conjunction with various cytokines and hormones. The binding of RANKL to RANK causes trimerisation of the receptor, which activates the signalling pathway and results in osteoclastogenesis from progenitor cells and the activation of mature osteoclasts receptor activator of the NF-KB. This domain is the second of four cysteine rich pseudo-repeat domains (CRDs) and so is known as CRD2. RANK moves via a hinge region between CRD2 and CRD3 to make close contact with RANKL.
Pfam PF19771: Family of unknown function (DUF6257) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces  tenjimariensis.
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 PF11610: Scaffold protein Ste5, Fus3-binding region (conserved_site)
This family of proteins represents the Fus3 binding region of Ste5. Ste5 functions in the yeast mating pathway and is required for signalling through the mating response MAPK pathway. Ste5 has separate binding sites for each member of the MAPK cascade. This region of Ste5 allosterically activates autophosphroylation of Fus3, a mitogen-activated protein kinase. Auto-activated Fus3 has a negative regulatory role, and promotes Ste5 phosphorylation which leads to a decrease in pathway transcriptional output.
Pfam PF12477: Sex factor F TraW protein N terminal (family)
This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. The traW gene of the E. coli K-12 sex factor, F, encodes one of the numerous proteins required for conjugative transfer of this plasmid.
Pfam PF22417: Cadherin-related hmr-1 E-cadherin-like (domain)
This entry represents a C-terminal region found in Cadherin-related hmr-1 from C.elegans and similar sequences from Caenorhabditis species which is homologous to the beta-catenin binding region of E-cadherin.
Pfam PF22929: Integrator complex subunit 1, INTS2-binding domain (repeat)
Integrator (INT) complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. It binds the C-terminal domain (CTD) of RNA polymerase II (Pol II) and functions as an RNA endonuclease to cleave different classes of RNAs, regulating the transcription of both protein-coding genes and noncoding elements. Integrator also associates with protein phosphatase 2A (PP2A) core enzyme to form the INTAC complex which regulates transcription through dephosphorylation of Pol II CTD. This entry includes the Integrator complex subunit 1 (INTS1) which forms the backbone module of the complex (it consists of four modules: backbone, shoulder, phosphatase and endonuclease) through the association with INTS2 and INTS7 to form a rigid scaffold. The backbone and shoulder modules form a central cruciform scaffold. INTS1 is an all-alpha helical protein with four repetitive helix hairpin domains towards the C-terminal (R1-R4). This entry represents a domain found at the N-terminal region of INTS1, after [pfam:PF12432], which interacts with the INTS2 subunit.
Pfam PF07839: Plant calmodulin-binding domain (domain)
The sequences featured in this family are found repeated  in a number of plant calmodulin-binding proteins (such as [swissprot:Q8W235], [swissprot:Q84ZT8] and [swissprot:Q8H6X1]), and are  thought to constitute the calmodulin-binding domains. Binding of the proteins to calmodulin depends on the presence of calcium ions. These proteins are thought to be  involved in various processes, such as plant defence responses and stolonisation or tuberization.
Wikipedia: In molecular biology, the plant calmodulin-binding domain is a protein domain found repeated in a number of plant calmodulin-binding proteins. These domains are thought to constitute the calmodulin-binding domains of these proteins. Binding of the proteins to calmodulin depends on the presence of calcium ions. These proteins are thought to be involved in various processes, such as plant defence responses and stolonisation or tuberization.
Pfam PF00700: Bacterial flagellin C-terminal helical region (domain)
Flagellins polymerise to form bacterial flagella. There is  some similarity between this entry and [pfam:PF00669], particularly the motif NRFXSXIXXL. It has been suggested that these two regions associate and this is shown to be correct as structurally this domain forms an extended helix that interacts with the N-terminal region ([pfam:PF00669]) to form the D0 and D1 structural domains. These domains are responsible for the activation of TLR5, with the C-terminal D0 region playing a key role.
Wikipedia: Flagellins are a family of proteins present in flagellated bacteria which arrange themselves in a hollow cylinder to form the filament in a bacterial flagellum. Flagellin has a mass on average of about 40,000 daltons. Flagellins are the principal component of bacterial flagella that have a crucial role in bacterial motility.
Pfam PF09782: NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit (family)
Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol.
Pfam PF15854: G-protein coupled receptor ligand 15 (family)
GPR15 is an orphan G protein-coupled receptor (GPCR) that is found in lymphocytes. It functions as a co-receptor of simian immunodeficiency virus and HIV-2 and plays a role in the trafficking of T cells to the lamina propria in the colon and to the skin. An activating ligand named GPR15L is shown to bind GPR15 and attract GPR15-expressing T cells including lymphocytes in colon-draining lymph nodes and thymic precursors of dermal epithelial T cell. This 9kDa CC-motif containing cationic polypeptide has been previously described as the 57 amino acid antimicrobial peptide AP-57, and as a Sushi Containing Domain-2 (SUSD2)-binding factor (CSBF), capable of inhibiting the growth of intestinal epithelial cancer cell lines. The chemokine is expressed by epithelial cells in gastrointestinal and genitourinary mucosae and in the skin. In humans GPR15L, is encoded by the gene C10ORF99 and has some features similar to the CC family of chemokines. However, it lacks significant homology to classic CC and CXC chemokines, yet shares many features with them, including a cationic domain predicted to comprise two disulfide bonds and a highly conserved GPCR-activating terminal peptide. Furthermore, the activating peptides of CC chemokines are typically located at the N-terminus, while that of GPR15L is C-terminal, a feature that it shares with some other GPCR ligands like chemerin and apela.
Pfam PF07116: Protein of unknown function (DUF1372) (family)
This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function 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 PF23260: SEMA5B-like, TSP-1 type 1 (domain)
This is a TSP-1 type 1 domain found in human Semaphorin-5B (SEMA5B) and similar sequences mainly found in animals. SEMA5B acts as an axonal guidance cue and regulates the development and maintenance of synapse size and number in hippocampal neurons.
Pfam PF00701: Dihydrodipicolinate synthetase family (domain)
This family has a TIM barrel structure.
Wikipedia: 4-Hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7, dihydrodipicolinate synthase, dihydropicolinate synthetase, dihydrodipicolinic acid synthase, L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing), dapA (gene)) is an enzyme with the systematic name L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing; (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate-forming). This enzyme catalyses the following chemical reactionpyruvate + L-aspartate-4-semialdehyde  (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
Pfam PF24335: Family of unknown function (DUF7503) (family)
This entry represents a group of uncharacterised archaeal proteins. These proteins are short in size (~50 residues long), contain a highly hydrophobic helix and are likely associated with the membrane.
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 PF17155: Gammaproteobacterial periplasmic sensor domain (family)
GAPES1 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcJ (YeaJ) that regulates biofilm formation and motility in Escherichia coli.
Pfam PF00242: DNA polymerase (viral) N-terminal domain (family)
This domain is at the N terminus of hepadnavirus P proteins and covers the so-called terminal protein and the spacer region of the protein. This domain is always associated with IPR000477 and IPR001462.
Pfam PF11180: Protein of unknown function (DUF2968) (family)
This 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 PF16592: REC lobe of CRISPR-associated endonuclease Cas9 (family)
The REC lobe of Cas9 - the CRISPR-associated endonuclease Cas9 - includes the REC1 and REC2 domains. REC1 forms an elongated, alpha-helical structure consisting of 25 alpha helices and two beta-sheets, whereas REC2 inserted within REC1 adopts a six-helix bundle structure. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive.
Pfam PF21400: Ndc10 N-terminal domain (domain)
Kinetochores link centromeric DNA to spindle microtubules and ensure faithful chromosome segregation during mitosis. In point-centromere yeasts, the CBF3 complex Skp1-Ctf13-(Cep3)(2)-(Ndc10)recognizes a conserved centromeric DNA element through contacts made by Cep3 and Ndc10. This entry represents the N-terminal domain of Ndc10.
Pfam PF21674: CCDC22 protein N-terminal domain (domain)
This entry represents the N-terminal helical domain from the CCDC22 protein. This protein is part of the complex termed the CCC complex that is composed of CCDC22, CCDC93 and various COMMD proteins.
Pfam PF02403: Seryl-tRNA synthetase N-terminal domain (domain)
This domain is found associated with the Pfam tRNA synthetase class II domain ([pfam:PF00587]) and represents the N-terminal domain of seryl-tRNA synthetase.
Pfam PF07365: Alpha conotoxin precursor (family)
This family consists of several alpha conotoxin precursor proteins from a number of Conus species. The alpha-conotoxins are small peptide neurotoxins from the venom of fish-hunting cone snails which block nicotinic acetylcholine receptors (nAChRs).
Pfam PF23807: Ribbon-helix-helix protein (domain)
This entry represents a family of phage Ribbon-helix-helix proteins. Members of the RHH superfamily are often parts of toxin/antitoxin systems, suggesting these proteins may form part of a phage immunity response.
Pfam PF16714: Tyrosyl-tRNA synthetase C-terminal domain (domain)
This domain is found at the C-terminus of fungal tyrosyl-tRNA synthetases. It binds to group I introns.
Pfam PF16383: Domain of unknown function (family)
This family around 150 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown.
Pfam PF12890: Dihydro-orotase-like (family)
This is a small family of dihydro-orotase-like proteins from various bacteria.
Pfam PF25057: Cuticlin N-terminal domain (domain)
This entry represents the N-terminal Ig-like domain of cuticlin proteins from C. elegans, a component of the cuticles, which contributes to the formation of extracellular envelopes protecting the organism from the environment. It also plays a role in alae formation in dauer larvae.
Pfam PF12481: Aluminium induced protein (domain)
This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: YGL and LRDR. This family is related to GATase enzyme domains.
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 PF13466: STAS domain (domain)
The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Pfam PF17504: Family of unknown function (DUF5436) (family)
This is a family of unknown function found in Orthopoxvirus.
Pfam PF06544: Small nuclear ribonucleoprotein Prp3, C-terminal domain (domain)
This domain is found at the C-terminal end of U4/U6 and U4/U5/U6- small nuclear ribonucleoprotein Prp3, part of the tri-RNA complex that form the spliceosome. Prp3 plays a key role in the recognition of the snRNA duplex. This binding domain, highly conserved among eukaryotes, interacts with the 3' end of U6 snRNA. It adopts a ferredoxin-like fold, showing a five-stranded mixed beta-sheet with three alpha-helices, two of them running parallel to the beta-strands on one side of the sheet and one on the other. This fold is extended with a long beta-hairpin, an extra beta-strand, an helix and a final loop at the C terminus. It is located C-terminal to [pfam:PF08572].
Pfam PF08677: GP11 baseplate wedge protein (family)
GP11 is a viral structural protein that connects short tail fibres to the baseplate.  The tail region is responsible for attachment to the host bacteria during infection.
Pfam PF19494: Family of unknown function (DUF6029) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in Bacteroidetes. Proteins in this family are typically between 531 and 570 amino acids in length. There is a conserved GGVCR 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 PF24921: E3 ubiquitin-protein ligase XB3/XBAT31 RING finger (domain)
This entry represents the RING finger domain found at the C-terminal of E3 ubiquitin-protein ligase XB3 from rice and XB3 ORTHOLOG 1 IN ARABIDOPSIS THALIANA, XBAT31. XB3 is an E3 ubiquitin-protein ligase required for full accumulation of the LRR receptor kinase XA21 and XA21-mediated disease resistance. Binding to XA21 may stabilize the receptor kinase and maintain its protein level. XBAT31 regulates thermoresponsive hypocotyl growth through mediating degradation of the thermosensor ELF3.
Pfam PF15170: Calcium/calmodulin-dependent protein kinase II inhibitor (family)
CaM-KIIN is the inhibitor of Calcium/calmodulin-dependent protein kinase II (CaMKII). CaMKII plays a central part in long-term potentiation, which underlies some forms of learning and memory. CaM-KIIN is a natural, specific inhibitor of CaMKII. This family is found in eukaryotes.
Pfam PF22725: GFO/IDH/MocA C-terminal domain (domain)
This entry includes the C-terminal domain found in a set of oxidorecuctases from GFO/IDH/MocA family, not included in [pfam:PF02894].
Pfam PF18428: BRCA1 C Terminus (BRCT) domain (domain)
Brca1 C-terminal (BRCT) domains are a common protein-protein interaction regions in proteins involved in the DNA damage response and DNA repair. For example 53BP1 which plays multiple roles in mammalian DNA damage repair, has a C-terminal tandem BRCT domain (BRCT2), which in its orthologs, Saccharomyces cerevisiae Rad9p and Schizosaccharomyces pombe Crb2, mediates binding to the equivalents of gammaH2AX. Structural and functional studies indicate that the 53BP1-BRCT2 domain is a competent binding module for phosphorylated peptides with a clear specificity for the DNA-damage marker gammaH2AX, and in isolation from other parts of 53BP1 is sufficient for localization to sites of DNA damage in cells associated with gammaH2AX.
Wikipedia: BRCA1 C Terminus (BRCT) domain  is a family of evolutionarily related proteins. It is named after the C-terminal domain of BRCA1, a DNA-repair protein that serves as a marker of breast cancer susceptibility.
Pfam PF18543: Intracellular delivery domain (domain)
This is a C-terminal domain found in BepA proteins from Bartonella henselae. It is a type IV secretion system (T4SS) effector protein. BepA from Bartonella henselae is composed of an N-terminal Fic domain and a C-terminal Bartonella intracellular delivery (ID) domain, the latter being responsible for T4SS-mediated translocation into host cells. The ID domain of BepA mediates inhibition of apoptosis and exhibits an OB (oligonucleotide/oligosaccharide binding)-fold.
Pfam PF11901: DM9 repeat (domain)
This repeat of unknown function was first identified in Diptera proteins; later on it was found in a wide range of invertebrates and vertebrates, such as natterin. It is often present in proteins comprising only two or four DM9 repeats and occasionally is linked to other domains at its N- or C-terminal. In the mannose-specific lectin CGL1 from Crassostrea gigas, DM9 exhibits high binding specificity and avidity toward D-mannose residue and served as a pattern recognition receptor (PRR) with a broad range of recognition spectrum to various pathogen-associated molecular patterns. It also mediates immune recognition and cellular encapsulation.