SII-SWORD/CoKE huggingface dataset:
Pfam PF24592: Family of unknown function (DUF7616) (family)
This entry represents a small family of uncharacterised proteins from enterobacterial phage. The proteins are around 56 residues 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 PF04626: Dec-1 protein, C terminal region (family)
The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). Alternative splicing generates different carboxyl terminal ends in different protein isoforms, so this is region is the most C terminal region that is present in the main isoforms.
Pfam PF18400: Thioredoxin-like domain (domain)
This is one of four TRXL(thioredoxin-like) domains found in UDP-glucose:glycoprotein glucosyltransferase (UGGT).
Wikipedia: Thioredoxins are small disulfide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulfide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol.
Pfam PF18420: CSN4/RPN5/eIF3a helix turn helix domain (domain)
Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). Enzymatically, CSN functions as an isopeptidase that removes the ubiquitin-like activator NEDD8 from CRLs, but it can also bind deneddylated CRLs and maintain them in an inactive state. The CSN subunits CSN1, CSN2, CSN3, CSN4, CSN7 and CSN8, share a common domain composition: an N-terminal array of tandem alpha-helical tetratricopeptide/-like repeats, a 34 residue motif, followed by a PCI domain, which encompasses a WH subdomain, a linker, and one or two alpha-helices at the C-terminus. This entry describes the C-terminal helices found on CSN4. The two helices from CSN4 (helices I and II) form a brace roughly perpendicular to the bundle axis in contact with the three C-terminal helices of CSN6. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle.  Both CSN1 and CSN4 are dependent on the presence of their C-terminal helix (CSN1 isoform-2 residues: 466-527; and CSN4: 364-406) for integration into CSN. COP9 signalosome shares common architecture with the 26S proteasome lid and eIF3 where the 19S lid subunit RPN5 and the eIF3 core subunit eIF3a share significant structural similarity with CSN4.
Pfam PF15304: A-kinase anchor protein 2 C-terminus (family)
This family includes the C-terminus of A-kinase anchor protein 2 (AKAP2). It includes the site where the regulatory subunits (RII) of protein kinase AII binds.
Pfam PF16640: Bacterial Ig-like domain (group 3) (domain)
This family consists of bacterial domains with an Ig-like fold.
Pfam PF07757: Predicted AdoMet-dependent methyltransferase (family)
Proteins in this family have been predicted to function as AdoMet-dependent methyltransferases.
Wikipedia: S-adenosylmethionine-dependent methyltransferase is a conserved protein domain and protein superfamily. SAM-MTase proteins are methyltransferases. There are five protein families within SAM-MTase,
Pfam PF11177: Protein of unknown function (DUF2964) (family)
This family of proteins with unknown function appears to be restricted to Proteobacteria.
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 PF01114: Colipase, N-terminal domain (domain)
SCOP reports duplication of common fold with Colipase C-terminal domain.
Wikipedia: Colipase, abbreviated CLPS, is a protein co-enzyme that counteracts the inhibitory effect of intestinal bile acid on the enzymatic activity of pancreatic lipase. It is secreted by the pancreas in an inactive form, procolipase, which is activated in the intestinal lumen by trypsin.
Pfam PF04455: LOR/SDH bifunctional enzyme conserved region (family)
Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme.  This conserved region is commonly found immediately  N-terminal to Saccharop_dh ([pfam:PF03435]) in eukaryotes.
Pfam PF19560: Family of unknown function (DUF6082) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a  protein from the kanamycin biosynthetic gene cluster from  Streptomyces kanamyceticus and appears to be predominantly found in actinobacteria.
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 PF13363: Beta-galactosidase, domain 3 (domain)
This is the third domain of the five-domain beta-galactosidase enzyme that altogether catalyses the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain has an Ig-like fold.
Pfam PF01737: YCF9 (family)
This family consists of the hypothetical protein product of the YCF9 gene from chloroplasts and  cyanobacteria. These proteins have no known function.
Wikipedia: In molecular biology, the PsbZ (Ycf9) is a protein domain, which is low in molecular weight. It is a transmembrane protein and therefore is located in the thylakoid membrane of chloroplasts in cyanobacteria and plants. More specifically, it is located in Photosystem II (PSII) and in the light-harvesting complex II (LHCII). Ycf9 acts as a structural linker, that stabilises the PSII-LHCII supercomplexes. Moreover, the supercomplex fails to form in PsbZ-deficient mutants, providing further evidence to suggest Ycf9's role as a structural linker. This may be caused by a marked decrease in two LHCII antenna proteins, CP26 and CP29, found in PsbZ-deficient mutants, which result in structural changes, as well as functional modifications in PSII.
Pfam PF14122: YokU-like protein, putative antitoxin (family)
The YokU-like protein family includes the B. subtilis YokU protein [swissprot:C0H434] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two conserved CXXC sequence motifs. This is likely to be a family of bacterial antitoxins, as the sequence bears remote homology to the RelE fold family.
Pfam PF09284: Rhamnogalacturonan lyase B, N-terminal (domain)
Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL).
Pfam PF23098: Nucleolar protein 10-like, N-terminal domain (repeat)
This domain is found at the N-terminal end of human Nucleolar protein 10 (NOL10) and similar eukaryotic sequences. This domain is normally found N-terminal to [pfam:PF23097]. This entry includes a entire beta-propeller structure and two alpha -helices.
Pfam PF24747: GIR1-like zinc ribbon domain (domain)
This domain is found in the Protein GL2-INTERACTING REPRESSOR 1 (GIR1), Protein GL2-INTERACTING REPRESSOR 2 (GIR2), Protein salt-induced and EIN3/EIL1-dependent 1 (SIED1) from Arabidopsis thaliana and related proteins. Proteins containing this domain are involved in the modulation of root hair development and act as negative regulators in this process. They may function as adapter proteins, interacting with other proteins to control gene expression related to root hair formation. Additionally, some proteins are implicated in ethylene-dependent salt stress responses, where they play a role in reducing the accumulation of reactive oxygen species, thereby protecting the plant from oxidative damage. This domain contains a pair of conserved cysteine residues and is predicted to adopt a fold typical for zinc-ribbon domains.
Pfam PF13877: Potential Monad-binding region of RPAP3 (domain)
This domain is found at the C-terminus of RNA-polymerase II-associated proteins.  These proteins bind to Monad and are involved in regulating apoptosis.                They contain TPR-repeats towards the N_terminus.
Pfam PF04018: Undecaprenyl phosphate translocase-like (family)
This family represents a group of prokaryotic proteins associated with transmembrane transport of undecaprenyl phosphate lipids, which is required for the biogenesis of microbial cell surface polymers, including VCA0040 ([swissprot:Q9KNC5]) from Vibrio cholerae. Family members have between 6 and 9 predicted transmembrane segments.
Pfam PF09142: tRNA Pseudouridine synthase II, C terminal (domain)
The C terminal domain of tRNA Pseudouridine synthase II adopts a PUA ([pfam:PF01472]) fold, with a four-stranded mixed beta-sheet flanked by one alpha-helix on each side. It allows for binding of the enzyme to RNA, as well as stabilisation of the RNA molecule.
Pfam PF14804: Jag N-terminus (domain)
This domain is found at the N-terminus of proteins containing [pfam:PF13083] and [pfam:PF01424], including the jag proteins.
Pfam PF06528: Phage P2 GpE (family)
This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2.
Pfam PF09735: Nck-associated protein 1 (family)
Nck-associated protein 1 is part of lamellipodial complex that controls Rac-dependent actin remodeling. It associates preferentially with the first SH3 domain of Nck and is a component of the WAVE2 complex composed of ABI1, CYFIP1/SRA1, NCKAP1/NAP1 and WASF2/WAVE2. It is also a component of the WAVE1 complex composed of ABI2, CYFIP2, C3orf10/HSPC300, NCKAP1 and WASF1/WAVE1. CYFIP2 binds to activated RAC1 which causes the complex to dissociate, releasing activated WASF1. The complex can also be activated by NCK1. Expression of this protein was found to be markedly reduced in patients with Alzheimer's disease.
Pfam PF15448: N-terminal segments of P. falciparum erythrocyte membrane protein (domain)
NTS_2 is a family of the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1). However, in this group of proteins conservation is high. PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors.
Pfam PF10987: Protein of unknown function (DUF2806) (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 PF19793: Family of unknown function (DUF6277) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001096) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the FR901464 biosynthetic gene cluster from Pseudomonas sp. 2663.
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 PF09774: Intermembrane space protein MIX23 (family)
Intermembrane space protein MIX23 regulates or stabilises the mitochondrial protein import machinery and is specifically up-regulated under stress conditions. It is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised. MIX23, also known as Caffeine-induced death protein 2 (Cid2), is evolutionarily conserved and a homologue of the human protein CCDC58.
Pfam PF19941: Family of unknown function (DUF6403) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001447) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the primycin biosynthetic gene cluster from Saccharomonospora azurea SZMC 14600.
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 PF08156: NOP5NT (NUC127) domain (domain)
This N terminal domain is found in RNA-binding proteins of the NOP5 family.
Pfam PF18934: Family of unknown function (DUF5682) (family)
This is a family of unknown function, mostly found in bacteria.
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 PF17463: Gene product 79 (family)
This is a domain of unknown function found in Mycobacterium phage. Family members include the full Gp79 protein found in Mycobacteriophage L5 [swissprot:Q05294]. Mycobacteriophage L5, is a phage isolated from Mycobacterium smegmatis. It forms stable lysogens in M. smegmatis and has a broad host range among the pathogenic mycobacteria. L5 encodes gene products (gp) toxic to the host M. smegmatis. Expression of gp79 interferes with the cell membrane or cell-wall synthesis of M. smegmatis, leading to altered cell morphology. It also has a bactericidal effect on E. coli. The N-terminal segment of gp79 (amino acids 1-41) shares sequence similarity with the signal peptide of the D-alanylD-alanine carboxypeptidase of Bacillus licheniformis. This enzyme removes C-terminal D-alanyl residues from sugarpeptide cell-wall precursors and is also a penicillin-binding protein (PBP). The homology of the hydrophobic N-terminal part of gp79 to a PBP (penicillin-binding protein) signal peptide may indicate an interaction of gp79 with proteins or metabolites involved in the peptidoglycan synthesis of M. smegmatis.
Pfam PF23068: M02D8_5-like, seventh CUB domain (domain)
This entry represents the seventh occurrence of the CUB domain in a family of uncharacterised proteins present in nematodes. Consecutive repetitions of this domain are common in this protein family. The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found predominantly in extracellular and plasma membrane-associated proteins, many of which undergo developmental regulation. CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding  partners.
Pfam PF11601: Shal-type voltage-gated potassium channels, N-terminal (domain)
This entry represents the short N-terminal helical domain of Shal-type voltage-gated potassium channels. The domain interacts with Kv channel-interacting proteins to modulate cell surface expression and the function of Kv4 channels. The interaction of the N-terminus of Shal-type protein Kv4.2 and the Kv interacting protein KChiP1 forms a structure which is like the structure between calmodulin and its target peptides when they interact. Interactions of an N terminal alpha helix in Kv4.2 and a C terminal alpha helix in KChIP1 are essential for the modulation of Kv4.2 by KChIPs.
Pfam PF22370: Flagellin, beta sheet domain (domain)
This domain is found in Flagellin from Salmonella dublin (FliC) and similar sequences from proteobacteria. FliC is the subunit protein which polymerises to form the filaments of bacterial flagella. Binding of FliC to the Toll-like receptor 5 (TLR5) leads to activation of innate immune responses against flagellated bacteria. It consists of four domains. This entry represents its third domain.
Pfam PF01903: CbiX (domain)
The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine-rich region at their C-terminus, which suggests that it might be involved in metal chelation.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF09368: Sas10 C-terminal domain (domain)
Sas10 is an Essential subunit of U3-containing Small Subunit (SSU) processome complex involved in the production of the 18S rRNA and assembly of the small ribosomal subunit.
Pfam PF13214: Protein of unknown function (DUF4022) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 85 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 PF13352: Protein of unknown function (DUF4100) (family)
This is a family of uncharacterised proteins. Some members have an aspartic peptidase domain at the C-terminal ([pfam:PF13650]).
Pfam PF09320: Domain of unknown function (DUF1977) (family)
Members of this family of functionally uncharacterised domains are predominantly found in dnaj-like proteins.
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 PF20142: Scaffold domain (domain)
This entry represents the scaffolding domain from the L,D-transpeptidases.
Pfam PF14478: Domain of unknown function (DUF4430) (domain)
Although this family has overlaps with SLBB, the majority of its sequences are unique. Several family members, eg UniProtKB:A0RGA8, that do not overlap have an LPXTG-cell wall anchor at their C-terminus, a SSF_Family 10_polysaccharide_lyase or Glycosyltransferase structure associated with them in the middle region, as shown by InterPro, as well as this domain at the N-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 PF10989: Protein of unknown function (DUF2808) (family)
This family of proteins with unknown function appears to be restricted to 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 PF02434: Fringe-like (family)
The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localised to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions.
Pfam PF24548: EFCAB10, C-terminal EF-hand (domain)
This is the second and C-terminal EF hand domain of human EF-hand calcium-binding domain-containing protein 10 (EFCAB10) and similar animal proteins.
Pfam PF12895: Anaphase-promoting complex, cyclosome, subunit 3 (repeat)
Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20.
Pfam PF19276: HD associated region (family)
This entry represents a region that forms part of a larger HD domain.According to the original paper describing the HD domain this family represents cluster 1.