SII-SWORD/CoKE huggingface dataset:
Pfam PF06975: Protein of unknown function (DUF1299) (family)
This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that many family members contain multiple copies of this region.
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 PF04745: VITF-3 subunit protein (family)
Family of Chordopoxvirus proteins composing one of the two subunits that make up VITF-3, a virally encoded complex necessary for intermediate stage transcription.
Pfam PF25136: Domain of unknown function (DUF7823) (domain)
This domain is found in uncharacterised proteins from Gammaproteobacteria. This domain is found usually associated with [pfam:PF11195].
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 PF23869: WD repeat-containing protein 75 first beta-propeller (repeat)
This entry represents the first beta-propeller found in WD repeat-containing protein 75 (WDR75) from animals. WDR75 has a crucial positive role in ribosome biogenesis and its malfunction activates p53, leading to cellular senescence. This domain forms a composite binding site with UTP4 protein in the SSU processome for the 5' external transcribed spacer.
Pfam PF13023: HD domain (domain)
HD domains are metal dependent phosphohydrolases.
Pfam PF19258: KxYKxGKxW signal peptide (conserved_site)
This entry represents a novel form of signal peptide that occurs as an N-terminal domain with a recognizable motif, reminiscent of the YSIRK signal peptide.
Pfam PF03666: Nitrogen Permease regulator of amino acid transport activity 3 (family)
This family, also known in yeasts as Rmd11, complexes with NPR2, [pfam:PF06218]. This complex heterodimer is responsible for inactivating TORC1. an evolutionarily conserved protein complex that controls cell size via nutritional input signals, specifically, in response to amino acid starvation.
Pfam PF03826: OAR motif (conserved_site)
The entry represents the OAR motif.
Pfam PF05219: DREV methyltransferase (family)
This family contains DREV protein homologues from several eukaryotes. The function of this protein is unknown. However, these proteins appear to be related to other methyltransferases (Bateman A pers obs).
Pfam PF14612: IEC3 subunit of the Ino80 complex, chromatin re-modelling (domain)
This entry includes fungal chromatin re-modelling proteins found in one of the chromatin-central complexes, Ino80. The function was identified in Schizosaccharomyces pombe but there is no orthologue in S. cerevisiae. INO80 complex remodels chromatin by shifting nucleosomes and is involved in DNA repair. This entry represents the helical section found at the N-terminal of this group of proteins.
Pfam PF22930: PDXDC1-like central domain (domain)
This entry represents a central domain found in Pyridoxal-dependent decarboxylase domain-containing protein 1 (PDXDC1) and related proteins. PDXDC1 has been associated with the modulation of prepulse inhibition of acoustic startle, perhaps through the metabolism of catecholamine neurotransmitters. The function of this domain is unknown.
Pfam PF13329: Autophagy-related protein 2 (repeat)
The Atg2 protein, an integral membrane protein, is required for a range of functions including the regulation of autophagy in conjunction with the Atg1-Atg13 complex. Atg2 is required for glucose-induced micropexophagy and ethanol-induced macropexophagy in yeast. Homologues of this protein have also been described in mammals and plants. Mammalian ATG2 proteins are thought to function both in autophagosome (a structure that enclose the cytoplasmic materials) formation and regulation of lipid droplet morphology and dispersion. In plants they have a role in programmed cell death, senescence and disease resistance.Atg2 is part of the RBG (repeating beta-grooves) superfamily together with VPS13, SHIP164, Csf1, and the Hob proteins, which all share the same structure consisting of long hydrophobic grooves made of multiple repeating modules of five beta-sheets followed by a loop.
Pfam PF23501: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AMU9] from the parasite Babesia bovis.
Pfam PF02952: L-fucose isomerase, C-terminal domain (domain)
L-fucose isomerase (5.3.1.25) converts the aldose L-fucose into the corresponding ketose L-fuculose during the first step in fucose metabolism using Mn2+ as a cofactor. The enzyme is a hexamer, forming the largest structurally known ketol isomerase, and each protomer consists of three domains. This entry represents the C-terminal domain.
Wikipedia: In enzymology, a L-fucose isomerase is an enzyme that catalyzes the chemical reactionL-fucose  L-fuculose
Pfam PF08167: rRNA processing/ribosome biogenesis (repeat)
Rix1 is a nucleoplasmic particle involved in rRNA processing/ribosome assembly. It associates with two other proteins, Ipi1 and Ipi3, to form the RIX1 complex that allows Rea1 - the AAA ATPase - to associate with the 60S ribosomal subunit. More than 170 assembly factors are involved in the construction and maturation of yeast ribosomes, and after these factors have completed their function they need to be released from the pre-ribosomes. Rea1 induces the release of the assembly protein complex in a mechanical fashion. This family is usually associated with NUC202, [pfam:PF08166].
Pfam PF14955: Mitochondrial ribosome subunit S24 (family)
This family of proteins corresponds to mitochondrial ribosomal subunit S24 in eukaryotes.
Pfam PF23318: Domain of unknown function (DUF7085) (domain)
This domain is found in a group of uncharacterised proteins from flatworms. It is predicted to adopt a PH-like fold with similarity to the PH-like domain found in Shulin and Spt16.
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 PF09115: DNA polymerase III, delta subunit, C terminal (domain)
Members of this family, which are predominantly found in prokaryotic DNA polymerase III, assume an alpha helical structure, with a core of five alpha helices, and an additional small helix. They are essential for the formation of the polymerase clamp loader.
Wikipedia: DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg and Malcolm Gefter in 1970. The complex has high processivity and, specifically referring to the replication of the E.coli genome, works in conjunction with four other DNA polymerases. Being the primary holoenzyme involved in replication activity, the DNA Pol III holoenzyme also has proofreading capabilities that corrects replication mistakes by means of exonuclease activity reading 3'→5' and synthesizing 5'→3'. DNA Pol III is a component of the replisome, which is located at the replication fork.
Pfam PF02819: Spider toxin (family)
This family of spider neurotoxins are thought to be calcium ion channel inhibitors.
Wikipedia: Spider toxins are a family of proteins produced by spiders which function as neurotoxins. The mechanism of many spider toxins is through blockage of calcium channels.
Pfam PF16568: Tyrosine-rich domain of Sam68 (domain)
Sam68-YY is a short tyrosine-rich domain on Src-associated in mitosis, 68 kDa protein (Sam68), a protein that regulates TCF-1 alternative splicing. It is a crucial binding-partner of the APC-Arm domain that forms a superhelix with a positively charged groove, the surface-residues of which groove form numerous interactions with Sam68-YY to fix it in a bent conformation. APC-Arm is the armadillo repeat domain of the tumour-suppressor protein adenomatous polyposis coli or APC. APC plays plays important roles in Wnt signalling and other cellular processes.
Pfam PF16242: Pyridoxamine 5'-phosphate oxidase like (domain)
This domain, approximately 140 residues in length, is mainly found in general stress proteins in various Xanthomonas species. It is composed of a six-stranded antiparallel beta-barrel flanked by five alpha-helices and can bind to FMN and FAD, suggesting that it may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant.
Pfam PF10876: Phage tail assembly chaperone protein, TAC (family)
This is a family of putative phage tail assembly chaperone proteins largely from Haemophilus and Xylella species.
Pfam PF21703: Major capsid protein (domain)
This protein family includes Major capsid protein from Bacteriophage T7 (Gp10A) and similar proteins from tailed bacteriophages and bacterial prophages. Gp10A subunits adopt an HK97-like conformation to form the viral shell.
Pfam PF19861: Family of unknown function (DUF6335) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001615) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular hexose-palythine-serine biosynthetic gene cluster from  Heteroscytonema crispum UCFS10.
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 PF13377: Periplasmic binding protein-like domain (domain)
This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognises Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF21590: AP5B1, C-terminal (domain)
AP5B1 is part of the AP-5 adaptor protein complex, which may be involved in endosomal transport. This entry represents a presumed alpha/beta domain found at the C-terminal of AP5B1 proteins. Structure predictions suggest that it consists of five beta-strands with three alpha-helices around them
Pfam PF14151: YfhD-like protein (family)
The YfhD-like protein family includes the B. subtilis YfhD protein [swissprot:O31572], which is functionally uncharacterised. Its expression is regulated by the sporulation-specific sigma factor sigma-F.  This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a single completely conserved residue E that may be functionally important.
Pfam PF10500: Nuclear RNA-splicing-associated protein (disordered)
SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway.
Pfam PF15610: PRTase ComF-like (family)
This PRTase family is related to the ComF PRTases. These genes are found in the smaller biosynthetic operon associated with the Ter  stress-response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress-response.
Pfam PF10365: Domain of unknown function (DUF2436) (family)
This domain is found on peptidase C25 proteins and 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 PF12368: Rhodanase C-terminal (family)
Rhodanase_C is found as the domain-extension to Rhodanase enzyme in some members of the Rhodanase family. Rhodanase is [pfam:PF00581].
Pfam PF22722: NACHT-associated inactive Restriction Endonuclease 1 (domain)
This entry represents a predicted sensor domain in bacterial NACHT conflict systems. It is likely to bind a ligand which could contribute to activation of enzymatic domains additionally fused to the N-terminus of the NACHT module.
Pfam PF11035: Small nuclear RNA activating complex (SNAPc), subunit 2 (family)
This family of proteins is snRNA-activating protein complex subunit 2 (SNAPc subunit 2). The SNAPc complex allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element, the TATA box. The family functions both to specifically recognise the proximal sequence element present in the core promoters of human snRNA genes and to stimulate TBP recognition of the neighbouring TATA box present in human U6 snRNA promoters.
Pfam PF13361: UvrD-like helicase C-terminal domain (domain)
This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pfam PF18929: Family of unknown function (DUF5678) (domain)
This presumed domain family is found in bacteria and archaea. Proteins in this family are typically between 64 and 76 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 PF14665: Rapamycin-insensitive companion of mTOR, phosphorylation-site (domain)
Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient- and growth-factor signalling. This short region is the phoshorylation site.  Rictor does interact with 14-3-3 in a Thr1135-dependent manner. Rictor can be inhibited by short-term rapamycin treatment showing that Thr1135 is an mTORC1-regulated site.
Pfam PF22372: BA_2335-like (family)
This protein family includes the uncharacterised protein BA_2335 from Bacillus anthracis and similar sequences from Bacilli. It adopts a beta-sandwich configuration.
Pfam PF22613: Transketolase-like TK C-terminal domain (domain)
This entry represents the C-terminal domain found in transketolase and transketolase-like enzymes, such as pyruvate  dehydrogenase E1 component (OPD1).
Pfam PF18949: Family of unknown function (DUF5693) (family)
This is a family of unknown function 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 PF03632: Glycosyl hydrolase family 65 central catalytic domain (repeat)
This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu. The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom.  The catalytic domain also forms the majority of the dimerisation interface.
Wikipedia: In molecular biology, glycoside hydrolase family 65 is a family of glycoside hydrolases.
Pfam PF08860: Domain of unknown function (DUF1827) (domain)
This presumed domain 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 PF15567: Immunity protein 35 (family)
A predicted immunity protein with an alpha+beta fold and a conserved tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a protease domain such as Tox-PL1 and Ntox40. In some instances, it is also fused to a papain-like toxin, ADP-ribosyl glycohydrolase and a S8-like peptidase. Based on these associations the domain is likely to be a protease inhibitor.
Pfam PF16763: Major ampullate spidroin 1, spider silk protein 1, N-term (domain)
Spidroin is produced by a number of arachnids. Spidrions are made up of repetitive segments flanked by conserved non-repetitive domains, and this domain is the conserved non-repetitive region. Aggregation to form the rigid silk occurs due to association at the repetitive regions, and the N-terminal domain is necessary to prevent premature aggregation during storage before extrusion. This N_terminal region inhibits precocious aggregation and then accelerates and directs self-assembly as the pH is lowered along the extrusion duct.
Wikipedia: Spidroins are the main proteins in spider silk. Different types of spider silk contain different spidroins, all of which are members of a single protein family. The most-researched type of spidroins are the major ampullate silk proteins (MaSp) used in the construction of dragline silk, the strongest type of spider silk. Dragline silk fiber was originally thought to be made up of two types of spidroins, spidroin-1 (MaSp1) and spidroin-2 (MaSp2) however recent transcriptomic analysis of over 1000 spider species has revealed multiple spidroins are expressed making it much more complex.
Pfam PF05568: African swine fever virus J13L protein (family)
This family consists of several African swine fever virus J13L proteins.
Pfam PF07945: Janus-atracotoxin (domain)
This family includes three peptides secreted by the  spider Hadronyche versuta ([swissprot:P82226], [swissprot:P82227], [swissprot:P82228]). These are insect-selective, excitatory neurotoxins that may function by antagonising muscle  acetylcholine receptors, or acetylcholine receptor  subtypes present in other invertebrate neurons. Janus atracotoxin-Hv1c (J-ACTX-Hv1c, [swissprot:P82228]) is organised into a disulphide-rich globular core (residues 3-19) and a beta-hairpin (residues 20-34). There are  4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance  of structure but critical for insecticidal activity.
Pfam PF19387: Family of unknown function (DUF5962) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000498) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF07693: KAP family P-loop domain (domain)
The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side.