SII-SWORD/CoKE huggingface dataset:
Pfam PF20079: Family of unknown function (DUF6474) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 208 and 230 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 PF22390: LntA, four-helical up-and-down bundle (domain)
This entry represents an helical domain present in LntA protein, a virulence factor from Listeria monocytogenes. LntA target the chromatin repressor BAHD1 in the host cell nucleus to activate interferon-stimulated genes.
Pfam PF04679: ATP dependent DNA ligase C terminal region (family)
This region is found in many but not all ATP-dependent DNA ligase enzymes  ([ec:6.5.1.1]).  It is thought to constitute part of the catalytic core of ATP dependent DNA ligase.
Pfam PF04644: Motilin/ghrelin (family)
Motilin is a gastrointestinal regulatory polypeptide produced by motilin cells in the duodenal epithelium. It is released into the general circulation at about 100-min intervals during the inter-digestive state and is the most important factor in controlling the inter-digestive migrating contractions. Motilin also stimulates endogenous release of the endocrine pancreas. This family also includes ghrelin, a growth hormone secretagogue synthesised by endocrine cells in the stomach. Ghrelin stimulates growth hormone secretagogue receptors in the pituitary. These receptors are distinct from the growth hormone-releasing hormone receptors, and thus provide a means of controlling pituitary growth hormone release by the gastrointestinal system.
Wikipedia: Motilin is a 22-amino acid polypeptide hormone in the motilin family that, in humans, is encoded by the MLN gene.
Pfam PF25087: GMPPB C-terminal domain (repeat)
This entry represents the C-terminal domain of GMPPB (Mannose-1-phosphate guanylyltransferase catalytic subunit beta), which consists of a left-handed parallel beta-helix composed of tandem repeats of a [LIV]-G-X(4) hexapeptide. This protein catalyses the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids. In S. pombe, it is required for proper septum structure and is involved cell cycle progression through cell-size checkpoint. In budding yeasts Mgp1 (also known as Psa1) plays an important part in maintenance of cell-wall integrity.
Pfam PF01259: SAICAR synthetase (domain)
Phosphoribosylaminoimidazole-succinocarboxamide synthase ([ec:6.3.2.6]) (SAICAR synthetase) catalyses the seventh step in the  de novo purine biosynthetic pathway; the ATP-dependent conversion of  5'-phosphoribosyl-5-aminoimidazole-4-carboxylic acid and aspartic  acid to SAICAR. This domain can be found in SAICAR synthetases as a monofunctional protein from the bacteria (purC), fungi (ADE1) and plants (Pur7). In animals, this domain can be found in the N-terminal domain of a multifunctional enzyme (ADE2) possessing both the SAICAR synthetase and the phosphoribosylaminoimidazole carboxylase (AIR carboxylase) activity.
Wikipedia: In molecular biology, the protein domain SAICAR synthase is an enzyme which catalyses a reaction to create SAICAR. In enzymology, this enzyme is also known as phosphoribosylaminoimidazolesuccinocarboxamide synthase. It is an enzyme that catalyzes the chemical reactionATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate  ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate
Pfam PF22583: UPF0425 C-terminal domain (domain)
This entry represents the C-terminal domain of UPF0425 pyridoxal phosphate-dependent protein MJ0158 from Methanocaldococcus jannaschii and similar archaeal sequences.
Pfam PF18360: Heterogeneous nuclear ribonucleoprotein Q acidic domain (domain)
This is an acidic sequence segment domain found in the splicing factor SYNCRIP (hnRNP Q) which is involved in viral replication, neural morphogenesis, modulation of circadian oscillation and the regulation of the cytidine deaminase APOBEC1. This domain is a self-folding globular domain with an all alpha-helix architecture with negatively charged surface areas. Additionally it contains a large hydrophobic cavity and a positively charged surface area as potential epitopes for inter-molecular interactions.
Pfam PF10893: Bacteriophage 186, Fil (family)
This family is represented by Bacteriophage 186, Fil, a protein that causes filamentation. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Pfam PF07529: HSA domain (family)
This domain is predicted to bind DNA and is often found associated with helicases. This region does not form a compact domain in the known structures.
Pfam PF18509: Magnetochrome domain (domain)
Magnetotactic bacteria (MTB) align along the Earth's magnetic field using an organelle called the magnetosome. The magnetosome-associated protein MamP is conserved in all MTB and has a PDZ domain, a small c-type cytochrome domain (the first magnetochrome domain, MCR1), a 17-residue linker and a second magnetochrome domain (MCR2). This entry describes the two tandem magnetochrome domains carrying c-type cytochrome motifs CX2CH.
Pfam PF05177: RCSD region (disordered)
Proteins contain this region include C.elegans UNC-89. This region is found repeated in UNC-89 and shows conservation in prolines, lysines and glutamic acids. Proteins with RCSD are involved in muscle M-line assembly, but the function of this region RCSD is not clear.
Pfam PF00004: ATPase family associated with various cellular activities (AAA) (domain)
AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF12065: Protein of unknown function (DUF3545) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 60 to 77 amino acids in length. This protein has two completely conserved residues (R and L) that may be functionally important.
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 PF18232: Chalcone isomerase N-terminal domain (domain)
This is the N-terminal domain of chalcone isomerase present in Eubacterium ramulus. Chalcone isomerase is involved in the degradation pathway of flavone naringenin.
Pfam PF10857: Protein of unknown function (DUF2701) (family)
This viral 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 PF06360: Euplotes raikovi mating pheromone (family)
This family consists of several Euplotes raikovi mating pheromone proteins. Diffusible polypeptide pheromones, which distinguish otherwise morphologically identical vegetative cell types from one another, are produced by some species of ciliates. In the marine sand-dwelling protozoan ciliate Euplotes raikovi, pheromone molecules promote the vegetative reproduction (mitogenic proliferation or growth) of the same cells from which they originate. As, understandably, such autocrine pheromone activity is primary to that of targeting and inducing a foreign cell to mate (paracrine functions), this finding provides an example of how the original function of a molecule can be obscured during evolution by the acquisition of a new one.
Pfam PF16952: Glutamine synthetase N-terminal domain (domain)
Glutamine synthetase (6.3.1.2) (GS)  plays an essential role in the metabolism of nitrogen by catalysing the condensation of glutamate and ammonia to form glutamine. This entry represents the glutamine synthetase N-terminal domain, which adopts a Î²-grasp fold  and contributes to the substrate binding pocket of the enzyme .
Pfam PF21274: Aromatic-ring hydroxylase, C-terminal (domain)
This is a thioredoxin-like domain found at the C-terminal of aromatic-ring hydroxylases, such as PgaE from Bacillus subtilis and Rifampicin monooxygenase from Streptomyces venezuelae. The function of this domain is not clear. It may be involved in folding and stability as it lacks the catalytic cysteine residues of thioredoxin, therefore, is not likely to have a redox function.
Pfam PF07005: Sugar-binding N-terminal domain (domain)
This is the N-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK).
Pfam PF03580: Herpesvirus UL14-like protein (family)
This is a family of Herpesvirus proteins including UL14. UL14 protein is a minor component of the virion tegument and is expressed late in infection. UL14 protein can influence the intracellular localisation patterns of a number of proteins belonging to the capsid or the DNA encapsidation machinery.
Pfam PF14581: SseB protein C-terminal domain (domain)
This family consists of several SseB proteins which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon.  This presumed domain is found at the C-terminus of SseB proteins.
Pfam PF04206: Tetrahydromethanopterin S-methyltransferase, subunit E (family)
The N5-methyltetrahydromethanopterin: coenzyme M ([ec:2.1.1.86]) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump.
Pfam PF10872: Protein of unknown function (DUF2740) (family)
This family of proteins with unknown function has a highly conserved sequence.
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 PF08433: Chromatin associated protein KTI12 (domain)
This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II.  The Elongator complex has histone acetyltransferase activity.
Pfam PF09172: Vitellinogen, open beta-sheet (domain)
This entry represents the open beta-sheet domain found in vitellinogen, which generally corresponds to a domain within the lipovitellin-1 peptide product. This domain adopts  a structure consisting of several large open beta-sheets.
Wikipedia: Vitellogenin is a precursor of egg yolk that transports protein and some lipid from the liver through the blood to the growing oocytes where it becomes part of the yolk. Normally, it is only found in the blood or hemolymph of females, and can therefore be used as a biomarker in vertebrates of exposure to environmental estrogens which stimulate elevated levels in males as well as females. "Vitellogenin" is a synonymous term for the gene and the expressed protein. The protein product is classified as a glycolipoprotein, having properties of a sugar, fat and protein. It belongs to a family of several lipid transport proteins.
Pfam PF23359: Lsr2 DNA-binding domain (domain)
Lsr2 is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression. This entry represents the DNA-binding domain found at the C-terminal, which binds AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates. This domain is also found in protein Ku from Mycobacterium phage Omega.
Pfam PF23516: YthB (family)
This protein family includes Protein YthB from Escherichia coli, a 32-residues micropeptide encoded by a small open reading frame (smORF) found antisense to nanS. Proteins 50 or fewer residues -long have been shown to regulate the functions of larger proteins in a variety of organisms.
Pfam PF22431: COG2p C-terminal (domain)
This entry represents the C-terminal region of COG2 from yeast, a component of the peripheral membrane COG complex involved in intra-Golgi protein trafficking. This domain adopts a six-helix bundle that seems to play an important structural role in the COG complex.
Pfam PF24435: NFXL1 RRM-like domain (domain)
This domain is found in NF-X1-type zinc finger protein NFXL1 from Arabidopsis thaliana and related proteins. AtNFXL1, a homologue of the human transcription repressor NF-X1, plays an important role in the trichothecene response, as well as the general defense response in Arabidopsis. This domain has a detectable sequence similarity to known RRM domains and it is predicted to adopt similar structure.
Pfam PF01951: Archease protein family (MTH1598/TM1083) (domain)
This archease family of proteins, has two SHS2 domains, with one inserted into another. It is predicted to be an enzyme. It is predicted to act as a chaperone in DNA/RNA metabolism.
Wikipedia: In molecular biology, the archease' superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing and therefore been predicted to be modulators or chaperones involved in DNA or RNA metabolism. Many of the roles of archeases remain to be established experimentally.
Pfam PF06827: Zinc finger found in FPG and IleRS (domain)
This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase [ec:3.2.2.23].
Wikipedia: The FPG IleRS zinc finger domain represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger.
Pfam PF00303: Thymidylate synthase (domain)
This is a family of proteins that are flavin-dependent thymidylate synthases.
Wikipedia: Thymidylate synthase (TS) is an enzyme that catalyzes the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP). Thymidine is one of the nucleotides in DNA. With inhibition of TS, an imbalance of deoxynucleotides and increased levels of dUMP arise. Both cause DNA damage.
Pfam PF09560: Sporulation protein YunB (Spo_YunB) (family)
Spo_YunB is the sporulation protein YunB. In Bacillus subtilis its expression is controlled by sigmaE.The gene YunB seems to code for a protein involved, at least indirectly, in the pathway leading to the activation of sigmaK. Inactivation of YunB delays sigmaK activation and results in reduced sporulation efficiency.
Pfam PF17725: YAP binding domain (domain)
TEA domain transcription factors contain an N-terminal TEA domain [pfam:PF01285] and a C-terminal YAP binding domain (YBD). This entry corresponds to the YBD that binds to the oncoproteins YAP and TAZ. The structure of the YBD shows that it has an Ig-like beta sandwich fold.
Pfam PF10102: Domain of unknown function (DUF2341) (family)
Members of this family are found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins. The exact function of this set of domains has not, as yet, been determined.
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 PF09554: HaeII restriction endonuclease (family)
This family includes the HaeII (recognises and cleaves RGCGC^Y) restriction endonuclease.
Pfam PF21454: Major structural protein 1, jelly-roll domain (domain)
This entry represents a beta barrel domain found towards the N-terminal of phage Tuc2009 receptor binding protein (RBP) which forms the head domain, involved in carbohydrate recognition.
Pfam PF01026: TatD related DNase (domain)
This family of proteins are related to a large superfamily of metalloenzymes.  TatD,  a member of this family has been shown experimentally to be a DNase enzyme.
Pfam PF13130: Domain of unknown function (DUF3952) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length. There is a conserved VMSAS sequence motif.
Pfam PF05775: Enterobacteria AfaD invasin protein (family)
This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface.  AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells.
Pfam PF13847: Methyltransferase domain (domain)
This family appears to have methyltransferase activity.
Pfam PF03478: KIB1-4 beta-propeller (repeat)
This entry represents the beta-propeller domain found in F-box proteins KIB1-4, from Arabidopsis thaliana, and similar plant proteins. This domain adopts a beta-propeller structure with 6 blades and is often found in association with F-box domain ([pfam:PF00646]). KIB1-4 are ubiquitin ligases that act as essential positive regulators in brassinosteroid signalling, mediating the ubiquitination, substrate interaction and degradation of GSK3 kinase BIN2.
Pfam PF24739: Domain of unknown function (DUF7690) (domain)
This entry represents a domain found in uncharacterised bacterial proteins. It is found N-terminal to [pfam:PF24736]. This domain is predicted to adopt a globular structure composed of four alpha- helices.
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 PF23691: YmgL-like (family)
This protein family includes Protein YmgL from Escherichia coli, a 36-residues long sequence predicted to adopt an alpha-helical configuration.
Pfam PF17768: RecJ OB domain (domain)
This OB-fold is found in RecJ proteins where is binds to ssDNA.
Pfam PF23553: NELF-A N-terminal domain (repeat)
The N-terminal domain of the NELF-A protein forms a novel helical fold, comprising five alpha-helices (residues 6-110). This domain shows structural similarity to the HIV integrase-binding domain present in the human PSIP1 protein. The N-terminal domain is highly conserved among metazoans and is crucial for NELF-A's interaction with the NELF-C subunit, forming a stable heterodimer interface. Two invariant tryptophan residues (W24 and W89) in this domain insert into hydrophobic pockets on NELF-C, mediating this interaction. NELF-A is a subunit of the Negative Elongation Factor (NELF) complex, which plays a key role in regulating transcription elongation by RNA Polymerase II. The NELF complex induces promoter-proximal pausing of Pol II, a rate-limiting step in transcription regulation that allows integration of additional signals before productive elongation.
Pfam PF23160: Periplakin spectrin-like repeat (domain)
This spectrin-like repeat is found N-terminal in human Periplakin and related proteins including Envoplakin-like protein. Periplakin is a component of the cornified envelope of keratinocytes. It coimmunoprecipitates with Envoplakin and both proteins form a network radiating from desmosomes. These two proteins probably provide a scaffolding onto which the cornified envelope is assembled. Envoplakin and periplakin are the two proteins that are most commonly targeted by pathogenic autoantibodies.
Pfam PF09630: Domain of unknown function (DUF2024) (domain)
This protein of 86 residues is expressed in bacteria.  It consists of four alpha helices and two beta strands. Its function is unknown. One UniProt entry gives the gene name as Traf5.
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 PF16885: Voltage-gated calcium channel subunit alpha, C-term (family)
CAC1F_C is the C-terminal region of voltage-gated calcium channel subunit alpha in higher eukaryotes. The exact function of this domain is not known.This region lies immediately downstream from the CDB motif, [pfam:PF08673].
Pfam PF06443: SEF14-like adhesin (family)
Family of enterotoxigenic bacterial adhesins.
Pfam PF20809: Msx2-interacting protein, MID domain (domain)
This is the Msx2-interacting domain (MID) found in Msx2-interacting protein (MINT), a widely expressed transcription repressor that regulates key transcription effectors in several signalling pathways, including MSX2, RBP-J, and nuclear receptors. This domain provides core activation functions to MINT; it confers OCFRE (osteocalcin (OC) FGF response element) activation. This domain partially overlaps the nuclear receptor-interacting domain (RID).