SII-SWORD/CoKE huggingface dataset:
Pfam PF19658: Family of unknown function (DUF6161) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 206 and 231 amino acids in length. There are two conserved sequence motifs: HLA and LFSR.
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 PF04951: D-aminopeptidase (family)
Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The structure reveals that DppA is a new example of a 'self-compartmentalising protease', a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organised in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterised by the SXDXEG key sequence. The only known substrates are D-ala-D-ala and D-ala-gly-gly.
Pfam PF12527: Protein of unknown function (DUF3727) (family)
This domain family is found in bacteria and eukaryotes, and is approximately 100 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 PF24514: Prealbumin-like fold domain (domain)
This entry represents a domain found in uncharacterised bacterial proteins. Some members are likely to contain an isopeptide bond.
Pfam PF12301: CD99 antigen like protein 2 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.
Pfam PF21962: Domain of unknown function (DUF6924) (domain)
This domain of unknown function is found mainly in bacterial proteins, either standalone or in combination with other domains. It is probably remotely related to the anticodon binding domain observed in histidyl, glycyl, threonyl and prolyl tRNA synthetases.
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 PF23447: Domain of unknown function (DUF7128) (domain)
This domain is found in a group of small proteins mainly from Halobacteria. It contains highly conserved cysteine and histidine residues arranged in two CxxC and HxxC motifs that likely coordinate zinc. This domain is predicted to adopt a fold similar to the classical C2H2 and variant C2HC zinc fingers containing beta-hairpin and an alpha helix. In addition, it is predicted to contain an extra N-terminal strand that contributes to the formation of a three-stranded antiparallel beta-sheet. This domain also has a number of highly conserved negatively charged residues.
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 PF02729: Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain (domain)
This entry contains two related enzymes:
 * Aspartate carbamoyltransferase (
2.1.3.2) (ATCase) catalyzes the conversion of aspartate and carbamoyl phosphate to carbamoylaspartate, the second step in thede novo biosynthesis of pyrimidine nucleotides . In prokaryotes ATCase consists of two subunits: a catalytic chain (gene pyrB) and a regulatory chain (gene pyrI), while in eukaryotes it is a domain in a multi- functional enzyme (called URA2 in yeast, rudimentary in Drosophila, and CAD in mammals ) that also catalyzes other steps of the biosynthesis of pyrimidines.
 * Ornithine carbamoyltransferase (2.1.3.3) (OTCase) catalyzes the conversion of ornithine and carbamoyl phosphate to citrulline. In mammals this enzyme participates in the urea cycle  and is located in the mitochondrial matrix. In prokaryotes and eukaryotic microorganisms it is involved in the biosynthesis of arginine. In some bacterial species it is also involved in the degradation of arginine  (the arginine deaminase pathway).
It has been shown  that these two enzymes are evolutionary related. The predicted secondary structure of both enzymes are similar and there are some regions of sequence similarities. One of these regions includes three residues which have been shown, by crystallographic studies , to be implicated in binding the phosphoryl group of carbamoyl phosphate and may also play a role in trimerization of the molecules . The carboxyl-terminal, aspartate/ornithine-binding domain is is described by IPR006131.
Wikipedia: In molecular biology, the ATCase/OTCase family is a protein family which contains two related enzymes: aspartate carbamoyltransferase EC 2.1.3.2 and ornithine carbamoyltransferase EC 2.1.3.3. It has been shown that these enzymes are evolutionary related. The predicted secondary structure of both enzymes is similar and there are some regions of sequence similarities. One of these regions includes three residues which have been shown, by crystallographic studies to be implicated in binding the phosphoryl group of carbamoyl phosphate and may also play a role in trimerisation of the molecules. The N-terminal domain is the carbamoyl phosphate binding domain. The C-terminal domain is an aspartate/ornithine-binding domain.
Pfam PF01933: 2-phospho-L-lactate transferase CofD (family)
This entry contains 2-phospho-L-lactate transferase (CofD), phosphoenolpyruvate transferase and related sequences. CofD catalyses the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2)diphospho-(5') guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterised so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. CofD monomer contains 12 beta- strands, seven of them form a Rossmann fold, and 13 alpha-helices.
Pfam PF03555: Influenza C non-structural protein (NS2) (family)
The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment  encodes a 286 amino acid non-structural protein NS1 [pfam:PF03506] as well as the NS2 protein. The NS2 protein is only about 60 amino acids in length and of unknown function.
Pfam PF02338: OTU-like cysteine protease (family)
This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases.
Pfam PF00818: Ice nucleation protein repeat (2 copies) (repeat)
This entry represents a beta solenoid repeat found in ice nucleation proteins.
Wikipedia: Bacterial ice-nucleation proteins are a family of proteins that enable Gram-negative bacteria to promote nucleation of ice at relatively high temperatures. These proteins are localised at the outer membrane surface and can cause frost damage to many plants. The primary structure of the proteins contains a highly repetitive domain that dominates the sequence. The domain comprises a number of 48-residue repeats, which themselves contain 3 blocks of 16 residues, the first 8 of which are identical. It is thought that the repetitive domain may be responsible for aligning water molecules in the seed crystal. [.........48.residues.repeated.domain..........]
 / / | | \ \
 AGYGSTxTagxxssli AGYGSTxTagxxsxlt AGYGSTxTaqxxsxlt
 [16.residues...] [16.residues...] [16.residues...]
Pfam PF01029: NusB family (domain)
The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.
Pfam PF01794: Ferric reductase like transmembrane component (domain)
This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein [swissprot:Q04800] from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain [swissprot:P04839] is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterised by the absence of a functional plasma membrane associated NADPH oxidase.  The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease.
Wikipedia: NADPH oxidase is a membrane-bound enzyme complex that faces the extracellular space. It can be found in the plasma membrane as well as in the membranes of phagosomes used by neutrophil white blood cells to engulf microorganisms. Human isoforms of the catalytic component of the complex include NOX1, NOX2, NOX3, NOX4, NOX5, DUOX1, and DUOX2.
Pfam PF04744: Monooxygenase subunit B protein (family)
Family of membrane associated monooxygenases (EC 1.13.12.-) which utilise O(2) to oxidise their substrate.  Family members include both ammonia and methane monooxygenases involved in the oxidation of their respective substrates.  These enzymes are multi-subunit  complexes.  This family represents the B subunit of the enzyme; the A subunit is thought to contain the active site..
Pfam PF19427: Protein inscuteable C-terminal (repeat)
This entry represents the C-terminal region of protein Inscuteable (Insc) containing four putative armadillo repeats and the conserved extreme C-terminal tetrapeptide Glu-Ser-Phe-Val which is in agreement with the class I PDZ-binding motif X-Ser/Thr-X-/ (X and /are unspecified and hydrophobic residues, respectively). Insc functions as an adaptor protein that binds simultaneously with Partner of Insc (Pins, consisting of alpha subunit (Ga) of heterotrimeric G proteins and its guanine nucleotide dissociation inhibitor) and Par3 (PDZ-containing proteins) to regulate their apical localisation in neuroblasts, which is required for the correct execution of the asymmetric division.
Pfam PF07491: Protein phosphatase inhibitor (family)
These proteins include Ypi1,  ([swissprot:P43587]), a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor and ppp1r11/hcgv ([swissprot:O60927]), annotated as having protein phosphatase inhibitor activity.
Pfam PF22241: PSMD12/CSN4, N-terminal (repeat)
The 26S proteasome consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The RP can be further divided into two subcomplexes, a base and a peripheral lid. The RP lid is structurally similar to the COP9 signalosome (CSN). The core CSN subunits (CSN4/5/7/6) show a remarkable one-to-one sequence correspondence with those of the RP lid (RPN5/11/9/8), suggesting a common ancestry and architecture. This entry represents the N-terminal region of PSMD12/RPN5) and CSN4 subunits, which consists of helical repeats.
Pfam PF00095: WAP-type (Whey Acidic Protein) 'four-disulfide core' (domain)
WAP belongs to the group of Elafin or elastase-specific inhibitors.
Wikipedia: In molecular biology, the Whey acidic proteins (WAP) have been identified as a major whey protein family in milk, and are important in regulating the proliferation of mammary epithelial cells. Additionally, their physiological function is thought to be similar to a protease inhibitor. It has been concluded, therefore, that WAP regulate the proliferation of mammary epithelial cells by preventing elastase-type serine proteases from carrying out laminin degradation and by suppressing the MAP kinase signal pathway in the cell cycle.
Pfam PF17916: LIM interaction domain (LID) (domain)
LIM-homeodomain (LIM-HD) proteins are transcription factors that are critical in the development of many cell types and tissues. The activity of LIM-HD proteins is dependent on the essential cofactor LIM domain-binding protein 1 (Ldb1). This entry represents a 30-residue LIM interaction domain (LID) that binds to the LIM domains of all LIM-HD and closely related LIM-only (LMO) proteins. Isl1 (Insulin gene enhancer protein 1) and Isl2 each contain a LID-like sequence in their C-terminal regions, the Lhx3-binding domain (LBD), which binds the LIM domains Lhx3 and Lhx4.
Pfam PF13902: R3H-associated N-terminal domain (domain)
This family is found at the N-terminus of R3H, [pfam:PF01424], domain-containing proteins.  The function is not known.
Pfam PF08202: Mis12-Mtw1 protein family (family)
Mis12-Mtw1 is a eukaryotic conserved kinetochore protein that is involved in chromosome segregation.
Pfam PF12296: Hydrophobic surface binding protein A (family)
This protein is found in eukaryotes. Proteins in this family are typically between 171 to 275 amino acids in length. Although the HsbA amino acid sequence suggests that HsbA may be hydrophilic, HsbA adsorbed to hydrophobic PBSA (Polybutylene succinate-co-adipate) surfaces in the presence of NaCl or CaCl2. When HsbA was adsorbed on the hydrophobic PBSA surfaces, it promoted PBSA degradation via the CutL1 polyesterase. CutL1 interacts directly with HsbA attached to the hydrophobic QCM electrode surface. These results suggest that when HsbA is adsorbed onto the PBSA surface, it recruits CutL1, and that when CutL1 is accumulated on the PBSA surface, it stimulates PBSA degradation.
Pfam PF20482: Family of unknown function (DUF6722) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 65 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 PF21861: Replication protein RepB, C-terminal (domain)
This entry represents the C-terminal oligomerisation domain (OD) of plasmid replication proteins, such as RepB. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence. They consist of a N-terminal origin binding domain (OBD, [pfam:PF01719]) which is the DNA-binding/catalytic domain that belongs to the HUH endonuclease superfamily and this C-terminal helical domain, which is responsible for the hexameric state of the protein [].
Pfam PF04879: Molybdopterin oxidoreductase Fe4S4 domain (domain)
This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface.
Pfam PF13199: Glycosyl hydrolase family 66 (domain)
This family is a set of glycosyl hydrolase enzymes including cycloisomaltooligosaccharide glucanotransferase ([ec:2.4.1.-]) and dextranase ([ec:3.2.1.11]) activities.
Wikipedia: In molecular biology, glycoside hydrolase family 66 is a family of glycoside hydrolases.
Pfam PF08674: Acetylcholinesterase tetramerisation domain (domain)
The acetylcholinesterase tetramerisation domain is found at the C terminus and forms a left handed superhelix.
Pfam PF09253: Pollen allergen Ole e 6 (domain)
Members of this family consist of two nearly antiparallel alpha-helices, that are connected by a short loop and followed by a long, unstructured C-terminal tail. They are highly allergenic, primarily mediating olive allergy.
Pfam PF16172: DOCK N-terminus (family)
This family is found near to the N-terminus of dedicator of cytokinesis (DOCK) proteins, between the variant SH3 domain ([pfam:PF07653]) and the C2 domain ([pfam:PF14429]).
Pfam PF03980: Nnf1 (family)
NNF1 is an essential yeast gene that is necessary for chromosome segregation.  It is associated with the spindle poles and forms  part of a kinetochore subcomplex called MIND.
Pfam PF24862: Sucrose synthase EPBD domain (domain)
This entry represents the EPBD domain (ENOD40 peptide binding domain, also referred to as SSN2) of sucrose synthases, which corresponds to the second domain and together with the N-terminal one, referred to as the cellular targeting domain (CTD) have regulatory functions in plant species, however, the function of these domains in bacteria is not yet clear. Sucrose synthases are sucrose-cleaving enzymes that provides UDP-glucose and fructose for various metabolic pathways.
Pfam PF11682: Probable zinc-ribbon (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. It is a probably zinc-ribbon.
Pfam PF04230: Polysaccharide pyruvyl transferase (family)
Pyruvyl-transferases involved in peptidoglycan-associated polymer  biosynthesis.  CsaB in Bacillus anthracis is necessary for the non-covalent anchoring of proteins containing an SLH (S-layer homology) domain to peptidoglycan-associated pyruvylated polysaccharides.  WcaK and AmsJ are involved in the biosynthesis of colanic acid in Escherichia coli and of amylovoran in Erwinia amylovora.
Pfam PF05592: Bacterial alpha-L-rhamnosidase concanavalin-like domain (domain)
This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria.
Wikipedia: In molecular biology, glycoside hydrolase family 78 is a family of glycoside hydrolases.
Pfam PF15195: TMEM210 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between and 149 amino acids in length. The function of this family is unknown.
Pfam PF18249: Calcium binding protein SSO6904 (domain)
This domain is SSO6904 present in Sulfolobus solfataricus. SSO6904 is a calcium binding protein thought to have a weak affinity for other cations such as Mg2+ and Zn2+. The structure of SSO6904 is similar to that of saposin-fold proteins. Saposin proteins are membrane-interacting glycoproteins required for the hydrolysis of certain sphingolipids by specific lysosomal hydrolases.
Pfam PF19137: Family of unknown function (DUF5820) (family)
This is a family of unknown function predominantly found in Halobacteria.
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 PF21460: GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal (domain)
GM-CSF/IL-3/IL-5 receptor common beta subunit (IL3RB) is a cell surface receptor that plays a role in immune response and controls the production and differentiation of haematopoietic progenitor cells into lineage-restricted cells. It participates in the signaling pathways of interleukin-3, interleukin-5 and granulocyte-macrophage colony-stimulating factor/CSF2 which have overlapping activities on haematopoietic cells and have been implicated in the pathogenesis of allergic diseases of the lung. IL3RB consists of four extracellular domains with an Ig-like fold. This entry represents the first domain.
Pfam PF15490: Telomere-capping, CST complex subunit (domain)
Ten1_2 is a family of primarily plant and vertebrate telomere-capping proteins that is evolutionarily related to the mostly fungal family of Ten1, [pfam:PF12658].
Pfam PF01963: TraB/PrgY/gumN family (family)
This entry includes Tiki1/2 from humans, TraB/PrgY from the gut flora Enterococcusfaecalis and gumN from the plant pathogen Xanthomonas. Tiki1 is homologous to TraB/PrgY. They have a pair of widely spaced GX2H motifs and a conserved glutamate. From the structural study, this group of proteins have been identified as an ancient metalloprotease clan with a common protein architecture (cobbled from the folds of the EreA/ChaN/PMT group) that mediates proteolytic activities. Tiki1 is a membrane-associated protease that inhibits Wnt via the cleavage of its amino terminus, diminishing Wnt's binding to receptors. TraB/PrgY is an inhibitor peptide that may act as a protease to inactivate the mating pheromone.
Pfam PF21427: Baseplate wedge protein gp7, domain V (domain)
This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents Domain V, which is an insertion into domain IV and consists of an eight-stranded beta- barrel followed by two short alpha-helices.
Pfam PF04473: Transglutaminase-like domain (domain)
This family of uncharacterised archaeal proteins are related to Transglutaminase-like domains. This family has previously been called DUF553 and UPF0252.
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.