SII-SWORD/CoKE huggingface dataset:
Pfam PF00326: Prolyl oligopeptidase family (domain)
This domain covers the active site serine of the serine peptidases belonging to MEROPS peptidase family S9 (prolyl oligopeptidase family, clan SC). The protein fold of the peptidase domain for members of this family resembles that of serine carboxypeptidase D, the type example of clan SC. Examples of protein families containing this domain are:


 * Prolyl endopeptidase (3.4.21.26) (PE) (also called post-proline cleaving enzyme). PE is an enzyme that cleaves peptide bonds on the C-terminal side of prolyl residues. The sequence of PE has been obtained from a mammalian species (pig) and from bacteria (Flavobacterium meningosepticum and Aeromonas hydrophila); there is a high degree of sequence conservation between these sequences.
 * Escherichia coli protease II (3.4.21.83) (oligopeptidase B) (gene prtB) which cleaves peptide bonds on the C-terminal side of lysyl and argininyl residues.
 * Dipeptidyl peptidase IV (3.4.14.5) (DPP IV). DPP IV is an enzyme that removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline.
 * Saccharomyces cerevisiae (Baker's yeast) vacuolar dipeptidyl aminopeptidases A and B (DPAP A and DPAP B), encoded by the STE13 and DAP2 genes respectively. DPAP A is responsible for the proteolytic maturation of the alpha-factor precursor.
 * Acylamino-acid-releasing enzyme (3.4.19.1) (acyl-peptide hydrolase). This enzyme catalyses the hydrolysis of the amino-terminal peptide bond of an N-acetylated protein to generate a N-acetylated amino acid and a protein with a free amino-terminus.


These proteins belong to MEROPS peptidase families S9A, S9B and S9C.
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .
Pfam PF21801: Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain (domain)
This domain is found at the N-terminal end of human Apoptosis -stimulating of p53 protein 2 (ASPP2) and similar sequences mainly from vertebrates. ASPP2 plays a central role in regulation of apoptosis and cell growth via its interactions with proteins such as TP53. This domain shows a mixed twisted beta-sheet and alpha -helices that pack on one side of the beta-sheet, with similarity to a Ras-association (RA) domain.
Pfam PF11043: Bacteriophage P22, anti-RecBCD protein 2 (family)
This phage protein modulates the activity of the host recBCD nuclease promoting phage growth and recombination, and protects the linear double stranded DNA from exonuclease degradation.
Pfam PF19310: Neurolysin/Thimet oligopeptidase, N-terminal domain (domain)
Thimet oligopeptidase and neurolysin are closely related zinc-dependent metallopeptidases that metabolize small bioactive peptides. They cleave many substrates at the same sites, but they recognise different positions on others. This entry represents the up-down alpha bundle domain found at the N terminus of these and related M3 peptidases.
Pfam PF03351: DOMON domain (domain)
The DOMON (named after dopamine beta-monooxygenase N-terminal) domain is 110-125 residues long. It is predicted to form an all beta fold with up to 11 strands and is secreted to the extracellular compartment. The beta-strand folding produces a hydrophobic pocket which appears to bind soluble haem. This is consistent with the predominant architectures where the protein is associated with cytochromes or enzymatic domains whose activity involves redox or electron transfer reactions potentially as a direct participant in the electron transfer process. The DOMON domain superfamily, of which this is just one member, shows (1) multiple hydrophobic residues that contribute to the hydrophobic core of the strands of the beta-sandwich, and small residues found at the boundaries of strands and loops, (2) a strongly conserved charged residue (usually arginine/lysine) at the end of strand 9, which possibly stabilises the loop between 9 and 10, and (3) a polar residue (usually histidine, lysine or arginine), that interacts or coordinates with ligands. The suggested superfamily includes both haem- and sugar-binding members: the haem-binding families being the ethyl-Benzoate dehydrogenase family EB_dh, [pfam:PF09459], the cellobiose dehydrogenase family CBDH and this family, and the sugar-binding families being the xylanases, CBM_4_9, [pfam:PF02018]. The common feature of the superfamily is the 11-beta-strand structure, although the first and eleventh strands are not well conserved either within families or between families.
Pfam PF17049: ATPase expression protein 1 (family)
ATPase expression protein 1 (AEP1) is a yeast mitochondrial protein. It is essential for the expression of subunit 9 of mitochondrial ATP synthase.
Pfam PF17707: Family of unknown function (DUF5553) (family)
This is a family of unknown function found in primates.
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 PF08542: Replication factor C C-terminal domain (domain)
This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA).  The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A.
Pfam PF03082: Male accessory gland secretory protein (family)
The accessory gland of male insects is a genital tissue that secretes many components of the ejaculatory fluid, some of which affect the female's receptivity to courtship and her rate of oviposition.  This protein is expressed exclusively in the male accessory glands of adult Drosophila melanogaster. The proteins are transferred to the female fly during copulation and are rapidly altered in the female genital tract.
Pfam PF08283: Geminivirus rep protein central domain (domain)
This is the cetral domain of the geminivirus rep proteins.
Pfam PF21291: Cyanate hydratase, N-terminal (domain)
Cyanate hydratase (also known as cyanate lyase)  catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate. It consists of an N-terminal five-helix bundle domain that shows structural similarity to DNA-binding HTH domains and a C-terminal catalytic domain, which has a unique fold.
Pfam PF15657: HNH/Endo VII superfamily nuclease toxins (family)
A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteristic conserved [ED]H motif and two histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion system.
Pfam PF11031: Bacteriophage T holin (family)
Bacteriophage effects host lysis with T holin along with an endolysin. T disrupts the membrane allowing sequential events which lead to the attack of the peptidoglycan. T has an usual periplasmic domain which transduces environmental information for the real-time control of lysis timing.
Pfam PF16373: Domain of unknown function (family)
This family around 100 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides, Prevotella and Prevotella species. The function of this family remains unknown.
Pfam PF17054: Microtubule-Associated protein Jupiter (family)
Is a microtubule-associated protein that binds to all microtubule populations in Drosophila.
Pfam PF24464: F54D1.6, Ig-like domain (domain)
This is an immunoglobulin-like domain of the uncharacterised protein F54D1.6 from Caenorhabditis elegans and similar animal sequences. It is often found associated to [pfam:PF06119] and [pfam:PF24462].
Pfam PF10090: Histidine phosphotransferase C-terminal domain (domain)
HPTransfase is a family of essential histidine phosphotransferases. It controls the activity of the master bacterial cell-cycle regulator CtrA through phosphorylation.  It behaves as a homodimer by adopting the domain architecture of the intracellular part of class I histidine kinases. Each subunit consists of two distinct domains: an N-terminal helical hairpin domain and a C-terminal [alpha]/[beta] domain. The two N-terminal domains are adjacent within the dimer, forming a four-helix bundle. The C-terminal domain adopts an atypical Bergerat ATP-binding fold.
Wikipedia: Histidine phosphotransfer domains and histidine phosphotransferases are protein domains involved in the "phosphorelay" form of two-component regulatory systems. These proteins possess a phosphorylatable histidine residue and are responsible for transferring a phosphoryl group from an aspartate residue on an intermediate "receiver" domain, typically part of a hybrid histidine kinase, to an aspartate on a final response regulator.
Pfam PF14850: DNA-binding domain of Proline dehydrogenase (domain)
This domain lies at the N-terminus of bifunctional proline-dehydrogenases and is found to bind DNA.
Pfam PF23688: YlcJ-like (family)
This protein family includes Protein YlcJ from Escherichia coli, a 49-residues long sequence predicted to adopt an alpha-helical configuration.
Pfam PF17756: RET Cadherin like domain 1 (domain)
RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that RET contains four consecutive cadherin-like domains (CLD). This entry relates to the first CLD at the N-terminal. Several regions within RET-CLD1 have been shown to be important for ligand-coreceptor binding. CLD1 and CLD2 have a distinctive clamshell shape and CLD1 is essential for CLD2 folding. CLD1 contains 2 sites for GDNF receptor alpha 1 binding.
Pfam PF24697: Domain of unknown function (DUF7661) (domain)
This entry represents a family of small uncharacterised bacterial proteins that adopts a compact domain composed of 5 beta strands and a single alpha helix.
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 PF09973: Predicted membrane protein (DUF2208) (family)
This domain, found in various hypothetical archaeal 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 PF19535: Family of unknown function (DUF6060) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001035) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide),  polyketide and other (Aminocoumarin). This family includes a  protein from the pneumocandin B0 biosynthetic gene cluster from Glarea lozoyensis ATCC 20868 and appear to be predominantly found in fungi.
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 PF10721: Protein of unknown function (DUF2514) (domain)
This family is conserved in bacteria and some viruses. The function is not known.
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 PF23613: ELP3 N-terminal domain (domain)
This domain is found N-terminal in the human Elongator complex protein 3 (ELP3) and related proteins. This protein is required for multiple modifications of tRNA. In the elongation complex, it acts as a tRNA uridine(34) acetyltransferase. It may also act as a lysine acetyltransferase by mediating acetylation of target proteins. The domain represented by this entry is predicted to fold into a globular structure consisting of two nearly orthogonal alpha-helical hairpins.
Pfam PF24965: TRS130-like four helical bundle domain (domain)
This entry represents a domain related to the four helical bundle domain found in the Trafficking protein particle complex II-specific subunit 130 (TRS130). In TRS130, this domain is inserted in the third Ig-like domain and contributes to the stability of the tandemly repeated Ig-like domains via extensive interactions with them.
Pfam PF13732: Domain of unknown function (DUF4162) (family)
This domain is found at the C-terminus of bacterial ABC transporter proteins. The function is not known.
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 PF09408: Betacoronavirus spike glycoprotein S1, receptor binding (domain)
This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is  arranged in trimers on the surface of the viral membrane and is  essential for viral entry. The spike protein is translated as a  large polypeptide that is subsequently cleaved to the distal S1,  responsible for receptor binding, and the membrane-anchored S2  responsible for membrane fusion. The coronavirus (SARS-CoV)  S1 subunit is composed of two distinct domains: an N-terminal  domain (S1 NTD) and a receptor-binding domain (S1 RBD) also  referred to as the S1 CTD or domain B. Each of these domains  have been implicated in binding to host receptors. However,  most coronaviruses are not known to utilise both the S1 NTD and  S1 RBD for viral entry. SARS-CoV makes use of its S1 RBD to  bind to the human angiotensin-converting enzyme 2 (ACE2) as its  host receptor.
Pfam PF19391: Family of unknown function (DUF5966) (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 PF11428: Protein of unknown function (DUF3196) (family)
This proteins is the product of the gene MPN330 and is thought to involved in a cellular function that has yet to be characterised. The proteins has 11 helices and a novel fold. No function is currently known for this protein.
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 PF23965: Family of unknown function (DUF7293) (family)
This entry represents an uncharacterized protein of approximately 54 amino acids found in T5-like bacteriophages that infect Escherichia coli and Salmonella.  Homologs have been identified in several T5-like phages including bacteriophage T5, Salmonella phage vB_SenS_SB13, and Escherichia phage vB_EcoS-26175V. Structure prediction suggests that this protein forms a strand swapped homodimeric arrangement. The dimeric structure forms two four stranded sheets that are connected by two alpha helices. The C-terminal of each protein is donated to the sheet made by the other monomer.
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 PF24060: Domain of unknown function (DUF7361) (domain)
This entry represents a domain of unknown function found at the C-terminal of SPbeta prophage-derived uncharacterized protein YomG from Bacillus subtilis (strain 168). This domain may be found in association with a prophage endopeptidase tail domain ([pfam:PF06605]).
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 PF05681: Fumarate hydratase (Fumerase) (family)
This family consists of several bacterial fumarate hydratase proteins FumA and FumB. Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre.
Wikipedia: Fumarase is an enzyme that catalyzes the reversible hydration/dehydration of fumarate to malate. Fumarase comes in two forms: mitochondrial and cytosolic. The mitochondrial isoenzyme is involved in the Krebs cycle and the cytosolic isoenzyme is involved in the metabolism of amino acids and fumarate. Subcellular localization is established by the presence of a signal sequence on the amino terminus in the mitochondrial form, while subcellular localization in the cytosolic form is established by the absence of the signal sequence found in the mitochondrial variety.
Pfam PF05422: Stress-activated map kinase interacting protein 1 (SIN1) (family)
SIN1 is the N-terminus of stress-activated map kinase interacting protein 1 (MAPKAP1 OR SIN1) sequences. This domain is likely to be the Ras-binding domain. The fission yeast Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. Sin1 interacts with Sty1/Spc1. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent. The separate CRIM and PH, pleckstrin-homology domains of the full-length SIN1 proteins have been separated into distinct families.
Pfam PF09501: Probable sporulation protein (Bac_small_yrzI) (family)
Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, while arrays of six members in tandem are found in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number of small acid-soluble spore proteins (SASP). A role in sporulation is possible.
Pfam PF13295: Domain of unknown function (DUF4077) (family)
This is the N-terminal region of methyl-accepting chemotaxis proteins from Bacillus spp. The function is not known.
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 PF21996: Histidyl-tRNA synthetase HisZ, C-terminal domain (domain)
HisZ is composed of two domains for the catalytic reaction and for anticodon binding. In contrast to other class-II aminoacyl-tRNA synthetases it lacks the essential editing domain. The C-terminal anicodon binding domain consists of three-stranded parallel beta-sheet flanked on each side with helices.