SII-SWORD/CoKE huggingface dataset:
Pfam PF02126: Phosphotriesterase family (domain)
Bacteria such as Brevundimonas diminuta (Pseudomonas diminuta) harbour a plasmid that carries the gene for phosphotriesterase (PTE also known as parathion hydrolase; 3.1.8.1). This enzyme has attracted interest because of its potential use in the detoxification of chemical waste and organophosphate warfare agents such as VX, soman, and sarin, and its ability to degrade agricultural pesticides such as parathion. It acts specifically on synthetic organophosphate triesters and phosphorofluoridates. It does not seem to have a naturally occurring substrate and may thus have optimally evolved for utilising paraoxon.

PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal centre, at the C-terminal end of a TIM Î±-Î² barrel motif. The native enzyme contains two zinc ions at the active site however these can be replaced with other metals such as cobalt, cadmium, nickel or manganese and the enzyme remains active .

PTE belongs to a family  of enzymes that possess a binuclear zinc metal centre at their active site. The two zinc ions are coordinated by six different residues, six of which being histidines. This family so far includes, in addition to the parathion hydrolase, the following proteins:


 * Sulfolobus solfataricus aryldialkylphosphatase that has a low paraoxonase activity .
 * E. coli php (phosphotriesterase homology) protein. The substrate of php is not yet known .
 * Mycobacterium tuberculosis phosphotriesterase homology protein Rv0230C.
 * Phospho-furanose lactonase from Mycoplasma .
 * Animal phosphotriesterase related protein (PTER) (RPR-1).
Wikipedia: Aryldialkylphosphatase is a metalloenzyme that hydrolyzes the triester linkage found in organophosphate insecticides:
Pfam PF05524: PEP-utilising enzyme, N-terminal (family)
This sequence identifies proteins which are a component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), a major carbohydrate active transport system. The PTS system is found throughout the bacterial kingdom, and is responsible for the coupled phosphorylation and translocation of numerous sugars across the cytoplasmic membrane . This entry represents the N-terminal domain of enzyme I (EIN) which transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) which in turn phosphorylates a group of membrane-associated proteins, known as enzyme II. The N-terminal domain of EI (EIN) extends from residues 1 to 259 and can be phosphorylated in a fully reversible manner by phosphorylated HPr. EIN, however, cannot be autophosphorylated by PEP .
Pfam PF16412: Domain of unknown function (DUF5020) (family)
This family of proteins is functionally uncharacterised. This family is found in various Bacteroides species. Proteins in this family are around 235 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 PF08350: Methanogenesis regulatory protein FilR1, middle domain (family)
This archaeal domain of unknown function has been found at the middle of Methanogenesis regulatory protein FilR1 and at the C-terminus of archaeal proteins, including several transcriptional regulators of the ArsR family (see [pfam:PF01022]). FilR1 is a member of the two-component regulatory system FilI/FilRs which is involved in the regulation of methanogenesis.
Pfam PF12366: Cancer susceptibility candidate 1 C-terminal (domain)
This is the C-terminal domain of Cancer susceptibility candidate 1  (Casc1) which has many SNPs associated with cancer susceptibility.
Pfam PF10117: McrBC 5-methylcytosine restriction system component (family)
Members of this family of bacterial proteins modify the specificity of mcrB restriction by expanding the range of modified sequences restricted.
Pfam PF18030: RimK PreATP-grasp domain (domain)
This is the N-terminal domain found in Escherichia coli RimK proteins (Ribosomal protein S6-L-glutamate ligase). This domain precedes the ATP-grasp domain [pfam:PF08443].
Pfam PF13124: Protein of unknown function (DUF3963) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 85 amino acids in length. There is a conserved DIQKW sequence motif.
Pfam PF01205: Uncharacterized protein family UPF0029 (family)
The Impact protein is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea .
This entry represents the N-terminal domain of the Impact proteins.
Pfam PF19692: Family of unknown function (DUF6193) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000087) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the lasalocid biosynthetic gene cluster from Streptomyces  lasaliensis. This family appears to be predominantly found in Actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00860: Permease family (family)
This family includes permeases for diverse substrates such as xanthine [swissprot:P42086], uracil [swissprot:P39766] and vitamin C [swissprot:Q9UGH3].  However many members of this family are functionally uncharacterised and may transport other substrates. Members of this family have ten predicted transmembrane helices.
Wikipedia: The Nucleobase cation symporter-2 (NCS2) family, also called the Nucleobase ascorbate transporter (NAT) family, consists of over 1000 sequenced proteins derived from gram-negative and gram-positive bacteria, archaea, fungi, plants and animals. The NCS2/NAT family is a member of the APC Superfamily of secondary carriers. Of the five known families of transporters that act on nucleobases, NCS2/NAT is the only one that is most widespread. Many functionally characterized members are specific for nucleobases including both purines and pyrimidines, but others are purine-specific. However, two closely related rat/human members of the family, SVCT1 and SVCT2, localized to different tissues of the body, co-transport L-ascorbate (vitamin C) and Na+ with a high degree of specificity and high affinity for the vitamin. Clustering of NCS2/NAT family members on the phylogenetic tree is complex, with bacterial proteins and eukaryotic proteins each falling into at least three distinct clusters. The plant and animal proteins cluster loosely together, but the fungal proteins branch from one of the three bacterial clusters forming a tighter grouping. E. coli possesses four distantly related paralogous members of the NCS2 family.
Pfam PF16595: PAM-interacting domain of CRISPR-associated endonuclease Cas9 (domain)
Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315.  Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively.
Pfam PF11837: Beta-fructofuranosidase, N-terminal domain (family)
This entry represents the N-terminal domain of beta-fructofuranosidase, which is involved in the hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides.
Pfam PF19827: Family of unknown function (DUF6308) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000699) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the hygromycin A biosynthetic gene cluster from Streptomyces hygroscopicus subsp. hygroscopicus. This family appears to be predominantly found in Actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10512: Cell division cycle-associated protein 8 (family)
The chromosomal passenger complex of Aurora B kinase, INCENP, and Survivin has essential regulatory roles at centromeres and the central spindle in mitosis. Borealin is also a member of the complex. Approximately half of Aurora B in mitotic cells is complexed with INCENP, Borealin, and Survivin. Depletion of Borealin by RNA interference delays mitotic progression and results in kinetochore-spindle mis-attachments and an increase in bipolar spindles associated with ectopic asters.
Pfam PF02833: DHHA2 domain (family)
This domain is often found adjacent to the DHH domain [pfam:PF01368] and is called DHHA2 for DHH associated domain. This domain is diagnostic of DHH subfamily 2 members. The domain is about 120 residues long and contains a conserved DXK motif at its amino terminus.
Pfam PF07960: CBP4 (family)
The CBP4 in S. cerevisiae is essential for the expression and activity  of ubiquinol-cytochrome c reductase.  This family describes fungal and human proteins..
Pfam PF15564: Immunity protein 25 (family)
A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in heterogeneous poly-immunity loci of polymorphic toxin systems.
Pfam PF15921: Coiled-coil domain-containing protein 158 (coiled_coil)
CCDC158 is a family of proteins found in eukaryotes. The function is not known.
Pfam PF15627: CEP76 C2 domain (domain)
Many ciliary proteins are involved in ciliogenesis and implicated for ciliophathies. A recent study has shown that many of them contain various new versions of C2 domains which are predicted to mediate membrane localizations for Y-shaped linkers of transition zone of cilia. This is the new C2 domain that is contained by ciliary  CEP76  proteins.
Pfam PF12357: Phospholipase D C terminal (family)
This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF00168], [pfam:PF00614]. There is a conserved FPD sequence motif.  This family is the C terminal of phospholipase D. PLD is a major plant lipid-degrading enzyme which is involved in signal transduction.
Pfam PF13120: Domain of unknown function (DUF3974) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 130 amino acids in length.
Pfam PF17605: Family of unknown function (DUF5501) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF06148: COG2 N-terminal (repeat)
The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function. The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficking proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs. This entry represents the N-terminal region.
Pfam PF23052: N4BP1, second type I KH-domain (domain)
This domain is found in the N4BP1 family which includes the NEDD4-binding protein 1, KHNYN and NYNRIN and other related proteins. Members of this family contain two type I K homology (KH) domains. This entry represents the second KH domain. Besides the typical for the KH domains secondary structures and topology, this domain contains a C-terminal extension consisting of three alpha-helices that define a small helical bundle domain.
Pfam PF15504: Domain of unknown function (DUF4647) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 282 and 480 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 PF21119: Ryanodine receptor junctional solenoid repeat (repeat)
This entry represents a region of the Ryanodine receptor composed of alpha helical ARM repeats. This region has been termed the Junctional solenoid region (Jsol).
Pfam PF07195: Flagellar hook-associated protein 2 C-terminus (family)
The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria. This alignment covers the C-terminal region of this family of proteins.
Pfam PF14743: DNA ligase OB-like domain (domain)
This domain has an OB-like fold, but does not appear to be related to [pfam:PF03120]. It is found at the C-terminus of the ATP dependent DNA ligase domain [pfam:PF01068].
Pfam PF02342: TerD domain (domain)
The TerD domain is found in TerD family proteins that include the paralogous TerD, TerA, TerE, TerF and TerZ proteins It is found in a stress response operon with TerB and TerC.  TerD has a maximum of two calcium-binding sites depending on the conservation of aspartates. It has various fusions to nuclease domains, RNA binding domains, ubiquitin related domains, and metal binding domains. The ter gene products lie at the centre of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing linked to novel pathways.
Pfam PF20679: Hantavirus glycoprotein Gn, base (domain)
The medium (M) genome segment of Hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins, Gn and Gc (also known as G1 and G2, respectively) as a polyprotein precursor. Gn and Gc forms homotetramers (spikes) at the surface of the virion which attach the virion to host cell receptors including integrin beta3/ITGB3 and induce internalisation predominantly through clathrin-dependent endocytosis. This entry represents the C-terminal region of the Gn ectodomain denoted as Gn base (Gn-B) which contributes the most to the intra-spike tetrameric contacts.
Pfam PF00518: Early Protein (E6) (family)
The papillomavirus E6 oncoproteins are small zinc-binding proteins that share a conserved zinc-binding CXXC motif and do not have identified intrinsic enzymatic activity. E6 proteins are thought to act as adapter proteins, thereby altering the function of E6-associated cellular proteins. This model for E6 function is best supported by observations of human papillomavirus type 16 (HPV-16) E6 (16E6), which can alter the metabolism of the p53 tumor suppressor through association with a cellular E3 ubiquitin ligase called E6AP. HPV-16 E6 interacts with an 18-amino-acid sequence in E6AP, and in an as yet ill-defined fashion the E6AP-16E6 complex binds to p53, inducing the ubiquitin-dependent degradation of the trimolecular complex. 16E6 apparently functions as an adapter protein in the complex with p53, since E6AP does not interact with p53 in the absence of E6 and since the degradation of p53 requires both E6 and E6AP .

Despite the similarity in structure of the E6 oncoproteins, studies have indicated surprising biochemical diversity among E6 oncoproteins of different papillomavirus types. E6 from the cancer-associated human papillomaviruses (HPVs) complex with a cellular protein termed E6-AP and together with E6-AP bind to the p53 tumor suppressor protein thereby degrading p53 through ubiquitin-mediated proteolysis. E6 from the non-cancer-associated HPV types do not bind E6-AP or degrade p53. Bovine papilloma virus E6 (BE6) binds E6-AP but fails either to complex with p53 or to degrade associated proteins, implying that BE6 might transform cells through a mechanism different from that of the HPVs. In addition to targeting p53, E6 of both cancer-associated HPVs and BPV-1 have been shown to associate with a cellular-calcium-binding protein localized to the endoplasmic reticulum .
Pfam PF06407: Borna disease virus P40 protein (family)
This family consists of several Borna disease virus P40 proteins. Borna disease (BD) is a persistent viral infection of the central nervous system caused by the single-negative-strand, nonsegmented RNA Borna disease virus (BDV). P40 is known to be a nucleoprotein.
Wikipedia: The Borna disease viruses 1 and 2 are members of the species Mammalian 1 orthobornavirus and cause Borna disease in mammals.
Pfam PF08249: Mastoparan protein (family)
Mastoparans are a family of tetradecapeptides from wasp venom, that have been shown to directly activate GTP-binding regulatory proteins.  These peptides show selectivity among G proteins: they strongly activate Go and Gi but not Gs or Gt.  The peptide of this family are composed by 14 amino acids but they can assume different structures.
Pfam PF24669: Ddi2 HDD domain (domain)
This domain is found in the human DNA-Damage-Inducible 2 (hDdi2) and related proteins. hDdi2 is a member of the Ddi1-like protein family which is intricately connected to the UBQ-proteasome. The better studied yeast homologue Ddi1 (yDdi1) has been implicated in cell cycle regulation, DNA-damage response and exocytosis. There are significant functional differences between hDdi2 and yDdi1. The domain represented by this entry is located central in the hDdi2, between the UBL and aspartic protease-like RVP domain. It is named HDD after "the helical domain of Ddi". It is composed of four alpha-helices that are arranged in a helical bundle. This domain may act as an interaction platform for an RVP substrate.
Pfam PF15739: Translin-associated factor X-interacting N-terminus (family)
This domain is found at the N-terminus of translin-associated factor X-interacting protein, a protein which may play a role in spermatogenesis.
Pfam PF08718: Glycolipid transfer protein (GLTP) (domain)
GLTP is a cytosolic protein that catalyses the intermembrane transfer of glycolipids.
Wikipedia: Glycolipid transfer protein is a cytosolic protein that catalyses the transfer of glycolipids between different intracellular membranes.
Pfam PF04312: Protein of unknown function (DUF460) (family)
Archaeal protein of unknown 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 PF08147: DBP10CT (NUC160) domain (domain)
This C terminal domain is found in the Dbp10p subfamily of hypothetical RNA helicases.
Pfam PF01677: Herpesvirus UL7 like (family)
This family consists of various functionally undefined proteins from the herpesviridae and UL7 from bovine herpes virus. UL7 is not essential for virus replication in cell culture, and is found localised in the cytoplasm of infected cells accumulated around the nucleus but could not be detected in purified virions.  Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication.
Pfam PF21049: Cilia- and flagella-associated protein 69, ARM repeat (repeat)
Cilia- and flagella-associated protein 69 is required for sperm flagellum assembly/stability. Truncating mutations of this protein induce autosomal-recessive MMAF (multiple morphological abnormalities of the flagella) and primary male infertility. In mice, it regulates the speed of activation and termination of the odour response and, thus, contributes to the robustness of olfactory transduction pathways. This entry represents the ARM-repeats domain.
Pfam PF19934: Family of unknown function (DUF6397) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000406) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular the phosphinothricintripeptide biosynthetic gene cluster from Streptomyces viridochromogenes. This family appears to be predominantly found in Actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22310: NMB0315-like, domain I (domain)
This entry represents the domain I of NMB0315, an outer membrane protein of Neisseria meningitidis serogroup B and a potential candidate for a broad-spectrum vaccine against meningococcal disease. This domain tightly associates with domain III, which blocks the active site and the substrate binding groove.
Pfam PF12308: Neurogenesis glycoprotein (family)
This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with [pfam:PF02191]. There are two conserved sequence motifs: SAQ and VQN. Noelin-1 is a glycoprotein which is secreted mainly by postmitotic neurogenic tissues in the developing central and peripheral nervous systems, first appearing after neural tube closure. It is likely that it forms large multimeric complexes.It has a divergent function in neurogenesis. In animal caps neuralized by expression of noggin, co-expression of Noelin-1 causes expression of neuronal differentiation markers several stages before neurogenesis normally occurs in this tissue. Finally, only secreted forms of the protein can activate sensory marker expression, while all forms of the protein can induce early neurogenesis.
Pfam PF24508: TXNDC16 N-terminal (domain)
This entry represents the N-terminal domain of TXNDC16, whose function is still unknown. This domain adopts a thioredoxin-like fold.