SII-SWORD/CoKE huggingface dataset:
Pfam PF13243: Squalene-hopene cyclase C-terminal domain (repeat)
Squalene-hopene cyclase, [ec:5.4.99.17], catalyses the cyclisation of squalene into hopene in bacteria.  This reaction is part of a cationic cyclisation cascade, which is homologous to a key step in cholesterol biosynthesis. This family is the C-terminal half of the molecule.
Wikipedia: Prenyltransferases (PTs) are a class of enzymes that transfer allylic prenyl groups to acceptor molecules. Prenyl transferases commonly refer to isoprenyl diphosphate syntheses (IPPSs). Prenyltransferases are a functional category and include several enzyme groups that are evolutionarily independent.
Pfam PF13441: YMGG-like Gly-zipper (domain)
This entry represents a YMGG-like Gly-zipper.
Pfam PF19051: Oxidoreductase family, C-terminal alpha/beta domain (domain)
This entry represents a domain found at the C-terminus of a variety of oxidoreductase enzymes. The domain is related to [pfam:PF02894].
Pfam PF01634: ATP phosphoribosyltransferase (family)
ATP phosphoribosyltransferase (2.4.2.17) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions . ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides.

ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity . This entry represents the catalytic region of this enzyme.

The structures of the long form enzymes from Escherichia coli (P60757) and Mycobacterium tuberculosis (P60759) have been determined . The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded Î²-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.
Wikipedia: In enzymology, an ATP phosphoribosyltransferase is an enzyme that catalyzes the chemical reaction1-(5-phospho-D-ribosyl)-ATP + diphosphate  ATP + 5-phospho-alpha-D-ribose 1-diphosphate
Pfam PF13509: S1 domain (domain)
The S1 domain was originally identified as a repeat motif in the ribosomal S1 protein. It was later identified in a wide range of proteins. The S1 domain has an OB-fold structure. The S1 domain is involved in nucleic acid binding.
Wikipedia: The S1 domain is a protein domain that was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site.
Pfam PF10584: Proteasome subunit A N-terminal signature (family)
This domain is conserved in the A subunits of the proteasome complex proteins.
Pfam PF20372: Family of unknown function (DUF6667) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 358 and 460 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 PF18064: Centromere-binding protein ParB C-terminal (domain)
This is the C-terminal domain found in centromere-binding protein ParB, which is used for stable segregation. The C-terminal domain has a ribbon-helix helix (RHH) motif with a C-terminal loop (residues 119-128) following helix alpha-2. The domain forms a dimer with the C-terminal of the beta chain. The function of the C-terminal domain is to bind to DNA.
Pfam PF12473: Kinesin protein (family)
This domain family is found in eukaryotes, and is typically between 131 and 151 amino acids in length. The family is found in association with [pfam:PF00225], [pfam:PF00498]. There is a single completely conserved residue W 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 PF04558: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 (family)
This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli.                          This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function.
Pfam PF09353: Domain of unknown function (DUF1995) (domain)
This family of proteins are functionally uncharacterised.
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 PF14629: Origin recognition complex (ORC) subunit 4 C-terminus (family)
This entry represents the C-terminus of origin recognition complex subunit 4.
Wikipedia: Origin recognition complex subunit 4 is a protein that in humans is encoded by the ORC4 (ORC4L) gene.
Pfam PF17660: Polyglycine hydrolase-like, structural repeat (repeat)
Polyglycine hydrolase from Fusarium vanettenii is a serine-type endopeptidase that cleaves Gly-Gly bonds in the polyglycine linker of host plant class IV chitinases to disrupt their chitin-binding, and thereby plays a role in lowering the defence responses of the host to fungi. It is formed by two distinct domains that are connected by a linker. The N-terminal domain is comprised of five nearly identical structural repeats consisting of three antiparallel beta-strands and an alpha-helix (this entry represents these structural repeats). This domain is often found associated to [pfam:PF00144].
Pfam PF14025: Protein of unknown function (DUF4241) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 205 and 315 amino acids in length. There is a conserved GDG sequence motif at the C-terminus.
Pfam PF20398: Family of unknown function (DUF6691) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 137 and 165 amino acids in length.  Proteins in this family are related to the thiosulfate transporter, but appear to be about half the length. Suggesting this family may operate as a dimer to make a functional transporter.
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 PF01672: Putative plasmid partition protein (family)
This family consists of conserved hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete, some of which are putative plasmid partition proteins.
Pfam PF21791: Monodehydroascorbate reductase 3-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Monodehydroascorbate reductase 3 (MDHAR3) from Oryza sativa and similar plant sequences. MDHAR3 transfers an electron directly to its substrate, monodehydroascorbate (MDHA), which binds to its active site pocket. It consists of three domains: an NAD(P)-binding domain, an FAD-binding domain, and a C-terminal domain (this entry). This domain shows an alpha-beta structure.
Pfam PF03431: RNA replicase, beta-chain (family)
This family is of Leviviridae RNA replicases.  The replicase is also known as RNA dependent RNA polymerase.
Pfam PF10727: Rossmann-like domain (domain)
This family of proteins contain a Rossmann-like domain.
Pfam PF05367: Phage endonuclease I (domain)
The bacteriophage endonuclease I is a nuclease that is selective for the structure of the four-way Holliday DNA  junction.
Pfam PF11082: Protein of unknown function (DUF2880) (family)
This bacterial 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 PF14960: ATP synthase regulation (family)
Members of this family are subunits of mitochondrial ATP synthase (F-ATPase) and vacuolar ATPase (V-ATPase). In F-ATPase, this subunit regulates mitochondrial ATP synthase population.
Pfam PF14350: Beta protein (family)
This family includes the beta protein from Bacteriophage T4, [swissprot:P13057]. Beta protein prevents the gop protein, [swissprot:P13058], from killing the bacterial host cell.
Pfam PF05548: Gametolysin peptidase M11 (family)
In the unicellular biflagellated alga, Chlamydomonas reinhardtii, gametolysin, a zinc-containing metallo-protease, is responsible for the degradation of the cell wall. Homologues of gametolysin have also been reported in the simple multicellular organism, Volvox.
Pfam PF24099: Diacylglycerol kinase theta, RNA-binding domain-like (domain)
This domain is found in human Diacylglycerol kinase theta (DGKtheta) and similar animal proteins. DGKtheta converts diacylglycerol/DAG into phosphatidic acid/phosphatidate/PA and regulates the respective levels of these two bioactive lipids. This domain is found between [pfam:PF00788] and [pfam:PF00781] and is predicted to adopt an RNA-binding domain (RBD)-like fold.
Pfam PF23635: F-box protein AT5G49610-like, beta-propeller (repeat)
This entry includes a group of plant proteins containing a F-box domain at the N-terminal, followed by a beta-propeller-like domain.  The F-box motif is a key component of the SCF (SKP1-cullin-F-box) complex, which functions as an E3 ligase. Members of this family are likely to play a role in the ubiquitination pathway, where they are responsible for targeting specific substrates for proteasomal degradation. The F-box domain facilitates the recognition and binding of substrate proteins, while the FBD (F-box associated domain), may contribute to the specificity and functionality of the SCF complex.
Pfam PF06679: Membrane protein FAM174-like (family)
This entry represents a group of animal membrane proteins, including human Membrane protein FAM174B, which is essential for Golgi structural integrity.
Pfam PF05259: Herpesvirus glycoprotein L (family)
This family consists of several herpesvirus glycoprotein L or UL1 proteins. Glycoprotein L is known to form a complex with glycoprotein H but the function of this complex is poorly understood.
Pfam PF21718: DTX3L, KH-like domain (domain)
DTX3L is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. This entry represents two copies of a domain found before the ZnF domain ([pfam:PF13923]) in DTX3L. According to structure predictions, it seems to be related to KH domains.
Pfam PF24981: Attractin/LZTR1 beta-propeller (repeat)
This entry represents the beta-propeller domain found in attracting (ATRN), LZTR1, among othes. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signaling pathways that regulate energy homeostasis and hair color. It was thought to have dipeptidase activity but it was shown later to lack that activity. LZTR1 is a substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates ubiquitination of Ras (K-Ras/KRAS, N-Ras/NRAS and H-Ras/HRAS). This domain can be found in a number of other proteins, such as KLHDC3, a substrate-recognition component of a Cul2-RING (CRL2) E3 ubiquitin-protein ligase complex of the DesCEND (destruction via C-end degrons) pathway.
Pfam PF09506: Glucosylglycerol-phosphate phosphatase (Salt_tol_Pase) (family)
Proteins in this family are glucosylglycerol-phosphate phosphatases, with the gene symbol stpA (Salt Tolerance Protein A). A motif characteristic of acid phosphatases is found, but otherwise this family shows little sequence similarity to other phosphatases. This enzyme acts on the glucosylglycerol phosphate, product of glucosylglycerol phosphate synthase and immediate precursor of the osmoprotectant glucosylglycerol.
Pfam PF06381: Phage portal protein (family)
This family represents phage and prophage portal proteins that form the portal of the phage particle. These proteins form a dodecamer assembly that defines a channel for DNA entry and exit. The dodecamer structure resembles a flying saucer with a central channel, which is filled with a rope-like DNA chain. Each subunit of the dodecamer is involved in interaction with capsomers. The dodecameric portal is connected with the neck, which comprises a dodecameric adaptor, a hexameric connector, and a hexameric terminator gp12, forming a continuous DNA injection channel at the center.
Pfam PF14178: YppF-like protein (family)
The YppF-like protein family includes the B. subtilis YppF protein [swissprot:P50834], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved LLDF sequence motif.
Pfam PF18080: Galactose mutarotase-like fold domain (domain)
This domain is found in endo-alpha-N-acetylgalactosaminidase present in Streptococcus pneumoniae. Endo-alpha-N-acetylgalactosaminidase is a cell surface-anchored glycoside hydrolase involved in the breakdown of mucin type O-linked glycans. The domain, known as domain 2, exhibits strong structural similarlity to the galactose mutarotase-like fold but lacks the active site residues. Domains, found in a number of glycoside hydrolases, structurally similar to domain 2 confer stability to the multidomain architectures.
Pfam PF18176: KptA in kinetoplastid DICER domain (domain)
KptA ADP-ribosyltransferase domain observed in kinetoplastid DICER-like (DCL) enzymes. Appears to have lost most residues required for catalyzing phospho-transfer to NAD; however, several positively-charged residues implicated in RNA end recognition remain well-conserved.
Pfam PF06630: Enterobacterial exodeoxyribonuclease VIII (family)
This family consists of several Enterobacterial exodeoxyribonuclease VIII proteins.
Pfam PF12159: Protein of unknown function (DUF3593) (family)
This family of proteins is functionally uncharacterised.This family of proteins is found in  bacteria and eukaryotes. Proteins in this family are typically between 98 and 228 amino acids in length. There is a conserved LHG sequence motif.
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 PF21086: ACT domain (domain)
This entry includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB.
Wikipedia: In molecular biology, the ACT domain is a protein domain that is found in a variety of proteins involved in metabolism. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The ACT domain is named after three of the proteins that contain it: aspartate kinase, chorismate mutase and TyrA. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure.
Pfam PF04111: Apg6 BARA domain (domain)
In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in  eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. This entry is the Beta-Alpha repeated, autophagy-specific (BARA) domain.
Pfam PF12927: Domain of unknown function (DUF3835) (domain)
This is a C-terminal domain conserved 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 PF09100: Quinohemoprotein amine dehydrogenase, alpha subunit domain IV (domain)
Members of this family, which are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase, adopt an immunoglobulin-like beta-sandwich fold, with seven strands arranged into two beta sheets; the fold is possibly related to the immunoglobulin and/or fibronectin type III superfamilies. The precise function of this domain has not, as yet, been defined.
Pfam PF22399: Family of unknown function (DUF6979) (family)
This is a family of uncharacterised proteins. They are predicted to fold into a globular structure consisting mainly of 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 PF23023: Anti-Pycsar protein Apyc1 (family)
This entry represents Anti-Pycsar protein Apyc1 and similar sequences which counteracts the endogenous Pycsar antiviral defense system. These are phosphodiesterases that enables metal-dependent hydrolysis of host cyclic nucleotide Pycsar defense signals such as cCMP and cUMP. These proteins have a metallo beta-lactamase (MBL)-like fold with homology to RNase and phosphodiesterase enzymes.
Pfam PF09296: NADH pyrophosphatase-like rudimentary NUDIX domain (domain)
The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP.
Wikipedia: NUDIX hydrolases are a superfamily of hydrolytic enzymes capable of cleaving nucleoside diphosphates linked to x, hence their name. The reaction yields nucleoside monophosphate (NMP) plus X-P. Substrates hydrolysed by nudix enzymes comprise a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, dinucleoside and diphosphoinositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity. Enzymes of the NUDIX superfamily are found in all types of organisms, including eukaryotes, bacteria and archaea.
Pfam PF22279: DGF-1 N-terminal domain (domain)
This entry represents the N-terminal domain present in DGF-1 from Typanosoma, one of the most abundant proteins in T. cruzi genome and it seems to have a preferential expression in amastigotes (intracellular replicative forms that develop in the mammalian host). The function of this protein is not yet clear, however, it is likely to play a role in cell-to-cell interactions or signal transduction.
Pfam PF05555: Coxiella burnetii protein of unknown function (DUF762) (family)
This family consists several of several uncharacterised proteins from the bacterium Coxiella burnetii. Coxiella burnetii is the causative agent of the Q fever disease.
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 PF04152: Mre11 DNA-binding presumed domain (domain)
The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication.  Mre11 has an intrinsic DNA-binding activity that is stimulated  by Rad50 on its own or in combination with Nbs1.