SII-SWORD/CoKE huggingface dataset:
Pfam PF12225: Methylene-tetrahydrofolate reductase C terminal (family)
This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme.
Pfam PF06507: Auxin response factor (family)
A conserved region of auxin-responsive transcription factors.
Pfam PF18711: Toxoflavin-degrading enzyme (domain)
This domain is found in toxoflavin-degrading enzymes such as toxoflavin lyase (TflA) also known as toxoflavin-degrading enzyme (TxDE). TflA/TxDE is structurally similar to the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity.
Pfam PF25022: Nephrocystin-3 domain (domain)
This domain is found in human Nephrocystin-3 (NPHP3) and similar animal proteins. NPHP3 is required for normal ciliary development and function and for proper convergent extension cell movements. It probably acts as a molecular switch between different Wnt signalling pathways. This domain is predicted to show a beta-sheet with alpha-helices at both sides.
Pfam PF22381: Transcriptional regulator SarA/Rot (domain)
This entry represents transcriptional regulatory proteins in Staphylococcal species including SarA and Rot. Sar is a global regulator with both positive and negative effects that controls expression of several virulence factors and biofilm formation process in a cell density-dependent manner. Rot plays a key role in regulating S. aureus virulence through activation or repression of promoters that control expression of a large number of critical virulence factors.
Pfam PF10679: Protein of unknown function (DUF2491) (family)
This is a bacterial family of uncharacterised proteins.
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 PF14453: ThiS-like ubiquitin (family)
A member of the ubiquitin superfamily that is often fused to the ThiF-like (E1)- ubiquitin activating enzyme and is present in gene neighborhoods with components of the thiamine biosynthesis pathway.
Pfam PF21857: Family of unknown function (DUF6913) (family)
This is a family of uncharacterized proteins. They share remote similarity to both domains of proteins members of UDP-glycosyltransferase superfamily. In contrast to them, these proteins are predicted to consist of a single standalone domain.
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 PF16940: Chloroplast envelope transporter (family)
Tic110 is a family of chloroplast envelope proteins. Some are involved in protein translocation and others are neurotransmitter receptor, cys loop, ligand-gated ion channel or LIC proteins.
Pfam PF16361: N-terminal of Subtilase family (family)
This is the N-terminal of Peptidase_S8 of subtilase family. It is around 100 residues in length from various Bacteroides species. The function of this family is unknown.
Pfam PF11604: Copper binding periplasmic protein CusF (domain)
CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein.
Pfam PF14646: MYCBP-associated protein family (family)
This family of eukaryotic proteins includes the mammalian MYCBP-associated proteins. These proteins may be synaptic processes and may have a role in spermatogenesis.
Pfam PF08522: BT_3987-like, N-terminal domain (domain)
This domain, previously known as DUF1735, is found in a number of proteins mainly found in firmicutes, including BT_3987 from Bacteroides thetaiotaomicron, which displays hydrolytic activity against Hy-type N-glycans, probably initiating the degradation of this type of glycan in the human gut. This domain adopts a beta-sandwich fold.
Pfam PF12168: DNA polymerase III subunits tau domain IV DnaB-binding (family)
This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with [pfam:PF00004]. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau.
Wikipedia: DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg and Malcolm Gefter in 1970. The complex has high processivity and, specifically referring to the replication of the E.coli genome, works in conjunction with four other DNA polymerases. Being the primary holoenzyme involved in replication activity, the DNA Pol III holoenzyme also has proofreading capabilities that corrects replication mistakes by means of exonuclease activity reading 3'→5' and synthesizing 5'→3'. DNA Pol III is a component of the replisome, which is located at the replication fork.
Pfam PF03967: Photosynthetic reaction centre, H-chain N-terminal region (family)
The family corresponds the N-terminal cytoplasmic domain.
Pfam PF24977: Family of unknown function (DUF7772) (family)
This entry represents a group of uncharacterised worm proteins. They contain highly conserved cysteine residues that are predicted to form disulfide bonds. It is likely that these proteins are secreted.
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 PF16985: Domain of unknown function (DUF5086) (domain)
This family includes uncharacterised proteins predominantly found in Proteobacteria, such as [swissprot:Q9I380] from Pseudomonas aeruginosa. This protein folds into a five-stranded antiparallel beta -sheet sandwiched between two short 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 PF11807: Mycotoxin biosynthesis protein UstYa (family)
Oxidase ustYa is involved in the production of ustiloxins, toxic cyclic peptides, in fungi. Ustiloxins were found to be the first example of cyclic peptidyl secondary metabolites that are ribosomally synthesized in filamentous fungi. The homologous genes ustYa and ustYb (which are found in the gene cluster for ustiloxins) have been shown to be involved in cyclization of the peptide.
Pfam PF21523: Plasmid segregation protein ParM, C-terminal (domain)
This entry consists of several bacterial ParM/StbA plasmid stability proteins. ParM is involved in the control of plasmid partition and required for the accurate segregation of the plasmid, which forms filaments to drive partition. This protein is an actin homologue and consists of two domains (I and II) with the same conformation. This entry represents the C-terminal domain.
Pfam PF01997: Translin family (family)
Members of this family include Translin [swissprot:Q15631] that interacts with DNA and forms a ring around the DNA. This family also includes [swissprot:Q99598], that was found to interact with translin with yeast two-hybrid screen.
Pfam PF24111: Family of unknown function (DUF7386) (family)
This is a family of archaeal sequences 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 PF15491: CST, telomere maintenance, complex subunit CTC1 (family)
CTC1 is one of the three components of the CST complex that assists Shelterin to protect the ends of telomeres from attack by DNA-repair mechanisms. This family largely represents sequences from plants species.
Pfam PF00561: alpha/beta hydrolase fold (domain)
This catalytic domain is found in a very wide range of enzymes.
Wikipedia: The alpha/beta hydrolase superfamily is a superfamily of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function that share a common fold. The core of each enzyme is an alpha/beta-sheet, containing 8 beta strands connected by 6 alpha helices. The enzymes are believed to have diverged from a common ancestor, retaining little obvious sequence similarity, but preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best-conserved structural features of the fold.
Pfam PF16071: Domain of unknown function (DUF4812) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with [pfam:PF03791], [pfam:PF03790]. There are two completely conserved residues (H and I) 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 PF15315: Facioscapulohumeral muscular dystrophy candidate 2 (family)
This family of proteins is found in eukaryotes. The family is localised close to the D4Z4 repeats on chromosome 4 and 10 that are associated with the autosomal dominant facioscapulohumeral muscular dystrophy (FSHD). FRG2 are transcriptionally upregulated in FSHD myoblast cultures suggesting involvement in the pathogenesis of FSHD.
Pfam PF06966: Protein of unknown function (DUF1295) (family)
This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long.
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 PF15327: Tankyrase binding protein C terminal domain (domain)
This protein domain family is found at the C-terminal end of the Tankyrase binding protein in eukaryotes. The precise function of this protein is still unknown. However, it is known interacts with the enzyme tankyrase, a telomeric poly(ADP-ribose) polymerase, by binding to it. Tankyrin catalyses poly(ADP-ribose) chain formation onto proteins. More specifically, it binds to the ankyrin domain in tankyrase. The protein domain is approximately 170 amino acids in length and contains two conserved sequence motifs: FPG and LKA.
Pfam PF17541: Type VI secretion system, TssC, VipB (family)
T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. VipB is a family of Gram-negative type VI secretion system components of the tail sheath. They have been known as COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell. VipA and VipB (TssB and TssC) proteins were shown to form a cog-wheel like tubular structure in V. cholerae that was noticed to resemble T4 phage gp18 polysheath. Two beta-strands of VipA and four beta-strands of VipB intertwine forming the middle layer of the sheath. The sheath assembles around an inner Hcp tube and is attached to a structure called a baseplate that spans the bacterial membranes. Importantly, VipA/VipB sheath was shown to form a long contractile organelle in V. cholerae and in E. coli, suggesting that sheath contraction powers the secretion.
Pfam PF19672: Family of unknown function (DUF6175) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 316 and 421 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 PF18148: Regulator of G-protein signalling DHEX domain (domain)
This domain is found in RGS9 (Class C) regulator of G-protein signalling (RGS) protein present in Mus musculus. RGS proteins attenuate heterotrimeric G-protein signalling by enhancing the intrinsic GTPase activity of G-alpha subunits and are vital for proper signal transduction kinetics. The domain is referred to as DEP helical extension (DHEX) because it is located next to N-terminal Dishevelled/Egl-10/Pleckstrin homology (DEP) domain. Both the DEP and DHEX domains are necessary, but not sufficient, to bind anchoring proteins such as RGS9 anchor protein. DHEX has no close structural homologs. This domain is also found in regulator of G-protein  signaling 7 (RGS7), the crystal structure of which has been solved.
Pfam PF01368: DHH family, N-terminal domain (domain)
It is predicted that this family of proteins all perform a phosphoesterase function. This domain is found at the N-terminal of the single stranded DNA exonuclease RecJ. It shows an alpha-beta configuration.
Wikipedia: In molecular biology, the DHH phosphatase family is a family of putative phosphoesterases. The family includes Drosophila prune protein and bacterial RecJ exonuclease. The RecJ protein of Escherichia coli plays an important role in a number of DNA repair and recombination pathways. RecJ catalyses processive degradation of single-stranded DNA in a 5'-to-3' direction. Sequences highly related to those encoding RecJ can be found in many of the eubacterial genomes sequenced to date.
Pfam PF06033: Nucleopolyhedrovirus protein of unknown function (DUF918) (family)
This family consists of several Nucleopolyhedrovirus proteins with 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 PF06015: Chordopoxvirus A30L protein (family)
This family consists of several short Chordopoxvirus proteins which are homologous to the A30L protein of Vaccinia virus. The vaccinia virus A30L protein is required for the association of electron-dense, granular, proteinaceous material with the concave surfaces of crescent membranes, an early step in viral morphogenesis. A30L is known to interact with the G7L protein and it has been shown that the stability of each is dependent on its association with the other.
Pfam PF18976: Family of unknown function (DUF5712) (family)
This is a family of unknown function mainly found in Bacteroidetes.
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 PF08341: Thioester domain (domain)
This domain is found near the N-terminus of a variety of bacterial surface proteins and pili. This domain contains an unusual covalent ester bond between a conserved cysteine and glutamine residue.
Pfam PF24365: Family of unknown function (DUF7521) (family)
This family includes a group of proteins from archaea.
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 PF02671: Paired amphipathic helix repeat (repeat)
This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene [swissprot:P22579] (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.
Pfam PF14597: Metallo-beta-lactamase superfamily (domain)
This is a small family of putative metal-dependent hydrolases.
Wikipedia: The metallo-β-lactamase (MBL) superfamily constitutes a group of proteins found in all domains of life that share a characteristic αββα fold with the ability to bind transition metal ions. Such metal binding sites may have divalent transition metal ions like Zn(II), Fe(II)/Fe(III) and Mn(II), and are located at the bottom of a wide cleft able to accommodate diverse substrates. The name was adopted after the first members of the superfamily to be studied experimentally: a group of zinc-dependent hydrolytic enzymes conferring bacterial resistance to β-lactam antibiotics. These zinc-β-lactamases (ZBLs) inactivate β-lactam antibiotics through hydrolysis of the β-lactam ring. Early studies on MBLs were conducted on the enzyme βLII isolated from strain 569/H/9 of Bacillus cereus. It was named βLII because it was the second β-lactamase shown to be produced by the bacterium; the first one, βLI, was a non-metallic β-lactamase, i.e., insensitive to inhibition with EDTA.
Pfam PF24566: Ints3-like, C-terminal HEAT repeats (repeat)
This is the C-terminal domain of human Integrator complex subunit 3 (Ints3) and similar animal proteins. Ints3 is a component of the Integrator (INT) complex, which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This domain forms a dimer, which binds single-stranded RNA/DNA.
Pfam PF09459: Ethylbenzene dehydrogenase (domain)
Eythylbenzene dehydrogenase is a heterotrimer of three subunits that catalyses the anaerobic degradation of hydrocarbons. The alpha subunit contains the catalytic centre as a Molybdenum cofactor-complex. This removes an electron-pair from the hydrocarbon and passes it along an electron transport system involving iron-sulphur complexes held in the beta subunit and a Haem b molecule contained in the gamma subunit. The electron-pair is then subsequently passed to an as yet unknown receiver. The enzyme is found in a variety of different bacteria.
Pfam PF11447: Protein of unknown function (DUF3201) (family)
This archaeal 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 PF13421: SPFH domain-Band 7 family (domain)
This is found in an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain .
Pfam PF04888: Secretion system effector C (SseC) like family (family)
SseC is a secreted protein that forms a complex together with SecB and SecD on the surface of Salmonella.  All these proteins are secreted by the type III secretion system. Many mucosal pathogens use type III secretion systems for the injection of effector proteins into target cells.  SecB, SseC and SecD are inserted into the target cell membrane.  where they form a small pore or translocon. In addition to SseC, this family includes the bacterial secreted proteins PopB, PepB, YopB and EspD which are thought to be directly involved in pore formation, and type III secretion system translocon.
Pfam PF24568: Peptidoglycan hydrolase PcsB, coiled-coil domain (domain)
This coiled-coil (CC) domain is found at the N-terminal of Peptidoglycan hydrolase PcsB from Streptococcus pneumoniae ([swissprot:Q8DMY4]) and similar bacterial proteins. PcsB forms a dimer, and the CC domain as a pair of molecular tweezers locking the catalytic domain of each dimeric partner in an inactive configuration.
Pfam PF03003: Pox virus entry-fusion-complex G9/A16 (family)
Pox_G9-A16 is a family of two of the eight entry-fusion complex proteins of pox viruses. the viral fusion proteins are components of the mature virion, MV, membrane. Extracellular enveloped virions (EVs), the infecting particles are MVs with an additional membrane that is opened or removed prior to the fusion of the MV and cell membrane during virus entry. G9 and A16 interact closely with each other and each is required for membrane fusion and virus entry as well as for interaction with A56/K2.
Pfam PF03554: UL73 viral envelope glycoprotein (family)
This family groups together the viral proteins BLRF1, U46, 53, and  UL73.  The UL73-like envelope glycoproteins, which associates in a  high molecular mass complex with its counterpart, gM, induce neutralising antibody responses in the host.  These glycoprotein are  highly  polymorphic, particularly in the N-terminal region.