SII-SWORD/CoKE huggingface dataset:
Pfam PF12794: Mechanosensitive ion channel inner membrane domain 1 (domain)
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains.
Pfam PF20483: Flavivirus RNA-directed RNA polymerase, thumb domain (domain)
Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteristic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry represents the thumb domain of NS5 RdRp. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.
Wikipedia: RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.
Pfam PF03621: MbtH-like protein (domain)
This domain is found in the MbtH protein [swissprot:O05821] as well as at the N terminus of the antibiotic synthesis protein NIKP1. MbtH and its homologues were first noted in gene clusters involved in non-ribosomal peptides and other secondary metabolites by Quadri et al. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues.  The structure of the PA2412 protein shows it adopts a beta-beta-beta-alpha-alpha topology with the short C-terminal helix forming the tip of an overall arrowhead shape. MbtH proteins have been shown to be required for the synthesis of antibiotics, siderophores and glycopeptidolipids.
Pfam PF24556: Unconventional myosin-XVIIIa SH3 domain (domain)
This entry represents the SH3 domain found in unconventional myosin-XVIIIa a protein that may play a role in Golgi membrane trafficking and could indirectly give its flattened shape to the Golgi apparatus. In macrophages, it regulates trafficking, expression, and activation of innate immune receptors.
Pfam PF18293: Caprin-1 dimerization domain (domain)
This domain is found in human Caprin-1 protein. Caprin-1 plays a role in many important biological processes, including cellular proliferation, innate immune response and synaptic plasticity. This domain is found in the highly conserved homologous region 1(HR1) and is responsible for the tight homodimerization of Caprin-1.
Wikipedia: Caprin-1 is a protein that in humans is encoded by the CAPRIN1 gene. It is suggested that Caprin1 is essential for the formation of long-term memory.
Pfam PF05856: ARP2/3 complex 20 kDa subunit (ARPC4) (family)
This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion.
Pfam PF19425: Csd3 second domain (domain)
This entry represents the second domain from the Csd3 peptidase. This domain has a similar structure to [pfam:PF18059] despite low sequence similarity.
Pfam PF12429: Protein of unknown function (DUF3676) (family)
This domain family is found in eukaryotes, and is approximately 230 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 PF23678: YqhI-like (family)
This protein family includes Protein YqhI from Escherichia coli and similar bacterial short sequences. YqhI is a 47-residues long protein encoded by a small open reading frame (smORF).
Pfam PF24830: Family of unknown function (DUF7714) (family)
This entry represents a group of uncharacterised prokaryotic proteins. They are likely to contain two domains that create a compact elongated structure. Toward the C terminus, these proteins have two highly conserved pairs of cysteines which are likely to be involved in metal coordination.
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 PF15633: HYD1 signature containing ADP-ribosyltransferase (family)
A predicted toxin of the ADP-ribosyltransferase superfamily present in bacterial polymorphic toxin systems. The domain has characteristic histidine, tyrosine and aspartate residues that comprise the active site. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, or type 7 secretion system. ART-HYD1 domain toxin from Photorhabdus has been shown to have antibacterial activity and arrest translation by ADP-ribosylating specific position of 23S rRNA.
Pfam PF15899: BNR-Asp box repeat (repeat)
This BNR repeat is found in proteins such as human sortilin. The model complements family BNR_5.
Pfam PF04501: Baculovirus major capsid protein VP39 (family)
This family constitutes the 39 kDa major capsid protein of the Baculoviridae.
Pfam PF23340: Chp1 domain II (domain)
Chp1 is required for RNA interference-dependent heterochromatin formation in fission yeast, and it is a member of the RNA-induced transcriptional silencing (RITS) complex  which maintains the heterochromatin regions, playing a role in stabilizing microtubules which allows accurate chromosome segregation. This entry represents the second domain (domain II) of Chp1 which resembles eukaryotic phosphatases and receiver domains of bacterial phosphotransferase signaling systems being part of the Rossmann fold superfamily. This domain makes the interaction surface between Chp1 and Tas3. Chp1 and Tas3 complex solid and versatile platform to recruit both RNAi-dependent and RNAi-independent gene-silencing pathways for locus-specific regulation of heterochromatin.
Pfam PF11422: Initiator binding protein 39 kDa (family)
IBP39 recognises the initiator which is solely responsible for transcription start site selection. IBP39 contains an N-terminal Inr binding domain connected to a C-terminal domain. The C domain structure indicates that it interacts with the T. vaginalis RNAP II large subunit C-terminal domain. Binding of IBP39 to Inr recruits RNAP II and initiates transcription.
Pfam PF12061: Late blight resistance protein R1 (family)
R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide. The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain  and a leucine-rich repeat domain. This protein is found associated with [pfam:PF00931].
Pfam PF24330: Family of unknown function (DUF7499) (family)
This entry represents uncharacterised proteins found in Chlamydiia. They adopt a globular alpha/beta structure consisting of a curved mixed beta-sheet and alpha-helices packed on both sides (PDB:6UXC).
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 PF05961: Chordopoxvirus A13L protein (family)
This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus.
Pfam PF19656: Family of unknown function (DUF6159) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 277 and 315 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 PF01812: 5-formyltetrahydrofolate cyclo-ligase family (family)
5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase [ec:6.3.3.2] catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin.
Pfam PF24735: Domain of unknown function (DUF7686) (domain)
This domain is found in uncharacterised bacterial proteins. It is usually found next to [pfam:PF24734]. It is predicted to adopt alpha/beta structure consisting of a four-stranded beta-sheet curved around an 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 PF15167: Domain of unknown function (DUF4581) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically 131 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 PF22540: RET, Cysteine Rich Domain (domain)
RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that the ligand-binding RET ectodomain (RET-ECD) contains four consecutive cadherin-like domains (CLD1-CLD4) followed by a membrane-proximal cysteine-rich domain (CRD). This entry relates to the Cysteine Rich Domain (CRD) domain.
Pfam PF11390: NADH-dependant formate dehydrogenase delta subunit FdsD (family)
FdsD is the delta subunit of the enzyme formate dehydrogenase. This subunit may play a role in maintaining the quaternary structure by means of electrostatic interactions with the other subunits. The delta subunit is not involved in the active centre of the enzyme.
Pfam PF05602: Cleft lip and palate transmembrane protein 1 (CLPTM1) (family)
This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family. This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis.
Wikipedia: Cleft lip and palate transmembrane protein 1 (Clptm1) is a multi-transmembrane protein that in humans is encoded by the CLPTM1 gene. Clptm1 was characterized in 1995 as a surface membrane protein in the thymus during embryonic development in mice and is suggested to have an important role in T-cell development. A more recent study shows a role in GABAA receptor subunit intracellular anchoring and regulation resulting in an influence on synaptic strength Clptm1 belongs to a family of several eukaryotic cleft lip and palate transmembrane protein 1 sequences.
Pfam PF07718: Coatomer beta C-terminal region (domain)
This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). This C-terminal domain probably adapts the function of the N-terminal [pfam:PF01602] domain.
Pfam PF09457: FIP domain (conserved_site)
The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterised regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes.
Pfam PF03334: Na+/H+ antiporter subunit (family)
This family includes PhaG from Rhizobium meliloti [swissprot:Q9ZNG0], MnhG from Staphylococcus aureus [swissprot:Q9ZNG0], YufB from Bacillus subtilis [swissprot:O05227].
Pfam PF09730: Microtubule-associated protein Bicaudal-D (coiled_coil)
BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER). For full functioning they bind with GSK-3beta [pfam:PF05350] to maintain the anchoring of microtubules to the centromere. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells.
Pfam PF22946: CPC1/SPEF2 domain D5 (domain)
This domain is found in the axoneme central apparatus (CA) associated proteins such as Chlamydomonas Central pair complex 1 (CPC1) and its mammalian orthologues Sperm flagellar protein 2 (SPEF2). CPC1 is located at C1 microtubule. Most of the distal components of the C1b projection bind CPC1 and its correct recruitment and positioning is critical to the formation of the C1b projection, and ciliary motility in Chlamydomonas and humans. CPC1 serves as the rachis of the entire C1b arm and this domain contributes to this function. It folds into a single long alpha-helix.
Pfam PF19404: Family of unknown function (DUF5977) (domain)
This entry represents a small domain that is found in tandem repeats in Bacteroidota bacterial surface proteins, commonly associated with PA14 adhesive domain. This domain is composed of a beta hairpin followed by an alpha helix. There is a conserved pair of cysteine residues in each domain that form a disulphide bridge that presumably stabilises this small 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 PF19087: Domain of unknown function (DUF5776) (domain)
Presumed stalk domain found in bacterial surface proteins forming  tandem repeats with high sequence identity. This domain is also  associated with other known bacterial surface protein stalks and  adhesive domains.
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 PF19618: Family of unknown function (DUF6123) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 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 PF23234: Large helicase-related protein, winged-helix domain (domain)
This is a winged-helix (WH) domain found in Large helicase -related protein from Escherichia coli (Lhr), DEAD/DEAH box helicase from Mycolicibacterium smegmatis ([swissprot:A0QT91]) and similar bacterial sequences. These proteins have a C-terminal domain composed of a series of five WH modules (named WH2 to WH6) and a beta-barrel module. This entry represents WH4. It shows three alpha-helices followed by two loops or 'wings' and two beta-strands forming an antiparallel beta-sheet.
Pfam PF00983: Tymovirus coat protein (domain)
This signature is found in coat proteins from the related tymoviruses. The coat protein is also known as the virion protein. The virus coat is composed of 180 copies of the coat protein arranged in an icosahedral shell.
Wikipedia: In molecular biology, the Tymovirus coat protein refers to the protein coat of a virus order, named Tymovirales. More specifically this protein signature is found only in coat proteins from the related tymoviruses. The coat protein (CP) is also known as the virion protein. The virus coat is composed of 180 copies of the coat protein arranged in an icosahedral shell.
Pfam PF22363: MrkH-like, YcgR-like domain (domain)
This entry represents the YcgR-like domain found at the N-terminal of MrkH ([swissprot:G3FT00]) from Klebsiella pneumoniae and similar sequences which contain a PilZ domain at the C-terminal. MrkH is a c-di-GMP-related transcriptional regulator that affects type 3 fimbrial expression in response to cellular c-di-GMP level, playing and important role in biofilm formation. This protein binds to the promoter regulation fragments of mrkHI and mrkA mainly through its PilZ domain and this YcgR-like domain also participates in DNA-binding.
Pfam PF19770: Family of unknown function (DUF6256) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001215) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the conglobatin biosynthetic gene cluster from Streptomyces conglobatus.
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 PF18295: M17 aminopeptidase N-terminal domain 2 (domain)
This domain is found in the N-terminal region of M17 aminopeptidase ([pfam:PF00883]) present in Homo sapiens and Mus musculus. M17 aminopeptidases are Zn-dependent exopeptidases that catalyse the removal of unsubstituted amino acid residues from the N-terminus of peptides.
Pfam PF04203: Sortase domain (domain)
The founder member of this family is S. aureus sortase,  a transpeptidase that attaches surface proteins by the  threonine of an LPXTG motif to the cell wall.
Wikipedia: Sortase refers to a group of prokaryotic enzymes that modify surface proteins by recognizing and cleaving a carboxyl-terminal sorting signal. For most substrates of sortase enzymes, the recognition signal consists of the motif LPXTG (Leu-Pro-any-Thr-Gly), then a highly hydrophobic transmembrane sequence, followed by a cluster of basic residues such as arginine. Cleavage occurs between the Thr and Gly, with transient attachment through the Thr residue to the active site Cys residue, followed by transpeptidation that attaches the protein covalently to cell wall components. Sortases occur in almost all Gram-positive bacteria and the occasional Gram-negative bacterium or Archaea, where cell wall LPXTG-mediated decoration has not been reported. Although sortase A, the "housekeeping" sortase, typically acts on many protein targets, other forms of sortase recognize variant forms of the cleavage motif, or catalyze the assembly of pilins into pili.
Pfam PF24120: Single-strand DNA deaminase toxin A, C-terminal (domain)
This domain is found at the C-terminal end of Single-strand DNA deaminase toxin A from Pseudomonas syringae (SsdA) and similar bacterial and fungal sequences. SsdA shows a typical alpha-beta deaminase configuration.
Pfam PF13358: DDE superfamily endonuclease (domain)
This family of proteins are related to [pfam:PF00665] and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.
Pfam PF13935: Ead/Ea22-like protein (family)
This family contains phage proteins and bacterial proteins that are likely to represent integrated phage proteins. This family includes the Lambda phage Ea22 early protein as well as the Bacteriophage P22 Ead protein.
Pfam PF04145: Ctr copper transporter family (family)
The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane.  A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport.