SII-SWORD/CoKE huggingface dataset:
Pfam PF23917: Domain of unknown function (DUF7256) (domain)
This entry represents a domain found in uncharacterised proteins from proteobacteria. This domain is sometimes found N-terminal to [pfam:PF21832].
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 PF15194: TMEM191C family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between and 302 amino acids in length. There are two conserved sequence motifs: QDC and RLF. The function of this family is unknown.
Pfam PF20946: DNA polymerase alpha-binding protein Ctf4, C-terminal domain (domain)
This domain is found at the C-terminal end of DNA polymerase alpha- binding protein Ctf4 from yeast, its human orthologue AND1, and similar proteins from eukaryotes. This accessory factor for DNA replication plays a role in accurately duplicating the genome in vivo. This domain folds into a helical extension that is linked to the beta-propeller domain ([pfam:PF12341]) and protrudes from one face of the disk-shaped trimer formed by the protein. It is essential for binding of dynamic partner proteins, such as Pol alpha-primase.
Pfam PF15176: Leucine-rich repeat family 19 TM domain (domain)
LRR19-TM is the single-span transmembrane region of LRRC19, a leucine-rich repeat protein family. LRRC19 functions as a transmembrane receptor inducing pro-inflammatory cytokines. This suggests its role in innate immunity. This family of proteins is found in eukaryotes.
Pfam PF12088: Protein of unknown function (DUF3565) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.
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 PF20521: Family of unknown function (DUF6736) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in fungi, and is approximately 130 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 PF07795: Protein of unknown function (DUF1635) (family)
The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids 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 PF14716: Helix-hairpin-helix domain (domain)
This domain is found at the N terminus of DNA polymerase beta, as well as in other X-type polymerases and DNA nucleotidylexotransferase (TdT).
Pfam PF23604: TRAPPC10-like, immunoglobulin-like (domain)
This domain is found in human Trafficking protein particle complex subunit 10 (TRAPPC10) and similar animal proteins. TRAPPC10 is a subunit of the TRAPP (transport protein particle) II complex, a highly conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether. This domain is predicted to adopt an immunoglobulin-like (Ig-like) fold.
Pfam PF18895: Type IV secretion system pilin (family)
This entry represents likely Type IV secretion system pilins.
Pfam PF22162: Plasmid Fertility inhibition factor (domain)
FiwA-like proteins are fertility inhibition factors (FIN), which are employed by plasmids to block import of rival plasmids. FiwA is encoded by plasmid RP1 and blocks the transfer of plasmid R388. A FiwA-like protein called Osa (oncogenic suppressive activity) inhibits the oncogenic properties of Agrobacterium tumefaciens. Osa is structurally similar to the ParB/Sulfiredoxin fold. Osa has been shown to have ATPase and DNAse activities, and can block T-DNA transfer into plants.
Pfam PF12856: Anaphase-promoting complex subunit 9 (family)
Apc9 is one of the subunits of the anaphase-promoting complex, or cyclosome, which is essential for regulating entry into anaphase and exit from mitosis. The APC is a ubiquitin-protein ligase complex. All APC subunits are members of the cullin family proteins, which bind to a ring-finger subunit via a conserved cullin domain. The APC is made up of four parts, the third of which is a tetratricopeptide repeat arm (TPR) that contains Apc9.
Pfam PF07232: Putative rep protein (DUF1424) (family)
This family consists of several archaeal proteins of around 320 residues in length. Members of this family seem to be found exclusively in Halobacterium and Haloferax species. The function of this family is unknown. This protein is probably a rep protein due to conservation of functional motifs.
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 PF18613: Tyrosine kinase receptor A trans-membrane domain (domain)
This receptor consists of 796 amino acids and can be divided in the extracellular ligand-binding domain, the trans-membrane domain, and the intracellular tyrosine kinase domain.This domain is the TMD of TrkA which has shown to be involved in the interaction with amyloid precursor protein (APP).
Wikipedia: Tropomyosin receptor kinase A (TrkA), also known as high affinity nerve growth factor receptor, neurotrophic tyrosine kinase receptor type 1, or TRK1-transforming tyrosine kinase protein is a protein that in humans is encoded by the NTRK1 gene.
Pfam PF17882: OAA-family lectin sugar binding domain (domain)
This domain is found in agglutinin family of lectins. Oscillatoria agardhii agglutinin (OAA)- family lectins comprise either one or two homologous domains, with a single domain possessing two glycan binding sites. OAA is one of the lectins with anti-HIV activity. This sugar binding domain is also found in Pseudomonas fluorescens agglutinin (PFA) and myxobacterial hemagglutinin (MBHA), where MBHA contains two sugar-binding domains (i.e. 4 sugar binding sites), whereas OAA and PFA are single-domain proteins (i.e. 2 sugar binding sites).
Pfam PF09265: Cytokinin dehydrogenase 1, FAD and cytokinin binding (domain)
Members of this family adopt an alpha+beta sandwich structure with an antiparallel beta-sheet, in a ferredoxin-like fold. They are predominantly found in plant cytokinin dehydrogenase 1, where they are capable of binding both FAD and cytokinin substrates. The substrate displays a 'plug-into-socket' binding mode that seals the catalytic site and precisely positions the carbon atom undergoing oxidation in close contact with the reactive locus of the flavin.
Pfam PF14901: Cleavage inducing molecular chaperone (domain)
Jiv90 is a fragment of the DnaJ protein in eukaryotes and in J-domain protein interacting with viral protein (Jiv) located in the N terminal region of the pestivirus viral polypeptide.  The viral protein interacts stably with non structural (NS) protein NS2, causing a conformational change in NS2-NS3 and stimulates NS2-NS3 cleavage in trans. Cleavage of NS2-NS3 increases cytopathogenicity and consequently aids viral replication. Jiv therefore acts as a regulating cofactor for NS2 auto-protease. The efficient release of NS3 from the viral polypeptide by Jiv is considered crucial to the pestivirus cytopathogenicity. In eukaryotes, it usually lies 40 residues downstream of DnaJ family [pfam:PF00226]. However, the function in eukaryotes is still unknown.
Pfam PF01121: Dephospho-CoA kinase (domain)
This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A [ec:2.7.1.24]. This enzyme uses ATP in its reaction.
Pfam PF11362: Protein of unknown function (DUF3161) (family)
This eukaryotic 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 PF23270: Glycerol-3-phosphate acyltransferase RAM2-like, HAD-like domain (domain)
This domain is found at the N-terminal end of Glycerol-3 -phosphate acyltransferase RAM2 from Medicago truncatula and similar plant proteins. RAM2 is involved in the production of cutin monomers, which act as plant signals that promote colonisation by arbuscular mycorrhizal fungi. This domain is predicted to adopt an alpha-beta structure similarly to this found in other haloacid dehalogenase (HAD) proteins.
Pfam PF02882: Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (domain)
This entry represents the NAD(P)-binding domain found in enzymes that belong to the tetrahydrofolate dehydrogenase/cyclohydrolase family, which are mainly found in bacteria but also in archaeal and eukaryotic organisms.
Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5), methenyl-THF cyclohydrolase (3.5.4.9) and formyl-THF synthetase (6.3.4.3) . The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase ; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein . Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site , and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds.
Pfam PF04568: Mitochondrial ATPase inhibitor, IATP (family)
ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface.  It is thought to inhibit ATP synthesis by preventing the release of ATP. The minimum inhibitory region for bovine inhibitor ([swissprot:P01096]) is from residues 39 to 72. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C terminal regions of two monomers.  At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity.
Wikipedia: ATPase inhibitor, mitochondrial is an enzyme that in humans is encoded by the ATPIF1 gene.
Pfam PF18346: Mind bomb SH3 repeat domain (domain)
The REP domain of Mind bomb which serves as the substrate recognition domain for a second, membrane-distal epitope of the Notch ligand (C-box).  Although the first Mib repeat of REP may play a dominant role in ligand binding, the two repeats appear to cooperate in the engagement of the Jag1 tail.  Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. The structure and functional analysis, show that Mib1 contains two independent substrate recognition domains that engage two distinct epitopes from the cytoplasmic tail of the ligand Jagged1, one in the intracellular membrane proximal region and the other near the C terminus. REP domains have a five-stranded anti-parallel twisted beta sheet topology similar to that of SH3 domains.
Pfam PF19663: Family of unknown function (DUF6166) (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 104 and 215 amino acids in length. There are two conserved sequence motifs: GDRTIDG and VVANF.
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 PF12077: Transmembrane protein of unknown function (DUF3556) (family)
This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 576 to 592 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 PF04293: SpoVR like protein (domain)
Family member [swissprot:P37875] is Bacillus subtilis stage V sporulation protein R, which is involved in spore cortex formation. Little is known about cortex biosynthesis, except that it depends on several sigma E controlled genes, including spoVR. Another family member is an uncharacterised protein YcgB. YcgB has been suggested to be part of a conserved signalling pathway with YeaH and YeaG. This  pathway may be involved in nitrogen metabolism (see Supplementary  note 5 in.). This is a domain found at the N-terminal of this group of proteins.
Pfam PF13013: F-box-like domain (family)
The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.
Pfam PF19122: Family of unknown function (DUF5806) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria and Methanomicrobia.
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 PF00184: Neurohypophysial hormones, C-terminal Domain (family)
N-terminal Domain is in hormone5
Wikipedia: The neurohypophysial hormones form a family of structurally and functionally related peptide hormones. Their representatives in humans are oxytocin and vasopressin. They are named after the location of their release into the blood, the neurohypophysis.
Pfam PF17489: L1 transposable element trimerization domain (coiled_coil)
This entry represents the trimerization domain.
Pfam PF10835: Protein of unknown function (DUF2573) (family)
Some members in this bacterial family of proteins are annotated as YusU however no function is currently known. This family of proteins appears to be restricted to Bacillus spp.
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 PF24713: TORTIFOLIA1 C-terminal (repeat)
This entry includes a group of plant microtubule-associated proteins, including TORTIFOLIA1/SPIRAL2 and SPIRAL2-like (SP2L) from Arabidopsis. They regulate the orientation of cortical microtubules and the direction of organ growth. TORTIFOLIA1-like protein 1 (also known as SPIRAL2) may regulate katanin-based microtubule (MT) severing. During virus infection, it may stabilize MT crossovers to support the formation and intercellular spread of the viral RNA complexes. This entry represents a domain found at the C-terminal of TORTIFOLIA1/SPIRAL2 and related proteins. This domain may consist of TPRs.
Pfam PF12465: Proteasome beta subunits C terminal (family)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00227]. There is a conserved GTT sequence motif. There is a single completely conserved residue Y that may be functionally important. This family includes the C terminal of the beta-type subunits of the proteasome, a multimeric complex that degrades proteins into peptides as part of the MHC class I-mediated Ag-presenting pathway.
Pfam PF01199: Ribosomal protein L34e (family)
This entry represents a number of eukaryotic and archaebacterial ribosomal proteins that belong to the eL34 family. These were previously known as vertebrate L34, mosquito L31 , plant L34 , yeast putative ribosomal protein YIL052c and archaebacterial L34e.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF00159: Pancreatic hormone peptide (family)
This entry represents a group of animal proteins, including Pancreatic hormone , also known as Pancreatic polypeptide is a peptide (PP), which is synthesized in pancreatic islets of Langherhans and acts as a regulator of pancreatic and gastrointestinal functions.

The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length  and has an amidated C terminus . The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a Î²-turn, and 14-32 an Î±-helix, held close to the first helix by hydrophobic interactions . Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution . Both N- and C- terminal ends are required for activity: receptor binding and activation functions may reside in the N and C termini respectively .

Pancreatic hormone is part of a wider family of active peptides that includes:


 * Neuropeptide Y (NPY or melanostatin) , one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotropin-releasing hormone.
 * Peptide YY (PYY) . PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictor action and inhibits jejunal and colonic mobility. Known as goannatyrotoxin-Vere1 in the venom of the pygmy desert monitor lizard (Varanus eremius) where it has a triphasic action: rapid biphasic hypertension followed by prolonged hypotension in prey animals .
 * Various NPY and PYY-like polypeptides from fish and amphibians .
 * Neuropeptide F (NPF) from invertebrates such as worms and snail.
 * Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity.
 * Polypeptide MY (peptide methionine-tyrosine). A regulatory peptide from the intestine of the sea lamprey (Petromyzon marinus) .


All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesised as larger protein precursors.
Wikipedia: The pancreatic islets or islets of Langerhans are the regions of the pancreas that contain its endocrine (hormone-producing) cells, discovered in 1869 by German pathological anatomist Paul Langerhans. The pancreatic islets constitute 1–2% of the pancreas volume and receive 10–15% of its blood flow. The pancreatic islets are arranged in density routes throughout the human pancreas, and are important in the metabolism of glucose.
Pfam PF09917: Uncharacterized protein conserved in bacteria (DUF2147) (domain)
This domain, found in various hypothetical prokaryotic 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.