SII-SWORD/CoKE huggingface dataset:
Pfam PF20330: Family of unknown function (DUF6625) (family)
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 292 and 338 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 PF22208: Cas_Csm6 CARF domain (domain)
This entry includes Csm6 from bacteria (i.e Enterococcus italicus), a Cas (CRISPR-associated) protein from type III-A CRISPR-Cas system. It consists of a CARF domain at the N-terminal, represented in this entry a six-helix domain ([pfam:PF22206]) and a C-terminal HEPN domain ([pfam:PF09659]), which has RNase activity. This domain is a ring nuclease.
Pfam PF01633: Choline/ethanolamine kinase (domain)
Choline kinase catalyses the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway. This alignment covers the protein kinase portion of the protein. The divergence of this family makes it very difficult to create a model that specifically predicts choline/ethanolamine kinases only.
Wikipedia: In molecular biology, the choline/ethanolamine kinase family includes choline kinase(EC 2.7.1.32) and ethanolamine kinase.
Pfam PF15926: E3 ubiquitin-protein ligase RNF220 (family)
This family represents the central region of the E3 ubiquitin-protein ligase RNF220.
Wikipedia: RING finger protein 220 is a protein that in humans is encoded by the RNF220 gene.
Pfam PF23067: Uncharacterised protein MG280 (family)
This entry includes uncharacterised proteins from Mycoplasma, such as MG280 from Mycoplasma vaginalis. These proteins are typically 260 aa long, with a hydrophobic predicted transmembrane alpha-helix toward each end.
Pfam PF00377: Prion/Doppel alpha-helical domain (domain)
The prion protein is thought to be the infectious agent that causes transmissible spongiform encephalopathies, such as scrapie and BSE. It is thought that the prion protein can exist in two different forms: one is the normal cellular protein, and the other is the infectious form which can change the normal prion protein into the infectious form. It has been found that the prion alpha-helical domain is also found in the Doppel protein.
Pfam PF15824: Spermatogenesis-associated protein 9 (family)
SPATA9, spermatogenesis-associated protein 9, or testis development protein NYD-SP16, is a family of eukaryotic proteins associated with sperm production. It is highly expressed in human testis and contains one transmembrane domain. Its localisation indicates it is likely to play an important role in testicular development and spermatogenesis and may be an important factor in male infertility.
Pfam PF20548: Family of unknown function (DUF6762) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicutes bacteria.  Proteins in this family are approximately 135 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 PF05453: BmTXKS1/BmP02 toxin family (domain)
This family consists of toxin-like peptides that are isolated from the venom of Buthus martensii Karsch scorpion. The precursor consists of 60 amino acid residues, with a putative signal peptide of 28 residues and an extra residue, and a mature peptide of 31 residues with an amidated C-terminal. The peptides share close homology with other scorpion K+ channel toxins and should present a common three-dimensional fold - the Cysteine -Stabilised alphabeta (CSalphabeta) motif. This family acts by blocking small conductance calcium activated potassium ion channels in their victim.
Pfam PF02010: REJ domain (family)
The REJ (Receptor for Egg Jelly) domain is found in PKD1 [swissprot:P98161], and the sperm receptor for egg jelly [swissprot:Q26627]. The function of this domain is unknown. The domain is 600 amino acids long so is probably composed of multiple structural domains. There are six completely conserved cysteine residues that may form disulphide bridges. This region contains tandem PKD-like domains.
Pfam PF20702: Novel STAND NTPase 2 (domain)
This is an inactive STAND-NTPase superfamily domain found in a mobile two-gene bacterial conflict systems. nSTAND2 is fused to various effector molecules. The neighbouring gene is an active STAND domain. These STAND NTPases define a novel family close to CR-ATPases, the mitochondrial apoptotic ribosomal protein S29/Dap3 and the mitochondria-associated STAND NTPase RNA12.
Pfam PF02481: DNA recombination-mediator protein A (family)
The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation.
Pfam PF11536: Protein of unknown function (DUF3226) (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 PF20211: Family of unknown function (DUF6571) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Actinobacteria. Proteins in this family are typically between 547 and 730 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 PF00767: Potyvirus coat protein (family)
This protease is found in genome polyproteins of potyviruses. The genome polyprotein contains: N-terminal protein (P1), helper component protease (3.4.22, HC-PRO), protein P3, 6KD protein (6K1), cytoplasmic inclusion protein (CI), 6KD protein 2 (6K2), genome-linked protein (VPG), nuclear inclusion protein A (3.4.22), nuclear inclusion protein B (2.7.7.48) and coat protein (CP). The coat protein is at the C terminus of the polyprotein.
Pfam PF22621: CurL-like, PKS C-terminal (domain)
This entry represents the polyketide synthase C-terminal extension from cyanobacterial CurL polyketide synthase and similar proteins from other bacteria and fungi.
Pfam PF00516: Envelope glycoprotein GP120 (domain)
The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein ([swissprot:P01730]) and a chemokine receptor on the cell surface. Gp160 us proteolytically cleaved n the trans-Golgi and activated by cellular furin or furin-like proteases to produce gp120 and gp41.
Wikipedia: Envelope glycoprotein GP120 is a glycoprotein exposed on the surface of the HIV envelope. It was discovered by Professors Tun-Hou Lee and Myron "Max" Essex of the Harvard School of Public Health in 1984. The 120 in its name comes from its molecular weight of 120 kDa. Gp120 is essential for virus entry into cells as it plays a vital role in attachment to specific cell surface receptors. These receptors are DC-SIGN, Heparan Sulfate Proteoglycan and a specific interaction with the CD4 receptor, particularly on helper T-cells. Binding to CD4 induces the start of a cascade of conformational changes in gp120 and gp41 that lead to the fusion of the viral membrane with the host cell membrane. Binding to CD4 is mainly electrostatic although there are van der Waals interactions and hydrogen bonds.
Pfam PF03037: Kinetoplastid membrane protein 11 (family)
Kinetoplastid membrane protein 11 is a major cell surface glycoprotein  of the parasite Leishmania donovani.
Pfam PF14197: Centrosome localisation domain of PPC89 (coiled_coil)
The N-terminal region of the fission yeast spindle pole body protein PPC89 has low similarity to the human Cep57 protein. The CLD or centrosome localisation domain of Cep57 and PPC89 is found at the N-terminus. This region localises to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerise with the N-terminus of other Cep57 molecules.  The C-terminal part, Family Cep57_MT_bd, [pfam:PF06657], is the microtubule-binding region of Cep57 and PPC89.
Pfam PF05459: Herpesvirus transcriptional regulator family (family)
This family includes UL69 and IE63 that are transcriptional regulator proteins.
Pfam PF04778: LMP repeated region (coiled_coil)
This family consists of a repeated sequence element found in the LMP group of surface-located membrane proteins of Mycoplasma hominis.  The the number of repeats in the protein affects the tendency of cells to spontaneously  aggregate.  Agglutination may be an important factor in colonisation. Non-agglutinating microorganisms might easily be distributed whereas  aggregation might provide a better chance to avoid an antibody response since some of the epitopes may be buried.
Pfam PF03385: STELLO glycosyltransferases (family)
This domain family is found in Metazoa and in Virdiplantae. Two of the family members are characterized in Arabidopsis thaliana. [swissprot:O22943] and [swissprot:Q9SCN0] and named STELLO1 (STL1) and STELLO2 (STL2) respectively. They are Golgi-localized proteins that can interact with CesAs (cellulose synthase A) and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. STL homologues are present throughout the plant kingdom, but STL proteins are distinct from distantly related proteins in nematodes, fungi and molluscs.
Pfam PF23232: Fungal AAA+ ATPase lid domain (domain)
This is the lid domain found C-terminal to the AAA domain ([pfam:PF00004]) in a group of fungal proteins. This domain is predicted to adopt an alpha-helical configuration.
Pfam PF12614: Ribosome recycling factor (family)
This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Pfam PF07886: BA14K-like protein (family)
The sequences found in this family are similar to the BA14K proteins expressed by Brucella abortus ([swissprot:Q44701]) and by Brucella suis ([swissprot:Q8FVU0]).  BA14K was found to be strongly immunoreactive; it induces both humoral and cellular responses in hosts throughout the infective process.
Pfam PF00088: Trefoil (P-type) domain (domain)
A cysteine-rich domain of approximately forty five amino-acid residues has been found in some extracellular eukaryotic proteins . It is known as either the 'P', 'trefoil' or 'TFF' domain, and contains six cysteines linked by three disulphide bonds with connectivity 1-5, 2-4, 3-6. This leads to a characteristic three leafed structure ('trefoil'). The P-type domain is clearly composed of three looplike regions. The central core of the domain consists of a short two-stranded antiparallel Î²-sheet, which is capped by an irregular loop and forms a central hairpin (loop 3). The Î²-sheet is preceded by a short Î±-helix, with majority of the remainder of the domain contained in two loops, which lie on either side of the central hairpin.

This domain has been found in a variety of extracellular eukaryotic proteins , including:


 * Protein pS2 (TFF1), a protein secreted by the stomach mucosa
 * Spasmolytic polypeptide (SP) (TFF2), a protein of about 115 residues that inhibits gastrointestinal motility and gastric acid secretion
 * Intestinal trefoil factor (ITF) (TFF3)
 * Xenopus laevis stomach proteins xP1 and xP4
 * Xenopus integumentary mucins A.1 (FIM-A.1 or preprospasmolysin) and C.1 (FIM-C.1), proteins which may be involved in defence against microbial infections by protecting the epithelia from the external environment
 * Xenopus skin protein xp2 (or APEG)
 * Zona pellucida sperm-binding protein B (ZP-B)
 * Intestinal sucrase-isomaltase (3.2.1.48 / 3.2.1.10), a vertebrate membrane bound, multifunctional enzyme complex which hydrolyses sucrose, maltose and isomaltose
 * Lysosomal alpha-glucosidase (3.2.1.20)
Wikipedia: The trefoil knot fold is a protein fold in which the protein backbone is twisted into a trefoil knot shape. "Shallow" knots in which the tail of the polypeptide chain only passes through a loop by a few residues are uncommon, but "deep" knots in which many residues are passed through the loop are extremely rare. Deep trefoil knots have been found in the SPOUT superfamily. including methyltransferase proteins involved in posttranscriptional RNA modification in all three domains of life, including bacterium Thermus thermophilus and proteins, in archaea and in eukaryota.
Pfam PF03176: MMPL family (family)
Members of this family are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport.
Pfam PF20516: PD-(D/E)XK nuclease superfamily (domain)
This entry contains a large family of uncharacterised fungal proteins. Structure prediction suggests it is likely to be an endonuclease enzyme related to the PD-(D/E)XK nuclease superfamily.
Pfam PF22756: E217 gateway protein gp29 (family)
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. The gateway protein gp29 is a neck factor of the E217 virion that connects the neck to the sheath lattice.
Pfam PF24679: Nodulin C-terminal domain (domain)
This domain is found in the Nodulin homeodomain protein from Arabidopsis thaliana and related plant proteins. Nodulin regulates COOLAIR, a set of antisense transcripts originating from the 3' end of FLOWERING LOCUS C. It associates with single-stranded DNA that is part of an RNA-DNA hybrid, or R-loop, that covers the COOLAIR promoter. This domain has a detectable partial sequence similarity to PUA domains but it is predicted to adopt a beta-barrel with SH3 topology.
Pfam PF10591: Secreted protein acidic and rich in cysteine Ca binding region (domain)
The SPARC_Ca_bdg domain of Secreted Protein Acidic and Rich in Cysteine is responsible for the anti-spreading activity of human urothelial cells. It is rich in alpha-helices. This extracellular calcium-binding domain contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2.
Pfam PF02083: Urotensin II (family)
Urotensin II (UII) is a vasoactive somatostatin-like or cortistatin-like peptide hormone. However, despite the apparent structural similarity to these peptide hormones, they are not homologous to UII. Urotensin II was first identified in fish spinal cord but later found in humans and other mammals . In fish, UII is secreted at the back part of the spinal cord, in a neurosecretory centre called uroneurapophysa, and is involved in the regulation of the renal and cardiovascular systems . In mammals, urotensin II is the most potent mammalian vasoconstrictor identified to date and causes contraction of arterial blood vessels, including the thoracic aorta .
This entry represents urotensin II.
Pfam PF24095: Domain of unknown function (DUF7378) (domain)
This domain is found in uncharacterised plant proteins. It is predicted to contain transmembrane helices that assemble in a four helical bundle.
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 PF21736: REC102 protein (domain)
The REC102 protein is required for formation of the SPO11-mediated double-strand breaks (DSBs) that initiate meiotic recombination. May mediate the interaction between SPO11 subunits during meiosis. Also needed for homolog chromosome pairing, synaptonemal complex formation, and for the proper timing of the first meiotic division. Not required for mitosis and mitotic DNA repair mechanisms.
Pfam PF23139: ATP-dependent DNA helicase YrrC, OB-fold domain (domain)
This entry represents a domain which is found N-terminal in ATP-dependent DNA helicase YrrC and related proteins. This domain is predicted to adopt a beta-barrel with an OB-fold topology.
Pfam PF23212: Domain of unknown function (DUF7064) (domain)
This is a domain of unknown function found in fungi and bacteria, which, according to structure predictions it adopts a lipocalin-like fold. This domain is found as a pair of two flattened, orthogonally packed, beta-barrels. This entry represents the C-terminal barrel of the pair.
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 PF09929: Putative PD-(D/E)XK phosphodiesterase (DUF2161) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in prokaryotes. Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses s have established this family to be a member of the PD-(D/E)XK superfamily.
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 PF03401: Tripartite tricarboxylate transporter family receptor (family)
These probable extra-cytoplasmic solute receptors are strongly overrepresented in several beta-proteobacteria.  This family, formerly known as Bug - Bordetella uptake gene (bug) product - is a family of bacterial tripartite tricarboxylate receptors of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. The TctABC system has been characterised in S. typhimurium, and TctC is the extracytoplasmic tricarboxylate-binding receptor which binds the transporters TctA and TctB, two integral membrane proteins. Complete three-component systems are found only in bacteria.
Pfam PF09743: E3 UFM1-protein ligase 1 (family)
The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme.
Pfam PF08737: Rgp1 (family)
Rgp1 forms heterodimer with Ric1 ([pfam:PF07064]) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor.
Pfam PF13223: Protein of unknown function (DUF4031) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 91 and 130 amino acids in length. There is a conserved HYD 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 PF22201: Conserved flagellar protein F, immunoglobulin-like domain (domain)
This domain is found in Conserved flagellar protein F from Sulfolobus acidocaldarius (FlaF, [swissprot:Q4J9K8]) and similar archaeal proteins. FlaF is essential for archaellum assembly with an extended N-terminal alpha-helix connected to a globular domain (this entry). This domain adopts a beta-sandwich fold with eight anti-parallel beta-strands in two sheets.
Pfam PF08071: RS4NT (NUC023) domain (domain)
This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains.
Pfam PF02803: Thiolase, C-terminal domain (domain)
Thiolase is reported to be structurally related to beta-ketoacyl synthase ([pfam:PF00109]), and also chalcone synthase.
Wikipedia: In molecular biology, Beta-ketoacyl-ACP synthase EC 2.3.1.41, is an enzyme involved in fatty acid synthesis. It typically uses malonyl-CoA as a carbon source to elongate ACP-bound acyl species, resulting in the formation of ACP-bound β-ketoacyl species such as acetoacetyl-ACP.
Pfam PF18413: Neuraminidase-like domain (repeat)
This is a neuraminidase-like domain, which is structurally homologous to neuraminidases. It can be found in TcA subunit in tripartite Tc toxin complexes of bacterial pathogens. Functional analysis suggest that the neuraminidase-like domain acts as an electrostatic lock that opens at high or low pH values.
Wikipedia: Exo-α-sialidase is a glycoside hydrolase that cleaves the glycosidic linkages of neuraminic acids:Hydrolysis of α-(2→3)-, α-(2→6)-, α-(2→8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates