SII-SWORD/CoKE huggingface dataset:
Pfam PF23009: Ubiquitin conjugating domain-like (domain)
This entry represents a domain that structurally resembles the ubiquitin conjugating enzyme domain [pfam:PF00179] and the RWD domain [pfam:PF05773]. This domain is somewhat smaller and apparently lacks the conserved cysteine that is used for ubiquitin conjugation.  This domain is commonly found in the LTN1 family that comprises E3 ubiquitin-protein ligases involved in the ribosome quality control complex (RQC). The RQC is a ribosome-associated complex that targets incompletely synthesized nascent chains for proteasomal degradation. Members of the LTN1 family are responsible for ubiquitinating stalled nascent chains on the 60S ribosomal subunit, a process facilitated by the recruitment of NEMF in some species. This ubiquitination signals the recruitment of cellular machinery such as VCP/p97, TER94/VCP, or CDC48, depending on the organism, to extract and degrade the incomplete translation products. The LTN1 family plays a crucial role in maintaining protein synthesis fidelity by ensuring the removal of defective ribosomal products, thereby preventing the accumulation of potentially toxic protein fragments within the cell.
Pfam PF00339: Arrestin (or S-antigen), N-terminal domain (domain)
Ig-like beta-sandwich fold.  Scop reports duplication with C-terminal domain.
Wikipedia: Arrestins are a small family of proteins important for regulating signal transduction at G protein-coupled receptors.
Arrestins were first discovered as a part of a conserved two-step mechanism for regulating the activity of G protein-coupled receptors (GPCRs) in the visual rhodopsin system by Hermann Kühn, Scott Hall, and Ursula Wilden and in the β-adrenergic system by Martin J. Lohse and co-workers.
Pfam PF20650: Family of unknown function (DUF6810) (family)
This is a highly conserved domain of unknown function found in bacteria from the phylum Chloroflexi. This domain contains the motifs ExRFY and WxEG.
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 PF16148: Domain of unknown function (DUF4856) (family)
This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this family is unknown.
Pfam PF15740: Protein phosphatase 1 regulatory subunit 26 N-terminus (family)
This domain represents the N-terminus of protein phosphatase 1 regulatory subunit 26.
Pfam PF08490: Domain of unknown function (DUF1744) (domain)
This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to [pfam:PF03104] and [pfam:PF00136].
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 PF11512: Agrobacterium tumefaciens protein Atu4866 (family)
Atu4866 is a protein with unknown function from Agrobacterium tumefaciens however the structure has been determined. Atu4866 adopts a streptavidin-like fold and has a beta-barrel/sandwich which is formed by eight antiparallel beta-strands. Atu4866 has a potential ligand-binding site where is has a stretch of conserved residues on the surface.
Pfam PF10436: Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase (family)
Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. This is the butyryl-CoA dehydrogenase, subunit A domain 3, a largely alpha-helical bundle of the enzyme BCDHK. This enzyme is the regulator of the dehydrogenase complex that breaks branched-chain amino-acids down, by phosphorylating and thereby inactivating it when synthesis is required. The domain is associated with family HATPase_c [pfam:PF02518] which is towards the C-terminal.
Pfam PF16832: Erythroid krueppel-like transcription factor, transactivation 1 (conserved_site)
This family is the first part of the minimal transactivation domain of erythroid-specific transcription factor EKFL in craniates. EKLF plays an important role in red blood cell development; it is posttranslationally modified by UBI on several lysine residues, and its turnover in the cell is regulated by ubiquitin-mediated degradation. In the first 90 residues at the N-terminus EKLF carries a minimal transactivation or TAD domain that is highly acidic. This minimal TAD of EKLF can be further subdivided into two independent domains EKLF_TAD1 (residues 1-40) and EKLF_TAD2 (residues 51-90), [pfam:PF16833], that are both capable of independently activating transcription.  TAD1, is able to form a non-covalent interaction with ubiquitin. Both TAD1 and TAd2 are highly acidic and carry a PEST (sequence rich in proline, glutamic acid, serine, and threonine) region. Deletion of either PEST domain significantly slows down degradation of EKLF by ubiquitin. The minimal TAD has an overlapping activation/degradation function that is critical for the role of EKLF in red blood cell development.
Pfam PF20235: PIR2-like, helical domain (domain)
This helical domain is found at the N-terminal of plant E3-ligase proteins, including PP2CA INTERACTING RING FINGER PROTEIN 2 (PIR2, also known as MND1-interacting protein 1) and its paralogues RF4 and RF298 from Arabidopsis. The  function of this domain is unknown. PIR2 is the closest homologue of PIR1 (PP2CA interacting RING finger protein 1) and both positively modulate ABA signaling by targeting PP2CA for degradation.
Pfam PF06935: Protein of unknown function (DUF1284) (family)
This family consists of several hypothetical bacterial and archaeal proteins of around 130 residues in length. The function of this family is unknown, although it is thought that they may be iron-sulphur binding 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 PF08365: Insulin-like growth factor II E-peptide (family)
This domain is found at the C-terminal domain of the insulin-like growth factor II (IGF-2, also see [pfam:PF00049]) in vertebrates and seems to represent the E-peptide.
Wikipedia: Insulin-like growth factor 2 (IGF-2) is one of three protein hormones that share structural similarity to insulin. The MeSH definition reads: "A well-characterized neutral peptide believed to be secreted by the liver and to circulate in the blood. It has growth-regulating, insulin-like and mitogenic activities. The growth factor has a major, but not absolute, dependence on somatotropin. It is believed to be a major fetal growth factor in contrast to insulin-like growth factor 1 (IGF-1), which is a major growth factor in adults."
Pfam PF23357: Domain of unknown function (DUF7088) (domain)
This domain is found at the N-terminal of a group of poorly characterised bacterial sequences. The function of this domain is unknown.
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 PF07779: 10 TM Acyl Transferase domain found in Cas1p (family)
Cas1p protein of Cryptococcus neoformans is required for the synthesis of O-acetylated glucuronoxylomannans, a consitutent of the capsule, and is critical for its virulence. The multi TM domain of the Cas1p was unified with the 10 TM Sugar Acyltransferase  superfamily. This superfamily is comprised of members from the  OatA, MdoC, OpgC, NolL and GumG families in addition to the Cas1p family. The Cas1p protein has a N terminal PC-Esterase domain with the opposing Acyl esterase activity.
Pfam PF09619: Type III secretion system lipoprotein chaperone (YscW) (family)
This entry is encoded within type III secretion operons. The protein has been characterised as a chaperone for the outer membrane pore component YscC. YscW is a lipoprotein which is itself localized to the outer membrane and, it is believed, facilitates the oligomerisation and localisation of YscC.
Pfam PF24864: Domain of unknown function (DUF7730) (domain)
This domain is found in uncharacterised fungal proteins. It contains a highly conserved EXR 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 PF23984: Pam3 gp33-like protein (family)
This entry represents a set of uncharacterised phage proteins that are related to the Pam3 phage gp33 protein.
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 PF02847: MA3 domain (repeat)
Domain in DAP-5, eIF4G, MA-3 and other proteins.  Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains.
Pfam PF03210: Paramyxovirus P/V phosphoprotein C-terminal (family)
Paramyxoviridae P genes are able to generate more than one product, using alternative reading frames and RNA editing. The P gene encodes the structural phosphoprotein P. In addition, it encodes several non-structural proteins present in the infected cell but not in the virus particle. This family includes phosphoprotein P and the non-structural phosphoprotein V from different paramyxoviruses.  Phosphoprotein P is essential for the activity of the RNA polymerase complex which it forms with another subunit, L [pfam:PF00946]. Although all the catalytic activities of the polymerase are associated with the L subunit, its function requires specific interactions with phosphoprotein P. The P and V phosphoproteins are amino co-terminal, but diverge at their C-termini. This difference is generated by an RNA-editing mechanism in which one or two non-templated G residues are inserted into P-gene-derived mRNA. In measles virus and Sendai virus, one G residue is inserted and the edited transcript encodes the V protein. In mumps, simian virus type 5 and Newcastle disease virus, two G residues are inserted, and the edited transcript codes for the P protein. Being phosphoproteins, both P and V are rich in serine and threonine residues over their whole lengths. In addition, the V proteins are rich in cysteine residues at the C-termini. This C-terminal region of the P phosphoprotein is likely to be the nucleocapsid-binding domain, and is found to be intrinsically disordered and thus liable to induced folding.
Pfam PF08653: DASH complex subunit Dam1 (family)
The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.  Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules.
Pfam PF05016: ParE toxin of type II toxin-antitoxin system, parDE (domain)
ParE is the toxin family of a type II toxin-antitoxin family. It is toxic towards DNA gyrase, but is neutralised by the antitoxin ParD. The family also encompasses RelE/ParE described in.
Wikipedia: The parDE type II toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). These systems preferentially guarantee growth of plasmid-carrying daughter cells in a bacterial population by killing newborn bacteria that have not inherited a plasmid copy at cell division.
Pfam PF20036: Major capsid protein 13-like (family)
This family represents phage capsid/coat proteins found in phages but also in bacteria. Included in this family is the Major capsid protein 13 from Bacillus phage SPP1 which is part of the icosahedral capsid together with the auxiliary protein gp12, which are organized in a T=7 lattice. This family contains some conserved motifs: GD, GxxxxV/IxxD and NW.
Pfam PF16734: Type IV pilin-like G and H, putative (family)
Pilin_GH is a family from Cyanobacteria. All the proteins are putatively annotated as being general secretion pathway proteins G and H, and are likely to be pilins of the type IV secretory pathway.
Pfam PF11424: Protein of unknown function (DUF3195) N-terminal domain (domain)
This archaeal family of proteins has no known function. This entry represents the N-terminal ferredoxin-like 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 PF15604: Novel toxin 15 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses a most all-alpha helical fold and a conserved HxxD motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion systems. This is shown to be a type IV secretion system protein that behaves as DNase.
Pfam PF12592: ATPase, RavA, C-terminal (domain)
This domain is found at the C-terminal of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) and is the second subdomain that forms the discontinuous triple helical domain. RavA forms an hexamer in which the triple helical domain mediates the lateral interactions between neighbouring RavA monomers.
Pfam PF20989: Sarcoglycan alpha/epsilon second domain (domain)
Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear. This family contains alpha and epsilon members and represents the second domain which has an Ig-like fold.
Wikipedia: The sarcoglycans are a family of transmembrane proteins involved in the protein complex responsible for connecting the muscle fibre cytoskeleton to the extracellular matrix, preventing damage to the muscle fibre sarcolemma through shearing forces.
Pfam PF23300: Nucleoporin nup120-like, HEAT repeats (repeat)
These HEAT repeats form an elongated alpha-helical stack at the C-terminal end of Nucleoporin nup120 from Schizosaccharomyces pombe and similar eukaryotic sequences. Nup120 functions as a component of the nuclear pore complex (NPC).
Pfam PF04680: Opioid growth factor receptor disordered repeat (disordered)
Proline-rich repeat found only in the C-terminus of the human opioid growth factor receptor ([swissprot:Q9NZT2]).
Wikipedia: Opioid growth factor receptor, also known as OGFr or the ζ-opioid receptor, is a protein which in humans is encoded by the OGFR gene. The protein encoded by this gene is a receptor for opioid growth factor (OGF), also known as [Met(5)]-enkephalin. The endogenous ligand is thus a known opioid peptide, and OGFr was originally discovered and named as a new opioid receptor zeta (ζ). However it was subsequently found that it shares little sequence similarity with the other opioid receptors, and has quite different function.
Pfam PF24694: PITM 1-3, LNS2 domain (domain)
This entry represents the LNS2 domain found at the C-terminal of Membrane-associated phosphatidylinositol transfer protein 1-3 (PITM1-3, class II PITPs) and RDGB from Drosophila. This domain, in contrast to lipins where it was first described, in class II PITPs can bind phosphatidic acid (PA) but not hydrolyse it. RDGB is required to regulate phosphoinositide turnover during G-protein activated phospholipase C signalling. PITM 1-3 catalyse the transfer of phosphatidylinositol (PI) between membranes.
Pfam PF24857: Threonine synthase, C-terminal (domain)
This domain is found at the C-terminal end of Threonine synthase from Saccharomyces cerevisiae (THR4), which catalyses the gamma-elimination of phosphate from L-phosphohomoserine and the beta-addition of water to produce L-threonine. This domain shows an alpha-beta configuration with a combined beta-sheet and an in-between helix.
Pfam PF24207: Family of unknown function (DUF7430) (family)
This entry represents a family of uncharacterised phage 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 PF20369: Family of unknown function (DUF6664) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 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 PF23734: Domain of unknown function (DUF7163) (domain)
This domain is found N-terminal in a group of uncharacterised proteins from Trypanosomes. It has a very weak similarity to the vWA-like domain of the SSL1 subunit of general transcription and DNA repair factor IIH and it is predicted to adopt a structure with similarity to known vWA-like 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 PF01949: Protein of unknown function DUF99 (family)
This family includes uncharacterised archaebacterial proteins. Sequence and structure analysis to identify RNase H-like superfamily members, has clustered this family in endonuclease Clade V, thus suggesting endonuclease activity of these 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 PF21308: Complement component 3, CUB domain, second segment (domain)
Complement C3 is major component in the both the classical and alternative complement activation pathways. C3 is cleaved into two chains (alpha and beta) by C3 convertases. This entry represents the second segment of the CUB domain, which is completed by [pfam:PF21406]. The CUB domain is interrupted by the TE domain. The CUB, TE and MG8 domains form a massive, tightly packed super domain. This entry also includes venom factors, also known as Complement C3 homologues. These are complement-activating proteins with structural and functional similarities to complement component C3b, the activated form of C3.
Pfam PF10720: Protein of unknown function (DUF2515) (family)
This family is conserved in Firmicutes. Several members are annotated as YppC. The function is not known.
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 PF11358: Protein of unknown function (DUF3158) (family)
Some members in this family of proteins are annotated as integrase regulator R however this cannot be confirmed. This family of proteins with unknown function appear to be restricted to Proteobacteria.
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 PF00584: SecE/Sec61-gamma subunits of protein translocation complex (family)
SecE is part of the SecYEG complex in bacteria which translocates proteins from the cytoplasm. In eukaryotes the complex, made from Sec61-gamma and Sec61-alpha  translocates protein from the cytoplasm to the ER.  Archaea have a similar complex.
Wikipedia: Sec61, termed SecYEG in prokaryotes, is a membrane protein complex found in all domains of life. As the core component of the translocon, it transports proteins to the endoplasmic reticulum in eukaryotes and out of the cell in prokaryotes. It is a doughnut-shaped pore through the membrane with 3 different subunits (heterotrimeric), SecY (α), SecE (γ), and SecG (β). It has a region called the plug that blocks transport into or out of the ER. This plug is displaced when the hydrophobic region of a nascent polypeptide interacts with another region of Sec61 called the seam, allowing translocation of the polypeptide into the ER lumen.