SII-SWORD/CoKE huggingface dataset:
Pfam PF09597: Small ribosomal subunit protein mS41 SAM domain (domain)
This entry represents a SAM-like domain found in fungal mitoribosome protein mS41.  The mitochondrion-specific ribosomal protein mS41 family comprises proteins that are integral components of the mitochondrial ribosome, also known as the mitoribosome. These proteins play a crucial role in the dedicated translation machinery that synthesizes mitochondrial genome-encoded proteins, which include essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are tethered to the mitochondrial inner membrane, ensuring that translation products are cotranslationally integrated into the membrane. Additionally, members of the mS41 family are implicated in the regulation of telomere length, a process essential for maintaining chromosome stability and cellular lifespan. Certain members are also required for survival upon exposure to specific environmental stressors, such as the K1 killer toxin.
Pfam PF15810: Coiled-coil domain-containing protein 117 (family)
CCDC117 is a family of coiled-coil proteins found in eukaryotes. Proteins in this family are typically between 203 and 279 amino acids in length. There is a conserved MELV sequence motif. The function is not known.
Pfam PF21477: FAK1/PYK2, FERM domain C-lobe (domain)
FAK1 (focal adhesion kinase 1) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells and it is involved in diverse cellular roles. The N-terminal region of FAK1 contains a FERM domain which is subdivided FERM_N or A-lobe, FERM_M or B-lobe and FERM_C or C-lobe. This entry represents the C-lobe, which is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. This domain is also present in protein-tyrosine kinase 2-beta (also known as PYK2),  a cytoplasmic, non-receptor tyrosine kinase which is a close paralogue to FAK in vertebrates. FRMPD1/3/4 also contain this domain; FRMPD1 regulates the subcellular location of activator of G-protein signaling 3 and its interaction with G-proteins. FRMPD4 has been shown to regulate dendritic spine morphogenesis and the function of FRMPD3 is not clear.
Pfam PF02901: Pyruvate formate lyase-like (family)
This family of enzymes includes pyruvate formate lyase, choline trimethylamine lyase, glycerol dehydratase, 4-hydroxyphenylacetate decarboxylase, and benzylsuccinate synthase.
Pfam PF20024: Family of unknown function (DUF6432) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 100 amino acids in length. Members in this family are thought to belong to the MarR family of transcriptional regulators.
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 PF04553: Tis11B like protein, N terminus (family)
Members of this family always contain a tandem repeat of CCCH zinc fingers [pfam:PF00642].  Tis11B, Tis11D and their homologues are thought to be regulatory proteins involved in the response to growth factors.  The function of the N terminus is unknown.
Pfam PF07095: Intracellular growth attenuator protein IgaA (family)
This family consists of several bacterial intracellular growth attenuator  (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the E. coli YrfF and P. mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in S. enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria.
Pfam PF13136: Protein of unknown function (DUF3984) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 393 and 442 amino acids in length.
Pfam PF06461: CHD subfamily II, SANT-like domain (domain)
CHD proteins (name derived from the presence of a Chromodomain, SWI2/SNF2 ATPase/Helicase and a motif with sequence similarity to a DNA)binding domain) are ATP-dependent chromatin remodelers found in plant and animals. In eukaryotes, there are three subfamilies, I, II and III. This domain is found in members of subfamily II which play a role in repression of genes involved in developmental regulation, including Mi-2 from Drosophila melanogaster, CHD3/4/5 from animals and PICKLE (a CHD3/4-related protein) from Arabidopsis. Sequence analysis revealed that this domain has a considerable similarity to SANT domains suggesting that it fold into this type of domain and it is integral to the DNA binding domain of CHD remodelers in subfamily II.
Pfam PF22625: Exosome RNA binding protein RRP4 N-terminal domain (domain)
This domain is found N-terminal in exosome RNA binding protein RRP4 and related proteins. RRP4 is a part of the exosome regulatory substrate recognition platform. This domain is structurally similar to ribosomal L27 protein.
Pfam PF16307: Domain of unknown function (DUF4949) (family)
This small family consists of uncharacterized proteins around 140 residues in length and is mainly found in various Legionella pneumophila and longbeachae species. The function of this family is unknown.
Pfam PF06836: Protein of unknown function (DUF1240) (family)
This family consists of a number of hypothetical putative membrane proteins which seem to be specific to Photorhabdus and Yersinia species. The function of this family 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 PF20694: TRADD-like N-terminal domain (domain)
This is the RRM fold domain prototyped by the version at the N-terminus of the TRADD protein. The TRADD-N domain is widely present in bacterial conflict systems and in a spectacular diversity of counter-invader systems in metazoa, especially in aggregating marine invertebrates. The domain is predicted to function as a signalling bridge linking invader sensing and effector deployment in multidomain proteins. Metazoans have two broad families of TRADD-N domains, the NCOA6 and the TRADD/DEDD-2 families respectively that are named after the prototypic vertebrate proteins in which they are found.
Pfam PF20365: Family of unknown function (DUF6660) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. 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 PF25157: Schizosaccharomyces Vps8, C-terminal domain (domain)
This domain is found towards the C-terminal end of Vacuolar protein sorting-associated protein 8 from Schizosaccharomyces pombe (Vps8), which is involved in the retention of proteins to the late-Golgi.
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 PF15280: Protein aurora borealis N-terminus (family)
This family of proteins is required for the activation of the protein kinase Aurora-A.
Pfam PF17632: Family of unknown function (DUF5513) (family)
This is a family of unknown function found in Bacillus.
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 PF14758: Non-essential region of nsp2 of arterivirus polyprotein (domain)
This non-essential region of the nsp2 subunit of the arterivirus polyprotein of such as porcine arterivirus PRRSV and equine arterivirus EAV may offer immunogenic surfaces to B-cells. It is associated with Peptidase_C33, [pfam:PF05412].
Pfam PF03481: Threonylcarbamoyl-AMP synthase, C-terminal domain (domain)
This domain can be found in the C terminus of threonylcarbamoyl-AMP synthases, including Sua5 from Saccharomyces cerevisiae and YwlC from Bacillus subtilis. Threonylcarbamoyl-AMP synthase is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t6A37) in tRNAs that read codons beginning with adenine. This domain adopts the Rossmann fold and may be involved in GTP and/or tRNA binding based on structural similarity with both GTP and tRNA binding proteins.
Pfam PF04109: Autophagy protein ATG9 (family)
In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in  eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, and it is the sole transmembrane protein in the autophagosome-forming machinery. It colocalises with Atg2 at the expanding edge of the isolation membrane where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Atg9 is a lipid scramblase that translocates phospholipids between outer and inner leaflets of liposomes. Phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, driving autophagosomal membrane expansion.
Pfam PF11948: Protein of unknown function (DUF3465) (domain)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif. These proteins are predicted to adopt a globular structure with OB-fold topology.
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 PF11046: Transcriptional repressor of hyc and hyp operons (family)
This family is conserved in Proteobacteria. It is likely to be the transcriptional repressor molecule for the hyc and hyp operons, which express, amongst others, the protein HycA. This protein may be harnessed for the reduction of technetium oxide, an unwelcome product of radio-nucleotide bioaccumulation. HycA produces formate hydrogenlyase, one of the key proteins necessary for metal compound reduction.
Pfam PF09507: DNA polymerase subunit Cdc27 (family)
This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.
Pfam PF06816: NOTCH protein (family)
NOTCH  signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated.
Pfam PF17275: Family of unknown function (DUF5340) (family)
This family of unknown function can be found in Cyanobacteria.
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 PF23662: Domain of unknown function (DUF7152) (domain)
This domain is found in plant proteins that are probably related to NOMO family of proteins. The latter are components of the multi-pass translocon (MPT) complex which mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes. The domain represented by this entry is predicted to adopt a globular beta-sandwich structure with a prealbumin-like topology.
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 PF05360: yiaA/B two helix domain (domain)
This domain consists of two transmembrane helices and a conserved linking section.
Pfam PF00559: Retroviral Vif (Viral infectivity) protein (family)
Human immunodeficiency virus type 1 (HIV-1) Vif is required for productive infection of T lymphocytes and macrophages. Virions produced in the absence of Vif have abnormal core morphology and those produced in primary T cells carry immature core proteins and low levels of mature capsid.
Wikipedia: Viral infectivity factor, or Vif, is an accessory protein found in HIV and other lentiviruses. Its role is to disrupt the antiviral activity of the human enzyme APOBEC by targeting it for ubiquitination and cellular degradation. APOBEC is a cytidine deaminase enzyme that mutates viral nucleic acids.
Pfam PF06817: Reverse transcriptase thumb domain (domain)
This domain is known as the thumb domain. It is composed of a four helix bundle.
Pfam PF21028: Protein of unknown function (DUF1285), C-terminal domain (domain)
This domain is found at the C-terminal end of several hypothetical bacterial proteins. The structure revealed a superficial similarity of this domain to pleckstrin homology-like folds.
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 PF14437: MafB19-like deaminase (family)
A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Neisseria MafB19. Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems.
Pfam PF10553: MSV199 domain (domain)
This domain was identified by Iyer and colleagues.
Pfam PF21912: Glycosyltransferase 99 family N-terminal domain (domain)
This entry represents the Glycosyltransferase 99 family N-terminal domain, which is found in a new family of glycosyltransferases (GTs) assigned as family GT99 in the CAZy database. The GT99 family includes a prototype beta-Kdo GT from WbbB, a modular protein participating in lipopolysaccharide (LPS) O-antigen synthesis in Raoultella terrigena. Kdo (3-deoxy-D-manno-oct-2-ulosonic acid) is an eight-carbon sugar mostly found in Gram-negative bacteria, where it is involved in attaching surface polysaccharides to their lipid anchors. Alpha-Kdo provides a bridge between lipid A and the core oligosaccharide in all bacterial LPSs, while an oligosaccharide of beta-Kdo residues links group 2 capsular polysaccharides to (lyso)phosphatidylglycerol. beta-Kdo is also found in a small number of other bacterial polysaccharides. The structure and function of the prototypical cytidine monophosphate-Kdo-dependent alpha-Kdo glycosyltransferase from LPS assembly is well characterized. The WbbB2-401 protein structure is built around two alpha/beta domains with recognizable Rossmann-fold topology, broadly meeting the criteria of conforming to a GT-B fold.
Pfam PF15964: Centrosomal colon cancer autoantigen protein family (coiled_coil)
CCCAP is a family of proteins found in eukaryotes. CCCAP is also known as SDCCAG8, serologically defined colon cancer antigen 8. It is associated with the centrosome.
Pfam PF17183: Get5, C-terminal domain (domain)
This entry represents the C-terminal domain of Get5 from Aspergillus fumigatus and similar proteins found mainly in Ascomycetes. Get5 is a component of the get4/get5/sgt2 sorting complex involved in the GET (guided entry of TA proteins) pathway that leads to the insertion of tail-anchored proteins into the endoplasmic reticulum.
Pfam PF17808: Fn3-like domain from Purple Acid Phosphatase (domain)
This entry represents an N-terminal Fn3-like domain found at the N-terminus of purple acid phosphatase enzymes.
Pfam PF06626: Protein of unknown function (DUF1152) (family)
This family consists of several hypothetical archaeal proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF03313: Serine dehydratase alpha chain (domain)
L-serine dehydratase ([ec:4.2.1.13]) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. Members included in this entry adopt and all-helical structure.
Pfam PF17402: Family of unknown function (DUF5408) (family)
This is a family of unknown function found in Helicobacteraceae. Family members are predicted to contain one trans-membrane region.
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 PF03024: Folate receptor family (domain)
This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anchor. The proteins contain 16 conserved cysteines that form eight disulphide bridges.
Wikipedia: Folate receptors bind folate and reduced folic acid derivatives and mediates delivery of tetrahydrofolate to the interior of cells. It is then converted from monoglutamate to polyglutamate forms - such as 5-methyltetrahydrofolate - as only monoglutamate forms can be transported across cell membranes. Polyglutamate forms are biologically active enzymatic cofactors required for many folate-dependent processes such as folate-dependent one-carbon metabolism. These proteins are attached to the membrane by a GPI anchor. A riboflavin-binding protein required for the transport of riboflavin to the developing oocyte in chicken also belong to this family.
Pfam PF13306: BspA type Leucine rich repeat region (6 copies) (repeat)
This family includes a number of leucine rich repeats. This family contains a large number of BSPA-like surface antigens from Trichomonas vaginalis.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF24891: Domain of unknown function (DUF7742) (domain)
This entry represents a likely uncharacterised phage protein. The protein is composed of three alpha helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12111: Polyribonucleotide phosphorylase C terminal (domain)
PNPase regulates the expression of small non-coding RNAs that control expression of outer-membrane proteins. The enzyme also affects complex processes, such as the tissue-invasive virulence of Salmonella enterica and the regulation of a virulence-factor secretion system in Yersinia. In Escherichia coli, PNPase is involved in the quality control of ribosomal RNA precursors and is required for growth following cold shock. This family contains the C terminal protomer domain of the PNPase core.  The function of the C terminal protomer is to catalyse phosphorolysis through its two active sites.