SII-SWORD/CoKE huggingface dataset:
Pfam PF14946: Domain of unknown function (DUF4501) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 167 and 308 amino acids in length. The exact function of this protein remains unknown, but it is thought to be a single-pass membrane protein. This family contains many highly conserved cysteine residues.
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 PF10134: Replication initiator protein A (family)
Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.
Pfam PF05102: holin, BlyA family (family)
BlyA, a small holin found in Borrelia circular plasmids that is encoded by a prophage.  BlyA contains two largely hydrophobic helices and a highly charged C-terminus and has two transmembrane segments.
Pfam PF00977: Histidine biosynthesis protein (family)
Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes.  The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold.  In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel e.g. [swissprot:P05325]. This family belong to the common phosphate binding site TIM barrel family.
Pfam PF12170: DNA polymerase III tau subunit V interacting with alpha (family)
This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with [pfam:PF00004]. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme.
Wikipedia: The τ and γ subunits are part of the DNA polymerase III holoenzyme of prokaryotes. The protein family is characterized by the well-conserved first N-terminal domain, approx. 365 amino acids. The eukaryotic equivalent to the DNA clamp loader is replication factor C, with the subunits RFC1, RFC2, RFC3, RFC4, and RFC5.
Pfam PF20055: Family of unknown function (DUF6454) (repeat)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 294 and 372 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 PF10251: Presenilin enhancer-2 subunit of gamma secretase (family)
This entry is a short 101 peptide protein which is the smallest subunit of the gamma-secretase aspartyl protease complex that catalyses the intramembrane cleavage of a subset of type I transmembrane proteins. The other active constituents of the complex are presenilin (PS) nicastrin and anterior pharynx defective-1 (APH-1) protein. PEN-2 adopts a hairpin orientation in the membrane with its N- and C-terminal domains facing the luminal/extracellular space, and the C-terminal domain maintains PS stability within the complex.
Pfam PF02421: Ferrous iron transport protein B (domain)
Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
Pfam PF16368: Cytoplasmic polyadenylation element-binding protein 1 N-terminus (family)
This is the N-terminal domain of cytoplasmic polyadenylation element-binding protein 1.
Wikipedia: Cytoplasmic polyadenylation element-binding protein 1 is a protein that in humans is encoded by the CPEB1 gene.
Pfam PF24036: Domain of unknown function (DUF7345) (domain)
This is a presumed domain found in uncharacterised proteins from archaea. It may adopt a ferredoxin-like fold.
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 PF11368: Protein of unknown function (DUF3169) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is 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 PF06841: T4-like virus tail tube protein gp19 (family)
This family consists of several tail tube protein gp19 sequences from the T4-like viruses.  This family also contains bacterial members which suggest lateral transfer of genes.
Pfam PF05532: CsbD-like (domain)
CsbD is a bacterial general stress response protein.  It's expression is mediated by sigma-B, an alternative sigma factor. The role of CsbD in stress response is  unclear.
Pfam PF16983: Molybdate transporter of MFS superfamily (family)
MFS_MOT1 is a family of molybdenate transporters. Molybdenum is an essential element that is taken up into the cell in the oxyanion molybdate. Molybdenum is used in the form of molybdopterin-cofactor, which participates in the active site of enzymes involved in key reactions of carbon, nitrogen, and sulfur metabolism.
Pfam PF09970: Nucleotidyl transferase of unknown function (DUF2204) (domain)
This domain, found in various hypothetical archaeal proteins, has no known function. However, this family was identified as belonging to the nucleotidyltransferase 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 PF20518: Anaphase-promoting complex subunit 1 middle domain (repeat)
Apc1 is the largest of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. Apc1 consists of a N-terminal WD40 beta-propeller domain, followed by the middle domain (Mid-N), a PC domain and the C-terminal domain (MidC). This entry represents the middle domain of Apc1, MidN (also referred to as the first helical domain), that coaleses with the C-terminal domain to form Apc1Mid that connects Apc1WD40 with Apc1PC. Apc1Mid consists of an alpha-solenoid capped by a beta-sandwich.
Pfam PF00002: 7 transmembrane receptor (Secretin family) (domain)
This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs). They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 ([swissprot:P48960]); calcium-independent receptors for latrotoxin (such as [swissprot:O94910]), and brain-specific angiogenesis inhibitors (such as [swissprot:O14514]) amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins (e.g. [swissprot:P83119]). Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling.
Wikipedia: Secretin receptor family consists of secretin receptors regulated by peptide hormones from the glucagon hormone family. The family is different from adhesion G protein-coupled receptors.
Pfam PF07387: Seadornavirus VP7 (family)
This family consists of several Seadornavirus specific VP7 proteins of around 305 residues in length. The function of this family is unknown. However, it appears to be distantly related to protein kinases.
Pfam PF04829: Pre-toxin domain with VENN motif (family)
This family represents a conserved region found in many bacterial porlymorphic toxins which is located before the C-terminal toxin modules.
Pfam PF07986: Tubulin binding cofactor C (domain)
Members of this family are involved in the folding pathway of tubulins and form a beta helix structure.
Pfam PF22822: MrpR, N-terminal core-binding domain (domain)
This family includes the MrpR protein from      Bacillus subtilis (also known as YopR), the master repressor of the lytic cycle of  the temperate phage SPbeta. MrpR, a DNA-binding protein that has  lost its recombinase function, shows a tyrosine recombinase fold with an N-terminal core-binding (CB) domain with four alpha -helices (this entry) and a C-terminal catalytic domain.
Pfam PF18359: Histone methyltransferase Tudor domain 1 (domain)
This is the first TUDOR domain found in SETDB1 enzymes ([ec:2.1.1.43]) in homosapiens, also known as Eggless in Drosophila. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4. SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase (HMT) that methylates lysine 9 on histone H3 (H3K9). The enzymatic activity of SETDB1, in association with MBD1-containing chromatin-associated factor 1 (MCAF1), converts H3K9me2 to H3K9me3 and represses subsequent transcription. SETDB1 is amplified in cancers such as melanoma and lung cancer, and increased expression of SETDB1 promotes tumorigenesis in a zebrafish melanoma model. In addition, SETDB1 is required for endogenous retrovirus silencing during early embryogenesis, inhibition of adipocyte differentiation, and differentiation of mesenchymal cells into osteoblasts. The tandem Tudor domains in the N-terminal region are involved in protein-protein interactions. The second tudor domain is [pfam:PF18385].
Pfam PF12146: Serine aminopeptidase, S33 (domain)
This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with [pfam:PF00561]. The majority of the members in this family carry the exopeptidase active-site residues of Ser-122, Asp-239 and His-269 as in UniProtKB:Q7ZWC2.
Pfam PF21970: HOXB-AS3 peptide (family)
This family represents human HOXB-AS3 peptide, a 53-residues peptide that suppresses colon cancer (CRC) growth but is associated with a poor prognosis in oral squamous cell carcinoma (OSCC).
Pfam PF03988: Repeat of Unknown Function (DUF347) (repeat)
This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan.
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 PF24577: RNA-dependent RNA polymerase 6 second domain (domain)
This entry represents the second domain of RNA-dependent RNA polymerase 6 (RDR6) from Arabidopsis and related plant sequences. RDR6 is involved in post-transcriptional gene silencing (PTGS) and natural virus resistance. It possess ssRNA and ssDNA-dependent polymerase activity. RDR6 is required for the production of trans-acting siRNA and other siRNA. This domain has similarity to PH domains and it is predicted to adopt similar beta-barrel structure.
Pfam PF16524: Periplasmic domain of Sensor histidine kinase RisS (domain)
RisS_PPD is the periplasmic domain of the sensor histidine kinase RisS. It is purported to be the region of the kinase that senses the pH of the environs.
Pfam PF03601: Conserved hypothetical protein 698 (family)
This entry represents a family of uncharacterised multi-pass membrane proteins.
Pfam PF20288: ABC-three component (ABC-3C) system Middle Component 2 (family)
Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses.
Pfam PF24616: Domain of unknown function (DUF7624) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to adopt a globular structure composed of alpha-helices. This domain has a number of conserved positively changed residues that in the predicted structure define a large positively charged patch on the surface.
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 PF01977: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain (domain)
This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+. This entry represents the central RIFT-related domain.
Wikipedia: In molecular biology this protein domain, refers to UbiD, which is found in prokaryotes, archaea and fungi, with two members in Archaeoglobus fulgidus. They are related to UbiD, a 3-octaprenyl-4-hydroxybenzoate carboxy-lyase from Escherichia coli that is involved in ubiquinone biosynthesis. The member from Helicobacter pylori has a C-terminal extension of just over 100 residues that is shared, in part, by the Aquifex aeolicus homologue.
Pfam PF16132: Domain of unknown function (DUF4843) (domain)
This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Bacteroides species.  Distant homology analysis suggest distant relation between this family and other families of proteins with immunoglobulin-like folds, which are often involved in substrate binding. However, specific function of this family is unknown. There is distant homology to the Calx-beta family [pfam:PF03160].
Pfam PF07557: Shugoshin C terminus (conserved_site)
Shugoshin-like proteins contain this conserved sequence at the C terminus, which is rich in basic amino-acids. Shugoshin (Sgo1) protects Rec8 at centromeres during anaphase I (during meiosis) so that sister chromatids remain tethered. Sgo2 is a paralogue of Sgo1 and is involved in correctly orienting sister-centromeres.
Pfam PF10052: Protein of unknown function (DUF2288) (family)
Members of this family of hypothetical bacterial proteins have 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 PF01606: Arterivirus envelope protein (family)
This family consists of viral envelope proteins from the arterivirus genus; this includes porcine reproductive and respiratory virus (PRRSV) envelope protein GP3 and lactate dehydrogenase elevating virus (LDV) structural glycoprotein. Arteriviruses consists of positive ssRNA and do not have a DNA stage.
Pfam PF25149: Domain of unknown function (DUF7825) (repeat)
This is a presumed domain found at the C-terminal of a group of uncharacterised sequences from bacteria. It may adopt a TPR-like fold. It is found associated with [pfam:PF20103] at the N-terminal and [pfam:PF25148] in the middle.
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 PF02705: K+ potassium transporter integral membrane domain (domain)
This is a family of K+ potassium transporters that are conserved across phyla, having bacterial (KUP), yeast (HAK), and plant (AtKT) sequences as members. This entry represents the N-terminal integral membrane domain.
Wikipedia: The potassium (K+) uptake permease (KUP) family (TC# 2.A.72) is a member of the APC superfamily of secondary carriers. Proteins of the KUP/HAK/KT family include the KUP (TrkD) protein of E. coli and homologues in both Gram-positive and Gram-negative bacteria. High affinity (20 μM) K+ uptake systems (Hak1, TC# 2.A.72.2.1) of the yeast Debaryomyces occidentalis as well as the fungus, Neurospora crassa, and several homologues in plants have been characterized. Arabidopsis thaliana and other plants possess multiple KUP family paralogues. While many plant proteins cluster tightly together, the Hak1 proteins from yeast as well as the two Gram-positive and Gram-negative bacterial proteins are distantly related on the phylogenetic tree for the KUP family. All currently classified members of the KUP family can be found in the Transporter Classification Database.
Pfam PF15650: Restriction endonuclease fold toxin 9 (family)
A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion system.
Pfam PF22104: Coronavirus Nsp3 DPUP domain (domain)
Non-structural protein 3 (Nsp3) is the largest Nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Murine hepatitis virus (MHV) Nsp3 contains the so-called DPUP (Domain Preceding Ubl2 and PLP2) domain that is represented by this entry. This domain precedes the papain-like protease 2 (PLP2) catalytic domain and the ubiquitin-like domain 2 (Ubl2). DPUP domain has close structural similarity to the severe acute respiratory syndrome coronavirus unique domain C (SUD-C), suggesting that this domain may not be unique to the severe acute respiratory syndrome coronavirus. It folds into five-stranded antiparallel curved beta-sheet with two alpha-helices packed on its convex side.
Pfam PF02166: Androgen receptor (family)
Steroid or nuclear hormone receptors (NRs) constitute an important super-family of transcription regulators that are involved in diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members include the steroid hormone receptors and receptors for thyroid hormone, retinoids and 1,25-dihydroxy-vitamin D3. The proteins function as dimeric molecules in the nucleus to regulate the transcription of target genes in a ligand-responsive manner .
Wikipedia: The androgen receptor (AR), also known as NR3C4, is a type of nuclear receptor that is activated by binding any of the androgenic hormones, including testosterone and dihydrotestosterone, in the cytoplasm and then translocating into the nucleus. The androgen receptor is most closely related to the progesterone receptor, and progestins in higher dosages can block the androgen receptor.
Pfam PF02602: Uroporphyrinogen-III synthase HemD (family)
This family consists of uroporphyrinogen-III synthase HemD [ec:4.2.1.75] also known as Hydroxymethylbilane hydrolyase (cyclizing) from eukaryotes, bacteria and archaea.  This enzyme catalyses the reaction: Hydroxymethylbilane  uroporphyrinogen-III + H(2)O.  Some members of this family are multi-functional proteins possessing other enzyme activities related to porphyrin biosynthesis, such as [swissprot:Q59294] with [pfam:PF00590], however the aligned region corresponds with the uroporphyrinogen-III synthase [ec:4.2.1.75] activity only. Uroporphyrinogen-III synthase is the fourth enzyme in the heme pathway. Mutant forms of the Uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria in humans a recessive inborn error of metabolism also known as Gunther disease.
Wikipedia: Uroporphyrinogen III synthase is an enzyme involved in the metabolism of the cyclic tetrapyrrole compound porphyrin. It is involved in the conversion of hydroxymethyl bilane into uroporphyrinogen III. This enzyme catalyses the inversion of the final pyrrole unit of the linear tetrapyrrole molecule, linking it to the first pyrrole unit, thereby generating a large macrocyclic structure, uroporphyrinogen III. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains.
Pfam PF13133: Protein of unknown function (DUF3949) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 69 and 87 amino acids in length.
Pfam PF20230: Family of unknown function (DUF6588) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 332 and 351 amino acids in length. There are several conserved Gly residues and two conserved motifs, AQ and GW.
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.