SII-SWORD/CoKE huggingface dataset:
Pfam PF01154: Hydroxymethylglutaryl-coenzyme A synthase N terminal (domain)
This entry represents the N-terminal domain of HMG-CoA synthase enzymes from both eukaryotes and prokaryotes.
Hydroxymethylglutaryl-CoA synthase (2.3.3.10) catalyses the condensation of acetyl-CoA with acetoacetyl-CoA to produce HMG-CoA and CoA, the second reaction in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA synthase contains an important catalytic cysteine residue that acts as a nucleophile in the first step of the reaction: the acetylation of the enzyme by acetyl-CoA (its first substrate) to produce an acetyl-enzyme thioester, releasing the reduced coenzyme A. The subsequent nucleophilic attack on acetoacetyl-CoA (its second substrate) leads to the formation of HMG-CoA .

HMG-CoA synthase occurs in eukaryotes, archaea and certain bacteria . In vertebrates, there are two isozymes located in different subcellular compartments: a cytosolic form that is the starting point of the mevalonate pathway (leads to cholesterol and other sterolic and isoprenoid compounds), and a mitochondrial form responsible for ketone body biosynthesis. HMG-CoA is also found in other eukaryotes such as insects, plants and fungi . In bacteria, isoprenoid precursors are generally synthesised via an alternative, non-mevalonate pathway, however a number of Gram-positive pathogens utilise a mevalonate pathway involving HMG-CoA synthase that is parallel to that found in eukaryotes .
Wikipedia: In biochemistry, hydroxymethylglutaryl-CoA synthase or HMG-CoA synthase EC 2.3.3.10 is an enzyme which catalyzes the reaction in which acetyl-CoA condenses with acetoacetyl-CoA to form 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). This reaction comprises the second step in the mevalonate-dependent isoprenoid biosynthesis pathway. HMG-CoA is an intermediate in both cholesterol synthesis and ketogenesis. This reaction is overactivated in patients with diabetes mellitus type 1 if left untreated, due to prolonged insulin deficiency and the exhaustion of substrates for gluconeogenesis and the TCA cycle, notably oxaloacetate. This results in shunting of excess acetyl-CoA into the ketone synthesis pathway via HMG-CoA, leading to the development of diabetic ketoacidosis.
Pfam PF22786: Tag1 C-terminal domain (domain)
This entry represents the C-terminal Ig-like domain of Tag1. Tag1 is a vacuolar membrane protein involved in termination of autophagy. It regulates autophagy termination during persistent nitrogen starvation through Atg1p-mediated re-phosphorylation of Atg13p and PAS disassembly. It shows homology to LEA-2 domain, and together with TMEM106B from humans and Vac7 from yeast, are all predicted to be lipid transfer proteins. It was proposed that Tag1 is composed of 3 tandemly repeated LEA-2 domains.
Pfam PF11344: Protein of unknown function (DUF3146) (family)
This family of proteins with unknown function appear to be restricted to 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 PF09538: Protein of unknown function (FYDLN_acid) (family)
Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Pfam PF04276: Protein of unknown function (DUF443) (family)
Family of uncharacterised 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 PF17574: Inhibitor of toxin/antitoxin system (Gp4.5) (family)
This is a family of prokaryotic toxin-antitoxin (TA) systems inhibitors, found in Podoviridae such as Enterobacteria phage T7. Family members such as Gene product 4.5 have been shown to neutralize TA-system-mediated abortive infection by inhibiting the Lon protease activity, thus preventing antitoxin degradation and toxin activation.
Pfam PF10176: NEDD4/Bsd2 (family)
Proteins in this entry includes NEDD4 family-interacting protein 1/2 (Ndfip1 and Ndfip2) and the yeast Bsd2 metal homeostasis proteins. Ndfip1 and Ndfip2 are endosomal membrane proteins that bind to and activate members of the Nedd4 family of E3 ubiquitin ligases. Ndfip1 plays a role in regulating metal transport in human neurons.
Pfam PF04991: LicD family (domain)
The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent. These proteins are part of the nucleotidyltransferase superfamily.
Wikipedia: Fukutin is a eukaryotic protein necessary for the maintenance of muscle integrity, cortical histogenesis, and normal ocular development. Mutations in the fukutin gene have been shown to result in Fukuyama congenital muscular dystrophy (FCMD) characterised by brain malformation - one of the most common autosomal-recessive disorders in Japan. In humans this protein is encoded by the FCMD gene, located on chromosome 9q31. Human fukutin exhibits a length of 461 amino acids and a predicted molecular mass of 53.7 kDa.
Pfam PF09343: Conserved hypothetical protein 2217 (DUF2460) (family)
This model represents a family of conserved hypothetical proteins. It is usually (but not always) found in apparent phage-derived regions of bacterial chromosomes.
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 PF21348: Rhamnogalacturonan lyase family 11, C-terminal domain (repeat)
This domain is found at the C-terminal end of Rhamnogalacturonan endolyase YesW and Rhamnogalacturonan exolyase YesX from Bacillus subtilis and other bacterial polysaccharide lyases from family 11 (RGL11). These proteins are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. They consist of an N-terminal domain [pfam:PF18370] and a C-terminal eight-bladed beta-propeller domain (this entry).
Pfam PF11039: Protein of unknown function (DUF2824) (family)
This family of proteins has no known function. Some members in the family are annotated as the P22 head assembly protein gp14 however this cannot be confirmed.
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 PF08747: BREX protein BrxB (domain)
This family includes BREX protein BrxB from Bacillus cereus, which is part of a type 1 BREX (bacteriophage exclusion) system, a system that provides immunity against bacteriophage, which allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA. The exact function of BrxB is not clear.
Pfam PF01976: Protein of unknown function DUF116 (family)
This archaebacterial protein has no known function. The protein contains seven conserved cysteines containing a CxxCxxC motif and may also be an integral membrane 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 PF23914: Cytochrome c-type biogenesis protein H TPR domain (repeat)
This entry represents the TPR domain found in cytochrome c-type biogenesis proteins CcmH and CycH from bacteria. These proteins are membrane-anchored thiol-oxidoreductases that are essential in the maturation of c-type cytochromes. In the case of CycH, it has been hypothesised that this TPR domain interacts with other proteins in order to mediate the assembly of c-type cytochromes. This entry also represents a TPR domain found in other proteins such as NRFG, NRFF and RNA polymerase-associated protein CDC27.
Pfam PF12120: Rifampin ADP-ribosyl transferase (domain)
This protein is found in bacteria. Proteins in this family are typically between 136 to 150 amino acids in length. The opportunistic pathogen Mycobacterium smegmatis is resistant to rifampin because of the presence of a chromosomally encoded rifampin ADP-ribosyltransferase (Arr-ms). Arr-ms is a small enzyme whose activity thus renders rifamycin antibiotics ineffective.
Pfam PF04630: Phage tail tube protein (family)
This is a family of phage tail tube proteins from Myoviridae.
Pfam PF02830: V4R domain (family)
The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons.
Pfam PF22148: Fervidolysin N-terminal prodomain (domain)
The founding member of this family is the N-terminal prodomain of fervidolysin, an extracellular subtilisin-like serine protease. This domain folds into a globular alpha/beta structure consisting of four-stranded antiparallel beta-sheet and two alpha-helices packed on one side of it. The prodomain is proteolytically cleaved and removed from the proenzyme.
Pfam PF03136: Pup-ligase protein (family)
Pupylation is a novel protein modification system found in some bacteria. This family of proteins are the enzyme that can conjugate proteins of the Pup family to lysine residues in target proteins marking them for degradation. The archetypal protein in this family is PafA (proteasome accessory factor) from Mycobacterium tuberculosis. It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases.
Pfam PF07564: Domain of Unknown Function (DUF1542) (domain)
This domain is found in several cell surface proteins,  such as extracellular matrix-binding protein ebh. Some members are involved in antibiotic resistance (e.g [swissprot:Q9RL69] and [swissprot:Q9LCJ9]) and/or cellular adhesion (e.g. [swissprot:Q931R6]). In some proteins it is repeated more than fifteen times, being the most repeated domain in streptococci. This is a predominantly alpha-helical domain that form a long, thin, fibre-like structure and it has been proposed to function as a stalk that helps the adhesive non-repeat region (NRR) of proteins protrude beyond the cell 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 PF12278: Sex determination protein N terminal (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 410 amino acids in length. This family is the N terminal end of the sex determination protein of many different animals. It plays a role in the gender determination of around 20% of all animals.
Pfam PF17170: 6-bladed beta-propeller (repeat)
This family is a 6-bladed beta-propeller structure of unknown function. There is a highly conserved FDxxG motif which might be important.
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 PF17832: Pre-PUA-like domain (domain)
This Pre-PUA-like domain is found in a wide variety of proteins including [swissprot:Q61211]. the eukaryotic translation initiation factor 2D, where it is found at the N-terminus.
Pfam PF21170: Fanconi-associated nuclease 1, TPR domain (repeat)
This is the TPR domain from Fanconi-associated nuclease 1 (FAN1), which mediates inter-domain interactions and is part of the dimerization interface. FAN1 is a DNA structure-specific nuclease involved in processing DNA interstrand crosslinks. FAN1 maintains genomic stability and prevents tissue decline in multiple organs. It mediates cancer drug resistance in several cancer subtypes.
Pfam PF18833: Tetratricopeptide repeat (repeat)
This Pfam entry includes outlying Tetratricopeptide-like repeats (two repeat units) that are not matched by [pfam:PF00515].
Pfam PF00904: Involucrin repeat (repeat)
Involucrin  is a protein present in keratinocytes of epidermis and other stratified squamous epithelia. Involucrin first appears in the cell cytosol, but ultimately becomes cross-linked to membrane proteins by transglutaminase thus helping in the formation of an insoluble envelope beneath the plasma membrane.

Structurally involucrin consists of a conserved region of about 75 amino acid residues followed by two extremely variable length segments that contain glutamine-rich tandem repeats. The glutamine residues in the tandem repeats are the substrate for the tranglutaminase in the cross-linking reaction. The total size of the protein varies from 285 residues (in dog) to 835 residues (in orangutan).
Wikipedia: Involucrin is a protein component of human skin and in humans is encoded by the IVL gene. In binding the protein loricrin, involucrin contributes to the formation of a cell envelope that protects corneocytes in the skin.
Pfam PF03875: Statherin (family)
Statherin functions biologically to inhibit the  nucleation and growth of calcium phosphate minerals. The N-terminus of statherin is highly charge, the glutamic acids of which  have been shown to be  important in the recognition hydroxyapatite.
Pfam PF00638: RanBP1 domain (domain)
Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran Binding Protein 1 (RanBP1) has guanine nucleotide dissociation inhibitory activity, specific for the GTP form of Ran and also functions to stimulate Ran GTPase activating protein(GAP)-mediated GTP hydrolysis by Ran. RanBP1 contributes to maintaining the gradient of RanGTP across the nuclear envelope high (GDI activity) or the cytoplasmic levels of RanGTP low (GAP cofactor) .

All RanBP1 proteins contain an approx 150 amino acid residue Ran binding domain. Ran BP1 binds directly to RanGTP with high affinity. There are four sites of contact between Ran and the Ran binding domain. One of these involves binding of the C-terminal segment of Ran to a groove on the Ran binding domain that is analogous to the surface utilised in the EVH1-peptide interaction . Nup358 contains four Ran binding domains. The structure of the first of these is known .
Pfam PF03257: Mycoplasma adhesin P1, C-terminal (domain)
This domain is found towards the C-terminal of adhesins from Mycoplasmas, such as adhesin P1, first identified as the major determinant for cytoadherence and gliding motility in M. pneumoniae. P1 forms a transmembrane adhesion complex with P40/P90, called 'Nap', which mediates motility and infectivity in these organisms. The C-terminal domain is smaller than the large N-terminal domain and is mostly conserved. It is followed by a transmembrane domain and acts as a stalk connecting the large N-terminal domain with the outer surface of the cell membranes. P1 N-terminal domain is highly variable ([pfam:PF12378]).
Pfam PF17471: Gene product 63 (family)
This is a family of unknown function found in Mycobacterium.
Pfam PF23856: Family of unknown function (DUF7219) (family)
This entry represents a domain of unknown function. The domain is found in bacteria, primarily in cyanobacteria and their phage. It is typically around 80-90 amino acids in length. AlphaFold prediction suggests this protein is composed of two longer paired alpha helices followed by a shorter third helix.
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 PF15165: Meiotic recombination protein REC114-like (family)
REC114-like members are necessary for meiotic DNA double-strand break formation. It functions in conjunction with Mei4. This family of proteins is found in eukaryotes. Proteins in this family are typically between 43 and 259 amino acids in length.
Pfam PF21351: Tetracyclin repressor-like, C-terminal domain (domain)
This domain is found at the C-terminal end of transcriptional regulators of the TetR family, including [swissprot:O53623] from Mycobacterium tuberculosis and [swissprot:Q1D4I5] from Myxococcus xanthus. This is the all-helical ligand-binding domain, which interacts with the respective effector molecule and transmits the signal to the DNA binding domain ([pfam:PF00440]).
Pfam PF23476: Family of unknown function (DUF7132) (family)
This entry represents a small family from archaebacteria based on protein PF1546. AlphaFold models show that a dimer of this protein forms a flattened 10 stranded beta barrel structure.
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 PF23806: Phage tail tube protein (domain)
This entry represents a family of bacteriophage tail tube proteins.  The tail tube forms the inner channel of the contractile tail which is used for DNA transfer from the capsid to the host during infection. The family is found in a wide variety of phages that infect bacteria.
Pfam PF19313: Domain of unknown function (DUF5916) (domain)
This entry represents a long region of similarity found to the C-terminus of a CBM9 domain. According to BOCTOPUS prediction this region has a membrane barrel topology suggesting this entry may represent a novel carbohydrate channel.
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 PF01454: MAGE homology domain (domain)
The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown.  This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis.
Wikipedia: The mammalian members of the MAGE gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors.
Pfam PF11888: Protein of unknown function (DUF3408) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 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 PF03553: Na+/H+ antiporter family (domain)
This family includes integral membrane proteins, some of which are NA+/H+ antiporters.
Pfam PF05958: tRNA (Uracil-5-)-methyltransferase (family)
This family consists of (Uracil-5-)-methyltransferases [ec:2.1.1.35] from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.
Pfam PF20458: Family of unknown function (DUF6711) (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 115 and 155 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 PF24339: P-granule-associated protein DEPS-1, third OB-fold domain (domain)
This domain is found in the P-granule-associated protein DEPS-1 from C.elegans and related proteins. DEPS-1 is a component of the P-granules and is required for their formation and integrity in adult germ cells. This protein is also involved in RNA-mediated silencing (RNAi) of germline-expressed genes. DEPS-1 is predicted to contain six OB-fold-like beta-barrel domains. This entry represents the third of these domains.