SII-SWORD/CoKE huggingface dataset:
Pfam PF18979: Family of unknown function (DUF5715) (family)
This is a family of unknown function, mainly found in bacteria.
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 PF21616: Topoisomerase V, second (HhH)2 tandem domain (domain)
This domain is found in Topoisomerase V from Methanopyrus kandleri (Topo-V), is a bifunctional enzyme carrying both topoisomerase and DNA repair lyase activities. Topo-V consists of an N-terminal topoisomerase domain followed by 12 tandem (HhH)2 domains, showing four active sites. This entry represents the second of these tandem domains.
Pfam PF00145: C-5 cytosine-specific DNA methylase (domain)
C-5 cytosine-specific DNA methylases (2.1.1.37) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine . In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA . The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A : the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.

This entry also includes tRNA (cytosine(38)-C(5))-methyltransferase (2.1.1.204), also known as DNMT2 (DNA (cytosine-5)-methyltransferase-like protein 2), that specifically methylates cytosine 38 in the anticodon loop of tRNA (Asp) .
Wikipedia: In biochemistry, the DNA methyltransferase family of enzymes catalyze the transfer of a methyl group to DNA. DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine (SAM) as the methyl donor.
Pfam PF24004: Archaeal microprotein (family)
This family includes a group of short archaeal proteins encoded by small open reading frames (sORFs).
Pfam PF14918: MDM2-binding (family)
MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle. MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilisation in an MDM2 RING finger-dependent manner. MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells. MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4). It is unclear which regions of MTBP interact with which binding-partner. See PF14919, PF14920.
Pfam PF02626: Carboxyltransferase domain, subdomain A and B (family)
Urea carboxylase (UC) catalyses a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein  (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the A and B subdomains of the CT domain. This domain covers the whole length of KipA (kinase A) from Bacillus subtilis. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity.
Pfam PF21447: Ppx/GppA phosphatase, domain III (domain)
Ppx/GppA phosphatases belong to ASKHA (acetate and sugar kinases, Hsp70, actin) which has an N-terminal ([pfam:PF02541]) nucleotide-binding domain (domains I/II), domain III which corresponds to the catalytic phosphohydrolase domain with the common helical fold and domain IV. This entry represents domain III.
Pfam PF12627: Probable RNA and SrmB- binding site of polymerase A (domain)
This region encompasses much of the RNA and SrmB binding motifs on polymerase A.
Pfam PF19088: TUTase nucleotidyltransferase domain (domain)
This nucleotidyltransferase domain is found in TUTase enzymes. Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species.
Pfam PF05086: Dictyostelium (Slime Mold) REP protein (family)
This family consists of REP proteins from Dictyostelium (Slime molds). REP protein is likely involved in transcription regulation and control of DNA replication, specifically amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity.
Pfam PF22451: Siroheme decarboxylase NirDL-like HTH domain (domain)
This entry represents the HTH domains found in siroheme decarboxylase NirdL from Hydrogenobacter thermophilus and related sequences. NirdL is involved in heme d1 biosynthesis. It catalyses the decarboxylation of siroheme into didecarboxysiroheme.
Pfam PF13503: Domain of unknown function (DUF4123) (domain)
This presumed domain is functionally uncharacterised. It is about 120 amino acids in length and contains several conserved motifs that may be functionally important.  This domain is sometimes associated with the FHA 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 PF18542: Transcription factor IIB C-terminal module 1 (domain)
In the pathogenic trypanosome, Trypanosoma brucei, transcription factor IIB (tTFIIB) is essential for spliced leader (SL) RNA gene transcription and cell viability, but has a highly divergent primary sequence in comparison to TFIIB in other eukaryotes. Structure analysis of the C-terminal region of trypanosome TFIIB, reveals 2, closely packed helical modules followed by a C-terminal extension of 32 aa. The trypanosome-specific region comprises the second helical module and the C-terminal extension.  Both helical modules contain the canonical 5-helix cyclin fold characteristic of TFIIB proteins. This domain is mostly found in Trypanosomatidae.
Pfam PF22440: SirC C-terminal domain (domain)
This entry represents the C-terminal helical domain of SirC from Bacillus megaterium and related sequences. This domain contains Arg159 which contributes to the active site from the alternate molecule of the homodimer.
Pfam PF09383: NIL domain (domain)
This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family.
Pfam PF08106: Formaecin family (family)
This family consists of the formaecin family of  antimicrobial peptides isolated from the bulldog  ant Myrmecia gulosa in response to bacterial  infection. Formaecins are inducible peptide  antibiotics and are active against growing  Escherichia coli but were inactive against other  Gram-negative and Gram-positive bacteria. Formaecin peptides are 16 amino acids long, are rich in proline  and have N-acetylgalactosamine O-linked to a conserved  threonine.
Pfam PF15697: Domain of unknown function (DUF4666) (family)
This family of proteins is found in plants. Proteins in this family are typically between 103 and 140 amino acids in length. There are two conserved sequence motifs: LQRS and FRR.
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 PF13225: Beta-carotene isomerase D27-like, C-terminal (domain)
This is the C-terminal domain of Beta-carotene isomerase D27 that may contain an iron binding domain. Beta-carotene isomerase D27 (also known as Protein DWARF-27) from plants is involved in strigolactones biosynthesis. It is a beta-carotene isomerase that converts all-trans-beta-carotene into 9-cis-beta-carotene, which is cleaved by CCD7 into a 9-cis-configured aldehyde. This is an iron-containing protein that localises in chloroplasts and is expressed mainly in vascular cells of shoots and roots.
Pfam PF19294: Diadenylate cyclase, N-terminal (domain)
This domain is found at the N-terminus of the DacZ diadenylate cyclase enzyme from euryarchaea. This domain appears to be distantly related to the C-terminal domain of pyruvate kinase [pfam:PF02887].
Pfam PF14043: WVELL protein (family)
This family includes the B. subtilis YfhJ protein [swissprot:O31578], which is functionally uncharacterised.  This is not a homologue of E. coli YfhJ, a synonym for IscX, which belongs to [pfam:PF04384]. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length and contain a highly conserved WVELL motif.
Pfam PF24051: Domain of unknown function (DUF7355) (domain)
This entry represents a small family of uncharacterised phage proteins. The family includes the y13F protein from bacteriophage T4 [swissprot:P39499]. Structure prediction shows this protein has a compact globular fold composed of three beta strands and two 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 PF19684: Family of unknown function (DUF6186) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001215) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the conglobatin biosynthetic gene cluster  from Streptomyces conglobatus. This family appears to be  predominantly found in Actinobacteria.
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 PF25025: Elongation factor Ts, mitochondrial, N-terminal (domain)
This domain is found at the N-terminal end of the mitochondrial Elongation factor Ts from Bos taurus (EF-Ts), which associates with the EF-Tu. GDP complex and induces the exchange of GDP to GTP. This domain consists of helical segments.
Pfam PF12605: Casein kinase 1 gamma C terminal (family)
This domain family is found in eukaryotes, and is typically between 54 and 99 amino acids in length. The family is found in association with [pfam:PF00069]. CK1gamma is a membrane-bound member of the CK1 family. Gain-of-function and loss-of-function experiments show that CK1gamma is both necessary and sufficient to transduce LRP6 signalling in vertebrates and Drosophila cells.
Pfam PF08830: Protein of unknown function (DUF1806) (family)
This is a bacterial family of uncharacterised proteins.  The structure of one of the proteins in this family has been solved and it adopts a beta barrel-like 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 PF22368: Response regulator protein ChxR, N-terminal domain (domain)
This domain is found at the N-terminal end of the response regulator protein ChxR from Chlamydia trachomatis ([swissprot:O84635]). ChxR is organised into a receiver domain (this entry) and a C -terminal effector domain ([pfam:PF00486]). Dimerisation occurs through the receiver domain. It shows an alpha-beta configuration.
Pfam PF09626: Dihaem cytochrome c (family)
Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway.  DHC acts as the physiological electron donor for SHP during phototrophic growth. In certain species DHC is found upstream of [pfam:PF01292].
Pfam PF14927: Neurensin/Transmembrane protein 74 (family)
This entry represents a group of proteins mainly found in vertebrates, including the neuronal membrane proteins neurensin-1 and neurensin-2 and the autophagosome protein TMEM74. Neurensin-1 plays a role in neurite extension.
Pfam PF03808: Glycosyl transferase WecG/TagA/CpsF family (family)
The WecG member of this family, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Pfam PF17951: Fatty acid synthase meander beta sheet domain (domain)
This domain is found in fungal fatty acid synthase beta chain proteins.
Pfam PF15518: L protein N-terminus (domain)
This endonuclease domain is found at the N-terminus of many bunyavirus L proteins.
Pfam PF06035: Bacterial transglutaminase-like cysteine proteinase BTLCP (family)
Members of this family are predicted to be bacterial transglutaminase-like cysteine proteinases. They contain a conserved Cys-His-Asp catalytic triad. Their structure is predicted to be similar to that of Salmonella typhimurium N-hydroxyarylamine O-acetyltransferase [swissprot:Q00267], in [pfam:PF00797], however they lack the sub-domain which is important for arylamine recognition.
Pfam PF07056: Protein of unknown function (DUF1335) (family)
This family represents a conserved region approximately 130 residues long within a number of proteins of unknown function that seem to be specific to the white spot syndrome virus (WSSV).
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 PF03557: Bunyavirus glycoprotein G1 (family)
Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase.  This family contains the G1 glycoprotein which is the viral attachment protein.
Pfam PF04769: Mating-type protein MAT alpha 1 HMG-box (family)
This family includes Saccharomyces cerevisiae mating type protein alpha 1 ([swissprot:P01365]).  Mat alpha 1 is a transcription activator which activates mating-type alpha-specific genes.  MAT alpha 1 and MCM 1 bind cooperatively to PQ elements upstream of alpha-specific genes. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone ([pfam:PF04648]) response pathway. In silico modelling of the MAT_Alpha1 domain indicates that its best scoring templates were structures of HMG-box proteins, and DOI: 10.4236/ojbiphy.2013.31001. Phylogenetic analysis suggests that the MAT_Alpha1 domain diverged from the MATA_HMG-box subfamily. The name of MATalpha_HMG-box was proposed for the MAT_alpha1 domain.
Pfam PF20663: Conserved oligomeric Golgi complex subunit 4, N-terminal (repeat)
COG4 is a component of the conserved oligomeric Golgi (COG) complex which mediates the proper glycosylation of proteins trafficking through the Golgi apparatus. It is a member of the CATCHR (complexes associated with tethering containing helical rods) family, which includes components of the exocyst, COG, GARP, and DSL1 complexes, sharing structural and functional features: the alpha-helical bundles at the middle/C-terminal and a N-terminal coiled-coil region. This is the N-terminal coiled-coil of COG4.
Pfam PF22358: Minor fimbrium tip subunit MfA4, C-terminal (domain)
This domain is found at the C-terminal end of Minor fimbrium tip subunit MfA4 from Porphyromonas gingivalis and similar sequences mainly found in bacteroidales. MfA4 is involved in biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome. This domain adopts a transthyretin-like fold that contains seven core beta-strands arranged in two beta-sheets.
Pfam PF01293: Phosphoenolpyruvate carboxykinase (family)
Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the first committed (rate-limiting) step in hepatic gluconeogenesis, namely the reversible decarboxylation of oxaloacetate to phosphoenolpyruvate (PEP) and carbon dioxide, using either ATP or GTP as a source of phosphate. The ATP-utilising (4.1.1.49) and GTP-utilising (4.1.1.32) enzymes form two divergent subfamilies, which have little sequence similarity but which retain conserved active site residues. ATP-utilising PEPCKs are monomers or oligomers of identical subunits found in certain bacteria, yeast, trypanosomatids, and plants, while GTP-utilising PEPCKs are mainly monomers found in animals and some bacteria . Both require divalent cations for activity, such as magnesium or manganese. One cation interacts with the enzyme at metal binding site 1 to elicit activation, while the second cation interacts at metal binding site 2 to serve as a metal-nucleotide substrate. In bacteria, fungi and plants, PEPCK is involved in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle.

PEPCK helps to regulate blood glucose levels. The rate of gluconeogenesis can be controlled through transcriptional regulation of the PEPCK gene by cAMP (the mediator of glucagon and catecholamines), glucocorticoids and insulin. In general, PEPCK expression is induced by glucagon, catecholamines and glucocorticoids during periods of fasting and in response to stress, but is inhibited by (glucose-induced) insulin upon feeding . With type II diabetes, this regulation system can fail, resulting in increased gluconeogenesis that in turn raises glucose levels .

PEPCK consists of an N-terminal and a catalytic C-terminal domain, with the active site and metal ions located in a cleft between them. Both domains have an Î±/Î² topology that is partly similar to one another . Substrate binding causes PEPCK to undergo a conformational change, which accelerates catalysis by forcing bulk solvent molecules out of the active site . PCK uses an Î±/Î²/Î± motif for nucleotide binding, this motif differing from other kinase domains. GTP-utilising PEPCK has a PEP-binding domain and two kinase motifs to bind GTP and magnesium.
This entry represents ATP-utilising phosphoenolpyruvate carboxykinase enzymes.
Wikipedia: Phosphoenolpyruvate carboxykinase is an enzyme in the lyase family used in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.
Pfam PF25148: Domain of unknown function (DUF7824) (repeat)
This is a presumed domain found in the middle region of bacterial sequences, which have a [pfam:PF20103] at the N-terminal.
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 PF03895: YadA-like membrane anchor domain (domain)
This region represents the C-terminal 120 amino acids of a family of surface-exposed bacterial proteins. YadA, an adhesin from Yersinia, was the first member of this family to be characterised. UspA2 from Moraxella was second. The Eib immunoglobulin-binding proteins from E. coli were third, followed by the DsrA proteins of Haemophilus ducreyi and others. These proteins are homologous at their C-terminal and have predicted signal sequences, but they diverge elsewhere. The C-terminal 9 amino acids, consisting of alternating hydrophobic amino acids ending in F or W, comprise a targeting motif for the outer membrane of the Gram negative cell envelope. This region is important for oligomerisation.
Wikipedia: In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.
Pfam PF09237: GAGA factor (domain)
Members of this family bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence.
Pfam PF20252: BIG2 C-terminal domain (domain)
This presumed domain is found at the C-terminus of BIG2 the brefeldin A-inhibited guanine nucleotide-exchange protein. The function of this region is unknown.
Pfam PF17205: Integrin plexin domain (domain)
This short disulphide rich domain is found at the N-terminus of integrin beta chains.