SII-SWORD/CoKE huggingface dataset:
Pfam PF23835: Domain of unknown function (DUF7205) (domain)
This entry represents a family of phage proteins that adopt a small beta barrel-like domain. The family is found in phages infecting members of the Enterobacteriaceae, such as Escherichia, Salmonella, Klebsiella, Cronobacter, Citrobacter, Erwinia, and Pectobacterium. The exact function of this protein within the phage tail is unknown. The family shows a highly conserved length of around 60-75 amino acids, with a few members having N- or C-terminal extensions.
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 PF03891: Domain of unknown function (DUF333) (domain)
This small domain of about 70 residues is found in a number of bacterial proteins.  It is found at the N-terminus the of [swissprot:O28332] protein. The proteins containing this domain are uncharacterised.
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 PF02259: FAT domain (repeat)
The FAT domain is named after FRAP, ATM and TRRAP.
Pfam PF03671: Ubiquitin fold modifier 1 protein (domain)
This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesised in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins,. While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme.
Pfam PF19818: Family of unknown function (DUF6301) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001381) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the brasilinolide A biosynthetic gene cluster from Nocardia terpenica. 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 PF07110: EthD domain (domain)
This family consists of several bacterial sequences which are related to the EthD protein of Rhodococcus ruber ([swissprot:Q93EX2]). In Rhodococcus ruber, EthD is thought to be involved in the degradation of ethyl tert-butyl ether (ETBE). EthD synthesis is induced by ETBE but it's exact function is unknown, it is however thought to be essential to the ETBE degradation system.
Pfam PF17358: Family of unknown function (DUF5384) (family)
This is a family of unknown function found in Proteobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF01679: Proteolipid membrane potential modulator (family)
Pmp3 is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organisms, stress-activated mitogen-activated protein kinases play crucial roles in transmitting environmental signals that will regulate gene expression for allowing the cell to adapt to cellular stress. Pmp3-like proteins are highly conserved in bacteria, yeast, nematode and plants.
Pfam PF17680: FlgO protein (domain)
This entry represents the FlgO protein. Mutation of this protein in Vibrio cholerae has been shown to reduce motility. FlgO is an outer membrane protein that localises throughout the membrane and not at the flagellar pole. Although FlgO and FlgP do not specifically localize to the flagellum, they are required for flagellar stability. Proteins in this family mostly contain an N-terminal lipoprotein attachment motif.
Pfam PF20744: Tail fibre protein gp37 trimerization region (repeat)
This entry represents part of the phage tail fibre. In T-even phages, gp37 and gp38 are components of the tail fibre that are critical for phage-host interaction.
Pfam PF12787: EcsC protein family (family)
Proteins in this family are related to EcsC from B. subtilis. This protein is found in an operon with EcsA and EcsB which are components of an ABC transport system. The function of this protein is unknown.
Pfam PF06345: DRF Autoregulatory Domain (conserved_site)
This motif is found in Diaphanous-related formins. It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of DAD to mammalian cells induces actin filament formation, stabilises microtubules,  and activates serum-response mediated transcription ().
Wikipedia: Formins (formin homology proteins) are a group of proteins that are involved in the polymerization of actin and associate with the fast-growing end (barbed end) of actin filaments. Most formins are Rho-GTPase effector proteins. Formins regulate the actin and microtubule cytoskeleton 
 and are involved in various cellular functions such as cell polarity, cytokinesis, cell migration and SRF transcriptional activity. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus.
Pfam PF01738: Dienelactone hydrolase family (domain)
Dienelactone hydrolases play a crucial role in chlorocatechol degradation via the modified ortho cleavage pathway. Enzymes induced in 4-fluorobenzoate-utilizing bacteria have been classified into three groups on the basis of their specificity towards cis- and trans-dienelactone . Some proteins contain repeated small fragments of this domain (for example rat kan-1 protein).
Pfam PF01432: Peptidase family M3 (family)
This is the Thimet oligopeptidase family, large family of mammalian and bacterial oligopeptidases that cleave medium sized peptides. The group also contains mitochondrial intermediate peptidase which is encoded by nuclear DNA but functions within the mitochondria to remove the leader sequence.
Pfam PF18696: Synaptotagmin-like, mitochondrial and lipid-binding domain (domain)
This is a lipid transport domain found in phospholipid transfer proteins such as C2CD2L-like (also known as TMEM24). The TMEM24-SMP domain is shown to bind glycerolipids with a preference for phosphatidylinositol (PI).The bound PI is then transferred to the plasma membrane (PM) where it is converted to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] to replenish pools of this lipid hydrolyzed during glucose-stimulated signaling. PI(4,5)P2 is required for Ca2+-dependent exocytosis hence, the SMP domain of TMEM24 is essential for sustaining the intracellular Ca2+ oscillations that trigger bursts of insulin granule release and hence insulin secretion. The SMP domain belongs to a superfamily of lipid/hydrophobic ligand-binding domains called TULIP for (tubular lipid-binding proteins) it adopts TULIP fold with two alpha helices and a highly curved antiparallel beta sheet forming a cornucopia-like structure.
Pfam PF10038: Protein of unknown function (DUF2274) (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 PF09362: Domain of unknown function (DUF1996) (domain)
This family of proteins are functionally uncharacterised.
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 PF01698: Floricaula / Leafy protein SAM domain (domain)
This family consists of various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY proteins have been shown to binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD. In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). This entry represents the SAM domain found in N -terminal of LFY proteins in plants. Crystallographic structure determination of LFY-N shows that LFY-N is a Sterile Alpha Motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFYbs (LFY-binding sites) and confers on LFY the ability to access closed chromatin regions. Experiments carried out in plants, revealed that altering the capacity of LFY to oligomerize compromised its floral function and drastically reduced its genome-wide DNA binding. SAM oligomerization has been suggested to have a profound effect on a TF binding landscape by promoting cooperative binding of LFY to DNA, as was proposed for other oligomeric TFs, and it gives LFY access to closed chromatin regions that are notably refractory to TF binding. It has also been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species.
Wikipedia: LEAFY is a plant gene that causes groups of undifferentiated cells called meristems to develop into flowers instead of leaves with associated shoots.
Pfam PF00319: SRF-type transcription factor (DNA-binding and dimerisation domain) (domain)
Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box , that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins.

In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation . Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic Î±-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel Î²-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see (IPR002487).
Pfam PF17214: Transcription termination factor FttA, KH domain (domain)
This entry represents the KH domain found at the N terminus of transcription termination factor FttA and similar archaeal proteins. FttA is a single-stranded endoribonuclease (endoRNase) that mediates cleavage at the RNA exit channel of RNA polymerase (RNAP); the 5'-3' exonuclease activity of this protein degrades the nascent RNA released from RNAP. It terminates transcription on the whole genome, a process that is linked to FttA-mediated RNA cleavage and does not require NTP hydrolysis. It also has weak activity 5'-3' exodeoxyribonuclease activity on ssDNA.
Pfam PF08517: Ataxin-1 and HBP1 module (AXH) (family)
AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1).  ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans.  The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression.
Pfam PF06437: IMP-specific 5'-nucleotidase (family)
The Saccharomyces cerevisiae ISN1 (YOR155c) gene encodes an IMP-specific 5'-nucleotidase, which catalyses degradation of IMP to inosine as part of the purine salvage pathway.
Pfam PF00716: Assemblin (Peptidase family S21) (family)
This group of serine peptidases belong to MEROPS peptidase family S21 (assemblin family, clan 21). Assemblin is a serine protease with a unique fold and an active site that comprises the unusual triad Ser-His-His. It is found in herpesviruses, one of the groups of DNA viruses. Assemblin is involved in the late stages of assembly of the viral prohead, breaking down the scaffold protein upon which the prohead is assembled. In Epstein-Barr virus (EBV), a member of the Gammaherpesvirus family, it is also known as the maturational protease (BVRF2) . The structure of assemblin has been revealed . The dimerization of assemblin may induce allosteric changes that activate this protease .
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .
Pfam PF13850: Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC) (domain)
This family is the N-terminal of ERGIC proteins, ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, [pfam:PF07970].
Pfam PF17606: Family of unknown function (DUF5502) (family)
This is a family of unknown function found in Listeria.
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 PF23044: UBE2O, ubiquitin binding SH3-C domain (domain)
This domain is found in the human E3-independent E2 ubiquitin-conjugating enzyme UBE2O and related proteins. UBE2O is involved in the monoubiquitination of diverse targets to mediate important processes such as targeting proteins for quality control, regulation of nuclear trafficking of chromatin-associated proteins and clearing ribosomes during erythropoiesis. UBE2O is a multidomain protein composed of several SH3-like domains, UBC domain and a CR3 helix. The domain represented by this entry folds into an open beta-barrel with typical SH3 topology. It binds ubiquitin via unique distinct interface and plays a key role in the UBE2O target selection.
Pfam PF02069: Prokaryotic metallothionein (domain)
Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds.
Wikipedia: Metallothionein (MT) is a family of cysteine-rich, low molecular weight proteins. They are localized to the membrane of the Golgi apparatus. MTs have the capacity to bind both physiological and xenobiotic heavy metals through the thiol group of its cysteine residues, which represent nearly 30% of its constituent amino acid residues.
Pfam PF13159: Domain of unknown function (DUF3994) (domain)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, and is typically between 97 and 111 amino acids in length, found at the C-terminal in most instances. According to structure predictions, it might have a beta-barrel 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 PF16317: Glycosyl hydrolase family 99 (domain)
This domain, around 350 residues, is mainly found in some uncharacterized proteins from bacteroides to human. Some proteins in this family, annotated as endo-alpha-mannosidases cleave mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. This domain reveals a (beta-alpha)(8) barrel fold in which the catalytic centre is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain, providing a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.
Pfam PF07890: Rrp15p (family)
Rrp15p is required for the formation of 60S ribosomal subunits.
Pfam PF10423: Bacterial AMP nucleoside phosphorylase N-terminus (domain)
This is the N-terminal domain of bacterial AMP nucleoside phosphorylase (AMNp). The N- and C-termini form distinct domains which intertwine with each other to form a stable monomer which associates with five other monomers to yield the active hexamer. The N-terminus consists of a long helix and a four-stranded sheet with a novel topology. The C-terminus binds the nucleoside whereas the N-terminus acts as the enzymatic regulatory domain. AMNp ([ec:3.2.2.4]) catalyses the hydrolysis of AMP to form adenine and ribose 5-phosphate. thereby regulating intracellular AMP levels.
Pfam PF21113: Lactate racemase C-terminal domain (domain)
This entry represents the C-terminal domain of the nickel-dependent lactate racemase enzyme (LarA). LarA is part of a superfamily containing many different enzymes. These include malate racemases, phenyllactate racemase, one alpha-hydroxyglutarate racemase, D-gluconate 2-epimerase, a short-chain aliphatic alpha-hydroxyacid racemase.
Pfam PF11892: Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal (family)
This domain is found at the C-terminal end of Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase from Escherichia coli (PpnN, also known as YgdH) and similar proteins mainly found in gammaproteobacteria. PpnN is a nucleosidase that catalyses the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates. The binding of (p)ppGpp, an alarmone molecule that plays a role in the bacterial stringent response, gives rise to a large conformational change in the terminal region that leads to the exposure of the catalytic pocket. This domain shows a completely alpha-helical fold with an extension that wraps around the central domain.
Pfam PF23441: SDR-like rossmann domain (domain)
This entry represents a set of short-chain dehydrogenases/reductases (SDRs) proteins.
Pfam PF09828: ChrB, C-terminal domain (domain)
This domain is found at the C-terminal end of Protein ChrB from the Proteobacteria Cupriavidus metallidurans, a protein involved in the reduction of chromate accumulation that is essential for chromate resistance. This domain may carry the metal detection motives that are important for its function.
Pfam PF18448: Carbohydrate binding domain (domain)
Carbohydrate active enzymes (CAZYmes) that target recalcitrant polysaccharides are modular enzymes containing noncatalytic carbohydrate-binding modules (CBMs) that direct enzymes to their cognate substrate, thus potentiating catalysis. The structure of Bacillus halodurans endo-beta-1,4-glucanase B (Cel5B) reveals that CBM46 is tightly associated with the catalytic module and, dependent on the glucan presented to the enzyme, can contribute directly to substrate binding or play a targeting role in directing the enzyme to regions of the plant cell wall rich in the polysaccharide hydrolyzed by the enzyme. The CBM46 domain displays a classic beta-sandwich jelly roll fold. Against beta-1,3-1,4-glucans CBM46 domain participates in productive substrate binding and thus plays a direct role in the hydrolytic activity of the enzyme.
Pfam PF18623: TnsE C-terminal domain (domain)
The bacterial transposon Tn7 facilitates horizontal transfer by directing transposition into actively replicating DNA with the element-encoded protein TnsE. Structural analysis of the C-terminal domain of TnsE identified a central V-shaped loop that toggles between two distinct conformations. It is suggested that a conformational change within the C-terminal domain of TnsE underlies target site selection by regulating stable engagement of the target DNA while providing a signal for activating transposition.