SII-SWORD/CoKE huggingface dataset:
Pfam PF07859: alpha/beta hydrolase fold (domain)
This catalytic domain is found in a very wide range of enzymes.
Wikipedia: The alpha/beta hydrolase superfamily is a superfamily of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function that share a common fold. The core of each enzyme is an alpha/beta-sheet, containing 8 beta strands connected by 6 alpha helices. The enzymes are believed to have diverged from a common ancestor, retaining little obvious sequence similarity, but preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best-conserved structural features of the fold.
Pfam PF16060: Domain of unknown function (DUF4802) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There are two conserved sequence motifs: CRC and YFDC.
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 PF06863: Protein of unknown function (DUF1254) (domain)
This family represents a conserved region about 130 residues long within hypothetical proteins of unknown function. Family members include eukaryotic, bacterial and archaeal 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 PF14215: bHLH-MYC and R2R3-MYB transcription factors N-terminal (family)
This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, [pfam:PF00010]. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).
Pfam PF02268: Transcription initiation factor IIA, gamma subunit, helical domain (domain)
Accurate transcription in vivo requires at least six  general transcription initiation factors, in addition to RNA  polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle.
Pfam PF02953: Tim10/DDP family zinc finger (domain)
Putative zinc binding domain with four conserved cysteine residues.  This domain is found in the human disease protein [swissprot:O60220].  Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import.       Members of this family seem to be localised to the mitochondrial intermembrane space.
Pfam PF08092: Magi peptide toxin family (family)
This family consists of Magi peptide toxins (Magi 1, 2 and 5) isolated from the venom of Hexathelidae spider. These insecticidal peptide toxins bind to sodium channels and induce flaccid paralysis when injected into lepidopteran larvae. However, these peptides are not toxic to mice when injected intracranially at 20 pmol/g.
Pfam PF22660: Ribonucleotide synthetase preATP-grasp domain (domain)
This domain precedes the ATP-grasp domain in a number of ribonucleotide synthetases.
Pfam PF16547: Proteasome-substrate-size regulator, N-terminal (domain)
The ordered regions of the yeast BLM10 or PA200 (human homologue), full-length protein encode 32 HEAT repeat (HR)-like modules, each comprising two helices joined by a turn, with adjacent repeats connected by a linker. Whereas a standard HEAT repeat is composed of ~50 residues, the BLM10 HEAT repeats are highly variable. The length of helices ranges from 8 to 35 residues, turns range from 2 to 87 residues, and linkers range from 1 to 88 residues, with the longest linker, between HR21 and HR22, containing additional secondary structures (two strands and three helices). BLM10_N is the N-terminal ordered region of the three in BLM10. BLM10 is found to surround the proteasome entry pore in the 1.2 MDa complex of proteasome and BLM10 to form a largely closed dome that is expected to restrict access of potential substrates. BLM10 and PA200 are predominantly nuclear and stimulate the degradation of model peptides, although they do not appear to stimulate the degradation of proteins, recognise ubiquitin, or utilise ATP.
Pfam PF05845: Bacterial phosphonate metabolism protein (PhnH) (family)
This family consists of several bacterial PhnH sequences which are known to be involved in phosphonate metabolism.
Pfam PF22400: Domain of unknown function (DUF6980) (domain)
This is a domain found in uncharacterised bacterial proteins. This domain occurs either standalone or in combination with other domains. It contains conserved cysteines and histidine that may be involved in Zn2+ coordination.
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 PF21789: TNP-like, RNase H C-terminal domain (domain)
This domain represents the C-terminal segment of the RNase H domain from Drosophila melanogaster transposable element P transposase (TNP) and its homologue from human THAP9. The catalytic RNase H domain of these proteins is interrupted by the GTP-binding insertion domain (GBD, [pfam:PF21788]). The N-terminal segment of the RNase H domain is represented in [pfam:PF21787].
Pfam PF02722: Major Outer Sheath Protein C-terminal domain (domain)
This is a family of spirochete major outer sheath protein C-terminal  regions. These proteins are present on the bacterial cell surface.  In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and  fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola. This domain forms an amphipathic beta rich structure with channel forming activity.
Pfam PF06926: Putative replisome organiser protein C-terminus (family)
This family represents the C-terminus (approximately 100 residues) of a putative replisome organiser protein in Lactococcus bacteriophages.
Pfam PF09386: Antitoxin ParD (domain)
ParD is a plasmid anti-toxin than forms a ribbon-helix-helix DNA binding structure.  It stabilises plasmids by inhibiting ParE toxicity in cells that express ParD and ParE.  ParD forms a dimer and also regulates its own promoter (parDE).
Wikipedia: The parDE type II toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). These systems preferentially guarantee growth of plasmid-carrying daughter cells in a bacterial population by killing newborn bacteria that have not inherited a plasmid copy at cell division.
Pfam PF10712: NAD-specific glutamate dehydrogenase (family)
The members of this are annotated as being NAD-specific glutamate dehydrogenase encoded in antisense gene pair with DnaK-J.
Pfam PF11944: Protein of unknown function (DUF3461) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 130 amino acids in length. This protein has two conserved sequence motifs: KFK and HLE.
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 PF07547: RSD-2 N-terminal domain (domain)
This domain is found in three copies in the N-terminus of the C. elegans RSD-2 protein. RSD-2 (RNAi spreading defective) is involved in systemic RNAi.  Mutations in the rsd-2 gene do not effect somatic genes but only germline expressed genes.
Pfam PF03285: Paralemmin (family)
Paralemmin was identified in the chicken lens as a protein with a molecular weight of 65kDa (isoform 1) and a splice variant of 60kDa (isoform 2). Isoform 2 is predominant during infancy and levels of isoform 1 increase with age. Paralemmin is localised to the plasma membrane of fibre cells, and was not detected in the annular pad cells. Its localisation to the short side of the fibre cell and the sites of fibre cell interlocking suggests that paralemmin may play a role in the development of such interdigitating processes . Palmitoylation is important for localising these proteins to the filopodia of dendritic cells where they have been implicated in the regulation of membrane dynamics and process outgrowth . Paralemmin-3 is an ATP-binding protein that was shown to interacts with single immunoglobulin IL-1 receptor-related molecule (SIGIRR) and may act as a adapter in the Toll-like receptor (TLR) signalling .
Pfam PF24526: ABCA12-like, C-terminal domain (domain)
This domain is found at the C-terminal end of ABC transporter A family member 12 from Arabidopsis thaliana (ABCA12) and similar plant proteins. This domain is predicted to show a two layer alpha-beta sandwich.
Pfam PF10874: Protein of unknown function (DUF2746) (family)
This family of proteins has 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 PF18966: Uncharacterised lipoprotein (family)
This entry includes members found in Actinobacteria (mostly streptomycetaceae, micromonosporales and  pseudonocardiales). Some members are annotated as lipoproteins.
Pfam PF05498: Rapid ALkalinization Factor (RALF) (family)
Family members found in Arabidopsis include RALF23. It has been shown to reduce plant growth upon overexpression while mature plants were dwarfed and bushy. It has also been suggested that RALF23 of Arabidopsis, counteracts brassinosteroid (BR) growth-promoting effects which may be relieved by the down-regulation of RALF23
Pfam PF06932: Protein of unknown function (DUF1283) (family)
This family consists of several hypothetical proteins of around 115 residues in length which seem to be specific to Enterobacteria. The function of the family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23752: WDR11 second beta-propeller (repeat)
This entry represents the second beta-propeller found in WD repeat-containing protein 11 (WDR11) from animals and similar eukaryotic proteins. Members of this family share a domain architecture consisting of two beta-propellers followed by a TPR domain. WDR11 has been implicated in human developmental genetic disorders characterised by delayed puberty and infertility. WDR11 modulates the Hedgehog (Hh) signalling pathway and is essential for adequate ciliogenesis. The beta-propellers in WDR11 are involved in protein-protein interaction. This are essential for proper interaction with EMX1, a homeodomain transcription factor involved in the development of olfactory neurons. Impaired pubertal development is suggested to result from a deficiency of productive WDR11 protein interaction. WDR11 is also involved in vesicle traffic as it binds TBC1D23, a vesicle-golgin adaptor required for endosome-to-Golgi trafficking.
Pfam PF00657: GDSL-like Lipase/Acylhydrolase (family)
GDSL esterases and lipases are hydrolytic enzymes with multifunctional properties . This new subclass of lipolytic enzymes possesses a distinct GDSL sequence motif different from the GxSxG motif found in many lipases . Members include; Aeromonas hydrophila lipase, Vibrio mimicus lecithinase, Vibrio parahaemolyticus thermolabile haemolysin, rabbit phospholipase (AdRab-B), and Arabidopsis thaliana anter-specific proline-rich protein. 3D structures of several enzymes of this family revealed several Î²-strands and Î±-helices arranged in alternating order and the substrate-binding pocket between the central Î²-strand and long Î±-helix appears to be highly flexible .
Pfam PF08909: Domain of unknown function (DUF1854) (family)
This potential domain is functionally uncharacterised. It is found at the C-terminus of a number of ATP transporter proteins suggesting this domain may be involved in ligand binding.
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 PF16223: Domain of unknown function (DUF4882) (family)
This small family consists of several uncharacterized proteins around 325 residues in length and is mainly found in various Acinetobacter species. The function of this family is unknown.
Pfam PF24431: Family of unknown function (DUF7554) (family)
This entry represents a small family of uncharacterised proteins found in archaea. These proteins are likely associated with the membrane. They are predicted to fold into a single 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 PF08201: BssC/TutF protein (family)
BssC short protein (57 amino acids) has been described as the gamma-subunit of benzylsuccinate synthase from Thauera aromatica strain K172.  TutF has been identified and described as highly similar to BssC in  T.aromatica strain T1.
Pfam PF13653: Glycerophosphoryl diester phosphodiesterase family (domain)
This family also includes glycerophosphoryl diester phosphodiesterases as well as agrocinopine synthase, the similarity to GDPD has been noted. This family appears to have weak but not significant matches to mammalian phospholipase C [pfam:PF00388], which suggests that this family may adopt a TIM barrel fold.
Pfam PF09277: Erythronolide synthase, docking (domain)
Members of this family of docking domains are found in prokaryotic erythronolide synthase. They adopt a structure consisting of a bundle of four alpha-helices, and mediate homodimerisation of the protein, stabilising the resulting complex.
Pfam PF20570: Domain of unknown function (DUF6779) (domain)
This presumed domain is functionally uncharacterised. This domain family is mainly found in bacteria, and is approximately 100 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 PF23154: KANSL3, helical domain (domain)
This domain is found in the homologues of the human KAT8 regulatory NSL complex subunit 3 (KANSL3). KANSL3 is a component of the non-specific lethal (NSL) complex which is involved in acetylation of nucleosomal histone H4 on several lysine residues and thus likely  involved in regulation of transcription. This domain is predicted to adopt a globular structure consisting of array of eight helices.
Pfam PF01383: CpcD/allophycocyanin linker domain (domain)
Ferredoxin-NADP(+) oxydoreductase (FNR) (1.18.1.2) transfers electrons from ferredoxin (or flavodoxin) to NADP(+) to generate NADPH. In eucaryotes, the nuclear-encoded, chloroplast-targeted enzyme contains two domains: an FAD-binding domain (see [prositedoc:PDOC51384]) and an NADP(+)-binding domain. With the exception of Gloeobacter violaceus PCC 7421, the predicted sequences of all cyanobacterial petH genes, encoding FNR, correspond to a protein containing three domains. Two domains at the C terminus correspond to the FAD- and NADP(+)-binding domains of higher plants FNR protein, which compose the catalytic domains of the enzyme. The N-terminal domain is similar to phycobilisome (PBS)-associated linker proteins from numerous cyanobacteria  and is associated with:


 * CpcD, the phycocyanin (PC)-associated, rod-capping, linker polypeptide of PBS. The similarity spans nearly the entire sequence of this linker class.
 * CpcC, the PC-associated rod linker polypeptide. The similarity is confined only to the C terminus of this linker class.
 * ApcC, the allophycocyanin (APC)-associated, core linker polypeptide. The similarity only correspond to about half of the molecule.


The CpcD-like domain has an elongated shape and consists of a three-stranded Î²-sheet, two Î±-helices, one of which has only about one turn, and the connecting random coil segments .
Pfam PF11657: Transcriptional activator TraM (family)
TraM is required for quorum dependence. It binds to and in-activates TraR which controls the replication of the tumour-inducing virulence plasmid. TraM interacts in a two-step process with DNA-TraR to form a large, stable anti-activation complex.
Pfam PF19330: Delta and Notch-like EGF-related receptor C-terminus (family)
This family represents the C-terminal region of the Delta and Notch-like epidermal growth factor-related receptor (DNER) containing the transmembrane domain and the short cytoplasmic region including AP-1-binding site required for its somatodendritic distribution. This receptor is highly expressed in Purkinje cells taking part in the differentiation and maturation of Bergmann glia via physical contact with Purkinje cells and granular cells. Recently, it has been demonstrated that DNER is induced in lung recruited macrophages after chronic inflammation in which induces IFNgamma expression via a non-canonical Notch NFkappaB pathway.
Pfam PF23267: ENOX1-like domain (domain)
This domain is found in human Ecto-NOX disulfide-thiol exchanger 1 (ENOX1) and similar sequences mainly found in animals. ENOX1 probably acts as a terminal oxidase of plasma electron transport from cytosolic NAD(P)H via hydroquinones to acceptors at the cell surface, playing a role in control of the ultradian cellular biological clock. This domain is predicted to form a long alpha-helix.
Pfam PF23943: PUS7L N-terminal domain (domain)
This domain is found N-terminal in the human Pseudouridylate synthase PUS7L and related proteins. PUS7L catalyses pseudouridylation of mRNAs and thus regulates pre-mRNA processing. This domain is predicted to adopt a globular structure consisting of a three-stranded antiparallel beta-sheet with two alpha-helices packed on one side of it.
Pfam PF03985: Paf1 (family)
Members of this family are components of the RNA polymerase II associated Paf1 complex.  The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i.
Pfam PF15542: Bacterial toxin 50 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains two conserved histidine, a serine, two lysine, and a threonine residue and a HxVP motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6, type 7, and MuF-type secretion systems.
Pfam PF05838: Glycosyl hydrolase 108 (domain)
This family acts as a lysozyme (N-acetylmuramidase), [ec:3.2.1.17]. It contains a conserved EGGY motif near the N-terminus, the glutamic acid within this motif is essential for catalytic activity. In bacteria, it may activate the secretion of large proteins via the breaking and rearrangement of the peptidoglycan layer during secretion. It is frequently found at the N-terminus of proteins containing a C-terminal [pfam:PF09374] domain.
Wikipedia: In molecular biology, glycoside hydrolase family 108 is a family of glycoside hydrolases.
Pfam PF20968: MASE8 (domain)
This entry represents the membrane-associated sensor domain MASE8, which is found in association with GGDEF domain ([pfam:PF00990]), histidine sensor kinases and adenylate cyclase output domain ([pfam:PF00211]). This domain is widespread among various classes of proteobacteria and is also found in other phyla.
Pfam PF03780: Asp23 family, cell envelope-related function (family)
The alkaline shock protein Asp23 was identified as an alkaline shock protein that was expressed in a sigmaB-dependent manner in Staphylococcus aureus. Following an alkaline shock Asp23 accumulates in the soluble protein fraction of the S. aureus cell. Asp23 is one of the most abundant proteins in the cytosolic protein fraction of stationary S. aureus cells, with a copy-number of >25000 per cell. A second Asp23-family protein, AmaP, which is  encoded within the asp23-operon, is required to localise Asp23  to the cell membrane. The overall function for the family  is thus a cell envelope-related one in Gram-positive bacteria.  UniProtKB:Q2FW64.
Pfam PF02572: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP (domain)
This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, [ec:2.5.1.17], involved in cobalamin (vitamin B12) biosynthesis.  These enzymes catalyse the adenosylation reaction: ATP + cob(I)alamin + H2O  phosphate + diphosphate + adenosylcobalamin.
Wikipedia: In molecular biology, cob(I)yrinic acid a,c-diamide adenosyltransferase EC 2.5.1.17 is an enzyme which catalyses the conversion of cobalamin into one of its coenzyme forms, adenosylcobalamin. Adenosylcobalamin is required as a cofactor for the activity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond.
Pfam PF19887: Family of unknown function (DUF6360) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 100 amino acids in length.
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.