SII-SWORD/CoKE huggingface dataset:
Pfam PF09096: Baseplate structural protein, domain 2 (domain)
Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27.
Pfam PF11598: Cartilage oligomeric matrix protein (family)
This family of proteins represents the five-stranded coiled-coil domain of cartilage oligomeric matrix protein (COMP). This region has a binding site between two internal rings formed by Leu37 and Thr40
Pfam PF02099: Josephin (family)
The Josephin domain is an eukaryotic protein module of about 180 residues, which occurs in stand-alone form in Josephin-like proteins, and as an amino- terminal domain associated with two or three copies of the ubiquitin- interacting motif (UIM) in ataxin 3-like proteins. Josephin domain-containing proteins function as de-ubiquitination enzymes . Although it has originally been proposed that the Josephin domain could be an all-Î± helical domain distantly related to ENTH and VHS domains involved in membrane trafficking and regulatory adaptor function , it is now believed that it is a mainly Î± helical cysteine-protease domain predicted to be active against ubiquitin chains or related substrates .

The Josephin domain contains two conserved histidines and one cysteine that is required for the ubiquitin protease activity  and two ubiquitin-binding sites .

Some proteins known to contain a Josephin domain are:


 * Animal Machado-Joseph disease protein 1 (Ataxin 3). It interacts with key regulators (CBP, p300 and PCAF) of transcription and represses transcription.
 * Plant Machado-Joseph disease-like protein (MJD1a-like) (Ataxin 3 homologue).
 * Mammalian Josephin 1 and 2.
 * Drosophila melanogaster Josephin-like protein.
 * Arabidopsis thaliana Josephin-like protein.
Pfam PF17364: Family of unknown function (DUF5389) (family)
This is a family of unknown function found in Pasteurellaceae. Family members are predicted to have 3 trans-membrane regions.
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 PF23909: Family of unknown function (DUF7251) (family)
This entry represents a family of protein of unknown function found in phage.  The protein are predicted to be largely disordered, with a C-terminal small beta barrel 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 PF13221: Protein of unknown function (DUF4029) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 119 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 PF11209: LmeA-like phospholipid-binding (family)
LmeA is a conserved cell-envelope protein critical for controlling  the mannan chain length of lipomannan/lipoarabinomannan.
Pfam PF10590: Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region (domain)
This domain represents one of the two dimerisation regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In [swissprot:P21159], S6 runs from residues 178-192, S7 from 200-206 and S8 from 211-215. the extended loop, of residues 167-177 may well be involved in the pocket formed between the two dimers that positions the FMN molecule.To date, the only time functional oxidase or phenazine biosynthesis activities have been experimentally demonstrated is when the sequences contain both [pfam:PF01243] and [pfam:PF10590]. It is unknown the role performed by each domain in bringing about molecular functions of either oxidase or phenazine activity.
Pfam PF15455: Proline-rich 19 (family)
This family includes proline-rich protein 19.
Pfam PF03648: Glycosyl hydrolase family 67 N-terminus (domain)
Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the N-terminal region of alpha-glucuronidase. The N-terminal domain forms a two-layer sandwich, each layer being formed by a beta sheet of five strands. A further two helices  form part of the interface with the central, catalytic, module ([pfam:PF07488]).
Wikipedia: In molecular biology, glycoside hydrolase family 67 is a family of glycoside hydrolases.
Pfam PF05008: Vesicle transport v-SNARE protein N-terminus (domain)
V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this. This domain is the N-terminal half of the V-Snare proteins.
Pfam PF14092: Domain of unknown function (DUF4270) (family)
This family of lipoproteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 444 and 534 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 PF05265: Protein of unknown function (DUF723) (family)
This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA-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 PF04089: BRICHOS domain (domain)
The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for it include (a) in targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialised intracellular protease processing system. This C-terminal domain is embedded in the endoplasmic reticulum lumen, and binds to the N-terminal, transmembrane, SP_C, [pfam:PF08999], provided that it is in non-helical conformation. Thus the Brichos domain of proSP-C is a chaperone that induces alpha-helix formation of an aggregation-prone TM region.
Wikipedia: The BRICHOS family consists of a variety of proteins linked to major diseases, each containing a 100 amino acid BRICHOS domain that is thought to have a chaperone function.
These include BRI2, which is related to familial British and Danish dementia ; Chondromodulin-I, related to chondrosarcoma; CA11, related to stomach cancer; and surfactant protein C (SP-C), related to respiratory distress syndrome (RDS).
Pfam PF06094: Gamma-glutamyl cyclotransferase, AIG2-like (family)
GGACT, gamma-glutamylamine cyclotransferase, is a ubiquitous enzyme found in bacteria, plants, and metazoans from Dictyostelium through to humans. It converts gamma-glutamylamines to free amines and 5-oxoproline.
Pfam PF23181: INO4 bHLH domain (domain)
The founding member of this family is the bHLH domain of yeast protein INO4. This protein is a positive regulatory factor involved in the transcriptional regulation of phospholipid biosynthetic genes. INO4 forms a heterodimer with INO2 and this complex specifically recognizes the inositol/choline-responsive element, followed by the transcription activation of the phospholipid biosynthetic gene. Ternary INO2(bHLH)/INO4(bHLH)/DNA complex showed that the recognition and binding of promoter DNA is mediated by the presence of both protein domains.
Pfam PF18467: Domain of unknown function (DUF5613) (domain)
This is a domain of unknown function 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 PF02020: eIF4-gamma/eIF5/eIF2-epsilon (repeat)
This domain of unknown function is found at the C-terminus of several translation initiation factors.
Wikipedia: In molecular biology, the protein domain eIF4-gamma/eIF5/eIF2-epsilon is a family of evolutionarily related proteins. This domain is found at the C-terminus of several translation Initiation factors. It was first detected at the very C-termini of the yeast protein GCD6, eIF-2B epsilon, and two other eukaryotic translation initiation factors, eIF-4 gamma and eIF-5 and it may be involved in the interaction of eIF-2B, eIF-4 gamma, and eIF-5 with eIF-2.
Pfam PF23478: YKL104W-A (family)
This protein family includes the uncharacterised protein YKL104W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF).
Pfam PF06852: Protein of unknown function (DUF1248) (domain)
This entry represents a conserved domain within a number of proteins of unknown function that seem to be specific to C. elegans. Note that some family members contain more than one copy of this region.
Pfam PF16280: Domain of unknown function (DUF4928) (family)
This family consists of uncharacterized proteins around 330 residues in length and is mainly found in various Bacteria species, such as Enterobacteriales, Clostridiales, Actinomycetales and so on. The function of this family is unknown.
Pfam PF06045: Rhamnogalacturonate lyase family (family)
Rhamnogalacturonate lyase ([ec:4.2.2.-]) degrades the rhamnogalacturonan  I (RG-I) backbone of pectin.  This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.
Pfam PF23233: Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat (repeat)
This entry includes a group of pre-mRNA-processing factors that are components of the spliceosome, involved in pre-RNA splicing, including Syf1 from human and its homologues from fungi, crooked neck from Drosophila and its homologues from human and fungi Crooked neck-like protein 1 (CRNKL1/SYF-3) and CFL1, respectively. These proteins contain HAT (Half A TPR) repeats which have a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs. The HAT repeats in these proteins can be divided in three segments, N-terminal, central and C-terminal. This entry represents the N-terminal HAT repeats of these proteins. The N-terminal HAT repeats of Syf1 and Syf3 contact the U2 core domain via the U2' protein.
Pfam PF23291: Transcription elongation factor SPT5, fourth KOW domain (domain)
This entry includes Transcription elongation factor SPT5, a component of the elongation factor DRB-sensitivity inducing factor (DSIF) that plays multiple roles during transcription. SPT5 is a multidomain protein consisting of an N-terminal NusG domain ([pfam:PF03439]), tandem of KOW domains and and a mobile C-terminal-repeat region. The KOW domains differ in number between yeast, which has five, and animals, which have seven. This entry represents the fourth KOW domain of SPT5. The KOW domains of these proteins play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors, and they are also involved in the binding of the eukaryotic SPT5 proteins to RNA polymerases.
Pfam PF04519: Polymer-forming cytoskeletal (repeat)
This is a family of bactofilins, a functionally diverse class of cytoskeletal, polymer-forming, proteins that is widely conserved among bacteria. In the example species C. crescentus, two bactofilins assemble into a membrane-associated laminar structure that shows cell-cycle-dependent polar localisation and acts as a platform for the recruitment of a cell wall biosynthetic enzyme involved in polar morphogenesis. Bactofilins display distinct subcellular distributions and dynamics in different bacterial species, suggesting that they are versatile structural elements that have adopted a range of different cellular functions.
Pfam PF07212: Hyaluronidase protein (HylP) (repeat)
This family consists of several phage associated hyaluronidase proteins ([ec:3.2.1.35]) which seem to be specific to Streptococcus pyogenes and Streptococcus pyogenes bacteriophages. The substrate of hyaluronidase is hyaluronic acid, a sugar polymer composed of alternating N-acetylglucosamine and glucuronic acid residues. Hyaluronic acid is found in the ground substance of human connective tissue and the vitreous of the eye and also is the sole component of the capsule of group A streptococci. The capsule has been shown to be an important virulence factor of this organism by virtue of its ability to resist phagocytosis. Production by S. pyogenes of both a hyaluronic acid capsule and hyaluronidase enzymatic activity capable of destroying the capsule is an interesting, yet-unexplained, phenomenon.
Wikipedia: Hyaluronidases are a family of enzymes that catalyse the degradation of hyaluronic acid. Karl Meyer classified these enzymes in 1971, into three distinct groups, a scheme based on the enzyme reaction products. The three main types of hyaluronidases are two classes of eukaryotic endoglycosidase hydrolases and a prokaryotic lyase-type of glycosidase.
Pfam PF07079: Protein of unknown function (DUF1347) (family)
This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this 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 PF05969: Photosystem II complex subunit Ycf12 (family)
Ycf12 has been identified as a core subunit in the photosystem II (PSII) complex.  PsbZ has been shown to be required for the association of PsbK and Ycf12 with PSII.
Pfam PF05831: GAGE protein (family)
This family consists of several GAGE and XAGE proteins which are found exclusively in humans. The function of this family is unknown although they have been implicated in human cancers.
Pfam PF21089: Polyketide synthase dehydratase domain (domain)
This domain is part of a dehydratase domain found in diverse PKS enzymes. This domain adopts a HotDog fold.
Pfam PF09469: Cordon-bleu ubiquitin-like domain (domain)
The Cordon-bleu protein domain is highly conserved among vertebrates. The sequence contains three repeated lysine, arginine, and proline-rich regions, the KKRAP motif. The exact function of the protein is unknown but it is thought to be involved in mid-brain neural tube closure. It is expressed specifically in the node. This domain has a ubiquitin-like fold.
Pfam PF23651: BTBD17 TRAF domain (domain)
This domain is found in human BTB/POZ domain-containing protein 17 and related proteins. It is predicted to adopt a beta-sandwich with permuted Ig-like topology. It has a significant sequence and structural similarity to TRAF domains.
Pfam PF12925: E2 domain of amyloid precursor protein (domain)
The E2 domain is the largest of the conserved domains of the amyloid precursor protein. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures.E 2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulfate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface.
Pfam PF12715: Abhydrolase family (domain)
This is a family of probable bacterial abhydrolases.
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 PF19679: Family of unknown function (DUF6181) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from  the kanamycin biosynthetic gene cluster from Streptomyces  kanamyceticus.
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 PF21778: Family of unknown function (DUF6873) (repeat)
This entry represents a family of uncharacterised proteins that have a five fold symmetric alpha/beta propeller fold belonging to the GME (guanidino-group modifying enzymes) superfamily.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07484: Phage Tail Collar Domain (domain)
This region is occasionally found in conjunction with [pfam:PF03335]. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance [swissprot:Q03314] from Rhizobium leguminosarum may be involved in plant-microbe interactions (). A related protein [swissprot:Q9L3N1] is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate ([swissprot:P10930]) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop () and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of [swissprot:P10930] appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.
Pfam PF22869: Protein PssL (family)
This family includes Protein PssL from Escherichia coli, the product of a small open reading frame (smORF), which may serve a regulatory role in expression of downstream gene.
Pfam PF06490: Flagellar regulatory protein FleQ (domain)
This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa.  It is clearly related to [pfam:PF00072], but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator ([pfam:PF00072]).
Pfam PF01494: FAD binding domain (family)
This domain is involved in FAD binding in a number of enzymes.
Wikipedia: Monooxygenases are enzymes that incorporate one hydroxyl group (−OH) into substrates in many metabolic pathways. In this reaction, the two atoms of dioxygen are reduced to one hydroxyl group and one H2O molecule by the concomitant oxidation of NAD(P)H. One important subset of the monooxygenases, the cytochrome P450 omega hydroxylases, is used by cells to metabolize arachidonic acid (i.e. eicosatetraenoic acid) to the cell signaling molecules, 20-hydroxyeicosatetraenoic acid or to reduce or totally inactivate the activate signaling molecules for example by hydroxylating leukotriene B4 to 20-hydroxy-leukotriene B5, 5-hydroxyeicosatetraenoic acid to 5,20-dihydroxyeicosatetraenoic acid, 5-oxo-eicosatetraenoic acid to 5-oxo-20-hydroxyeicosatetraenoic acid, 12-hydroxyeicosatetraenoic acid to 12,20-dihydroxyeicosatetraenoic acid, and epoxyeicosatrienoic acids to 20-hydroxy-epoxyeicosatrienoic acids.