SII-SWORD/CoKE huggingface dataset:
Pfam PF07832: Cfr10I/Bse634I restriction endonuclease (domain)
Cfr10I ([swissprot:P56200]) and Bse634I ([swissprot:Q8RT53]) are two Type II restriction endonucleases. They exhibit a conserved  tetrameric architecture that is of functional importance, wherein two dimers are arranged 'back-to-back' with their  putative DNA-binding clefts facing opposite directions.  These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet.The monomer may be split into  separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3.
Wikipedia: In molecular biology, the Cfr10I/Bse634I family of restriction endonucleases includes the type II restriction endonucleases Cfr10I and Bse634I. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged, back-to-back, with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet. The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3. Both Cfr10I and Bse634I recognise the double-stranded sequence RCCGGY and cleave after the purine R.Recognition sequence Cut
5' RCCGGY 5' ---R CCGGY--- 3'
3' YGGCCR 	 3' ---YGGCC R--- 5'
Pfam PF01421: Reprolysin (M12B) family zinc metalloprotease (domain)
The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.  Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins such as [swissprot:P78325], and fertilin [swissprot:Q28472].  Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.
Pfam PF17466: Family of unknown function (family)
This is a family of unknown function found in Enterobacteria phage P22 and Enterobacteria phage lambda.
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 PF18128: Hydrogen maturase F dimerization domain (domain)
This domain is found in Hydrogen maturase F (HydF) present in Thermotoga neapolitana. HydF is a GTPase, containing an FeS cluster-binding motif, that is able to are able to activate HydA produced so that HydA can drive the reversible reduction of protons to molecular H2. This domain, referred to as domain II, is responsible for HydF dimerization through the formation of a continuous beta-sheet comprising eight beta-strands from two monomers.
Pfam PF10486: Phosphoinositide 3-kinase gamma adapter protein p101 subunit (family)
Class I PI3Ks are dual-specific lipid and protein kinases involved in numerous intracellular signaling pathways. Class IB PI3K, p110gamma, is mainly activated by seven-transmembrane G-protein-coupled receptors (GPCRs), through its regulatory subunit p101 and G-protein beta-gamma subunits.
Pfam PF12418: Acyl-CoA dehydrogenase N terminal (family)
This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with [pfam:PF02770], [pfam:PF00441], [pfam:PF02771]. This family is one of the enzymes involved in AcylCoA interaction in beta-oxidation.
Pfam PF14402: 7 transmembrane helices usually fused to an inactive transglutaminase (family)
A family of seven transmembrane helices fused to an inactive transglutaminase domain. The transglutaminase domain is predicted to be extracellularly located. Members of this family are associated in gene neighborhoods with a pepsin-like peptidase and an ATP-grasp of the RimK-family. The ATP-grasp is predicted to modify the 7TM protein or a cofactor that interacts with it.
Pfam PF07151: Protein of unknown function (DUF1391) (family)
This family consists of several Enterobacterial proteins of around 50 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi where they are often known as YdfA. 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 PF23922: Family of unknown function (DUF7261) (family)
This entry represents uncharacterised proteins found mainly in Halobacteria.
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 PF11325: Domain of unknown function (DUF3127) (domain)
This bacterial family of proteins has no known function. However, it does show distant similarity to [pfam:PF00436], with proteins such as [swissprot:D1W984] being similar to both families. This suggests that this family may have a DNA-binding 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 PF00511: E2 (early) protein, C terminal (domain)
E2 is an early regulatory protein found in the dsDNA papillomaviruses. The viral genome is a 7.9-kb circular DNA that codes for at least eight early and two late (capsid) proteins. The products of the early genes E6 and E7 are oncoproteins that destabilise the cellular tumour suppressors p53 and pRB. The product of the E1 gene is a helicase necessary for viral DNA replication. The products of the E2 gene play key roles in the regulation of viral gene transcription and DNA replication. During early stages of viral infection, the E2 protein represses the transcription of the oncogenes E6 and E7, reintroduction of E2 into cervical cancer cell-lines leads to repression of E6/E7 transcription, stabilisation of the tumour suppressor p53, and cell-cycle arrest at the G1 phase of the cell cycle. E2 can also induce apoptosis by a p53-independent mechanism.
Pfam PF03283: Pectinacetylesterase (family)
This family includes protein Notum from animals and pectinacetylesterase (PAE) from plants. Notum is a carboxylesterase that removes an essential palmitoleate moiety from Wnt proteins. Notum constitutes the first known extracellular protein deacylase . PAEs catalyse the deacetylation of pectin, a major compound of primary cell walls .
Pfam PF14185: Antitoxin SpoIISB, type II toxin-antitoxin system (family)
Members of this family act as antitoxins. They bind to the SpoIISA toxin, [pfam:PF14171]. They are disordered proteins which adopt structure only when bound to SpoIISA.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF16735: Unconventional myosin-X coiled coil domain (coiled_coil)
This coiled coil domain is found in unconventional myosin-X and is responsible for dimerisation.
Pfam PF13637: Ankyrin repeats (many copies) (repeat)
The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators , cytoskeletal, ion transporters and signal transducers . The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it.

The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures . Each repeat folds into a helix-loop-helix structure with a Î²-hairpin/loop region projecting out from the helices at a 90oangle. The repeats stack together to form an L-shaped structure .
Wikipedia: The ankyrin repeat is a 33-residue motif in proteins consisting of two alpha helices separated by loops, first discovered in signaling proteins in yeast Cdc10 and Drosophila Notch. Domains consisting of ankyrin tandem repeats mediate protein–protein interactions and are among the most common structural motifs in known proteins. They appear in bacterial, archaeal, and eukaryotic proteins, but are far more common in eukaryotes. Ankyrin repeat proteins, though absent in most viruses, are common among poxviruses. Most proteins that contain the motif have four to six repeats, although its namesake ankyrin contains 24, and the largest known number of repeats is 34, predicted in a protein expressed by Giardia lamblia.
Pfam PF24743: Domain of unknown function (DUF7692) (domain)
This domain is found in a group of proteins from Halobacteria. It is predicted to adopt a structure that is reminiscent of ribbon-helix-helix fold. Members of this entry are likely to form dimers. They have a stretch of positively charged residues at the N terminus.
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 PF08314: Secretory pathway protein Sec39 (repeat)
Mnaimneh et al identified Sec39p as a protein involved in ER-Golgi transport in a large scale promoter shut down analysis of essential yeast genes.  Kraynack et al. (2005) showed that Sec39p (Dsl3p) is required for Golgi-ER retrograde transport and is part of a very stable protein complex that also includes Dsl1p (in mammals ZW10), Tip20p (Rint-1) and the ER localized Q-SNARE proteins Ufe1p (syntaxin-18), Sec20p and Use1p. This was confirmed in a genome-wide analysis of protein complexes by Gavin et al (2006).
Pfam PF07010: Endomucin (family)
This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Pfam PF19605: Family of unknown function (DUF6110) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in Firmicute bacteria. Proteins in this family are typically between 88 and 109 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 PF04261: Dyp-type peroxidase, N-terminal (domain)
Dyp-type (dye-decolorizing) peroxidases are a family of heme proteins found in a wide range of bacteria and fungi. They have a wide substrate specificity and lack homology to most other peroxidases, with the ability to function well under much lower pH conditions compared with the other plant peroxidases. They consist of two domains that adopt a ferredoxin-like fold, connected by a loop. This entry represents the N-terminal domain.
Wikipedia: In molecular biology, the DyP-type peroxidase family is a family of haem peroxidase enzymes.
Haem peroxidases were originally divided into two superfamilies, namely, the animal peroxidases and the plant peroxidases, which include fungal and bacterial peroxidases. The DyP family constitutes a novel class of haem peroxidase. Because these enzymes were derived from fungal sources, the DyP family was thought to be structurally related to the class II secretory fungal peroxidases. However, the DyP family exhibits only low sequence similarity to classical fungal peroxidases, such as LiP and MnP, and does not contain the conserved proximal and distal histidines and an essential arginine found in other plant peroxidase superfamily members.
Pfam PF18687: Family of unknown function (DUF5637) (domain)
This is a domain of unknown function found in predicted cysteine knot peptides.
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 PF02019: WIF domain (family)
The WIF domain is found in the RYK tyrosine kinase receptors [swissprot:P34925] and WIF the Wnt-inhibitory- factor. The domain is extracellular and contains two conserved cysteines that may form a disulphide bridge.  This domain is Wnt binding in WIF, and it has been suggested that RYK may also bind to Wnt. The WIF domain is a member of the immunoglobulin superfamily, and it comprises nine beta-strands and two alpha-helices, with two of the beta-strands (6 and 9) interrupted by four and six residues of irregular secondary structure, respectively. Considering that the activity of Wnts depends on the presence of a palmitoylated cysteine residue in their amino-terminal polypeptide segment, Wnt proteins are lipid-modified and can act as stem cell growth factors, it is likely that the WIF domain recognises and binds to Wnts that have been activated by palmitoylation and that the recognition of palmitoylated Wnts by WIF-1 is effected by its WIF domain rather than by its EGF domains. A strong binding affinity for palmitoylated cysteine residues would further explain the remarkably high affinity of human WIF-1 not only for mammalian Wnts, but also for Wnts from Xenopus and Drosophila.
Wikipedia: In molecular biology, the protein domain, WIF N-terminal refers to the N terminal domain of the protein, WIF. It stands for, Wnt-inhibitory factor, whereby wnt is a signalling molecule also known as wingless. Wnt is a molecule in the wnt signaling pathway. The WIF domain binds to the wnt ligand since it inhibits it.
Pfam PF10498: Intra-flagellar transport protein 57 (family)
Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.
Pfam PF22112: OmcA-like N-terminal domain (domain)
This entry represents the N-terminal domain of OmcA ([swissprot:Q8EG33]) from Shewanella oneidensis and similar proteins. OmcA is a decaheme c-type cytochrome homologue of MtrF and MtrC. OmcA may be able to receive electrons from the MtrCAB or MtrFDE complexes through the interaction with MtrC or MtrF. OmcA, MtrF and MtrC are involved in the use of manganese and iron as terminal electron acceptors.
Pfam PF18603: L-amino acid ligase C-terminal domain 2 (domain)
l-amino-acid ligases (LALs; EC 6.3.2.28) were discovered to be ATP-grasp superfamily enzymes that catalyze the formation of an alpha-peptide bond between two l-amino acids in an ATP-dependent manner. The members of this family share a common structural architecture that consists of three domains referred to as the A-domain, B-domain and C-domain. The C domain can be further divided into the C1-subdomain and the C2-subdomain. This entry represents the C2 subdomain.
Pfam PF01050: Mannose-6-phosphate isomerase C-terminal (family)
All of the members of this Pfam entry belong to family 2 of the mannose-6-phosphate isomerases. The type II phosphomannose isomerases are bifunctional  enzymes. This Pfam entry covers the isomerase domain.  The guanosine diphospho-D-mannose pyrophosphorylase domain is in another Pfam entry, see [pfam:PF00483].
Pfam PF24102: FAD synthase, middle domain (domain)
This domain is found in human FAD synthase (FLAD1) and similar sequences mainly found in eukaryotes. FLAD1 catalyses the adenylation of flavin mononucleotide (FMN) to form flavin adenine dinucleotide (FAD) coenzyme. This domain, which is predicted to show an alpha-beta configuration, is often found C-terminal to [pfam:PF00994] and N-terminal to [pfam:PF01507].
Pfam PF24059: Domain of unknown function (DUF7360) (domain)
This entry represents a domain of unknown function found in SPbeta prophage-derived uncharacterized protein YomG from Bacillus subtilis (strain 168). This domain may can be found in association with a prophage endopeptidase tail domain ([pfam:PF06605]).
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 PF15036: Interleukin 34 (domain)
Interleukins (IL) are a group of cytokines that play an important role in the immune system. They modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells.

This entry represents interleukin-34 (IL-34), it was identified via functional screening of a library of secreted proteins . This cytokine promotes the differentiation and viability of monocytes and macrophages through the colony-stimulating factor-1 receptor (CSF1R) .
Wikipedia: Interleukin 34 (IL-34) is a protein belonging to a group of cytokines called interleukins. It was originally identified in humans, by large scale screening of secreted proteins; chimpanzee, murine, rat and chicken interleukin 34 orthologs have also been found. The protein is composed of 241 amino acids, 39 kilodaltons in mass, and forms homodimers. IL-34 increases growth or survival of immune cells known as monocytes; it elicits its activity by binding the Colony stimulating factor 1 receptor.
Pfam PF07391: NPR nonapeptide repeat (2 copies) (repeat)
This nine residue repeat which I have called NPR after NonaPeptide Repeat.  It is found in two malarial proteins and has the consensus EEhhEEhhP where h stands for a hydrophobic amino acid.
Pfam PF18300: Domain of unknown function (DUF5604) (domain)
This domain is often found in the N-terminal region of proteins carrying the SET domain ([pfam:PF00856]), such as the SETDB1 protein present in Homo sapiens. SETDB1 is a histone methyltransferase that suppresses gene expression and modulates heterochromatin formation through H3K9me2/3.
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 PF21013: LOC400499 family (family)
This entry represents a human protein of unknown function. It has a remarkable high confidence structure prediction showing an extended single beta sheet composed of a single long meander. No obvious sequence repeat is present in the sequence. Some members of this family contain lipovitellin homologous regions additionally to the N-terminus of this family. Lipovitellin contains similar open beta structures which are used to bind to lipids suggesting that this family is also involved in lipid binding and storage.
Pfam PF24785: RXYLT1 C-terminal domain (domain)
This domain is found in human Ribitol-5-phosphate xylosyltransferase 1 (RXYLT1) and related proteins. RXYLT1 acts as an UDP-d-xylose,ribitol-5-phosphate beta1,4-xylosyltransferase in the biosynthetic pathway of O-mannosyl glycan. This domain has a detectable similarity to domains members of Glycosyl transferase clan GT-B and it is predicted to adopt similar structure.
Pfam PF23701: Micropeptide inhibiting actin cytoskeleton (family)
This protein family includes human Micropeptide inhibiting actin cytoskeleton (MIAC) and similar sequences from vertebrates. MIAC is a 51-residues long protein that reduces filamentous actin fibers by interacting with aquaporin AQP2. It also inhibits the activation of the EREG/EGFR signalling pathway. Low expression of this micropeptide is associated with poor survival of head and neck squamous cell carcinoma (HNSCC).
Pfam PF15220: Hypoxia-inducible lipid droplet-associated (family)
This family of proteins stimulate intracellular lipid accumulation, function as autocrine growth factors and enhance cell growth.
Pfam PF16971: Rough colony protein B, tight adherence - tad - subunit (family)
RcpB is part of the Tad operon of proteins. The Tad (tight adherence) macromolecular transport system, present in many bacterial and archaeal species, represents an ancient and major new subtype of type II secretion. The three Rcp proteins (RcpA, RcpB, and RcpC) and TadD, a putative lipoprotein, are localised to the bacterial outer membrane.