SII-SWORD/CoKE huggingface dataset:
Pfam PF02914: Bacteriophage Mu transposase (domain)
This transposase is essential for integration, replication-transposition and excision of Bacteriophage Mu DNA. The crystal structure of the core domain of Mu transposase, MuA, exhibits that the first of two subdomains contains the active site and, despite very limited sequence homology, exhibits a striking similarity to the core domain of Human immunodeficiency virus 1 integrase. The enzymatic activity of MuA is known to be activated by formation of a DNA-bound tetramer of the protein.
Pfam PF14100: Family of unknown function (DUF6807) (family)
This family includes bacterial proteins of unknown function.
Pfam PF17189: Glycosyl hydrolase family 30 beta sandwich domain (domain)
This Î² sandwich domain is found in proteins from the glycosyl hydrolase family 30.
Glycoside hydrolase family 30 GH30 comprises enzymes with only one known activity; glucosylceramidase (3.2.1.45).

Family 30 encompasses the mammalian glucosylceramidases. Human acid beta-glucosidase (D-glucosyl-N-acylsphingosine glucohydrolase), cleaves the glucosidic bonds of glucosylceramide and synthetic beta-glucosides . Any one of over 50 different mutations in the gene of glucocerebrosidase have been found to affect activity of this hydrolase, producing variants of Gaucher disease, the most prevalent lysosomal storage disease .
Wikipedia: In molecular biology, glycoside hydrolase family 30 is a family of glycoside hydrolases.
Pfam PF17154: Gammaproteobacterial periplasmic sensor domain (family)
GAPES3 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases/phosphodiesterases, including the c-di-GMP phosphodiesterases PdeK (YhjK) of Escherichia coli and HmsP of Yersinia pestis.
Pfam PF18045: ISP3 C-terminal (domain)
This is the C-terminal domain of ISP3 protein, which plays a role in asexual daughter cell formation, for example in T.gondii. The domain consists of a seven-stranded antiparallel beta-sandwich bordered on one end by a interstrand loop (open end) and capped at the other end by an amphipathic C-terminal helix (closed end). The loop between beta 5 and beta 6 is extended and variable. The domain adopts a pleckstrin homology (PH) fold, despite having neglible sequence similarity. PH domains are often found in proteins that support protein-lipid and play a role in mediating membrane localization through IP binding. However, the Phospholipid Binding Properties of PH domains is not conserved in the ISP3. Unlike PH domains, ISP3 is cysteine rich. The cysteine-rich nature of the ISP3s and the number of surface-exposed cysteines may result in redox instability and may also facilitate higher order multimerization. There are no disulfide bonds in ISP3 unlike in ISP1. It is worth noting that ISP1 and ISP3 share low sequence identity but contain the same secondary core elements.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF22967: NUP210 Ig-like domain 1 (domain)
This domain is found in the homologues of human Nuclear pore membrane glycoprotein 210 (NUP210). NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.
Pfam PF09037: Stf0 sulphotransferase (domain)
Members of this family are essential for the biosynthesis of sulpholipid-1 in prokaryotes. They adopt a structure that belongs to the sulphotransferase superfamily, consisting of a single domain with a core four-stranded parallel beta-sheet flanked by alpha-helices.
Wikipedia: Stf0 sulfotransferases are essential for the biosynthesis of sulfolipid-1 in prokaryotes. They adopt a structure that belongs to the sulfotransferase superfamily, consisting of a single domain with a core four-stranded parallel beta-sheet flanked by alpha-helices.
Pfam PF24347: FIGL1 N-terminal domain (domain)
This domain is found N-terminal in the ATPase family AAA domain-containing protein FIGL1 from Arabidopsis thaliana and related proteins. FIGL1 is involved in DNA double-strand break repair via homologous recombination (HR). This protein Limits class II meiotic crossover formation by regulating the invasion step of meiotic HR. This domain is predicted to fold into a three-helical bundle and precedes the AAA domain [pfam:PF00004] and separated from it via disordered linker.
Pfam PF13553: Function to find (domain)
The function to find (FIIND) was initially discovered in two proteins, NLRP1 (aka NALP1, CARD7, NAC, DEFCAP) and CARD8 (aka TUCAN, Cardinal). NLRP1 is a member of the Nod-like receptor (NLR) protein  superfamily and is involved in apoptosis and inflammation. To date,  it is the only NLR protein known to have a FIIND domain. The FIIND domain is also present in the CARD8 protein where, like in NLRP1,  it is followed by a C-terminal CARD domain. Both proteins are described to form an "inflammasome", a macro-molecular complex able to process caspase 1 and activate pro-IL1beta. The FIIND domain is present in only a very small subset of the kingdom of life, comprising  primates, rodents (mouse, rat), carnivores (dog) and a few more, such as horse. Publications describing the newly discovered NLRP1 protein  failed to identify it as a separate domain; for example, it was taken as part of the adjacent leucine rich repeat domain (LRR). Upon discovery of CARD8 it was noted that the N-terminal region shared significant sequence identity with an undescribed region in NLRP1. Before getting its final name, FIIND, this domain was termed NALP1-associated domain (NAD). This is a peptidase domain of the ZU5 superfamily that is predicted to be involved in autoproteolytic cleavage.
Pfam PF16821: C protein from hendra and measles viruses (family)
This is a family of C proteins from a number of Morbillivirus species.
Pfam PF23885: Family of unknown function (DUF7238) (family)
This entry represents a domain of unknown function. It is found in uncharacterized phage proteins in the size range 90 to 120 amino acids.  The domain does not appear to be related to any other known Pfam domain. The function of this domain remains to be determined.
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 PF10159: Multiple myeloma tumor-associated (domain)
This is a glycine-rich domain that is the most highly conserved region of a family of proteins that in vertebrates are associated with tumours in multiple myelomas. The region may contain nuclear localisation signals, so it might act as a signal molecule in the nucleus.
Pfam PF22962: NUP210 Ig-like domain 7 (domain)
This domain is found in the homologues of Nuclear pore membrane glycoprotein 210 (NUP210). NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.
Pfam PF19577: DcaP outer membrane protein (domain)
This entry includes DcaP which is the most abundant outer membrane channel protein in Acinetobacter baumannii. X-ray crystallography reveals a trimeric porin-like structure and suggests dicarboxylic acids as potential substrates.
Pfam PF22497: Domain of unknown function (DUF6989) (domain)
This domain is found in a number of uncharacterised bacterial proteins that are likely associated with the membrane.
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 PF08658: Rad54 N terminal (family)
This is the N terminal of the DNA repair protein Rad54.
Pfam PF09701: CRISPR-associated protein (Cas_Cmr5) (family)
CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species.
Pfam PF07084: Thyroid hormone-inducible hepatic protein Spot 14 (family)
This family consists of several thyroid hormone-inducible hepatic protein (Spot 14 or S14) sequences. Mainly expressed in tissues that synthesise triglycerides, the mRNA coding for Spot 14 has been shown to be increased in rat liver by insulin, dietary carbohydrates, glucose in hepatocyte culture medium, as well as thyroid hormone. In contrast, dietary fats and polyunsaturated fatty acids, have been shown to decrease the amount of Spot 14 mRNA, while an elevated level of cAMP acts as a dominant negative factor. In addition, liver-specific factors or chromatin organisation of the gene have been shown to contribute to the regulation of its expression. Spot 14 protein is thought to be required for induction of hepatic lipogenesis.
Pfam PF13462: Thioredoxin (domain)
Several biological processes regulate the activity of target proteins through changes in the redox state of thiol groups (S2 to SH2), where a hydrogen donor is linked to an intermediary disulphide protein. Such processes include the ferredoxin/thioredoxin system, the NADP/thioredoxin system, and the glutathione/glutaredoxin system . Several of these disulphide proteins share a common structure, consisting of a three-layer Î±/Î²/Î± core.
Pfam PF19780: Domain of unknown function (DUF6265) (domain)
This family of domains is functionally uncharacterised. This family of proteins is primarily found in bacteria. Proteins in this family are typically between 159 and 170 amino acids in length. The domain is found in some proteins associated with carbohydrate binding domains. The domain has some conserved aromatic residues that may suggest a carbohydrate 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 PF11059: Protein of unknown function (DUF2860) (family)
This bacterial 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 PF20898: P-type Type IV secretion system, TraN (family)
TraN, a subunit of the P-type Type IV secretion system (T4SS) encoded by the conjugative plasmid pKM101 from Escherichia coli, is the homologue of the F-type T4SS protein VirB7 ([pfam:PF17413]). This protein forms spokes radially crossing the entire assembly of the T4SS in the periphery of the outer membrane complex. It forms a complex with TraO (the homologue of VirB9) that surrounds the inner ring formed by TraF (VirB10 homologue).
Pfam PF01696: Adenovirus EB1 55K protein / large t-antigen (repeat)
This family consists of adenovirus E1B 55K protein or large t-antigen. E1B 55K binds p53 the tumour suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site.  This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the adenovirus E1A protein.  The E1B region of adenovirus encodes two proteins E1B 55K the large t-antigen as found in this family and E1B 19K [pfam:PF01691] the small t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis.  This family shows distant similarities to the pectate lyase superfamily.
Pfam PF13297: Replication stress response SDE2 C-terminal (domain)
This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved from its N-terminal at a diglycine motif within the ubiquitin-like fold, after Proliferating cell nuclear antigen (PCNA) interaction. This generates a functional protein that negatively regulates damage-inducible PCNA monoubiquitination, which then is proteolytically degraded to allow S phase progression and replication fork recovery in response to DNA damage.
Pfam PF09189: Domain of unknown function (DUF1952) (domain)
Members of this family are found in various Thermus thermophilus proteins. Their exact function has not, as yet, been determined.
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 PF22997: Chitin synthase 4-like domain (domain)
This domain is found in a group of fungal proteins, including Chitin synthase 4 from Gibberella zeae (CHS4), which plays a role in the polymerisation of chitin. This domain is predicted to adopt a globular structure with similarity to Cytochrome b5-like heme/steroid binding domain ([pfam:PF00173]). Despite this global similarity this domain lacks haem coordinating residues and is probably not involved in haem binding.
Pfam PF07609: Protein of unknown function (DUF1572) (family)
These proteins, from several diverse bacteria, share a short conserved sequence towards their N termini.
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 PF15965: TRAF-like zinc-finger (domain)
This entry represents TRAF-type zinc finger domains. Some of the proteins that have this domain are mammalian signal transducers associated with the cytoplasmic domain of the 75kDa tumour necrosis factor receptor . A heterocomplex, homodimer or heterodimer of TRAF1 and TRAF2, binds to the N-terminal of the inhibitor of apoptosis proteins 1 and 2 (IAPS) and recruits them to the tumour necrosis factor receptor 2. Other proteins containing this domain include F45G2.6 protein from Caenorhabditis elegans and DG17 protein from Dictyostelium discoideum (Slime mold).
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Pfam PF14140: YpzI-like protein (disordered)
The YpzI-like protein family includes the B. subtilis YpzI protein [swissprot:C0H446] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.
Pfam PF16055: Domain of unknown function (DUF4798) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 80 and 365 amino acids in length. There is a single completely conserved residue H that may be functionally important.
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 PF21949: Negative regulator of P-body association (family)
This protein family includes human Negative regulator of P-body association, also known as Protein NoBody, and similar sequences from vertebrates. NoBody is a microprotein of 68 residues that interacts with mRNA decapping proteins, which participate in mRNA turnover and nonsense-mediated decay (NMD).
Pfam PF25099: Patellin-1-like, C-terminal GOLD domain (domain)
This GOLD domain is found at the C-terminal end of Patellin-1 from Arabidopsis thaliana (PATL1) and similar plant proteins. PATL1 is a carrier protein that may be involved in membrane -trafficking events associated with cell plate formation during cytokinesis. It binds to some hydrophobic molecules and promotes their transfer between the different cellular sites. This domain is predicted to adopt a compact beta sandwich fold.
Pfam PF00370: FGGY family of carbohydrate kinases, N-terminal domain (domain)
This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain.
Wikipedia: In molecular biology the FGGY carbohydrate kinase family is a family of evolutionarily related carbohydrate kinase enzymes. These enzymes include L-fuculokinase EC 2.7.1.51 ; gluconokinase EC 2.7.1.12 ; glycerol kinase EC 2.7.1.30 ; xylulokinase EC 2.7.1.17 ; D-ribulose kinase EC 2.7.1.47 ; and L-xylulose kinase EC 2.7.1.53. These enzymes are proteins of from 480 to 520 amino acid residues.
Pfam PF01430: Hsp33 protein (family)
Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localised protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidising conditions like H2O2 cause disulfide bonds to form in Hsp33, a process that leads to the activation of its chaperone function.
Wikipedia: Hsp33 protein is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function.
Pfam PF14451: Mut7-C ubiquitin (family)
This member of the ubiquitin superfamily is found at the N-terminus of Mut7-C like RNAses, suggestive of an RNA-binding role.
Pfam PF22648: Histone H3 K4-specific methyltransferase SET7 N-terminal (repeat)
This entry includes histone-lysine N-methyltransferase SETD7 (also known as SET7/9) which specifically monomethylate Lys-4 of histone H3, creating a specific tag for epigenetic transcriptional activation. This entry represents the N-terminal region, which consists of MORN repeats.
Pfam PF17812: RET Cadherin like domain 3 (domain)
RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that RET contains four consecutive cadherin-like domains (CLD). This entry relates to CLD3. Classical cadherin calcium-coordinating motifs can be found between CLD2 and CLD3.
Pfam PF24466: Domain of unknown function (DUF7578) (domain)
This domain is found in uncharacterised eukaryotic proteins. It is sometimes found in tandem. This domain is predicted to adopt a globular structure consisting of alpha helices with some similarity to SAM domains.
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 PF04344: Chemotaxis phosphatase, CheZ (family)
This family represents the bacterial chemotaxis phosphatase, CheZ. This protein forms a dimer characterised by a long four-helix bundle, composed of two helices from each monomer. CheZ dephosphorylates CheY in a reaction that is essential to maintain a continuous chemotactic response to environmental changes. It is thought that CheZ's conserved residue Gln 147 orientates a water molecule for nucleophilic attack at the CheY active site.