SII-SWORD/CoKE huggingface dataset:
Pfam PF17450: Alpha galactosidase A C-terminal beta sandwich domain (domain)
Alpha-galactosidase (melibiase) catalyses the hydrolysis of melibiose into galactose and glucose . Alpha-N-acetylgalactosaminidase catalyses the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides .

This entry represents the C-terminal domain of these enzymes .
Wikipedia: In molecular biology, glycoside hydrolase family 27 is a family of glycoside hydrolases.
Pfam PF02635: DsrE/DsrF-like family (domain)
DsrE is a small soluble protein involved in intracellular sulfur reduction. This family also includes DsrF and the homologues TusD/C. n E. coli, the DsrEFH homologue TusBCD interacts with the DsrC homologue TusE in a sulfur relay system during 2-thiouridine biosynthesis.
Pfam PF05656: Protein of unknown function (DUF805) (family)
This family consists of several bacterial proteins of unknown 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 PF13193: AMP-binding enzyme C-terminal domain (domain)
This is a small domain that is found C terminal to [pfam:PF00501]. It has a central beta sheet core that is flanked by alpha helices.
Pfam PF05715: Piccolo Zn-finger (domain)
This (predicted) Zinc finger is found in the  bassoon and piccolo proteins (e.g. [swissprot:Q9JKS6]). There are eight conserved cysteines, suggesting  that it coordinates two zinc ligands.
Pfam PF00132: Bacterial transferase hexapeptide (six repeats) (repeat)
A variety of bacterial transferases contain a repeat structure composed of tandem repeats of a [LIV]-G-X(4) hexapeptide, which, in the tertiary structure of LpxA (Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase) , has been shown to form a left-handed parallel Î²-helix. A number of different transferase protein families contain this repeat, such as the bifunctional protein GlmU, galactoside acetyltransferase-like proteins , the gamma-class of carbonic anhydrases , and tetrahydrodipicolinate-N-succinlytransferases (DapD), the latter containing an extra N-terminal 3-helical domain . It has been shown that most hexapeptide acyltransferases form catalytic trimers with three symmetrical active sites .
Pfam PF21958: SOGP N-terminal domain (domain)
This is the N-terminal domain of 1,2-beta oligoglucan phosphorylase (SOGP). This enzyme phosphorolyzes beta-1,2-glucooligosaccharides (sophorooligosaccharides, Sops) with degrees of polymerization (DP) of 3 or more. It consists of four domains: two beta-sandwich domains, (alpha/alpha)6 catalytic domain and a beta-sheet domain. The N-terminal domain adopts a supersandwich fold in which 18 beta-strands define two beta-sheets.
Pfam PF24350: Family of unknown function (DUF7510) (family)
This entry represents a family of uncharacterised archaeal proteins. They are predicted to have a structure composed of seven nearly orthogonally packed strands, four of which are located at the N-terminus and three at the C-terminus. The N- and C-terminal strands clamp to form a beta-sandwich. They are separated by a ~50 aa long disordered region which contains a repetitive SPY sequence motif.
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 PF10729: Cell division activator CedA (domain)
CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet..
Pfam PF14970: Tubulin epsilon and delta complex protein 1 (family)
This family represents the tubulin epsilon and delta complex protein 1 (TEDC1). This complex is required for centriole maintenance and it is a component of several ciliary structures. It acts as a positive regulator of hedgehog signalling, which play key roles in embryonic development and in cancers. Additionally, this protein may play a role in counteracting perturbation of actin filaments, such as after treatment with the actin depolymerising microbial metabolite Chivosazole F.
Pfam PF18790: KfrB Domain (domain)
This is a domain found in polyvalent proteins of conjugative element or often in the neighbourhood of one. The KfrB domain has been speculated to play a role in discrimination of self from non-self in plasmid conjugation systems. This domain has been described as having an OB-fold. Additionally in some proteins it has a four stranded beta sheet elaboration to the N-terminus that packs against the side of the OB barrel that is not included in this entry. The KfrB domain is also found at the C-terminus of some zeta toxin proteins.
Pfam PF23176: Transcription factor LHW bHLH domain (domain)
This bHLH domain is found in Arabidopsis thaliana Transcription factor LONESOME HIGHWAY (LHW) and related proteins from plants. LHW is a transcription activator that regulates root development. Mutations in this protein eliminate bilateral symmetry and reduce the number of cells in the center of the root, resulting in roots with only single xylem and phloem poles.
Pfam PF00951: Arterivirus GL envelope glycoprotein (family)
Arteriviruses encode 4 envelope proteins, Gl, Gs, M and N. Gl envelope protein, is encoded in ORF5, and is 30- 45 kDa in size. Gl is heterogenously glycosylated with N-acetyllactosamine in  a cell-type-specific manner. The Gl glycoprotein expresses the neutralisation determinants.
Pfam PF23031: ELAPOR1-like, galactose binding domain (domain)
This domain is found in Endosome/lysosome-associated apoptosis and autophagy regulator family member 2 from humans (ELAPOR1), which may protect cells from cell death by inducing cytosolic vacuolisation and up-regulating the autophagy pathway and may play a role in apoptosis and cell proliferation. It is predicted to form a beta sandwich with a jelly roll topology typical of a galactose binding domain (GBD).
Pfam PF25104: Domain of unknown function (DUF7812) (domain)
This domain is found in uncharacterised plant proteins. It is predicted to fold into an alpha-helical structure with similarity to alpha-solenoid 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 PF20660: Family of unknown function (DUF6812) (family)
This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria. There is a conserved RxxD sequence motif.
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 PF18010: Cry35Ab1 HTH C-terminal domain (domain)
This is the C-terminal domain found in Bacillus thuringiensis protein Cry35Ab1 (an insecticidal protein). The domain has three helices held in a hydrophobic core, the first two form a typical helix-loop-helix whilst the third helix is perpendicular. The domain is structurally homologous to BinB and proteins containing similar beta-trefoil lectin-like domains. The domain is not required for insecticidal activity or for immuno-reactivity and its function is likely to be to bind to WCR brush border membrane vesicles.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF16554: Dimerisation domain of d-ornithine 4,5-aminomutase (domain)
This family is the short dimerisation domain of the enzyme D-ornithine 4,5-aminomutase. It sits between the TIM-barrel [pfam:PF09043] and [pfam:PF02310]. The enzyme is an alpha2-beta2-heterodimer that converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor.
Pfam PF06668: Inter-alpha-trypsin inhibitor heavy chain C-terminus (family)
This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix. All family members contain the [pfam:PF00092] domain.
Pfam PF01981: Peptidyl-tRNA hydrolase PTH2 (family)
Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.
Pfam PF07722: Peptidase C26 (domain)
These peptidases have gamma-glutamyl hydrolase activity; that is they catalyse the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to [pfam:PF00117], but contain extensions in four loops and at the C terminus.
Pfam PF23763: GLAA-B beta-barrel domain I (domain)
This entry represents the first beta-barrel domain found towards the N-terminal in Alpha-1,3-galactosidase A-B (GLAA-B)from bacteria. This proteins share a domain architecture consisting of a core beta-helix surrounded by two small beta-barrel domains (domains I and II), which are involved in protein dimerization. GLAA-B are alpha-galactosidases grouped in the GH110 subfamily by its narrow subtract specificity. This proteins remove branched alpha-1,3-linked galactose residues present in blood group B antigens.
Pfam PF18377: FERM F2 acyl-CoA binding protein-like domain (domain)
This is an F2 lobe domain consisting of an acyl-CoA binding protein fold found in FERM region of Jak-family tyrosine kinases. Multidomain JAK molecules interact with receptors through their FERM and SH2-like domains, triggering a series of phosphorylation events, resulting in the activation of their kinase domains.  Overall, the FERM region maintains the typical three-lobed architecture, with an F1 lobe consisting of a ubiquitin-like fold, an F2 lobe consisting of an acyl-CoA binding protein fold, and an F3 lobe consisting of a pleckstrin-homology (PH) fold. JAK1 FERM-F2 domain has been shown to act as the interaction site for the IFNLR1 box1 motif (PxxLxF) of class II cytokine receptors which is essential for kinase activation.
Wikipedia: In molecular biology, the FERM domain is a widespread protein module involved in localising proteins to the plasma membrane. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus in the majority of proteins in which it is found.
Pfam PF21358: Ezh2, MCSS domain (domain)
This entry represents the MCSS domain found in the middle region of the Histone-lysine N-methyltransferase EZH2. It makes contacts with the adjacent SANT domain and the Vefs domain from EED. Additionally, this domain contains a zinc-binding motif and contributes two cysteine residues for a second one, formed with two cysteines from the SANT domain.
Pfam PF12764: Glycine-rich region of argonaut (domain)
This domain is often found at the very N-terminal of argonaut-like proteins.
Pfam PF12954: Protein of unknown function (DUF3843) (family)
A family of uncharacterized proteins found by clustering human gut metagenomic sequences.
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 PF05025: RbsD / FucU transport protein family (family)
The Escherichia coli high-affinity ribose-transport system consists of six proteins encoded by the rbs operon (rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). RbsD was originally thought to be a high affinity ribose transport protein, but further analysis shows that it is a D-ribose pyranase . It catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. It also catalyzes the conversion between beta-allofuranose and beta-allopyranose. This family also includes FucU a component of the fucose operon and is a L-fucose mutarotase, involved in the anomeric conversion of L-fucose. It also exhibits a pyranase activity for D-ribose. Both have been classified in the RbsD/FucU family of proteins. Members of this family are ubiquitous having been found in organisms from eubacteria to mammals.
Pfam PF04817: Umbravirus long distance movement (LDM) family (family)
The long distance movement protein of Umbraviruses mediates the movement of viral RNA through the phloem of infected plants.
Pfam PF11848: Domain of unknown function (DUF3368) (family)
This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 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 PF06401: Alpha-2-macroglobulin RAP, C-terminal domain (domain)
The alpha-2-macroglobulin receptor-associated protein (RAP)  is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of  all currently known ligands of these receptors.   Two different studies have provided conflicted domain boundaries.
Wikipedia: Low density lipoprotein receptor-related protein-associated protein 1 also known as LRPAP1 or RAP is a chaperone protein which in humans is encoded by the LRPAP1 gene.
Pfam PF03039: Interleukin-12 alpha subunit (domain)
Interleukin 12 (IL-12) is a disulphide-bonded heterodimer consisting of a 35kDa alpha subunit (e.g. [swissprot:P29459]) and a 40kDa beta subunit (e.g. [swissprot:P29460]). It is involved in the stimulation and maintenance of Th1 cellular immune responses, including the normal host defence against various intracellular pathogens, such as Leishmania, Toxoplasma, measles virus and HIV. IL-12 also has an important role in pathological Th1 responses, such as in inflammatory bowel disease and multiple sclerosis. Suppression of IL-12 activity in such diseases may have therapeutic benefit.  On the other hand, administration of recombinant IL-12 may have therapeutic benefit in conditions associated with pathological Th2 responses.
Wikipedia: Interleukins (ILs) are a group of cytokines that are expressed and secreted by white blood cells (leukocytes) as well as some other body cells. The human genome encodes more than 50 interleukins and related proteins.
Pfam PF18633: Zinc-finger antiviral protein (ZAP) zinc finger domain 3 (domain)
Zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of certain viruses, such as HIV-1, by targeting viral mRNA for degradation. N-terminal domain of ZAP is the major functional domain which contains four zinc-finger motifs. This entry represents the third zinc finger type CCCH.
Pfam PF17032: zinc-ribbon family (domain)
This zinc-ribbon region is found on a set of largely microsporidia-specific proteins.
Pfam PF14704: Dermatopontin (family)
Members of this family mediate cell adhesion via cell surface integrin binding. They also induce haemagglutination and aggregation of amebocytes.
Pfam PF08886: Glutamate-cysteine ligase (family)
This is a rare family of glutamate--cysteine ligases, [ec:6.3.2.2], demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.  The structure of this family has been solved, and is similar to that of human glutathione synthetase and very different to gamma-glutamylcysteine synthetase from Escherichia coli.
Pfam PF19092: Family of unknown function (DUF5780) (domain)
This entry adopts a Greek-key beta sandwich topology, with long loops in some of the members. While a  structure is known, the function of this domain is yet 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 PF09112: Peptide-N-glycosidase F, N terminal (domain)
Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins.
Pfam PF19711: Family of unknown function (DUF6207) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001709) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the nystatin biosynthetic gene cluster from Streptomyces albulus. This family appears to be predominantly found in Actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11441: Pilot protein MxiM (domain)
MxiM, a Shigella pilot protein, is essential for the assembly and membrane association of the Shigella secretin MxiD. MxiM contains an orthologous secretin component and has a specific binding domain for the acyl chains of bacterial lipids. The C terminal domain of MxiD hinders lipid binding to MxiM.
Pfam PF19095: Family of unknown function (DUF5783) (family)
Family of unknown function predominantly found 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 PF19716: Family of unknown function (DUF6211) (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 PF14649: Spatacsin C-terminus (family)
This family includes the C-terminus of spatacsin.
Pfam PF22723: NACHT-associated inactive Restriction Endonuclease 2 (domain)
This entry represents a predicted sensor domain in bacterial NACHT conflict systems. It is likely to bind a ligand which could contribute to activation of enzymatic domains additionally fused to the N-terminus of the NACHT module.
Pfam PF09957: Bacterial antitoxin of type II TA system, VapB (domain)
VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC, [pfam:PF05016]. The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerises with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the Toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all antitoxins.
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 PF23778: Putative phage holin family 2 (family)
This entry represents a family of putative holin proteins found in various phages infecting actinobacterial hosts, particularly Gordonia, Mycobacterium, Arthrobacter, and Microbacterium. Holins are small membrane proteins involved in the timing of host cell lysis during bacteriophage infection. Members of this family typically range from 94 to 151 amino acids in length and contain 3 to 4 predicted transmembrane helices. While some members have an N-terminal signal peptide or lipoprotein signal, most do not. It is unclear where the annotation for these proteins as holins arose.  However it appears plausible based on their sequence features. This entry shows similarity to [pfam:PF19447] a bacterial family of unknown function.