SII-SWORD/CoKE huggingface dataset:
Pfam PF23555: Vps41 C-terminal RING finger domain (domain)
This entry represents the C-terminal RING finger domain of Vps41, a component of the endosomal sorting complexes required for transport (ESCRT) machinery in eukaryotic cells. These cells utilize conserved membrane tethering complexes like CORVET and HOPS to regulate endomembrane fusion, with each complex comprising six subunits, including unique C-terminal zinc-finger domains. Biochemical studies in human CORVET and HOPS reveal direct interaction between the zinc-containing RING domains of VPS18 and VPS41, forming a stable heterodimer. Within cells, these domains integrate into endogenous HOPS, with the VPS18 RING domain recruiting VPS41 to the core complex. However, yeast Vps41 lacks a C-terminal zinc-finger motif. In human CORVET, the analogous subunit VPS8 requires both its RING and disordered C-terminal domains for integration into endogenous complexes, suggesting distinct molecular interactions for recruiting VPS41 and VPS8 to HOPS and CORVET, respectively.
Pfam PF13445: RING-type zinc-finger (domain)
This zinc-finger is a typical RING-type of plant ubiquitin ligases.
Pfam PF02520: SXP/RAL-2 family protein Ani s 5-like, metal-binding domain (domain)
This domain is found in proteins from nematodes, including SXP/RAL-2 family protein Ani s 5 (ANIS5) from Anisakis simplex, and comprises two conserved motifs: SXP1 and SXP2. Although the function of this domain is not clear, structural information from ANIS5 revealed an alpha helical arrangement with a Calmodulin-like fold. Functional studies indicates that ANIS5 can bind magnesium and calcium, suggesting that this domain plays a role in cation binding. These proteins are interesting targets to develop control strategies against the diseases caused by parasites.
Pfam PF15867: Dynein attachment factor N-terminus (family)
This family represents the N-terminus of a dynein arm attachment factor which is required for dynein arm assembly and cilia motility.
Pfam PF01153: Glypican (family)
Glypicans  are a family of heparan sulphate proteoglycans which are anchored to cell membranes by a glycosylphosphatidylinositol (GPI) linkage. Six members (GPC1-6) are known in vertebrates . The main function of glypicans is to regulate several signaling pathways, including those of Wnts, Hedgehogs, fibroblast growth factors and bone morphogenetic proteins (BMPs) .

Structurally, these proteins consist of three separate domains:


 * A signal sequence;
 * An extracellular domain of about 500 residues that contains 12 conserved cysteines probably involved in disulphide bonds and which also contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains;
 * A C-terminal hydrophobic region which is post-translationally removed after formation of the GPI-anchor.
Wikipedia: Glypicans constitute one of the two major families of heparan sulfate proteoglycans, with the other major family being syndecans. Six glypicans have been identified in mammals, and are referred to as GPC1 through GPC6. In Drosophila two glypicans have been identified, and these are referred to as dally and dally-like. One glypican has been identified in C. elegans. Glypicans seem to play a vital role in developmental morphogenesis, and have been suggested as regulators for the Wnt and Hedgehog cell signaling pathways. They have additionally been suggested as regulators for fibroblast growth factor and bone morphogenic protein signaling.
Pfam PF06514: Photosystem II 12 kDa extrinsic protein (PsbU) (family)
This family consists of several photosystem II 12 kDa extrinsic protein (PsbU) proteins from cyanobacteria and algae. PsbU is an extrinsic protein of the photosystem II complex of cyanobacteria and red algae. PsbU is known to stabilise the oxygen-evolving machinery of the photosystem II complex against heat-induced inactivation. This family appears to be related to the Helix-hairpin-helix domain.
Pfam PF04400: (Na+)-NQR maturation NqrM (family)
The NqrM gene is often found adjacent to the nqr operons that encode (Na+)-NQR subunits. It is involved in the maturation of (Na+) translocating NADH:quinone oxidoreductase in proteobacteria. The four conserved Cys residues found in NqrM are required for (Na+)- NQR maturation and may serve as ligands for a metal ion or metal cluster used to build up the (Na+)-NQR molecule.
Pfam PF20857: Immunodominant antigen Pgp3, helical domain (domain)
This domain is found in Immunodominant antigen Pgp3, a virulence protein from Chlamydia trachomatis involved in stimulating host immune responses and thought to be required for growth within mammalian cells. Pgp3 consists of globular N- and C-terminal domains ([pfam:PF05475] is the latter) connected by a triple-helical coiled coil (THCC, this entry).
Pfam PF24439: Family of unknown function (DUF7558) (family)
This entry represents a small family of uncharacterised proteins found in archaea. They contain four pairs of conserved cysteines as well as several conserved histidines. It is likely that these residues are involved in metal coordination.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22507: Family of unknown function (DUF6994) (family)
This is a family of uncharacterised bacterial proteins. They are probably remotely related to His-Me finger endonucleases. The conservation of the putative active site residues in this family is not strict, in particular the position of the catalytic histidine. The residues involved in metal coordination are conserved. The presence in the vicinity of two invariant aspartate residues that point toward the putative active site suggests that these proteins may still function as enzymes but probably via a somewhat different catalytic mechanism. They may still retain their catalytic activity by employing these conserved aspartates that in the predicted AF2 models are well positioned to undertake a role in a potential nucleophilic attack.
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 PF00822: PMP-22/EMP/MP20/Claudin family (family)
This family of evolutionarily related integral membrane proteins includes PMP22, EMP, claudins and voltage-gated calcium channel gamma subunits, many of which perform diverse functions at specialised cell-cell contacts . Family members from vertebrates and invertebrates are highly divergent.
Wikipedia: Claudins are a family of proteins which, along with occludin, are the most important components of the tight junctions. Tight junctions establish the paracellular barrier that controls the flow of molecules in the intercellular space between the cells of an epithelium. They have four transmembrane domains, with the N-terminus and the C-terminus in the cytoplasm.
Pfam PF02918: Pertussis toxin, subunit 2 and 3, C-terminal domain (domain)
A large group of bacterial exotoxins are referred to as "A/B toxins", essentially because they are formed from two subunits . The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit .

Bordetella pertussis is the causative agent of whooping cough, and is a Gram-negative aerobic coccus. Its major virulence factor is the pertussis toxin, an A/B exotoxin that mediates both colonisation and toxaemic stages of the the disease . Recombinant, inactive forms of the 5 subunits that make up the toxin have proven to be good vaccines. The S2 and S3 subunits of the toxin form part of the "B" moiety. They are responsible for binding the whole toxin to host cells prior to invasion, and are classed as adhesins . S2 attaches to a host receptor called lactosylceramide. It has also been speculated that the S3 unit may preferentially bind phagocytes.

The crystal structure of pertussis toxin has been determined to 2.9A resolution . The catalytic A-subunit (S1) shares structural similarity with other ADP-ribosylating bacterial toxins, although differences in the C-terminal portion explain its unique activation mechanism. Despite its heterogeneous subunit composition, the structure of the cell-binding B-oligomer (S2, S3, two copies of S4, and S5) resembles the symmetrical B-pentamers of the cholera and shiga toxin families, but it interacts differently with the A-subunit and there is virtually no sequence similarity between B-subunits of the different toxins. Two peripheral domains that are unique to the pertussis toxin B-oligomer share structural similarity with a calcium-dependent eukaryotic lectin, and reveal possible receptor-binding sites.
Wikipedia: Pertussis toxin (PT) is a protein-based AB5-type exotoxin produced by the bacterium Bordetella pertussis, which causes whooping cough. PT is involved in the colonization of the respiratory tract and the establishment of infection. Research suggests PT may have a therapeutic role in treating a number of common human ailments, including hypertension, viral infection, and autoimmunity.
Pfam PF22528: Arginine methyltransferase oligomerization subdomain (domain)
This entry represents a domain found C-terminal in protein arginine methyltransferases. This domain is involved in oligomerisation.
Pfam PF11282: Protein of unknown function (DUF3082) (family)
This family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23946: Family of unknown function (DUF7280) (family)
This entry represents an uncharacterized protein domain found in bacteriophage proteins, predominantly from mycobacteriophages and Gordonia phages. The domain is typically between 80-130 amino acids in length. It folds into a compact domain composed of a sheet of five beta strands with an alpha helix packed on one side.
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 PF01559: Zein seed storage protein (family)
Zeins are seed storage proteins. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats.
Wikipedia: Zein is a class of prolamine protein found in maize. It is usually manufactured as a powder from corn gluten meal. Zein is one of the best understood plant proteins. Pure zein is clear, odorless, tasteless, hard, water-insoluble, and edible, and it has a variety of industrial and food uses.
Pfam PF14457: Prokaryotic E2 family A (family)
A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are very similar to the eukaryotic E2 proteins. Members of this family are usually fused to E1 and JAB domains C-terminal to the E2 domain. The protein is usually in the gene neighborhood of a gene encoding a distinct metallobetalactamase family protein.
Pfam PF08225: Pseudin antimicrobial peptide (family)
Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Pseudidae).  The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides.
Pfam PF14535: 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 PF20912: DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain (domain)
This domain is found in the subunit RPC3 (also known as RPC62) of the eukaryotic DNA-directed RNA polymerase III, which synthesises small RNAs, such as 5S rRNA and tRNAs. RPC3 shows four defined domains folded around a fifth C-terminal domain consisting of two long alpha- helices (this entry). This domain appears to be reminiscent of coiled- coil motifs.
Pfam PF06777: Helical and beta-bridge domain (domain)
HBB is the domain on DEAD-box eukaryotic DNA repair helicases ([ec:3.6.1.-]) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein verifies the presence of damage to DNA and allows DNA repair to proceed. XPD is an assembly of several domains to form a doughnut-shaped molecule that is able to separate two DNA strands and scan the DNA for damage. HBB helps to form the overall DNA-clamping architecture.  This family represents a conserved region within a number of eukaryotic DNA repair helicases ([ec:3.6.1.-]).
Pfam PF17430: Uncharacterized YqgC-like (family)
This is a family of unknown function found in Enterobacteriaceae such as E.coli and Shigella.
Pfam PF04349: Periplasmic glucan biosynthesis protein, MdoG (family)
This family represents MdoG, a protein that is necessary for the synthesis of periplasmic glucans. The function of MdoG remains unknown. It has been suggested that it may catalyse the addition of branches to a linear glucan backbone.
Pfam PF15501: Nuclear protein MDM1 (family)
This family of proteins is present in the nucleus. The function of MDM1 is not known.
Pfam PF15631: NTF2 fold immunity protein (family)
A predicted immunity protein of the NTF2 fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-NucA family. This domain is also fused to ankyrin repeats and the PFAM:PF14025.
Pfam PF18343: Dda helicase SH3 domain (domain)
This is a Src homology-3 (SH3) like beta-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second beta-ribbon that is referred to as the hook and a beta-ribbon/two-helix substructure that is referred to as the tower. The tower region within the domain is rigidly connected to domain 2A in Dda and appears to be specifically designed for the task of supporting the extended pin. Hence, it is suggested that 2A and this SH3 domain move as one unit during the ATP-driven translocation of ssDNA while maintaining contact with the pin. In this scenario, the pin-tower interaction can be considered as an additional transmission site that serves to more efficiently couple the energy from ATP binding and hydrolysis to the unwinding of dsDNA.
Pfam PF05183: RNA dependent RNA polymerase (family)
This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates.
Wikipedia: RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.
Pfam PF14355: Abortive infection C-terminus (family)
This domain is found at the C-terminus of the Lactococcus lactis abortive infection protein Abi-859, [swissprot:Q48620]. This protein confers bacteriophage resistance.
Pfam PF01163: RIO domain (domain)
This is the atypical serine kinase domain found in RIO family of proteins and related sequences, which is conserved in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined. This domain is also found at the C-terminal of EKC/KEOPS complex subunit BUD32 from Fungi and Kae1/Bud32 from archaea.
Pfam PF02228: Major core protein p19 (family)
p19 is a component of the inner protein layer of the viral nucleocapsid.
Pfam PF03088: Strictosidine synthase (repeat)
Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid  biosynthesis.  It catalyses the condensation of tryptamine with  secologanin to form strictosidine.
Pfam PF16097: Fragile X-related 1 protein C-terminal region 3 (family)
FXR_C1 is a small highly conserved region at the very C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with [pfam:PF05641], [pfam:PF00013], PF16096.
Pfam PF24160: Root UVB sensitive protein, C-terminal (domain)
This domain is found at the C-terminal of a group of root UVB sensitive plant proteins and their eukaryotic RUS homologues. It is predicted to adopt an alpha-beta configuration. This domain is found associated with [pfam:PF04884].
Pfam PF03855: M-factor (family)
The M-factor is a pheromone produce upon nitrogen starvation. The production of M-factor is increased by the pheromone signal. The protein undergoes post-translational modification, to remove the C-terminal signal peptide, the carboxy-terminal cysteine residue is carboxy-methylated  and S-alkylated, with a farnesyl residue.
Pfam PF08022: FAD-binding domain (domain)
This entry represents FAD binding domain that is associated with ferric reductase NAD binding proteins and the heavy chain of Cytochrome b-245. Members of this group are predominantly found in eukaryotes and bacteria.
Pfam PF20484: Family of unknown function (DUF6723) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 81 and 125 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 PF01052: Type III flagellar switch regulator (C-ring) FliN C-term (family)
This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, [pfam:PF02154] and family FliN_N [pfam:PF16973].
Pfam PF01403: Sema domain (repeat)
The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance.  Sema domains also occur in [swissprot:P08581] the hepatocyte growth factor receptor and [swissprot:P51805]
Wikipedia: The Sema domain is a structural domain of semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor, Plexin-A3 and in viral proteins.
Pfam PF08329: Chitinase A, N-terminal domain (domain)
This domain is found in a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin. It is separated by a hinge region from the catalytic domain ([pfam:PF00704]); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution.
Wikipedia: In molecular biology, the chitinase A N-terminal domain is found at the N-terminus of a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin. It is separated by a hinge region from the catalytic domain; this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution.
Pfam PF11246: Base plate wedge protein 53 (family)
The baseplate of bacteriophage T4 controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The structure of the baseplate suggests a mechanism of baseplate structural transition during the initial stages of T4 infection. The baseplate is assembled from six identical wedges that surround the central hub. Gp53, along with other T4 gene products, combine sequentially to assemble a wedge.
Pfam PF15109: TMEM125 protein family (family)
The function of this family of transmembrane proteins, TMEM125, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 55 and 232 amino acids in length.
Pfam PF16456: YmgD protein (domain)
This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
Pfam PF09027: GTPase binding (domain)
The GTPase binding domain binds to the G protein Cdc42, inhibiting both its intrinsic and stimulated GTPase activity. The domain is largely unstructured in the absence of Cdc42.
Pfam PF14011: EspG family (family)
This family of proteins contains the the EspG1, EspG2 and EspG3 proteins from M. tuberculosis.  These proteins are involved in the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis which is important for virulence and intercellular spread. Proteins in this family are typically between 254 and 295 amino acids in length.
Pfam PF16460: Phage tail tube, TTP, lambda-like (domain)
This family represents the phage-tail-tube protein from a set of Siphoviridae from Gammaproteobacteria. Tail tube proteins polymerise with the assistance of the Tail-tip complex, a tape measure protein and two chaperones. Infectivity of host is delivered through the tube.
Pfam PF00920: Dihydroxy-acid/6-phosphogluconate dehydratase N-terminal (domain)
This is the N-terminal domain of Ilv/ED dehydratase protein family which includes dihydroxy-acid/6-phosphogluconate dehydratases, and pentonate dehydratases. Members of this entry are involved in various biosynthetic and carbohydrate metabolic pathways. Dihydroxy-acid dehydratase catalyses the fourth step in the biosynthesis of isoleucine and valine, the dehydratation of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyses the first step in the Entner-Doudoroff pathway, the dehydratation of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. They consist of two domains, N- and C-terminal. This domain is composed of a beta-sheet with four parallel beta-strands surrounded by four alpha-helices and forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion.