SII-SWORD/CoKE huggingface dataset:
Pfam PF22043: Domain of unknown function (DUF6935) (domain)
This is a domain found in uncharacterised bacterial proteins either as standalone or in combination with other domains. It is remotely related to soluble lipid-binding protein MlaC and it is predicted to adopt a similar structure with a typical NTF2-like topology.
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 PF00927: Transglutaminase family, C-terminal ig like domain (domain)
Transglutaminases catalyse the post-translational modification of proteins at glutamine residues, with formation of isopeptide bonds. Members of the transglutaminase family usually have three domains: N-terminal (IPR001102), middle (IPR013808) and C-terminal. The middle domain is usually well conserved, but family members can display major differences in their N- and C-terminal domains, although their overall structure is conserved . This entry represents the C-terminal domain found in transglutaminases, which consists of an immunoglobulin-like Î²-sandwich consisting of seven strands in two sheets with a Greek key topology.

The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. Protein-glutamine gamma-glutamyltransferases (2.3.2.13) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the Î³-carboxyl group of a glutamine in one polypeptide chain and the Îµ-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins .

Proteins containing this domain also include Protein 4.2 (also known as Epb42), which is one of the most abundant protein components of the erythrocyte membrane. The protein shares significant sequence homology with transglutaminases, but lacks the catalytic triad residues required for transglutaminase activity . The complete or nearly complete absence of protein 4.2 is associated with an atypical form of hereditary spherocytosis (HS) .
Wikipedia: Transglutaminases are enzymes that in nature primarily catalyze the formation of an isopeptide bond between γ-carboxamide groups ( -(C=O)NH2 ) of glutamine residue side chains and the ε-amino groups ( -NH2 ) of lysine residue side chains with subsequent release of ammonia ( NH3 ). Lysine and glutamine residues must be bound to a peptide or a protein so that this cross-linking (between separate molecules) or intramolecular (within the same molecule) reaction can happen. Bonds formed by transglutaminase exhibit high resistance to proteolytic degradation (proteolysis). The reaction isGln-(C=O)NH2 + NH2-Lys → Gln-(C=O)NH-Lys + NH3
Pfam PF10601: LITAF-like zinc ribbon domain (family)
Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure.
Pfam PF24722: Domain of unknown function (DUF7674) (domain)
This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 127 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 PF04464: CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase (family)
Wall-associated teichoic acids are a heterogeneous class of phosphate-rich polymers that are covalently linked to the cell wall peptidoglycan of gram-positive bacteria. They consist of a main chain of phosphodiester-linked polyols and/or sugar moieties attached to peptidoglycan via a linkage unit. CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase is responsible for the polymerisation of the main chain of the teichoic acid by sequential transfer of glycerol-phosphate units from CDP-glycerol to the linkage unit lipid.
Pfam PF01555: DNA methylase (domain)
Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.
Wikipedia: In biochemistry, the DNA methyltransferase family of enzymes catalyze the transfer of a methyl group to DNA. DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine (SAM) as the methyl donor.
Pfam PF24481: CT398-like coiled coil hairpin domain (domain)
This entry, previously known as DUF7581, represents a coiled coil hairpin domain found N-terminal in CT398 from C. trachomatis, MSMEG_4306 M. smegmatis and related bacterial sequences predominantly from actinobacteria. Both CT398 and MSMEG_4306 proteins have been structurally characterised. CT398 protein is involved in several aspects of chlamydial biology and pathogenesis, and is capable of interacting with multiple binding partners. The coiled coil hairpin domain of CT398 engages in interaction with RpoN as well as both T3SS ATPase-regulators FliH and CdsL.
Pfam PF06874: Firmicute fructose-1,6-bisphosphatase (family)
This family consists of several bacterial fructose-1,6-bisphosphatase proteins ([ec:3.1.3.11]) which seem to be specific to phylum Firmicutes. Fructose-1,6-bisphosphatase (FBPase) is a well known enzyme involved in gluconeogenesis. This family does not seem to be structurally related to [pfam:PF00316].
Wikipedia: The enzyme fructose bisphosphatase (EC 3.1.3.11; systematic name D-fructose-1,6-bisphosphate 1-phosphohydrolase) catalyses the conversion of fructose-1,6-bisphosphate to fructose 6-phosphate in gluconeogenesis and the Calvin cycle, which are both anabolic pathways:D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate
Pfam PF01683: EB module (family)
This domain has no known function. It is found in several C. elegans proteins. The domain contains 8 conserved cysteines that probably form four disulphide bridges. This domain is found associated with kunitz domains [pfam:PF00014].
Pfam PF05614: Circovirus ORF3 (family)
This family consists porcine circovirus ORF3 protein which plays a role in modulating host cell signalling by binding to and degrading host RGS16. This protein is not necessary for virus replication.
Pfam PF23157: Domain of unknown function (DUF7055) (domain)
This is a presumed domain found in a group of uncharacterised sequences from bacteria. According to structure predictions, this domain is found at the C-terminal and may adopt an all-beta structure consisting of eight anti-parallel beta-sheets.. These proteins also have a glycosyltransferase domain at the N-terminal ([pfam:PF13231]).
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 PF01381: Helix-turn-helix (domain)
This large family of DNA binding helix-turn helix proteins includes Cro [swissprot:P03036] and CI [swissprot:P03034]. Within the protein [swissprot:Q5F9C2], the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family.
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 PF17762: HTH domain found in ParB protein (domain)
This entry represents the HTH domain found in ParB and its homologue, Spo0J . ParB is involved in chromosome partition. It localize to both poles of the predivisional cell following completion of DNA replication .
Pfam PF23338: PTHB1 hairpin (domain)
This entry represents a hairpin domain found in PTHB1 protein (also known as Bardet-Biedl syndrome 9 protein, BBS9). This protein forms a part of the BBSome complex, which is required for ciliogenesis. PTHB1 is the major binding subunit of IFT38 C-terminal domain, which assists the BBSome in some of its roles.
Pfam PF21591: RNA helicase Hera, dimerization domain (domain)
This domain is found at the C-terminal region of Heat resistant RNA dependent ATPase from Thermus thermophilus (also known as Hera) the first DEAD box helicase that forms a stable dimer in the absence of ligands. This dimerization domain (DD) folds into a single turn of a left-handed super-helix.
Pfam PF19594: Family of unknown function (DUF6099) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000222) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from  the FD-594 biosynthetic gene cluster from Streptomyces sp. TA-0256  and it 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 PF13813: Membrane bound O-acyl transferase family (family)
This domain is found in membrane bound O-acyltransferases, including long-chain-alcohol O-fatty-acyltransferase (wax synthases) from plants and fungi  and acyl-CoA sterol acyl transferase 1 from Arabidopsis .
Wikipedia: The MBOAT family of membrane proteins is a family of various acyltransferase enzymes. All family members contain multiple transmembrane domains and most carry two conserved residues, a conserved histidine (His) embedded in a hydrophobic stretch of residues and an asparagine (Asn) or histidine within a more hydrophilic region some 30-50 residues upstream.
Pfam PF04947: Poxvirus Late Transcription Factor VLTF3 like (family)
Members of this family are approximately 26 KDa, and are involved in trans-activator of late transcription.
Pfam PF11009: Monothiol bacilliredoxin BrxC (family)
Bacillithiol (BSH) functions as a general thiol reductant, analogous to glutathione, in a wide range of bacterial species. Bacilliredoxins reduce those proteins that are modified by disulfide bond formation with BSH (S-bacillithiolation). This entry represents BrxC from Bacillus subtilis (formerly known as YtxJ) and similar bacterial proteins related to BSH. BrxC is a monothiol bacilliredoxin responsible for the removal of BSH from oxidized cytosolic proteins. It can also debacillithiolate the mixed disulfide form of the bacilliredoxin BrxB. It has a similar fold to thioredoxin. The homologue in Deinococcus radiodurans, named AbxC, plays a role in the response to oxidative stress.
Pfam PF12739: ER-Golgi trafficking TRAPP I complex 85 kDa subunit (family)
This family is one of the subunits of the TRAPP Golgi trafficking complex. TRAPP subunits are found in two different sized complexes, TRAPP I and TRAPP II, and this Trs85 is in the smaller complex. TRAPP I, but Not TRAPP II, functions in ER-Golgi transport. Trs85p was reported to function in the cytosol-to-vacuole targeting pathway, suggesting a role for this subunit in autophagy as well as in secretion. The overall architecture of TRAPP I shows the other components to be Bet3p (TRAPPC3), Bet5p (TRAPPC1), Trs20p (TRAPPC2) , Trs23p (TRAPPC4), Trs31p (TRAPPC5), Trs33p (TRAPPC6a and b) and Trs85p.
Pfam PF25138: Phage head-tail joining protein (domain)
This entry is related to [pfam:PF05521] which is a phage protein that acts as a stopper to retain phage DNA in the capsid as well performing a head tail connector function.
Pfam PF14889: Penicillin-binding protein Tp47 domain a (domain)
This is the first domain in this unusual penicillin-binding protein PBP), Tp47 is mainly composed of beta-strands and is sequentially non-contiguous. The first three domains in Tp47 interact with each other through intimate domain-domain interfaces. Domain A contacts domain B through its N-terminal segment. Domain A also interacts tightly with domain C, Tp47 is unusual in that it displays beta-lactamase activity, and thus it does not fit the classical structural and mechanistic paradigms for PBPs, and thus Tp47 appears to represent a new class of PBP.
Pfam PF21734: 10-bladed beta propeller domain (repeat)
This entry represents a family of beta propeller repeats identified in metagenomics data. They have 10 blades in an arrangement similar to the sortilin protein.
Pfam PF01988: VIT family (family)
This family includes the vacuolar Fe2+/Mn2+ uptake transporter [swissprot:P47818], Ccc1 and the vacuolar iron transporter VIT1 [swissprot:Q9ZUA5].
Pfam PF13001: Proteasome component ECM29, N-terminal (repeat)
The proteasome consists of two subunits, and the capacity of the proteasome to degrade protein depends crucially on the interaction between these two subunits. This interaction is affected by a wide range of factors including metabolites, such as ATP, and proteasome-associated proteins such as ECM29. ECM29 is an adapter/scaffolding protein that tethers the proteasome core particle to the regulatory particle, stabilising the interaction between the two subunits. This entry represents a HEAT-repeats containing domain found at the N-terminal of ECM29. The N-terminal half of the protein binds the endocytic components Vps11, Rab11-FIP4, and rabaptin.
Pfam PF18939: Family of unknown function (DUF5686) (family)
This is a family of unknown function, mostly found in bacteria. Family members can be found at the C-terminal region of [pfam:PF13715].
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 PF20644: Rrn7/TAF1B, N-terminal cyclin domain (domain)
Rrn7 from yeast and its orthologue TATA box-binding protein-associated factor RNA polymerase I subunit B (TAF1B) from human, are TFIIB-like factors components of RNA polymerase I core factor complex. They contain two cyclin fold domains which interact with both Rrn6 and Rrn11 and form the fingers of the core factor which resembles a right hand. N-terminal regions of both Rrn11 and Rrn6 compose the palm, the thumb is composed by the C-terminal of Rrn11 and the knuckles consist of the C-terminal half of Rrn6. This is the first cyclin domain (cyclin I) from yeast Rrn7 and its orthologues from animals and plants TAF1B.
Pfam PF09581: Stage III sporulation protein AF (Spore_III_AF) (family)
This family represents the stage III sporulation protein AF (Spore_III_AF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). These proteins have the typical RBM fold conserved in T3SS/flagellar systems. The RBM fold of SpoIIIAF contains two unique features, extended N-terminal helix, associated with multimerization and an insertion at a loop region that can adopt two distinct conformations.
Pfam PF15188: Coiled-coil domain-containing protein 167 (coiled_coil)
The function of this family of coiled-coil domains, has not, as yet, been determined. Members of this family remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 103 amino acids in length.
Pfam PF02863: Arginine repressor, C-terminal domain (domain)
This is the C-terminal domain of the arginine repressor, responsible for arginine binding and multimerization. It binds mainly Arg, but also ornithine, Pro and Tyr (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: In molecular biology, the arginine repressor (ArgR) is a repressor of prokaryotic arginine deiminase pathways.
Pfam PF17986: EMP3-KAHRP-like N-terminal domain (domain)
This is the N-terminal domain which is found at the N terminus of the erythrocyte cytoskeleton-associated protein (EMP3) and the knob-associated histidine-rich protein (KAHRP). KAHRP found in protozoan parasites such as Plasmodium falciparum, is involved in both rigidifying the host cell and the formation of cytoadherent knob structures.
Wikipedia: KAHRP is a protein expressed by Plasmodium falciparum infecting erythrocytes. KAHRP is a major component of knobs, feature found on Plasmodium falciparum infected erythrocytes.
Pfam PF14645: Chibby family (family)
This family includes the eukaryotic chibby proteins. These proteins inhibit the wingless/Wnt pathway by binding to beta-catenin and inhibiting beta-catenin-mediated transcriptional activation. Chibby is Japanese for small, and is named after the RNAi phenotype seen in Drosophila.
Pfam PF03898: Satellite tobacco necrosis virus coat protein (family)
This entry represents coat proteins found in several satellite viruses, including satellite panicum mosaic virus , satellite tobacco necrosis virus, and satellite St. Augustine decline virus. The coat proteins of satellite viruses consist of a Î²-sandwich jelly-roll fold, with usually eight strands making up the two sheets, although some members can have an extra 1-2 strands. The characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies. Although the satellite virus coat proteins share the same jelly-roll fold, they differ in the arrangement of their secondary structural elements and in the interactions of adjacent subunits .
Pfam PF09693: Phage uncharacterised protein (Phage_XkdX) (family)
This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Pfam PF06069: PerC transcriptional activator (family)
PerC is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria.
Pfam PF05125: Phage major capsid protein, P2 family (family)
This entry represents Capsid proteins from Bacteriophage P2 (GpN) and similar proteins from tailed bacteriophages and bacterial prophages mainly among Proteobacteria.

GpN undergoes proteolytic cleavage into three products:


 * Minor capsid protein H1, a 39 kDa protein
 * Minor capsid protein H2, 38.6 kDa
 * Major capsid protein N*, 36.7 kDa 


The capsid of P4, the satellite phage of P2, consists of those same gene products encoded by P2, although in this case the resulting capsids are smaller than those usually formed by P2 alone. P2 procapsid have a dextro HK97 fold with T = 7 symmetry .
Pfam PF04526: Protein of unknown function (DUF568) (family)
Family of uncharacterised plant proteins.
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 PF08965: Domain of unknown function (DUF1870) (domain)
This domain is found in a set of hypothetical bacterial proteins. It contains a helix-turn-helix domain so may be a DNA-binding protein.
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 PF05383: La domain (domain)
This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.
Wikipedia: In molecular biology, the La domain is a conserved protein domain. Human 60 kDa SS-A/Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La. The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjögren syndrome. In the nucleus, La acts as a RNA polymerase III transcription factor, while in the cytoplasm, La acts as a translation factor. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and an RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif.
Pfam PF14112: Immunity protein 22 (family)
A predicted immunity protein with an alpha+beta fold and conserved  tryptophan,tyrosine and an acidic residues. 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  ColD/E5, Tox-REase-4, Ntox49 or Ntox14  families. The domain is also found in heterogeneous  polyimmunity loci.
Pfam PF05951: Bacterial protein of unknown function (DUF882) (family)
This family consists of a series of hypothetical bacterial proteins of unknown function.
Pfam PF14181: YqfQ-like protein (family)
The YqfQ-like protein family includes the B. subtilis YqfQ protein [swissprot:P54474], also known as VrrA, which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY.
Pfam PF15524: Novel toxin 17 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses a mostly all-beta fold and a conserved ExD motif and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 7 or TcdB/TcaC-type secretion system.