SII-SWORD/CoKE huggingface dataset:
Pfam PF04837: MbeB-like, N-term conserved region (family)
This family represents an N-terminal conserved region of MbeB/MobB proteins. These proteins are essential for specific plasmid transfer.
Pfam PF06925: Monogalactosyldiacylglycerol (MGDG) synthase (family)
This family represents a conserved region of approximately 180 residues within plant and bacterial monogalactosyldiacylglycerol (MGDG) synthase ([ec:2.4.1.46]). In Arabidopsis, there are two types of MGDG synthase which differ in their N-terminal portion: type A and type B.
Pfam PF14116: YyzF-like protein (family)
The YyzF-like protein family includes the B. subtilis YyzF protein [swissprot:C0H3T9] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.
Pfam PF15488: Domain of unknown function (DUF4645) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 200 and 298 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 PF00574: Clp protease (domain)
The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. [swissprot:P48254] has lost all of these active site residues and is therefore inactive. [swissprot:P42379] contains two large insertions, [swissprot:P42380] contains one large insertion.
Wikipedia: In molecular biology, the CLP protease family is a family of serine peptidases belong to the MEROPS peptidase family S14. ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP, although the P subunit alone does possess some catalytic activity.
Pfam PF10769: Protein of unknown function (DUF2594) (family)
This family of proteins with unknown function appear to be restricted to Enterobacteriaceae.
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 PF02428: Potato type II proteinase inhibitor family (domain)
Members of this family are proteinase inhibitors that contain eight cysteines that form four disulphide bridges. The structure of the proteinase-inhibitor complex is known.
Pfam PF01535: PPR repeat (repeat)
This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins.  This family appears to be greatly expanded in plants. This repeat occurs in PET309 [swissprot:P32522] that may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing.  This repeat is associated with a predicted plant protein [swissprot:O49549] that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR.
Wikipedia: The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide-repeat-containing proteins are a family of proteins commonly found in the plant kingdom. They are distinguished by the presence of tandem degenerate PPR motifs and by the relative lack of introns in the genes coding for them.
Pfam PF06242: Transcriptional cell cycle regulator TrcR (family)
This family represents a transcriptional cell cycle regulator (TrcR) found in Proteobacteria, mainly Alphaproteobacteria. It has been shown to associate with promoters and coding sequences in vivo in a rifampicin-dependent manner and to interact physically and genetically with RNA polymerase, resulting in the integration of cell cycle and antibiotic stress control with the general transcriptional machinery.
Pfam PF02493: MORN repeat (repeat)
The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton.
Pfam PF12259: Baculovirus F protein (family)
This protein is found in a variety of baculoviruses. It is known as the F protein. Matches to this family are additionally found in some presumed transposons.
Pfam PF24025: DR_A0283-like, Ig-like domain (domain)
This domain with an immunoglobulin (Ig)-like fold is found in the probable subtilase-type serine protease DR_A0283 from Deinococcus radiodurans. It shows high  structural similarity with the first beta-sandwich domain (SD1) from Fervidolysin from Fervidobacterium pennivorans.
Pfam PF21875: Calpain-13-like, C-terminal EF-hand (domain)
This domain is found at the C-terminal end of human Calpain-13 (CAPN13) and similar sequences from vertebrates. CAPN13 is thought to be a non-lysosomal thiol-protease. This entry represents the last EF-hand domain of this protein.
Pfam PF22682: Large ribosomal subunit protein uL24m (domain)
This entry represents a domain found in the homologues of large ribosomal subunit protein uL24m. This protein is a component of the mitochondrial ribosome (mitoribosome).
Pfam PF05704: Capsular polysaccharide synthesis protein (family)
This family consists of several capsular polysaccharide proteins. Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae.
Pfam PF00847: AP2 domain (domain)
This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins.
Wikipedia: Apetala 2 (AP2) is a gene and a member of a large family of transcription factors, the AP2/EREBP family. In Arabidopsis thaliana AP2 plays a role in the ABC model of flower development. It was originally thought that this family of proteins was plant-specific; however, recent studies have shown that apicomplexans, including the causative agent of malaria, Plasmodium falciparum encode a related set of transcription factors, called the ApiAP2 family.
Pfam PF04720: PDDEXK-like family of unknown function (family)
PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix. The family is not in general fused with any other domains, so its function cannot be predicted.
Pfam PF03203: MerC mercury resistance protein (family)
The mercury resistance protein, MerC, is an inner membrane protein that mediates Hg2+transport into the cytoplasm . MerA then converts the inorganic form of mercury Hg2+ to the less toxic form Hg0, thereby conferring mercury resistance .
Pfam PF08354: Fatty acid synthase subunit beta/Fas1-like, helical (domain)
This domain has been identified in fungi and bacteria. It is found in fatty acid synthase beta subunit from fungi, including Fas1 from yeasts and aflB from Aspergillus parasiticus. This is an inserted helical domain, whose function is not clear, and is found together with the MaoC-like domain ([pfam:PF01575]) and the acyltransferase domain ([pfam:PF00698]). Fas1 is a fatty acid synthetase that catalyses the formation of long-chain fatty acids from  acetyl-CoA, malonyl-CoA and NADPH. AflB is part of the gene cluster that mediates the biosynthesis of aflatoxins.
Pfam PF01007: Inward rectifier potassium channel transmembrane domain (domain)
Inwardly-rectifying potassium channels (Kir) are the principal class of two-TM domain potassium channels. They are characterised by the property of inward-rectification, which is described as the ability to allow large inward currents and smaller outward currents. Inwardly rectifying potassium channels (Kir) are responsible for regulating diverse processes including: cellular excitability, vascular tone, heart rate, renal salt flow, and insulin release . To date, around twenty members of this superfamily have been cloned, which can be grouped into six families by sequence similarity, and these are designated Kir1.x-6.x .

Cloned Kir channel cDNAs encode proteins of between ~370-500 residues, both N- and C-termini are cytoplasmic, and the N terminus lacks a signal sequence. Kir channel alpha subunits possess only 2TM domains linked with a P-domain. The two 'transmembrane passes' place the C-terminal tail on the cytoplasmic side of the membrane . It is thought that four Kir subunits assemble to form a tetrameric channel complex, which may be hetero- or homomeric .
Wikipedia: Inward-rectifier potassium channels (Kir, IRK) are a specific lipid-gated subset of potassium channels. To date, seven subfamilies have been identified in various mammalian cell types, plants, and bacteria. They are activated by phosphatidylinositol 4,5-bisphosphate (PIP2). The malfunction of the channels has been implicated in several diseases. IRK channels possess a pore domain, homologous to that of voltage-gated ion channels, and flanking transmembrane segments (TMSs). They may exist in the membrane as homo- or heterooligomers and each monomer possesses between 2 and 4 TMSs. In terms of function, these proteins transport potassium (K+), with a greater tendency for K+ uptake than K+ export. The process of inward-rectification was discovered by Denis Noble in cardiac muscle cells in 1960s and by Richard Adrian and Alan Hodgkin in 1970 in skeletal muscle cells.
Pfam PF04383: KilA-N domain (domain)
The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease.
Wikipedia: In molecular biology, the KilA-N domain is a conserved DNA-binding domain found at the N-terminus of the poxvirus D6R/NIR proteins. It is also found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. Putative proteins with homology to the KilA-N domain have also been identified in Maverick transposable elements of the parabasalid protozoa Trichomonas vaginalis. The KilA-N domain has been suggested to be homologous to the fungal DNA-binding APSES domain. In all proteins shown to contain the KilA-N domain, it occurs at the extreme amino terminus accompanied by a wide range of distinct carboxy-terminal domains. These carboxy-terminal modules may be enzymes, such as the nuclease domains, or might mediate additional, specific interactions with nucleic acids or proteins, like the RING or CCCH fingers in the poxviruses. The KilA-N domain is predicted to adopt an alpha-beta fold with four conserved strands and at least two conserved helices. Some proteins known to contain a KilA-N domain are listed below:Bacteriophage P1 protein kilA
Fowlpox virus (FPV) protein FPV236.
Trichomonas vaginalis G3 Putative uncharacterised protein
Vaccinia virus hypothetical 21.7 kDa HindIII-C protein
Pfam PF11875: DnaJ-like protein C11, C-terminal (domain)
This is the C-terminal domain found in DnaJ-like proteins, including DnaJ homolog subfamily C member 11 (DNAJC11) from mammals and Chaperone protein dnaJ 13 from Arabidopsis. DNAJC11 is a mitochondrial outer membrane protein involved in mitochondrial biogenesis and in the response to microenvironment changes and requirements. The J-domain is mediated its mitochondrial localization, while this domain is critical for protein-protein interactions. This domain adopts a SUEL/RBL-like fold and contains the conserved motif FxDPCxxxxxK in common with the carbohydrate-binding loop of the SUEL/RBL lectin domain ([pfam:PF02140]).
Pfam PF19619: Family of unknown function (DUF6124) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 85 and 119 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 PF21936: Pcf11, C-terminal domain (domain)
This entry represents the C-terminal domain of Pcf11, a CCHC zinc-finger domain which contains a conserved interface for potential binding partners. Mutational studies revealed that mutations in key residues in this conserved region disrupts 3'-end processing. Pfc11 is a highly conserved multidomain protein that links transcriptional elongation, 3'-end processing, and transcription termination.
Pfam PF02829: 3H domain (family)
This domain is predicted to be a small molecule binding domain, based on its occurrence with other domains. The domain is named after its three conserved histidine residues.
Wikipedia: In molecular biology, the 3H domain is a protein domain named after its three highly conserved histidine residues. The 3H domain appears to be a smarr molecure-binding domain, based on its occurrence with other domains. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products. The 3H domain has a 2-layer alpha/beta sandwich fold.
Pfam PF18522: Domain of unknown function (DUF5620) (domain)
This is a domain of unknown function predicted to be a carbohydrate binding module.
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 PF24305: Probiotic-derived P8 protein (family)
This entry represents the Probiotic-derived P8 protein from Lactobacillus rhamnosus and related proteins found mainly in Lactobacillales. P8 has anti-cancer properties in colorectal cancer (CRC) cells via inducing apoptosis through regulation of Ring finger protein 152 (RNF152) and thus inhibiting the development of CRC. P8 adopts a globular structure consisting of a three-helical bundle (PDB:6J98).
Pfam PF17236: SU10 major capsid protein (family)
This family (previously known as DUF5309) represents the bacteriophage SU10 major capsid protein and related proteins found in phages and bacteriophages. The capsid of SU10 is organised in fivefold symmetry and build from 715 copies of major capsid protein. The major capsid protein of SU10 adopts an HK97 fold, which is common among tailed bacteriophages and herpesviruses. This protein forms a capsomers of two types: pentamers and hexamers.
Pfam PF23911: Domain of unknown function (DUF7253) (domain)
This entry represents a domain of unknown function, which is found in phage proteins, predominantly from Arthrobacter and Gordonia phages. The domain is approximately 110 amino acids in length. It shows similarity to the Phage_barrel superfamily. These proteins are often components of the phage neck complex.
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 PF10047: Protein of unknown function (DUF2281) (domain)
Members of this family of hypothetical bacterial proteins have 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 PF01591: 6-phosphofructo-2-kinase (domain)
This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyses both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. This enzyme contains a P-loop motif.
Wikipedia: Phosphofructokinase-2 (6-phosphofructo-2-kinase, PFK-2) or fructose bisphosphatase-2 (FBPase-2), is an enzyme indirectly responsible for regulating the rates of glycolysis and gluconeogenesis in cells. It catalyzes formation and degradation of a significant allosteric regulator, fructose-2,6-bisphosphate (Fru-2,6-P2) from substrate fructose-6-phosphate. Fru-2,6-P2 contributes to the rate-determining step of glycolysis as it activates enzyme phosphofructokinase 1 in the glycolysis pathway, and inhibits fructose-1,6-bisphosphatase 1 in gluconeogenesis. Since Fru-2,6-P2 differentially regulates glycolysis and gluconeogenesis, it can act as a key signal to switch between the opposing pathways. Because PFK-2 produces Fru-2,6-P2 in response to hormonal signaling, metabolism can be more sensitively and efficiently controlled to align with the organism's glycolytic needs. This enzyme participates in fructose and mannose metabolism. The enzyme is important in the regulation of hepatic carbohydrate metabolism and is found in greatest quantities in the liver, kidney and heart. In mammals, several genes often encode different isoforms, each of which differs in its tissue distribution and enzymatic activity. The family described here bears a resemblance to the ATP-driven phospho-fructokinases; however, they share little sequence similarity, although a few residues seem key to their interaction with fructose 6-phosphate.
Pfam PF15318: Putative Bcl-2 like protein of testis (family)
This family of proteins is found in eukaryotes. The family may represent a set of Bcl-2-like proteins involved in apoptosis, see UniProt:Q9BQM9.
Pfam PF00704: Glycosyl hydrolases family 18 (domain)
The glycosyl hydrolases family 18 (GH18) GH18 is widely distributed in all kingdoms and contains hydrolytic enzymes with chitinase or endo-N-acetyl-beta-D-glucosaminidase (ENGase) activity as well as chitinase-like lectins (chi-lectins/proteins (CLPs). Chitinases (3.2.1.14) are hydrolytic enzymes that cleave the beta-1,4-bond releasing oligomeric, dimeric (chitobiose) or monomeric (N-actetylglucosamine, GlcNAc) products. ENGases (3.2.1.96) hydrolyze the beta-1,4 linkage in the chitobiose core of N-linked glycans from glycoproteins leaving one GlcNAc residue on the substrate. CLPs do not display chitinase activity but some of them have been reported to have specific functions and carbohydrate binding property . This family also includes glycoproteins from mammals, such as oviduct-specific glycoproteins.

This entry represents the catalytic domain of GH18s, which has a common (Î²/Î±)8 triosephosphate isomerase (TIM)-barrel structure that consists of a barrel-like framework made from eight internal parallel Î²-strands that are alternately connected by eight exterior Î±-helices. The active site motif DxxDxDxE is essential for the activity of the GH18 catalytic domain. .
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Wikipedia: In molecular biology, Glycoside hydrolase family 18 is a family of glycoside hydrolases.
Pfam PF12386: Pseudomurein endo-isopeptidase Pei (family)
This peptidase has the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. It catalyses the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteristics of metal-activated peptidases.
Pfam PF03469: XH domain (domain)
The XH (rice gene X Homology) domain is found in a family of plant proteins including gene X [swissprot:Q9SBW2].  The molecular function of these proteins is unknown.  However these proteins usually contain an XS domain that is also found in the PTGS protein SGS3. This domain contains a conserved glutamate residue that may be functionally important.
Pfam PF09216: Pfg27 (domain)
Members of this family are essential for gametocytogenesis in Plasmodium falciparum. They contain a fold composed of two pseudo dyad-related repeats of the helix-turn-helix motif, serving as a platform for RNA and Src homology-3 (SH3) binding.
Pfam PF03294: RNA polymerase-associated transcription specificity factor, Rap94 (family)
The Poxvirus RNA polymerase-associated transcription specificity factor Rap94 associates with RNA polymerase and may mediate binding of the core polymerase to VetF. It is required for transcription of early genes.
Pfam PF15011: Ribosome biogenesis protein C1orf109-like (family)
Ribosome biogenesis protein C1orf109 is involved in the cytoplasmic maturation steps of pre-60S ribosomal particles by promoting the release of shuttling protein RSL24D1/RLP24 from the pre-ribosomal particles. It has been first identified as the downstream target of a protein kinase, casein kinase 2 (CK2) which is upregulated in cancer cells. C1orf109 has been found upregulated in cancer cells and therefore, it has been suggested to be important in the regulation of cancer cell proliferation. The precise mechanism of CK2 targeting C1orf109 is not well characterised. It is found to be localised in the nucleus and cytoplasm.
Pfam PF12878: SICA extracellular beta domain (domain)
The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies.  There can be between 1 and 10 copies of this cysteine-rich domain.