SII-SWORD/CoKE huggingface dataset:
Pfam PF17905: GLD-3 4th KH domain (aka KH5) (domain)
This KH domain is found in the C. elegans GLD-3 protein. GLD-3 is a protein required maternally for germline survival and embryogenesis. This domain is known as the KH5 domain based on a prior identification of five KH domains in the GLD-3 protein. However, based on recent structure predictions using AlphaFold is appears that the KH1 domain is not a KH domain at all. Therefore the 4th KH domain is known as KH5. This is the fourth KH domain of the globular structure unit also formed by KH2, KH3 and KH4. GLD-3 interacts with the cytoplasmic poly(A)-polymerase GLD-2. The two proteins cooperate to recognize target mRNAs and convert them into a polyadenylated, translationally active state.
Pfam PF15942: Domain of unknown function (DUF4751) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 140 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 PF03293: Poxvirus DNA-directed RNA polymerase, 18 kD subunit (family)
DNA-directed RNA polymerases 2.7.7.6 (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.

Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:


 * RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.
 * RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.
 * RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.


Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.
The Poxvirus DNA-directed RNA polymerase (2.7.7.6) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18kDa subunit.
Pfam PF00288: GHMP kinases N terminal domain (domain)
This entry represents a conserved domain with a Gly/Ser-rich region found in galacto-, homoserine, mevalonate and phosphomevalonate kinases (GHMP) which is involved in the binding of ATP.
Wikipedia: In molecular biology, the GHMP kinase family is a family of kinase enzymes. Members of this family include homoserine kinases EC 2.7.1.39, galactokinases EC 2.7.1.6, and mevalonate kinasesEC 2.7.1.36. These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. These enzymes contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, creates a novel nucleotide binding fold.
Pfam PF18486: PNGase/UBA- or UBX-containing domain (domain)
This is a PUB domain (PNGase/UBA- or UBX-containing domain), found in E3 ubiquitin-protein ligase RNF31, also known as Ring finger protein 31 and HOIL-1-interacting protein (HOIP) ([ec:2.3.2.27]). RNF31/HOIP is observed to contribute to inborn human immunity disorders, in which RNF31/HOIP missense mutation at PUB domain gives rise to the de-stabilized LUBAC complex (linear ubiquitin chain assembly complex) and subsequently causes the auto-inflammation and immunodeficiency. In addition, RNF31 is reported to modify ERK and JNK pathways leading to cisplatin resistance. Functional studies indicate that HOIP and OTULIN interact and act as a bimolecular editing pair for linear ubiquitin signals where the HOIP-PUB domain binds to the PUB interacting motif (PIM) of OTULIN and the chaperone VCP/p9. This interaction plays an important role where the HOIP binding to OTULIN is required for the recruitment of OTULIN to the TNF receptor complex and to counteract HOIP-dependent activation of the NF-KB pathway.
Pfam PF12442: Protein of unknown function (DUF3681) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 112 and 212 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12244: Protein of unknown function (DUF3606) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13965: dsRNA-gated channel SID-1 (family)
This is a family of proteins that are transmembrane dsRNA-gated channels. They passively transport dsRNA into cells and do not act as ATP-dependent pumps. They are required for systemic RNA interference. This family of proteins belong to the CREST superfamily, which are distantly related to GPCRs.
Pfam PF22269: Teichoic acid transporter subunit TagH, SH3-like domain (domain)
This domain is found in TagH from Staphylococcus epidermidis, the ATPase subunit of the two-component transporter TagGH, which is involved in the synthesis of bacterial polysaccharides-wall teichoic acids. This entry represents the middle SH3-like subdomain that consists of a twisted antiparallel beta-sheet and two beta-hairpins tightly packed forming a barrel structure. It is usually found C-terminal to [pfam:PF00005] and N-terminal to [pfam:PF22096].
Pfam PF13190: PDGLE domain (domain)
This short presumed domain is usually found on its own. However, it is also found associated with [pfam:PF01891] suggesting it may have a role in cobalt uptake. The domain is named after a short motif found within many members of the family.
Pfam PF16886: ATPsynthase alpha/beta subunit barrel-sandwich domain (domain)
This barrel-sandwich domain is found in the alpha-beta catalytic subunit of VATA or V-type proton ATPase catalytic subunit at the N-terminal end. This domain has a circularly permuted topology compared to other barrel-sandwich domains. In VATA barrel-sandwich domain the C-terminal strand is circularly permuted and occupies the spatial position of the N-terminal strand in other hybrid domains.
Pfam PF05132: RNA polymerase III RPC4 (family)
Specific subunit for Pol III, the tRNA specific polymerase.
Pfam PF02140: D-galactoside/L-rhamnose binding SUEL lectin domain (domain)
The D-galactoside binding lectin purified from sea urchin (Anthocidaris crassispina) eggs exists as a disulphide-linked homodimer of two subunits; the dimeric form is essential for hemagglutination activity. The sea urchin egg lectin (SUEL) forms a new class of lectins that binds D-galactoside and L-rhamnose, with preference for L-rhamnose.
Wikipedia: In molecular biology, the galactose binding lectin domain is a protein domain. It is found in many proteins including the lectin purified from sea urchin eggs, SUEL. This lectin exists as a disulfide-linked homodimer of two subunits; the dimeric form is essential for hemagglutination activity. The sea urchin egg lectin (SUEL) forms a new class of lectins. Although SUEL was first isolated as a D-galactoside binding lectin, it was later shown that it binds to L-rhamnose preferentially. L-rhamnose and D-galactose share the same hydroxyl group orientation at C2 and C4 of the pyranose ring structure.
Pfam PF14985: TM140 protein family (family)
This family of uncharacterised membrane proteins are called transmembrane protein 140. They are found in mammals.
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 PF15845: Cysteine-rich C-terminal 1 family (disordered)
NICE-1 is family of proteins found in primates. Proteins in this family are typically between 51 and 105 amino acids in length.
Pfam PF21475: PaaA-like, N-terminal domain (domain)
This domain is found at the N-terminal end of PaaA from Enterobacter agglomerans, an enzyme involved in post-translational modification and host immunity. PaaA is composed of two domains: [pfam:PF00899] and the domains represented by this entry, which folds into a globular domain and has similarity to RiPP precursor peptide recognition elements or RREs.
Pfam PF17074: Darcynin, domain of unknown function (family)
Darcynin is a bacterial protein family. Its function is unknown.
Pfam PF10441: Urb2/Npa2 family (family)
This family includes the Urb2 protein from yeast that are involved in ribosome biogenesis.
Pfam PF22475: YhfS-like, C-terminal domain (domain)
This entry represents the C-terminal domain of the uncharacterised protein YhfS from E.coli and similar sequences. This is an alpha/beta domain commonly found in PLP-dependent enzymes.
Pfam PF16446: Domain of unknown function (DUF5043) (family)
This family consists of several uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
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 PF24913: Fungal AAA protein, C-terminal winged helix domain (domain)
This domain is found at the C-terminal end of a group of fungal proteins that contain the AAA ATPase domain [pfam:PF13191] at the N-terminal end. This domain is predicted to have a winged helix configuration.
Pfam PF17919: RNase H-like domain found in reverse transcriptase (domain)
DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection . This domain can also be found in animal retrotransposon-like proteins .
This entry represents the RNase H-like domain found in a group of reverse transcriptases .
Pfam PF03759: PRONE (Plant-specific Rop nucleotide exchanger) (family)
This is a functional guanine exchange factor (GEF) of plant Rho GTPase.
Pfam PF01374: Glycosyl hydrolase family 46 (domain)
This family are chitosanase enzymes.
Wikipedia: In molecular biology, glycoside hydrolase family 46 is a family of glycoside hydrolases.
Pfam PF22204: CRISPR-associated endonuclease C2c1, wedge domain, second region (domain)
This domain is found in CRISPR-associated endonuclease Cas12b from Alicyclobacillus acidoterrestris and similar sequences from firmicutes. Cas12b, also known as C2c1, is a type V-B CRISPR-Cas system dual-RNA-guided DNA endonuclease that site-specifically targets and cleaves dsDNA. This entry represents the second region of the wedge domain (WED-II). It adopts an oligonucleotide-binding (OB) fold with eight beta-stranded distorted beta-sheets flanked by two alpha-helices and one beta-hairpin.
Pfam PF13324: Grap2 and cyclin-D-interacting, N-terminal (domain)
GCIP, or Grap2 and cyclin-D-interacting protein (also Human homologue of murine maternal Id-like molecule (HHM)), is found in eukaryotes, and in the protein [swissprot:O95273], residues 149-190 constitute a helix-loop-helix domain, residues 190-240 an acidic region, and 240-261 a leucine zipper domain. GCIP interacts with full-length Grap2 protein and with the COOH-terminal unique and SH3 domains (designated QC domain) of Grap2. It is potentially involved in the regulation of cell differentiation and proliferation through Grap2 and cyclin D-mediated signalling pathways. In mice, it is involved in G1/S-phase progression of hepatocytes, which in older animals is associated with the development of liver tumours. In vitro it acts as an inhibitory HLH protein, for example, blocking transcription of the HNF-4 promoter. In its function as a cyclin D1-binding protein it is able to reduce CDK4-mediated phosphorylation of the retinoblastoma protein and to inhibit E2F-mediated transcriptional activity. GCIP has also been shown to have interact physically with Rad (Ras associated with diabetes), Rad being important in regulating cellular senescence. GCIP adopts a V-shaped conformation, with N and C-terminal five-helix bundles. This entry represents the N-terminal domain.
Pfam PF15019: C9orf72-like protein family (family)
The entry includes Guanine nucleotide exchange factor C9orf72 protein, a component of the C9orf72-SMCR8 complex, which has guanine nucleotide exchange factor activity and regulates autophagy. The C9orf72 protein is proposed to be a catalytic component for the exchange of GDP to GTP and promoting autophagosome maturation by converting inactive GDP-bound RAB8A and RAB39B into their active forms. Defects in the gene, C9orf72, are the cause of frontotemporal dementia and/or amyotrophic lateral sclerosis (FTDALS) which is an autosomal dominant neurodegenerative disorder. The disorder is caused by a large expansion of a GGGGCC hexa-nucleotide within the first C9orf72 intron located between the first and the second non-coding exons. The expansion leads to the loss of transcription of one of the two transcripts encoding isoform 1 and to the formation of nuclear RNA foci.
Pfam PF10662: Ethanolamine utilisation - propanediol utilisation (domain)
Members of this family function in ethanolamine and propanediol degradation pathways. PduV may be involved in the association of the bacterial microcompartments (BMCs) to filaments.
Pfam PF21131: eEFSec C-terminal RIFT domain (domain)
This entry represents the C-terminal RIFT beta barrel domain found in the Selenocysteine-specific elongation factor eEFSec. Selenocysteine is the only proteinogenic amino acid encoded by a recoded in-frame UGA codon that does not operate as the canonical opal stop codon. A specialised translation elongation factor, eEFSec in eukaryotes and SelB in prokaryotes, promotes selenocysteine incorporation into selenoproteins.
Pfam PF20022: vWA-MoxR associated protein middle region 19 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF13768: von Willebrand factor type A domain (domain)
The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders . In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins . Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands . A number of human diseases arise from mutations in VWA domains.
Wikipedia: The von Willebrand factor type A (vWA) domain is a protein domain named after its occurrence in von Willebrand factor (vWF), a large multimeric glycoprotein found in blood plasma. Mutant forms of vWF are involved in the aetiology of bleeding disorders. This type A domain is the prototype for a protein superfamily.
Pfam PF15229: POM121 family (family)
Wikipedia: Nuclear envelope pore membrane protein POM 121 is a protein that in humans is encoded by the POM121 gene. Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined.
Pfam PF02212: Dynamin GTPase effector domain (family)
This entry represents the dynamin GTPase effector domain (GED) found in proteins related to dynamin. Its C-terminal region constitutes one of the helices of the bundle signalling element (BSE) or neck together with the N- and C-terminal regions from the GTPase domain, being in close proximity and functionally linked to it. The N-terminal region of GED is part of the stalk domain .

Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis .
Pfam PF11719: DNA replication and checkpoint protein (family)
Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent re-licensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication.
Pfam PF13982: YbfN-like lipoprotein (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. Members of this family are lipoproteins.
Pfam PF24269: Domain of unknown function (DUF7467) (domain)
This entry represents a beta sandwich domain found in a variety of bacterial cell surface 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 PF17448: Uncharacterized YqaH-like (family)
This is a family of unknown function found in Bacillus.
Pfam PF19524: Family of unknown function (DUF6054) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in Firmicute bacteria. Proteins in this family are approximately 110 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 PF14070: Putative motility protein (family)
This family of proteins is regulated in B. subtilis by SigD, and is likely to be involved in motility or flagellin production, Proteins in this family are approximately 60 amino acids in length, and contain two highly conserved asparagine residues.
Pfam PF19719: Family of unknown function (DUF6213) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the lavendiol  biosynthetic gene cluster from Streptomyces lavendulae. 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 PF20627: T-box transcription factor 2/3, repressor domain (domain)
This is the repressor domain (RD) found at the C-terminal of T-box transcription factors 2 and 3.