SII-SWORD/CoKE huggingface dataset:
Pfam PF19833: ATP-dependent DNA helicase RecG, domain 3, C-terminal (domain)
This domain is found in ATP-dependent DNA helicase RecG from bacteria the homologue from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteristic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.
Pfam PF24063: Domain of unknown function (DUF7363) (domain)
This entry represents a domain of unknown function found in CHAT domain-containing protein, such as SwissProt:A0A100JVW6, from Streptomyces scabiei. This domain may be found in association with TCAD7 ([pfam:PF19973]) and CHAT ([pfam:PF12770]) domains.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09553: Eco47II restriction endonuclease (family)
This family includes the Eco47II (which recognises GGNCC, but the cleavage site unknown) restriction endonuclease.
Pfam PF11769: Protein of unknown function (DUF3313) (family)
This a bacterial family of proteins which are annotated as putative lipoproteins.
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 PF08841: Diol dehydratase reactivase ATPase-like domain (family)
Diol dehydratase (DDH, [ec:4.2.1.28]) and its isofunctional homologue glycerol dehydratase (GDH, EC.4.2.1.30) are enzymes which catalyse the conversion of glycerol 1,2-propanediol, and 1,2-ethanediol to aldehydes.  These reactions require coenzyme B12.  Cleavage of the Co-C bond of coenzyme B12 by substrates or coenzyme analogues results in inactivation during which coenzyme B12 remains tightly bound to the apoenzyme.  This family comprises of the large subunit of the diol dehydratase and glycerol dehydratase reactivating factors whose function is to reactivate the holoenzyme by exchange of a damaged cofactor for intact coenzyme.
Pfam PF00483: Nucleotidyl transferase (family)
This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars.
Pfam PF10220: Smg8_Smg9 (family)
Smg8 and Smg9 are two subunits of the Smg-1 complex. They suppress Smg-1 kinase activity in the isolated Smg-1  complex, and are involved in nonsense-mediated mRNA  decay (NMD) in both mammals and nematodes.
Pfam PF24874: Piezo, THU9 and anchor domain (domain)
Piezo is a family of proteins that form mechanosensitive non-specific cation channels whose conductance is higher for Li+, intermediate for Na+ and lowest for Li+. Divalent ions except for Mn2+ permeate the channel but more slowly than monovalent ions and can reduce K+ currents. These channels have a homotrimeric three-blade propeller-shaped structure that use a cap-motion and plug-and-latch mechanism to gate their ion-conducting pathways. Each protomer consists of 38 TM helices that form unusual non-planar blades, and an extracellular cap-like structure ([pfam:PF12166]). This entry represents a TM segment comprising TM33-36 (THU9) and the anchor domain of Piezo proteins, found towards the C-terminal before the cap domain.
Pfam PF01268: Formate--tetrahydrofolate ligase (family)
Formate--tetrahydrofolate ligase (6.3.4.3) (formyltetrahydrofolate synthetase) (FTHFS) is one of the enzymes participating in the transfer of one-carbon units, an essential element of various biosynthetic pathways. FTHFS catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2fixation (acetogenesis) and the glycine synthase/reductase pathways of purinolysis. The key physiological role of this enzyme in acetogens is to catalyze the formylation of tetrahydrofolate, an initial step in the reduction of carbon dioxide and other one-carbon precursors to acetate. In purinolytic organisms, the enzymatic reaction is reversed, liberating formate from 10-formyltetrahydrofolate with concurrent production of ATP . In many of these processes the transfers of one-carbon units are mediated by the coenzyme tetrahydrofolate (THF). In eukaryotes the FTHFS activity is expressed by a multifunctional enzyme, C-1-tetrahydrofolate synthase (C1-THF synthase), which also catalyses the dehydrogenase and cyclohydrolase activities. Two forms of C1-THF synthases are known , one is located in the mitochondrial matrix, while the second one is cytoplasmic. In both forms the FTHFS domain consists of about 600 amino acid residues and is located in the C-terminal section of C1-THF synthase. In prokaryotes FTHFS activity is expressed by a monofunctional homotetrameric enzyme of about 560 amino acid residues .

The crystal structure of N(10)-formyltetrahydrofolate synthetase from Moorella thermoacetica shows that the subunit is composed of three domains organised around three mixed Î²-sheets. There are two cavities between adjacent domains. One of them was identified as the nucleotide binding site by homology modelling. The large domain contains a seven-stranded Î²-sheet surrounded by helices on both sides. The second domain contains a five-stranded Î²-sheet with two Î±-helices packed on one side while the other two are a wall of the active site cavity. The third domain contains a four-stranded Î²-sheet forming a half-barrel. The concave side is covered by two helices while the convex side is another wall of the large cavity. Arg 97 is likely involved in formyl phosphate binding. The tetrameric molecule is relatively flat with the shape of the letter X, and the active sites are located at the end of the subunits far from the subunit interface .
Pfam PF04632: Fusaric acid resistance protein family (family)
This family includes a conserved region found in two proteins associated with fusaric acid resistance, [swissprot:P24128] from Burkholderia cepacia and [swissprot:Q48403] from Klebsiella oxytoca. These proteins are likely to be membrane transporter proteins.
Pfam PF03273: Baculovirus gp64 envelope glycoprotein (family)
This entry includes the gp64 glycoprotein from baculovirus as well as other viruses e.g. [swissprot:P28970], a protein that facilitates their entry into host cells. This Gp adopts the typical fold of a class III viral fusion proteins.
Pfam PF12673: SipL, SPOCS domain (domain)
This is the SPOCS domain found in three copies in SipL from C. difficile, N-terminal to the LysM domain ([pfam:PF01476]). SipL (for SpoIVA-interacting protein) is involved in coat localization, and, together with SpoIVA, is a critical spore morphogenetic protein.
Pfam PF21965: Small archaeal modifier protein 2 (domain)
The ubiquitin-like small archaeal modifer protein 2 (SAMP2) is involved in sulfur transfer during molybdenum cofactor biosynthesis. SAMP2 has been demonstrated to form covalent conjugates with substrate proteins through an isopeptide linkage via C-terminal di-glycine motif in a streamlined archaeal E1-dependent pathway. SAMP2 also forms homo-conjugates through the intermolecular isopeptide bond between the C-terminal glycine and the Lys58 side chain, a feature that likely resembles polyubiquitination. This protein adopt a typical ubiquitin-like fold.
Pfam PF16914: Bacterial transcriptional repressor C-terminal (domain)
This domain is found at the C terminus of a small group of bacterial putative TetR transcriptional regulator proteins.
Pfam PF11920: Protein of unknown function (DUF3438) (family)
This family of proteins appear to be structurally distantly related to TraK proteins suggesting they have an important tole in a type IV secretion system likely involved in conjugation.
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 PF12982: Protein of unknown function (DUF3866) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 352 and 374 amino acids in length.
Pfam PF21249: GyrB, hook (domain)
This entry represents the N-terminal section of the 'Toprim hook' as described in, which is localised between the Toprim ([pfam:PF01751]) and the insert ([pfam:PF18053]) domains. The C-terminal section of the hook is included in ([pfam:PF00986]). The hook is flexible towards the Toprim domain.
Pfam PF12407: Homeobox protein (disordered)
This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with [pfam:PF00046]. This family is a homeobox protein involved in differentiation of embryonic cells to form the abdominal region.
Pfam PF17149: Periplasmic sensor domain found in signal transduction proteins (domain)
CHASE5 is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins. In Pseudomonas aeruginosa, CHASE5 is the sensor domain in the c-di-GMP phosphodiesterase BifA that regulates biofilm formation and in sensor kinase AruS that regulates arginine degradation pathways. These results suggest that CHASE5 might bind arginine or a related compound.
Pfam PF05793: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) (family)
Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II.
Pfam PF08396: Spider toxin omega agatoxin/Tx1 family (family)
The Tx1 family lethal spider neurotoxin induces excitatory symptoms in mice.
Pfam PF04428: Choline kinase N terminus (family)
Found N terminal to choline/ethanolamine kinase regions ([pfam:PF01633]) in some plant and fungal choline kinase enzymes ([ec:2.7.1.32]).  This region is only found in some members of the choline kinase family, and is therefore unlikely to contribute to catalysis.
Pfam PF05707: Zonular occludens toxin (Zot) (domain)
This family consists  of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers
Pfam PF06872: EspG protein (family)
This family consists of several EspG like proteins from Citrobacter rodentium and Escherichia coli. EspG is secreted by the type III secretory system and is translocated into host epithelial cells. EspG is homologous with Shigella flexneri protein VirA and can rescue invasion in a Shigella virA mutant, indicating that these proteins are functionally equivalent in Shigella.  EspG plays an accessory but as yet undefined role in EPEC virulence that may involve intestinal colonisation.
Pfam PF05438: Thyrotropin-releasing hormone (TRH) (family)
This family consists of several thyrotropin-releasing hormone (TRH) proteins. Thyrotropin-Releasing Hormone (TRH; pyroGlu-His-Pro-NH2), originally isolated as a hypothalamic neuropeptide hormone, most likely acts also as a neuromodulator and/or neurotransmitter in the central nervous system (CNS). This interpretation is supported by the identification of a peptidase localised on the surface of neuronal cells which has been termed TRH-degrading ectoenzyme (TRH-DE) since it selectively inactivates TRH. TRH has been used clinically for the treatment of spinocerebellar degeneration and disturbance of consciousness in humans.
Wikipedia: Thyrotropin-releasing hormone (TRH) is a hypophysiotropic hormone produced by neurons in the hypothalamus that stimulates the release of thyroid-stimulating hormone (TSH) and prolactin from the anterior pituitary.
Pfam PF15754: Sperm equatorial segment protein 1 (family)
Equatorial segment protein (ESP) been localised to the equatorial segment of the acrosome in sperm. It defines a discrete acrosomal subcompartment that persists throughout acrosomal biogenesis  and is required for fully fertile sperm .
Pfam PF09062: PI-PfuI Endonuclease subdomain (domain)
The endonuclease subdomain, found in the prokaryotic protein ribonucleotide reductase, assumes an alpha-beta-beta-alpha-beta-beta-alpha-alpha topology. The four stranded beta-sheet forms a saddle-shaped surface and assembles together through an interface made of alpha-helices. The presence of 14 basic residues on the surface of the beta-sheets suggests that this large groove may be involved in DNA binding.
Pfam PF07243: Phlebovirus glycoprotein G1 (family)
This family consists of several Phlebovirus glycoprotein G1 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi.
Pfam PF21856: ESX-1 secretion-associated protein EspB, PPE domain (domain)
This entry represents the PPe domain of ESX-1 secretion- associated protein EspB, a member of the PE/PPE family and the only one described to date to form higher-order oligomers. It contains PE (Pro-Glu) and PPE (Pro-Pro-Glu) domains, and a C-terminal domain, which is processed by MycP1 protease during secretion. EspB oligomerises into a cylinder-like heptamer through its N-terminal domain, that form channel-like structures.
Pfam PF01575: MaoC like domain (domain)
The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase.  The MaoC protein is found to share similarity with a wide variety of enzymes; estradiol 17 beta-dehydrogenase 4, peroxisomal hydratase-dehydrogenase-epimerase, fatty acid synthase beta subunit. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl-CoA hydratase activity. This domain is also present in the NodN nodulation protein N.
Pfam PF05325: Protein of unknown function (DUF730) (family)
This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12551: Poly-beta-hydroxybutyrate polymerase N terminal (family)
This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with [pfam:PF07167], [pfam:PF00561]. There is a single completely conserved residue W that may be functionally important. PHBC is the third enzyme of the poly-beta-hydroxybutyrate biosynthetic pathway.
Pfam PF07733: Bacterial DNA polymerase III alpha NTPase domain (domain)
This is a conserved region found in the the DNA polymerase III alpha subunit, (2.7.7.7). DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase .
Wikipedia: DnaE, the gene product of dnaE, is the catalytic α subunit of DNA polymerase III, acting as a DNA polymerase. This enzyme is only found in prokaryotes.
Pfam PF20160: C-JID domain (domain)
C-terminal jelly roll/Ig-like domain (C-JID) was defined in cryogenic electron microscopy (cryoEM) structures of plant intracellular immune receptors containing Toll/interleukin-1 receptor (TIR, PF01582), nucleotide-binding (NB-ARC, PF00931) and leucine-rich repeat (LRR) domains (TIR-NLRs). Structurally, the C-JID core is represented by a beta-sandwich made up of 8 to 9 beta-strands. C-JID matches the so-called post-LRR or C-terminal non-LRR domain detected earlier via MEME and BLAST searches. The domain showed a strong distribution bias towards TIR-NLRs of dicotyledonous plant species despite broader taxonomic distribution of TIR-NLR in plant groups. Structure-function analyses of cryoEM structures suggest that C-JID domains play a role in substrate recognition, such as binding to effector proteins from pathogens, and thus are involved in the initiation of signaling by TIR-NLR receptors. Presence of C-JID (or post-LRR) and its importance for the function of Arabidopsis TIR-NLR RPS4 that partners with RRS1 for effector recognition suggest that C-JID has additional functions.
Pfam PF19416: Astrovirus VPg protein (family)
This entry represents the presumed VPg protein from human astrovirus. Viral genome-linked proteins (VPgs) are virus-encoded small proteins that are covalently linked to the 5' terminus of many RNA viral genomes through a phosphodiester bond.  Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The protein resulting from this putative VPg coding region is a highly disordered protein. A common feature of VPgs is that they are rich in basic amino acids [mostly Lys (K), Gly (G), Thr (T), and Arg (R)], which favors the interaction with the negatively charged RNA. Tyr-693 at the conserved TEEEY-like motif has been postulated to be the residue responsible for the covalent linkage to viral RNA. Mutagenesis of Tyr-693 in the VPg protein is lethal for HAstV replication.
Pfam PF03948: Ribosomal protein L9, C-terminal domain (domain)
This entry represents the large ribosomal subunit protein bL9. In Escherichia coli, bL9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities .

The crystal structure of Bacillus stearothermophilus bL9 shows the 149-residue protein comprises two globular domains connected by a rigid linker . Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an Î±-helix and a three-stranded mixed parallel, anti-parallel Î²-sheet packed against the central Î±-helix. The long central Î±-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF13463: Winged helix DNA-binding domain (domain)
The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. The MarR family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds .

The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel Î²-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the Î²-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers .
Pfam PF24438: IML1, N-terminal, fungi (domain)
This entry represents the N-terminal double psi beta-barrel domain found in IML1 proteins from fungi. In Saccharomyces cerevisiae, Iml1 is a GAP subunit of both the SEA (Seh1-associated) and Iml1 complexes (Iml1-Npr2-Npr3). SEA complex is associated dynamically with the vacuole and is involved in autophagy. Iml1 complex is required for non-nitrogen-starvation (NNS)-induced autophagy.
Pfam PF13067: Protein of unknown function (DUF3930) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 51 and 67 amino acids in length.