SII-SWORD/CoKE huggingface dataset:
Pfam PF14260: C4-type zinc-finger of DNA polymerase delta (domain)
In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1.  Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pfam PF05444: Domain of unknown function (DUF753) (domain)
This domain contains is found in many copies in a variety of uncharacterised fly proteins. This domain has a Ly6/uPAR/alpha-neurotoxin-like domain structure.
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 PF09827: CRISPR associated protein Cas2 (family)
This entry represents members of the family of Cas2, one of the first four protein families found to be associated with prokaryotic genomes containing multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterised as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. The cas genes usually are found near the palindromic repeats. The structural subunit of Cas2, belongs to the VapD family of interferases. The interferase catalytic site is intact in the majority of the Cas2 proteins but is disrupted in some, and is not required for spacer acquisition. This entry also includes the endoribonuclease VapD.
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF07165: Protein of unknown function (DUF1397) (family)
This family consists of several insect specific proteins. [swissprot:Q25513] is annotated as being a haemolymph glycoprotein precursor. 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 PF08078: PsaX family (family)
This family consists of the PsaX family of photosystem I (PSI) protein subunits.                          PSI is a large multi-subunit pigment protein complex embedded in the thylakoid membranes of green plants and cyanobacteria. PsaX is one of the 12 protein subunits found in PSI and these subunits are arranged as monomers or trimers within the membrane as shown by the structure of the trimeric complex from Synechococcus elongatus.
Pfam PF13196: Protein of unknown function (DUF4012) (family)
This is a family of uncharacterised proteins found in archaea and bacteria.
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 PF16693: YscD/CdsD-like Bon-like domain 1 (domain)
Yop-YscD-ppl is the periplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus.  This entry represents the first of three periplasmic BON domains.
Pfam PF13078: Protein of unknown function (DUF3942) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length.
Pfam PF09837: Uncharacterized protein conserved in bacteria (DUF2064) (family)
This family has structural similarity to proteins in the nucleotide-diphospho-sugar transferases superfamily. The similarity suggests that it is an enzyme with a sugar substrate.
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 PF09897: Uncharacterized protein conserved in archaea (DUF2124) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF03785: Peptidase family C25, C terminal ig-like domain (domain)
This domain is found in almost all members of MEROPS peptidase family C25, (clan CD). Peptidase family C25 is a protein family found in the bacteria Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes . It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor . Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes .
Pfam PF11591: Ferredoxin chloroplastic transit peptide (family)
The structure of chloroplast ferredoxin in water is unstructured however in a 30:70 molar-ratio mixture of 2,2,2-trifluoroethanol, residues 3 to 13 form an alpha-helix. The rest of the peptide remains unstructured. This family is the N-terminal of the [2Fe-2S) ferredoxin from C.reinhardtii. This protein catalyses the final reaction in a pathway which allows the production of H(2) from water in the chloroplast.
Pfam PF01034: Syndecan domain (family)
Syndecans are transmembrane heparin  sulphate  proteoglycans which  are   implicated  in  the binding of extracellular matrix components  and growth factors.
Wikipedia: Syndecans are single transmembrane domain proteins that are thought to act as coreceptors, especially for G protein-coupled receptors. More specifically, these core proteins carry three to five heparan sulfate and chondroitin sulfate chains, i.e. they are proteoglycans, which allow for interaction with a large variety of ligands including fibroblast growth factors, vascular endothelial growth factor, transforming growth factor-beta, fibronectin and antithrombin-1. Interactions between fibronectin and some syndecans can be modulated by the extracellular matrix protein tenascin C.
Pfam PF22115: T6SS, Peptidoglycan muramidase Tse3, catalytic domain (domain)
This domain is found in Peptidoglycan muramidase Tse3 from Pseudomonas aeruginosa and similar sequences from bacteria. Tse3 is a toxin secreted by the H1 type VI (H1-T6SS) secretion system into the periplasm of recipient cells. This protein degrades peptidoglycan via muramidase activity. It is organised into a small N-terminal domain with a C-terminal catalytic domain (this entry), which contains two major lobes that form an an open, accessible catalytic groove with three calcium-binding ions.
Pfam PF19369: Family of unknown function (DUF5944) (family)
This entry represents a member of a biosynthetic gene cluster (BGC).  This BGC (BGC0001797) is described by MIBiG as an example of the  following biosynthetic class, RiPP (ribosomally synthesised and  post-translationally modified peptide).
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 PF23467: WWE domain (domain)
This entry represents a WWE domain found in a family of plant protein.  The protein family includes probable inactive ADP-ribosyltransferases that are involved in the regulation of oxidative stress, hormonal and developmental responses in Arabidopsis thaliana. Members of the family, such as SRO1 and RCD1, may regulate stress-responsive genes and play distinct roles in plant development. While they are characterized as inactive due to their inability to bind NAD in vitro, they still contribute to critical processes such as embryogenesis, vegetative and reproductive development, and abiotic stress responses. The family highlights a functional partnership between its members in managing plant responses to environmental challenges.
Pfam PF24664: Viral fusion glycoprotein (family)
This family of proteins are likely viral fusion glycoproteins. Comparison of the predicted structure suggests similarity to Herpesvirus Glycoprotein B. This family includes Monjiviricetes. Many proteins come from non-viral species.
Pfam PF24003: Domain of unknown function (DUF7319) (domain)
This domain is found in uncharacterised archaeal 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 PF04832: SOUL heme-binding protein (family)
This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologues.
Pfam PF24824: FACT complex subunit SPT16 PH-like domain (domain)
This domain is found in human FACT complex subunit SPT16 and related proteins. SPT16 is a component of the FACT complex which acts to reorganise the nucleosome. The domain represented by this entry has similarity to known PH domains.
Pfam PF08075: NOPS (NUC059) domain (domain)
This domain is found at the C-terminus of NONA and PSP1 proteins adjacent to 1 or 2 [pfam:PF00076] domains.
Pfam PF09480: Type III secretion system protein PrgH-EprH (PrgH) (family)
In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion and is a structural component of the needle complex, which is the core component of type III secretion systems.
Pfam PF05042: Caleosin related protein (family)
This family contains plant proteins related to caleosin. Caleosins contain calcium-binding domains and have an oleosin-like association with lipid  bodies. Caleosins are present at relatively low levels and are mainly bound to microsomal membrane fractions at the early stages of seed development. As the seeds mature, overall levels of caleosins increased dramatically and they were associated almost exclusively with storage lipid bodies. This family is probably related to EF hands [pfam:PF00036].
Pfam PF09764: N-terminal glutamine amidase (family)
This protein is conserved from plants to humans. It represents a family of N terminal glutamine amidases. The enzyme removes the NH2 group from a Gln, at the N-terminal, rendering it a Glu.
Pfam PF13599: Pentapeptide repeats (9 copies) (repeat)
These repeats were first identified in many cyanobacterial proteins but they are also found in bacterial as well as in plant proteins . The repeats were first identified in hglK . Pentapeptide repeat proteins (PRPs) are characterised by the repetition of the pentapeptide repeat motif , which allows it to adopt a right-handed Î²-helical structure conformation . The functions of these repeats is unknown but it has been shown that members of this family share the ability to interact with DNA-binding proteins, such as DNA gyrase. For example, McbG (from Escherichia coli) protects the DNA gyrase from microcin B17 toxicity, MfpAMt (from Mycobacterium tuberculosis) and Qnr (from Klebsiella pneumoniae and other enterobacteria) are involved in resistance to fluoroquinolones .
Wikipedia: Pentapeptide repeats are a family of sequence motifs found in multiple tandem copies in protein molecules. Pentapeptide repeat proteins are found in all species, but they are found in many copies in cyanobacterial genomes. The repeats were first identified by Black and colleagues in the hglK protein. The later Bateman et al. showed that a large family of related pentapeptide repeat proteins existed. The function of these repeats is uncertain in most proteins. However, in the MfpA protein a DNA gyrase inhibitor it has been suggested that the pentapeptide repeat structure mimics the structure of DNA. The repeats form a regular right handed four sided beta helix structure known as the Rfr-fold.
Pfam PF23470: PF0610 rubredoxin-like zinc beta-ribbon domain (domain)
This rubredoxin-like zinc beta-ribbon domain is found in PF0610, a protein from the hyperthermophile Pyrococcus furiosus, and related homologous proteins. This domain is embedded in winged HTH fold.
Pfam PF01074: Glycosyl hydrolases family 38 N-terminal domain (domain)
Glycosyl hydrolases are key enzymes of carbohydrate metabolism.
Wikipedia: In molecular biology, glycoside hydrolase family 38 is a family of glycoside hydrolases.
Pfam PF10267: Predicted transmembrane and coiled-coil 2 protein (coiled_coil)
This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Pfam PF11725: AvrE-family Type-III effector proteins (T3Es) (family)
This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system.  The family is long and carries a number of predicted functional regions, including in Erwinia stewartii ([swissprot:Q9FCY7]) an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas. A double beta-propeller structure is found towards the N-terminus. Furthermore, AvrE1, an AvrE-family T3E from Pseudomonas syringae pv. tomato strain DC3000, associates with specific PP2A B- subunit proteins from its susceptible host Arabidopsis. In a similar fashion, the WtsE (AvrE-family T3E from the maize pathogen Pantoea stewartii subsp. Stewartii) has been shown to target maize protein phosphatase 2A (PP2A) heterotrimeric enzyme complexes via direct interaction with B- regulatory subunits. Taken together, it has been indicated that that sub-component specific PP2A complexes are targeted by bacterial T3Es, including direct targeting by members of the widely conserved AvrE-family. Additionally, DspE, a type-III effector encoded by the broad-host-range bacterial soft-rot pathogen Pectobacterium carotovorum subsp. carotovorum (Pcc), has been indicated to be required and sufficient for disease-associated cell death in host plants.
Pfam PF23761: DDB1- and CUL4-associated factor 4 beta-propeller (repeat)
This entry represents the beta-propeller domain found in DDB1- and CUL4-associated factor 4 (DCAF4) and DCAF4-like proteins 1 and 2 (DCAF4L1 and DCAF4L2) from mammals. These proteins are substrate receptors for the Cullin-DDB1 ubiquitin ligase complexes. DCAF4 has been identified as a key protein in proper proteostasis of Cu, Zn superoxide dismutase (SOD1) and has been associated to Leukocyte telomere length (LTL) in humans, which in turn has been link to human diseases, including sporadic melanoma. The function of this domain is unknown. The entry also includes partial hits to other beta-propeller domains from animal proteins such as WDR5.
Pfam PF23714: Carboxypeptidase Rv3627c-like, N-terminal domain (domain)
This is the short N-terminal domain of Carboxypeptidase Rv3627c from Mycobacterium tuberculosis and similar sequences found in actinobacteria. This domain is predicted to form an alpha helix.
Pfam PF08892: YqcI/YcgG family (family)
This family of proteins are functionally uncharacterised. The family include YqcI and YcgG from B. subtilis. The alignment contains a conserved FPC motif at the N-terminus and CPF at the C-terminus.
Pfam PF15071: Transmembrane family 220, helix (family)
Transmembrane 220 (TMEM220) is a domain of unknown function. It is thought to be a transmembrane helix. The length of this protein is typically between 150 and 160 amino acids. In humans, it is found in the chromosomal position 17p13.1.
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 PF16712: Coiled-coil regions of plant-specific actin-binding protein (family)
SCAB_CC is the two coiled-coil, dimerisation domains of plant-specific actin-binding proteins or SCABs, CC1 and CC2, both of which contribute independently to dimerisation.  CC1 is also required for actin binding, indicating that SCAB1 is a bivalent actin cross-linker. since CC1 adopts an antiparallel helical hairpin that further dimerises into a four-helix bundle. SCAB proteins bind, bundle and stabilise actin filaments and regulate stomatal movement,
Pfam PF09838: Uncharacterized protein conserved in bacteria (DUF2065) (family)
This domain, found in various prokaryotic proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF04375: HemX, putative uroporphyrinogen-III C-methyltransferase (family)
This is a family of bacterial putative uroporphyrinogen-III C-methyltransferase proteins. It forms one of the members of a complex of proteins involved in the biogenesis of the inner membrane in E.coli.  Uroporphorphyrin-III C-methyltransferase (HemX) is a single spanning inner membrane protein that regulates the activity of NAD(P)H:glutamyl-tRNA reductase (HemA) in the tetrapyrrole biosynthesis pathway.
Pfam PF10252: Casein kinase substrate phosphoprotein PP28 (domain)
This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II.
Pfam PF06444: NADH dehydrogenase subunit 2 C-terminus (domain)
This family consists of the C-terminal region specific to the eukaryotic NADH dehydrogenase subunit 2 protein and is found in conjunction with [pfam:PF00361].
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF16538: Flagellar assembly protein T, C-terminal domain (domain)
FlgT_C is the C-terminal domain of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilise both ring structures. FlgT_C is not essential but stabilises the H-ring structure..
Pfam PF16564: p55-binding region of Methyl-CpG-binding domain proteins MBD (domain)
MBDa is a second MBD domain of Methyl-CpG-binding domain proteins. region implicated in binding the RbAp46/48 (retinoblastoma protein-associated protein) homologue p55, which is one of the components of the MBD2-NuRD complex. The MBD2-NuRD complex is a nucleosome remodelling and deacetylation complex.
Pfam PF20038: Helix-turn-helix domain (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 63 and 82 amino acids in length. This domain is a helix-turn-helix suggesting it is likely a DNA-binding transcriptional regulator.
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 PF11420: Bacteriocin subtilosin A (family)
Subtilosin A is a bacteriocin from Bacillus subtilis.The protein has a cyclized peptide backbone and forms three cross-liks between the sulphurs of Cys13, Cys7 and Cys4 and the alpha-positions of Phe22,Thr28 and Phe31.
Wikipedia: Microcins are very small bacteriocins, composed of relatively few amino acids. For this reason, they are distinct from their larger protein cousins. The classic example is microcin V, of Escherichia coli. Subtilosin A is another bacteriocin from Bacillus subtilis. The peptide has a cyclized backbone and forms three cross-links between the sulphurs of Cys13, Cys7 and Cys4 and the alpha-positions of Phe22, Thr28 and Phe31.
Pfam PF16490: Putative oxidoreductase C terminal domain (domain)
This is the putative C-terminal domain of a bacterial oxidoreductase.  It lies C-terminal to family GFO_IDH_MocA [pfam:PF01408] in some members.