SII-SWORD/CoKE huggingface dataset:
Pfam PF05891: AdoMet dependent proline di-methyltransferase (family)
This protein is expressed in the tail neuron PVT and in uterine cells in C. elegans [worm-base]. In Saccharomyces cerevisiae this is AdoMet dependent proline di-methyltransferase. This enzyme catalyses the di-methylation of ribosomal proteins Rpl12 and Rps25 at N-terminal proline residues. The methyltransferases described here specifically recognise the N-terminal X-Pro-Lys sequence motif, and they may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and human proteins also share the recognition motif and may be similarly modified. As with other methyltransferases, this family carries the characteristic GxGxG motif.
Pfam PF15450: Coiled-coil domain-containing protein 154 (coiled_coil)
CCDC154 is an osteopetrosis-related protein that suppresses cell proliferation by inducing G2/M arrest.
Pfam PF17120: RING/Ubox like zinc-binding domain (domain)
This entry represents a RIGN zinc finger domain commonly found in the C-terminal region of various animal and fungal proteins, including WDR59 Q6PJI9 , a component of the GATOR complex in vertebrates  and the fungal protein RTC1 Q08281 , which is a component of the SEA complex .
Pfam PF13102: Phage integrase SAM-like domain (domain)
A family of uncharacterised proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.
Pfam PF11439: Type III secretion system filament chaperone CesA (family)
This family represents a chaperone protein for the type III secretion system - TTSS - translocon protein EspA, to prevent the latter's self-polymerisation. The TTSS is a highly specialised bacterial protein secretory pathway, similar in many ways to the flagellar system, that is essential for the pathogenesis of many Gram-negative bacteria. The twenty or so proteins making up the TTSS apparatus, referred to as the needle complex, allow the injection of virulence proteins (known as effectors) directly into the cytoplasm of the eukaryotic host cells they infect; however, the injection process itself is mediated by a subset of extracellular proteins that are secreted by the needle complex to the bacterial surface and assembled into the type III translocon - EspA. EspB and EspD. EspA polymerises into an extracellular filament, and, as with other fibrous proteins, is apt to undergo massive polymerisation when overexpressed. CesA is the secretion chaperone protein that binds to EspA. CesA is dimeric and helical, and it traps EspA in a monomeric state and inhibits its polymerisation.
Pfam PF16569: Gram-positive pilin backbone subunit 2, Cna-B-like domain (domain)
GramPos_pilinBB is one of the major backbone units of Gram-positive pili, such as those from S.pneumoniae.  There are three major pilin subunits that form the polymeric backbone of the pilin from S.  pneumoniae, constructed of three transthyretin-like, CnaB, domains along with a crucial N-terminal domain, D1. The three Cna-B like domains are stabilised by internal Lys-Asn isopeptdie bonds, Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base.
Pfam PF13613: Helix-turn-helix of DDE superfamily endonuclease (domain)
This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4.
Pfam PF09986: Uncharacterized protein conserved in bacteria (DUF2225) (repeat)
This domain, found in various hypothetical bacterial 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 PF23363: Family of unknown function (DUF7089) (family)
This entry represents a family of uncharacterised proteins from halobacteria. Members are predicted to adopt an alpha-beta configuration.
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 PF15736: Domain of unknown function (DUF4684) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 531 and 1277 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 PF08832: Steroid receptor coactivator (domain)
This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding.  The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.
Pfam PF15994: Domain of unknown function (DUF4770) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 169 and 182 amino acids in length. There is a single completely conserved residue L 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 PF03117: UL49 family (family)
Members of this family, found in several herpesviruses, include EBV BFRF2 [swissprot:P14347] and other UL49 proteins (e.g. HCMVA UL49 [swissprot:P16786], HSV6 U33 [swissprot:P52441]). There are eight conserved cysteine residues in this alignment, all lying towards the C-terminus. Their function is unknown.
Pfam PF16644: Regulatory region of Na+/H+ exchanger NHE binds to calmodulin (domain)
NEXCaM_BD is a coiled-coil domain found as part of the regulatory, C-terminal region of the 12-14 TM sodium/proton exchangers (NHEs)2 of the solute carrier 9 (SLC9) family in all animal kingdoms. The C- lobe of CaM binds the first alpha-helix of the NHE, or NEXCaM_BD region, and the N-lobe of CaM binds the second helix of NEXCaM_BD.
Pfam PF19187: PafC helix-turn-helix domain (domain)
This entry is an N-terminal HTH domain found in the PafC protein. Transcriptional activator PafBC is responsible for upregulating the majority of genes induced by DNA damage.
Pfam PF13908: Shisa, N-terminal domain (domain)
Shisa is a transmembrane, transcription factor-type protein that physically interacts with immature forms of the Wnt receptor Frizzled and the FGF receptor within the endoplasmic reticulum to inhibit their post-translational maturation and trafficking to the cell surface. Vertebrate homologues play roles in development, cancer and apoptosis. This entry represents a domain found in the N-terminal region, which contains six conserved cysteines.
Pfam PF11687: Domain of unknown function (DUF3284) (domain)
This family of proteins with unknown function appears to be restricted to Firmicutes.
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 PF06340: Vibrio cholerae toxin co-regulated pilus biosynthesis protein F (family)
This family consists of several Vibrio cholerae toxin co-regulated pilus biosynthesis protein F (TcpF) sequences. TcpF is known to be a secreted virulence protein but its exact function is unknown.
Pfam PF19279: YegS C-terminal NAD kinase beta sandwich-like domain (domain)
This entry represents the C-terminal domain found in the YegS protein. It is related to the beta sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site crevice found between the two domains. The C-terminal domain contains 13 beta-strands and two alpha-helices. The likely substrate for YegS is phosphatidylglycerol.
Pfam PF04922: DIE2/ALG10 family (family)
The ALG10 protein from Saccharomyces cerevisiae encodes the alpha-1,2 glucosyltransferase of the endoplasmic reticulum. This protein has been characterised in rat as potassium channel regulator 1.
Pfam PF17097: Spindle pole body component Kre28 (family)
In Saccharomyces cerevisiae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation.
Pfam PF23329: EF-hand found in PLCG1 (domain)
This entry represents an EF-hand like domain found in phosphoinositol-specific phospholipase C gamma proteins.
Pfam PF24092: Domain of unknown function (DUF7373) C-terminal (domain)
This domain is found C-terminal in uncharacterised bacterial proteins. It is predicted to adopt a seven-stranded antiparallel beta-sheet with similarity to Mog1p/PsbP-like domains. Some proteins containing this domain have a lipoprotein attachment motif at the N-terminus suggesting they may be associated with the membrane. This domain is usually found in two copies that share little if any sequence similarity to each other.
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 PF01002: Flavivirus non-structural protein NS2B (family)
Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex.
Pfam PF08521: Two-component sensor kinase N-terminal (family)
This domain is found in bacterial two-component sensor kinases towards the N-terminus. It recognises Autoinducer 3 (AI-3), epinephrine, norepineprhine and Fe(III) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF08306: Glycosyl hydrolase family 98 (domain)
This domain is the putative catalytic domain of glycosyl hydrolase family 98 proteins.
Wikipedia: In molecular biology, glycoside hydrolase family 98 is a family of glycoside hydrolases.
Pfam PF12802: MarR family (family)
The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR.  A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Pfam PF24372: Family of unknown function (DUF7528) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt an alpha-beta 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 PF02880: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III (domain)
This entry represents domain III found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer Î±/Î²/Î± topology.
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (5.4.2.2) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (5.4.2.2; 5.4.2.8) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (5.4.2.3) and PAGM (5.4.2.10) are involved in the biosynthesis of UDP-N-acetylglucosamine .
Pfam PF11993: VC2046 family (family)
This family of proteins largely uncharacterised. They were annotated as ribosomal SSU S4 p proteins but there is not evidence supporting this, and it is, apparently, a miss annotation. Sequences in this entry are found in Gammaproteobacteria. Proteins in this family are typically between 162 to 178 amino acids in length.
Pfam PF04912: Dynamitin (family)
Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS).
Wikipedia: Dynactin is a 23 subunit protein complex that acts as a co-factor for the microtubule motor cytoplasmic dynein-1. It is built around a short filament of actin related protein-1 (Arp1).
Pfam PF18577: Astrotactin-2 C-terminal beta-hairpin domain (domain)
This is a beta-hairpin domain found at the C-terminal region of astrotactin 2 proteins (ASTN-2). ASTN-2 is an integral membrane perforin-like protein linked to the planar cell polarity pathway in hair cells. it consists of multiple polypeptide folds: a perforin-like domain, a minimal epidermal growth factor-like module, a fibronectin type III domain Fn (III) and an annexin-like domain as well as the beta hairpin domain which packs across the fibronectin domain.
Pfam PF14079: Domain of unknown function (DUF4260) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 126 amino acids in length. There is a conserved GLK sequence motif.
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 PF00316: Fructose-1-6-bisphosphatase, N-terminal domain (domain)
This family represents the N-terminus of this protein family.
Wikipedia: The enzyme fructose bisphosphatase (EC 3.1.3.11; systematic name D-fructose-1,6-bisphosphate 1-phosphohydrolase) catalyses the conversion of fructose-1,6-bisphosphate to fructose 6-phosphate in gluconeogenesis and the Calvin cycle, which are both anabolic pathways:D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate
Pfam PF22828: HphA N-terminal heme-binding domain (domain)
HphA is a secreted hemophore that binds and acquires heme from hemoglobin. It consists of two domains: N-terminal heme binding domain (this entry) and C-terminal beta-barrel that is related to domains members of the Outer membrane beta-barrel superfamily. The N-terminal domain has a clamp-like structure consisting of six antiparallel beta-strands and an alpha-helix. Two histidines located on loops coordinate the heme.
Pfam PF16608: TNRC6-PABC binding domain (disordered)
TNRC6-PABC_bdg is a natively unstructured region on the higher eukaryote TNRC6 subset of GW182 proteins that carries the binding motif for the interaction with Polyadenylate-binding protein 1, PABC. TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localised to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay.  Thus GW182 proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells being a major component of miRISCs. The interaction motif that binds to PABC is ShNWPPEFHPGVPWKGLQ. This region lies between a Q-rich region and the RRM, or RNA-recognition motif, [pfam:PF13893].
Pfam PF23774: GEMI5 TPR domain (repeat)
This entry represents the TPR domain found towards the C-terminal of Gem-associated protein 5 (GEMI5) from animals and related eukaryotic sequences. GEMI5 is a component of the survival of motor neurons (SMN) complex, that binds small nuclear RNAs (snRNAs). The SMN complex assembles the heptameric Sm protein core on snRNAs playing a critical role in the biogenesis of small nuclear ribonucleoproteins (snRNPs). GEMI5 is also implicated in translation control, and gene expression reprogramming. The TPR domain in GEMI5 mediates the dimerization of the protein. This is possible thanks to the helical repeats stretched in an alpha-solenoid rod that provides an extensive flat surface for self-dimerization. Mutations in this domain have been shown to cause a neurodevelopmental disorder characterised by cerebellar atrophy, intellectual disability (ID), and motor dysfunction. Also included in this entry is Protein rigor mortis (RIG) TPR domain from Drosophila melanogaster. RIG is a nuclear receptor-interacting protein required for the response to steroid hormone ecdysone during larval development.
Pfam PF08608: Wyosine base formation (family)
Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs.  It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Pfam PF04295: D-galactarate dehydratase/Altronate hydrolase, second domain (domain)
This entry includes D-galactarate dehydratase (GarD, [ec:4.2.1.42]) which catalyses the reaction D-galactarate = 5-keto-4-deoxy-D glucarate + H2O, and altronate hydrolase (altronic acid hydratase, [ec:4.2.1.7]), which catalyses D-altronate = 2-keto-2- deoxygluconate + H2O. As purified, both enzymes are catalytically inactive in the absence of added Fe2+, Mn2+, and beta-mercaptoethanol. Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of  the single bound Fe2+ ion is unknown. The hydratase has no Fe-S core. GarD structure revealed that it is a dimer in solution; each monomer has three domains, an N-terminal SAF domain ([pfam:PF08666]), a second domain represented in this entry and a C-terminal domain. This domain consists of three parallel beta-strands, surrounded by three alpha-helices and it interacts with the C-terminal domain from the second chain to form a dimerisation surface.
Pfam PF22178: Bacteriophage T4 gp5 C-terminal trimerisation domain (repeat)
This entry represents the C-terminal trimerisation domain of bacteriophage T4 gp5. This domain associates to form a triple-stranded beta-helix that forms an equilateral triangular prism, which acts as a membrane-puncturing needle. The interior of the beta-helix has an increased hydrophobicity toward the C terminus. The middle part of the helix has a pore, enriched with polar and charged side chains.
Pfam PF09613: Bacterial type III secretion protein (HrpB1_HrpK) (repeat)
This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Pfam PF00569: Zinc finger, ZZ type (domain)
Zinc finger present in dystrophin, CBP/p300.  ZZ in dystrophin binds calmodulin.  Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure.
Wikipedia: In molecular biology the ZZ-type zinc finger domain is a type of protein domain that was named because of its ability to bind two zinc ions. These domains contain 4-6 Cys residues that participate in zinc binding, including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains. ZZ-type zinc finger domains are found in:Transcription factors P300 and CBP.
Plant proteins involved in light responses, such as Hrb1.
E3 ubiquitin ligases MEX and MIB2.
Dystrophin and its homologues
Pfam PF17648: Luciferase (family)
This family includes fungal luciferase which is part of the gene cluster that mediates the fungal bioluminescence cycle. It may use the fungal luciferin 3-hydroxyhispidin as a substrate to produce an endoperoxide as a high-energy intermediate with decomposition that yields oxyluciferin (also known as caffeoylpyruvate) and light emission. The fungal bioluminescence cycle begins with the hispidin synthetase that catalyses the formation of hispidin which is further hydroxylated by the hispidin-3-hydroxylase,  yielding the fungal luciferin 3-hydroxyhispidin. The luciferase then produces an endoperoxide as a high-energy intermediate with decomposition  that yields oxyluciferin and light emission. Oxyluciferin can be recycled to caffeic acid by caffeoylpyruvate hydrolase. This entry also includes uncharacterised bacterial sequences.
Pfam PF11880: Domain of unknown function (DUF3400) (family)
This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length.  This domain is found associated with [pfam:PF02754], [pfam:PF02913], [pfam:PF01565].
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 PF20828: Acidianus two-tailed virus, ORF273 protein (family)
Acidianus two-tailed virus (ATV) develops two tails to infect extremely thermophilic and acidophilic archaea. This entry represents one of its proteins, ORF273, which adopts a tetramer assembly and shows flexible loops and surface pockets in an alpha-beta structure typical of hyper thermostable folds.