SII-SWORD/CoKE huggingface dataset:
Pfam PF13843: Transposase IS4 (domain)
This entry represents a domain found in the human PiggyBac transposable element-derived proteins (PGBDs) and some uncharacterised proteins. Its function is not clear.
Wikipedia: The PiggyBac (PB) transposon system employs a genetically engineered transposase enzyme to insert a gene into a cell's genome. It is built upon the natural PiggyBac (PB) transposable element (transposon), enabling the back and forth movement of genes between chromosomes and genetic vectors such as plasmids through a "cut and paste" mechanism. During transposition, the PB transposase recognizes transposon-specific inverted terminal repeat sequences (ITRs) located on both ends of the transposon vector and efficiently moves the contents from the original sites and integrates them into TTAA chromosomal sites. The powerful activity of the PiggyBac transposon system enables genes of interest between the two ITRs in the PB vector to be easily mobilized into target genomes. The TTAA-specific transposon piggyBac is rapidly becoming a highly useful transposon for genetic engineering of a wide variety of species, particularly insects. They were discovered in 1989 by Malcolm Fraser at the University of Notre Dame.
Pfam PF12346: Holliday junction recognition protein-associated repeat (domain)
Vertebral Holliday junction recognition proteins carry an SCM3 domain at their N-terminus as do the eukaryotic fungi, but they also carry this central, conserved region. The function of this family is not known. Further downstream there is also a repeated domain, also of unknown function. Investigation of Scm3 and associated proteins is likely to be directly relevant to understanding the mechanism of HJURP-mediated CENP-A chromatin assembly at human centromeres.
Pfam PF06416: Effector protein NleG (family)
Many bacterial pathogens deliver effector proteins into host cells via a type III secretion system. These effector proteins then alter the host cell's biology in ways that are advantageous to the pathogen. The NleG protein and its homologues form the largest family of effector proteins in the enterohemorrhagic Escherichia coli O157:H7, with 14 members identified in the Sakai strain alone.
Pfam PF08956: Domain of unknown function (DUF1869) (domain)
This domain is found in a set of hypothetical bacterial 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 PF09187: RNA-directed DNA methylation 1 (domain)
This family of plant proteins includes RDM1 from Arabidopsis, which is a component of the RNA-directed DNA methylation (RdDM) effector  complex and may have a role in linking siRNA production with  pre-existing or de novo cytosine methylation. As part of the DDR complex with two other RdDM components, it has been shown to facilitate association of PolV to chromatin.
Pfam PF08559: Cut8, nuclear proteasome tether protein (family)
In Schizosaccharomyces pombe, Cut8 is a nuclear envelope protein that physically interacts with and tethers 26S proteasome in the nucleus resulting in the nuclear accumulation of proteasome. Cut8 comprises three functional domains. An N-terminal lysine-rich segment which binds to the proteasome when ubiquitinated, a central dimerisation domain and a C-terminal nine-helix, pdb:3q5w, bundle which shows structural similarity to 14-3-3 phosphoprotein-binding domains. The helical bundle is necessary for liposome and cholesterol binding. Cut8 is a proteasome substrate and the N-terminal segment is polyubiquitinated and functions as a degron tag. Ubiquitination of the amino N-terminal segment is essential for the function of Cut8. Lysine residues in the N-terminal segment of Cut8 are required for physical interaction with proteasome. In fission yeast the function of Cut8 has been demonstrated to be regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating enzymes Ubr1. Cut8 homologues have been identified in Drosophila melanogaster, Anopheles gambiae and Dictyostelium discoideum.
Pfam PF16865: Glutathione S-transferase, C-terminal domain (domain)
Leishmania major and Trypanosoma cruzi glutathione-S-transferase (GST) has undergone gene duplication, diversification, and gene fusion leading to an four domain enzyme which contains two repeats of a GST N-terminal domain followed by a GST C-terminal domain.
Pfam PF22429: Formimidoylglutamate deiminase HutF, N-terminal domain (domain)
This small domain is found at the N-terminal end of Formimidoylglutamate deiminase from Pseudomonas aeruginosa (also known as N-formimino-L-Glutamate Iminohydrolase, HutF) and similar proteins predominantly found in proteobacteria. HutF catalyzes he deamination of N-formimino-l-glutamate to N-formyl-l-glutamate and ammonia in the histidine degradation pathway. The domain represented by this entry folds into an open beta-barrel which is completed by two strands located at the C terminus of the protein.
Pfam PF24058: Domain of unknown function (DUF7359) (domain)
This entry represents a domain of unknown function found in SPbeta prophage-derived uncharacterized protein (YomG) from Bacillus subtilis (strain 168). This domain may adopt a FN3-like fold and can be found in association with a prophage endopeptidase tail domain ([pfam:PF06605]).
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 PF24665: Domain of unknown function (DUF7652) (domain)
This is an Ig-like domain found towards the C-terminal of a group of uncharacterised sequences from Strongyloides spp. and similar sequences from nematodes.
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 PF03040: CemA family (family)
Members of this family are probable integral membrane proteins. Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane. A cyanobacterial member of this family has been implicated in CO2 transport, but is probably not a CO2 transporter itself. They are predicted to be haem-binding however this has not been proven experimentally.
Pfam PF03811: InsA N-terminal domain (domain)
This appears to be a short zinc binding domain found in IS1 InsA family protein. It is found at the N-terminus of the protein and may be a DNA-binding domain.
Pfam PF09557: Domain of unknown function (DUF2382) (domain)
This entry describes an uncharacterized domain, sometimes found in association with a PRC-barrel domain [pfam:PF05239] which is also found in rRNA processing protein RimM and in a photosynthetic reaction centre complex protein). This domain is found in proteins from Bacillus subtilis, Deinococcus radiodurans, Nostoc sp. PCC 7120, Myxococcus xanthus, and several other species. The function is not known.
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 PF01022: Bacterial regulatory protein, arsR family (domain)
Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
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 PF03939: Ribosomal protein L23, N-terminal domain (family)
The N-terminal domain appears to be specific to the  eukaryotic ribosomal proteins L25, L23, and L23a.
Pfam PF14744: WASH complex subunit 7 (family)
This family is the central, conserved region of proteins that form subunit 7 of the WASH complex. In species such as Drosophila this protein is the only component of the 'complex'. This complex is a nucleation promoting factor necessary for the activation of Arp2/3 that nucleates and organises actin filaments by associating with a pre-existing filament to induce the assembly of a branching filament.  WASH thus effectively nucleates actin on endosomes.
Pfam PF01872: RibD C-terminal domain (domain)
The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG [swissprot:P25539], in combination with [pfam:PF00383], as well as in isolation in some archaebacterial proteins [swissprot:P95872].  This family appears to be related to [pfam:PF00186].
Pfam PF07671: Protein of unknown function (DUF1601) (family)
This repeat is found in a small number of proteins and is apparently limited to Coxiella and related species.
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 PF07504: Fungalysin/Thermolysin Propeptide Motif (conserved_site)
This motif is found in both the bacterial M4 peptidase propeptide and the fungal M36 propeptide. Its exact function is not clear, but it is likely to either  inhibit the peptidase, so as to prevent its premature activation, or has a chaperone activity. Both of these roles have been ascribed to the M4 and M36 propeptides (,).
Pfam PF04394: Protein of unknown function, DUF536 (family)
This family aligns the C-terminal region from several bacterial proteins of unknown function that may be involved in a theta-type replication mechanism.
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 PF19130: Family of unknown function (DUF5813) (family)
This is a family of unknown function found predominantly in Halobacteria.
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 PF18267: Rubredoxin NAD+ reductase C-terminal domain (domain)
This is the C-terminal domain of NADH rubredoxin oxidoreductase present in Clostridium acetobutylicum. The majority of obligatory anaerobes detoxify micro-aerobic environments by consuming O2 via H2O-forming NADH oxidase. This enzyme offers an alternate reaction pathway for scavenging of O2 and reactive oxygen species, wherein the reducing equivalent is obtained from NADH.
Pfam PF06677: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) (family)
This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
Pfam PF17268: Family of unknown function (DUF5334) (family)
This is a family of unknown function which can is found mainly in Proteobacteria.
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 PF08231: SYF2 splicing factor (domain)
Proteins in this family are involved in cell cycle progression and pre-mRNA splicing.
Pfam PF01517: Hepatitis delta virus delta antigen (family)
The hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg).  The central region of this protein has been shown to bind RNA.  Several interactions are also mediated by a coiled-coil region at the N terminus of the protein.
Wikipedia: Hepatitis D is a type of viral hepatitis caused by the hepatitis delta virus (HDV). HDV is one of five known hepatitis viruses: A, B, C, D, and E. HDV is considered to be a satellite because it can propagate only in the presence of the hepatitis B virus (HBV). Transmission of HDV can occur either via simultaneous infection with HBV (coinfection) or superimposed on chronic hepatitis B or hepatitis B carrier state (superinfection).
Pfam PF05709: Phage tail protein RIFT-related domain (domain)
This family consists of several Siphovirus and other phage tail component proteins as well as some bacterial proteins of unknown function. This entry represents the N-terminal RIFT-related barrel domain.
Pfam PF19587: Uncharacterised methyltransferase family (DUF6094) (family)
This family of proteins is functionally uncharacterised, but The C-terminus appears to be related to methyltransferases. This family of proteins is found in bacteria. Proteins in this family are typically between 362 and 396 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 PF09578: Spore cortex protein YabQ (family)
This protein is predicted to span the membrane several times. It is only found in genomes of species that perform sporulation, such as Bacillus subtilis, Clostridium tetani, and other members of the Firmicutes (low-GC Gram-positive bacteria). Mutation of this sigmaE-dependent gene blocks development of the spore cortex. The length of the C-terminal region, which includes some hydrophobic regions, is variable.
Pfam PF17152: Periplasmic sensor domain (family)
CHASE8 is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcN (YfiN) that regulates biofilm formation and motility in Escherichia coli. In Pseudomonas aeruginosa, CHASE8 is the sensor domain in the diguanylate cyclase TpbB that regulates biofilm formation by controlling the levels of extracellular DNA.
Pfam PF22249: Endoplasmic reticulum metallopeptidase 1, TM domain (domain)
Endoplasmic reticulum metallopeptidase 1 (ERMP1, also known as Felix-ina, FXNA or Fxna peptidase) is a multi-pass membrane protein located in the endoplasmic reticulum membrane. In humans, it may play a crucial role in processing proteins required for the organisation of somatic cells and oocytes into discrete follicular structures, although which proteins are hydrolysed has not yet been determined. According to AlphaFold structure predictions, these proteins consists of a M28 peptidase domain ([pfam:PF04389]), a transmembrane domain and a C-terminal elongated banana-shaped, all beta-sheet domain ([pfam:PF22248]) structurally similar to the Mu homology domain ([pfam:PF00928], based on structure comparisons). This entry represents the transmembrane (TM domain).
Pfam PF10288: Cytoplasmic tRNA 2-thiolation protein 2 (family)
CTU2 is a family of proteins necessary for the formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. The family is conserved from plants to humans ]1]. It plays a central role in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine, or the wobble nucleoside. This wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), is required for the proper decoding of NNR codons in eukaryotes. The 2-thio group gives rigidity by largely fixing the C3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing.
Pfam PF07662: Na+ dependent nucleoside transporter C-terminus (family)
This family consists of nucleoside transport proteins. [swissprot:Q62773] is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. [swissprot:Q62674] is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters.
Wikipedia: Human concentrative nucleoside transporters include SLC28A1, SLC28A2 and SLC28A3 proteins. SLC28A2 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane. SLC28A1 is a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine. It also transports the anti-viral nucleoside analogues Zidovudine and Zalcitabine.
Pfam PF02616: Segregation and condensation protein ScpA (family)
This is a family of proteins that from part of the condensin complex that regulates chromosome segregation.  This is the A subunit, which binds to the ScpB subunit, [pfam:PF04079], and SMC, [pfam:PF02463], to participate in chromosomal partition during cell division. The condensin complex pulls DNA away from the mid-cell into both cell halves. These proteins are part of the Kleisin superfamily.
Pfam PF07615: YKOF-related Family (domain)
This entry represents YkoF-related proteins. YkoF is involved in the hydroxymethyl pyrimidine (HMP) salvage pathway . The domain is found in pairs in these proteins.
Pfam PF11081: Adenovirus L4-33K/L4-22K (family)
Adenoviruses express up to 20 distinct mRNAs from five major late transcription unit (MLTU) regions, L1 to L5. The L4 region expresses L4-33K and a related protein, L4-22K. L4-22K and L4-33K have complementary but not redundant functions that provide the normal pattern of mRNA production during the late phase of infection. L4-33K is an alternative RNA splicing factor that up-regulates several MLTU splice acceptor sites as the late phase progresses. L4-22K plays a role in genome packaging via its binding, in association with IVa2, to the A2 sequence within the packaging signal. Additionally, L4-22K plays an important role in the temporal switch from the early to late phase of infection by regulating both early and late gene expression.
Pfam PF10993: Protein of unknown function (DUF2818) (family)
This bacterial family of 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 PF17385: Lacto-N-biose phosphorylase central domain (domain)
The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme ([ec:2.4.1.211]), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by bifidobacteria is important for human health, especially in pediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides.
Pfam PF14052: Capsule assembly protein Wzi (family)
Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organisation of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 1 capsule biosynthesis. It is likely to be involved in the later stages of capsule assembly. It is likely to consist of a beta-barrel structure.
Pfam PF02611: CDP-diacylglycerol pyrophosphatase (family)
This is a family of CDP-diacylglycerol pyrophosphatases, [ec:3.6.1.26].  This enzyme catalyses the reaction CDP-diacylglycerol + H2O  CMP + phosphatidate.
Pfam PF01896: DNA primase small subunit (family)
DNA primase synthesises the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits.  This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme. The family also contains many bacterial DNA primases.
Wikipedia: DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
Pfam PF23258: Domain of unknown function (DUF7072) (domain)
This domain is found in a group of uncharacterised proteins mainly from Fungi. It shares a weak sequence similarity to the C-terminal domain of the Escherichia Coli ProQ RNA binding protein ([pfam:PF17516]) and it is predicted to adopt a similar structure with SH3-like topology.
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 PF15702: Hermansky-Pudlak syndrome 6 protein N-terminal domain (repeat)
This entry represents the N-terminal beta propeller domain of the HPS6 protein.
Wikipedia: Hermansky–Pudlak syndrome 6 (HPS6), also known as ruby-eye protein homolog (Ru), is a protein that in humans is encoded by the HPS6 gene.