SII-SWORD/CoKE huggingface dataset:
Pfam PF00476: DNA polymerase family A (family)
Synonym(s): DNA nucleotidyltransferase (DNA-directed)

DNA-directed DNA polymerases(2.7.7.7) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for thede novosynthesis of a DNA chain. A number of polymerases belong to this family .
DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains .
Wikipedia: A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create two identical DNA duplexes from a single original DNA duplex. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones.
These enzymes catalyze the chemical reactiondeoxynucleoside triphosphate + DNAn ⇌ pyrophosphate + DNAn+1.
Pfam PF07705: CARDB (domain)
Cell adhesion related domain found in bacteria.
Pfam PF22330: Small ribosomal subunit protein mS39, PPR (repeat)
This entry represents the a PPR section found at the N-terminal of Small ribosomal subunit protein mS39 (also known as PPR domain protein 3 (PTCD3)), a mitochondrial RNA-binding protein that has a role in mitochondrial translation.
Pfam PF07202: T-complex protein 10 C-terminus (repeat)
This entry represents a repeating unit commonly found in the C terminus of the eukaryotic T-complex protein 10. The T-complex is  involved in spermatogenesis in mice. The repeating unit is  commonly found 3-4 times, but there is often a gap between the first  and second repeats, which is big enough to accommodate another repeat  unit. However, the score is insufficient to be included, and could  be a degenerate repeat.
Pfam PF17202: Single cache domain 3 (domain)
Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2 channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors.
This entry represents the single cache domain 3 (sCache_3) .
Wikipedia: In molecular biology, the cache domain is an extracellular protein domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria such as Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions.
Pfam PF05883: Baculovirus U-box/Ring-like domain (domain)
This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Pfam PF20074: Family of unknown function (DUF6470) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, predominantly in Firmicutes, but also in eukaryotes. Proteins in this family are typically between 185 and 202 amino acids in length. There is a conserved motif ID.
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 PF18519: SAGA-associated factor 11 N-terminal domain (domain)
The SAGA (Spt-Ada-Gcn5-Acetyltransferase) transcriptional co-activator is a protein complex that regulates inducible yeast genes by performing multiple functions including acetylating core histones, recruiting the RNA polymerase II preinitiation complex, and deubiquitinating histone H2B.  The deubiquitinating activity of SAGA resides in a distinct sub-complex called the deubiquitinating module (DUBm), which consists of four proteins that are conserved across eukaryotes: Ubp8, Sgf11, Sus1 and Sgf73. The DUBm proteins are organized into two lobes around the globular domains of Ubp8. In SAGA, Sus1 binds to Sgf11 by wrapping around this N-terminal domain of Sgf11, forming a stable dimer.
Pfam PF09536: Protein of unknown function (DUF2378) (family)
This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus DK 1622 and and 12 in Stigmatella aurantiaca DW4/3-1. Members are about 200 amino acids in length. The function 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 PF14138: Cytochrome c oxidase assembly protein COX16 (family)
This family represents homologues of COX16 which has been shown to be involved in assembly of cytochrome oxidase. Protein in this family are typically between 106 and 134 amino acids in length.
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF23131: DotY (family)
This entry represent the type 4 apparatus protein DotY from Legionella pneumophila and related proteins found mainly in Gammaproteobacteria. DotY is a component of Type 4B secretion (T4BS) system that translocates over 300 effectors into the host cell during infection. This protein is part of a subcomplex which recruits effector proteins and delivers them to the core transmembrane subcomplex. In the membrane-embedded T4 coupling complex (T4CC), DotY makes extensive contacts with DotZ. The DotLMNYZ components form a hetero-pentameric core of the T4CC complex from which the flexible IcmSW module protrudes. These hetero-pentameric complexes assemble and form an inner membrane channel for effectors to pass through. DotY and DotZ play a role in effector translocation and optimise secretion by modulating the delivery trajectory of the IcmSW module.
Pfam PF06336: Coronavirus 5a protein (family)
This family consists of several Coronavirus 5a proteins. The function of this family is unknown.
Pfam PF14553: YqbF, hypothetical protein domain (domain)
This N-terminal domain is found in Bacillus and related spp. The function is not known.
Pfam PF14834: Glutathione S-transferase, C-terminal domain (domain)
GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants.  Stringent starvation proteins in E. coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain.
Wikipedia: Glutathione S-transferase, C-terminal domain  is a structural domain of glutathione S-transferase (GST).
Pfam PF02128: Fungalysin metallopeptidase (M36) (family)
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .
This group of metallopeptidases belong to MEROPS peptidase family M36 (fungalysin family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH.

Fungalysin is produced by fungi, Aspergillus and other species, to aid degradation of host lung cell walls on infection. The enzyme is a 42kDa single chain protein, with a pH optimum of 7.5-8.0 and optimal temperature of 60 celcius .
Pfam PF11980: C-terminal domain of neuropilin glycoprotein (family)
This domain is found in eukaryotes at the C-terminus of neuropilins. It represents the transmembrane region of these transmembrane glycoproteins, that are predominantly co-receptors for another class of proteins known as semaphorins. The domain is found associated with [pfam:PF00754], [pfam:PF00431], [pfam:PF00629].
Wikipedia: Neuropilin is a protein receptor active in neurons.
Pfam PF10277: Frag1/DRAM/Sfk1 family (family)
This family includes Frag1, DRAM and Sfk1 proteins.  Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans.  There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced.  This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton.
Pfam PF22098: Family of unknown function (DUF6942) (family)
This is a family of uncharacterised bacterial proteins. They are probably distantly related to uracil-DNA glycosylases and other related DNA glycosylases given their predicted 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 PF10384: Centromere protein Scm3 (family)
Scm3 is a centromere protein that has been shown in Saccharomyces cerevisiae to be required for G2/M progression and Cse4 localisation.  The C terminal region of Scm3 proteins is variable in size and sometimes consists of DNA binding motifs.
Pfam PF21971: Transcriptional regulator PINT87aa (family)
This protein family represents human Transcriptional regulator PINT87aa (LINC-PINT), an 87-residues peptide encoded by a circular RNA (circRNA) that suppresses glioblastoma cell proliferation in vitro and in vivo. It has been established as a biomarker and a key regulator of cellular senescence in hepatocellular carcinoma (HCC).
Pfam PF05872: Helicase HerA-like C-terminal (domain)
HerA is a DNA helicase able to utilise either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus. This entry represents the C-terminal domain of HerA which seems to be involved in the conversion of ATP hydrolysis into DNA translocation.
Pfam PF11254: Protein of unknown function (DUF3053) (family)
Some members in this family of proteins are annotated as the membrane protein YiaF. No function is currently 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 PF22829: HphA C-terminal domain (domain)
HphA is a secreted hemophore that binds and acquires heme from hemoglobin. It consists of two domains: N-terminal heme binding domain and C-terminal beta-barrel (this entry) that is related to domains members of the Outer membrane beta-barrel superfamily.
Pfam PF07125: Protein of unknown function (DUF1378) (family)
This family consists of hypothetical bacterial and phage proteins of around 59 residues in length. Bacterial members of this family seem to be specific to Enterobacteria. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids.
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 PF09157: Pseudouridine synthase II TruB, C-terminal (domain)
Members of this family adopt a secondary structure consisting of a four-stranded beta sheet and one alpha helix. They are predominantly RNA-binding domains, mostly found in Pseudouridine synthase II TruB.
Pfam PF06540: Galanin message associated peptide (GMAP) (family)
This family consists of several galanin message associated peptides. In rat preprogalanin, galanin is C-terminally flanked by a 60 amino acid long peptide: galanin message-associated peptide (GMAP). GMAP sequences in different species show high degree of homology, but the biological function of this family is unknown.
Wikipedia: Galanin is a neuropeptide encoded by the GAL gene, that is widely expressed in the brain, spinal cord, and gut of humans as well as other mammals. Galanin signaling occurs through three G protein-coupled receptors.
Pfam PF01102: Glycophorin A (family)
This entry represents a family of mammal proteins, including human Glycophorin A and B (GYPA/B). GYPA and B are components of the ankyrin-1 complex, a multiprotein complex involved in the stability and shape of the erythrocyte membrane .
Wikipedia: A glycophorin is a sialoglycoprotein of the membrane of a red blood cell. It is a membrane-spanning protein and carries sugar molecules. It is heavily glycosylated (60%). Glycophorins are rich in sialic acid, which gives the red blood cells a very hydrophilic-charged coat. This enables them to circulate without adhering to other cells or vessel walls.
Pfam PF02575: YbaB/EbfC DNA-binding family (family)
This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure. The conformation of the DNA is changed when bound to these proteins. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage.
Pfam PF07376: Prosystemin (family)
This family consists of several plant specific prosystemin proteins. Prosystemin is the precursor protein of the 18 amino acid wound signal systemin which activates systemic defence in plant leaves against insect herbivores.
Wikipedia: Systemin is a plant peptide hormone involved in the wound response in the family Solanaceae. It was the first plant hormone that was proven to be a peptide having been isolated from tomato leaves in 1991 by a group led by Clarence A. Ryan. Since then, other peptides with similar functions have been identified in tomato and outside of the Solanaceae. Hydroxyproline-rich glycopeptides were found in tobacco in 2001 and AtPeps were found in Arabidopsis thaliana in 2006. Their precursors are found both in the cytoplasm and cell walls of plant cells, upon insect damage, the precursors are processed to produce one or more mature peptides. The receptor for systemin was first thought to be the same as the brassinolide receptor but this is now uncertain. The signal transduction processes that occur after the peptides bind are similar to the cytokine-mediated inflammatory immune response in animals. Early experiments showed that systemin travelled around the plant after insects had damaged the plant, activating systemic acquired resistance, now it is thought that it increases the production of jasmonic acid causing the same result. The main function of systemins is to coordinate defensive responses against insect herbivores but they also affect plant development. Systemin induces the production of protease inhibitors which protect against insect herbivores, other peptides activate defensins and modify root growth. They have also been shown to affect plants' responses to salt stress and UV radiation. AtPEPs have been shown to affect resistance against oomycetes and may allow A. thaliana to distinguish between different pathogens. In Nicotiana attenuata, some of the peptides have stopped being involved in defensive roles and instead affect flower morphology.
Pfam PF18340: DNA relaxase TraI 2B/2B-like domain (domain)
This is the 2B and 2B-like sub-domain found in TraI ([ec:5.99.1.2]) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components.  The 2B sub-domains in TraI are formed by residues 625-773 in the vestigial helicase domain and residues 1255-1397 in the active helicase domain. The 2B/2B-like sub-domain interacts with ssDNA where it contributes to the surface area where ssDNA bind. In other words the ssDNA-binding site is located in a groove between the 2B and 2B-like parts of the sub-domain. The sub-domain parts appear to act as clamps holding the ssDNA in place, resulting in the ssDNA being completely surrounded by protein. In previous studies, the 2B/2B-like sub-domain of the TraI vestigial helicase domain has been identified as translocation signal A (TSA) since it contains sequences essential for the recruitment of TraI to the T4S system. Thus, the 2B/2B-like sub-domain plays two major roles in relaxase function: (1) interacting with the DNA and possibly promoting high processivity and (2) mediating recruitment of the relaxosome to the T4S system.
Pfam PF02130: Endoribonuclease YbeY (family)
YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both  the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices.
Pfam PF02757: YLP motif (conserved_site)
The YLP motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in [swissprot:Q15303] may suggest it could be a substrate for tyrosine kinases.
Pfam PF25060: Tetratricopeptide repeat protein 21 second ARM domain (repeat)
This entry represents the second ARM-repeats domain found towards the N-terminal of Tetratricopeptide repeat protein 21 (TT21) from human and its homologues. TT21 is an intraflagellar transport (IFT)-associated protein required for spermatogenesis. It is involved in sperm flagellar formation and intraflagellar transport.
Pfam PF03719: Ribosomal protein S5, C-terminal domain (domain)
This entry represents the C-terminal of the ribosomal protein uS5, which is related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (O05641). Ribosomal protein uS5 is one of the proteins from the small ribosomal subunit. In Escherichia coli, uS5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in uS5 have been shown to increase translational error frequencies.
Pfam PF01541: GIY-YIG catalytic domain (domain)
This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.  The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.
Wikipedia: The homing endonucleases are a collection of endonucleases encoded either as freestanding genes within introns, as fusions with host proteins, or as self-splicing inteins. They catalyze the hydrolysis of genomic DNA within the cells that synthesize them, but do so at very few, or even singular, locations. Repair of the hydrolyzed DNA by the host cell frequently results in the gene encoding the homing endonuclease having been copied into the cleavage site, hence the term 'homing' to describe the movement of these genes. Homing endonucleases can thereby transmit their genes horizontally within a host population, increasing their allele frequency at greater than Mendelian rates.