SII-SWORD/CoKE huggingface dataset:
Pfam PF18648: Tse2 ADP-ribosyltransferase toxin (domain)
Tse2 from P. aeruginosa has structural features similar to ADP-ribosylating toxins. It is a cytoactive toxin secreted by a type six secretion apparatus of Pseudomonas aeruginosa and found mostly in gamma proteobacteria. It naturally attacks a target in the cytoplasm of bacterial cells. Structural analysis shows similarity between Tse2 and nicotinamide adenine dinucleotide (NAD)-dependent enzymes from bacteria, notably the mono-ADP-ribosyltransferase toxins (ADPRTs). Furthermore, it revealed that the Tse2 active site is occluded upon binding the cognate immunity protein Tsi2. The abrogation of toxicity for the R14A, S80A, and H122A mutant Tse2 proteins indicates the importance of these amino acids in the mechanism of Tse2 toxicity and, given their conservation with NAD-reactive enzymes, also supports their assignment as being involved in a catalytic reaction.
Pfam PF11701: Myosin-binding striated muscle assembly central (repeat)
The UNC-45 or small muscle protein 1 of C.elegans is expressed in two forms from different genomic positions in mammals, as a general tissue protein UNC-45a and a specific form Unc-45b expressed only in striated and skeletal muscle. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) domains towards their N-terminal, a UCS domain at the C-terminal that contains a number of Arm repeats [pfam:PF00514] and this central region of approximately 400 residues. Both the general form and the muscle form of UNC-45 function in myotube formation through cell fusion. Myofibril formation requires both GC and SM UNC-45, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organised myofibrils. The S. pombe Rng3p, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins. Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90. The exact function of this central region is not known.
Pfam PF07642: Putative beta-barrel porin-2, OmpL-like. bbp2 (family)
BBP2 is a family of putative porin proteins that are likely to be outer membrane beta barrel proteins porins.
Pfam PF22005: Parp14 WWE domain (domain)
WWE domains are characterized by the presence of a Trp-Trp-Glu region, which is important for PARP14 protein structure stabilization. WWE domains can bind to ADP-Ribose derivatives, including iso-ADP-ribose, a molecule specifically found in PAR and promote interactions with ubiquitinated proteins. The PARP14 WWE domain, however, is unable to bind to any ADP-ribose derivatives and whether it interacts with iso-ADP ribose or ubiquitinated targets is unknown.
Pfam PF15653: URI fold toxin 2 (family)
A predicted toxin of the URI nuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system.
Pfam PF18521: Transactivation domain 2 (conserved_site)
This is a N-terminal transactivation domain (TAD) domain 2 found in p53 proteins. In p53 two TAD domains are found termed TAD1 (residues 1-39) and TAD2 (residues 40-61), both of which have been shown to be able to independently activate gene transcription and are intrinsically disordered protein domains that adopt a helical conformation for at least part of their length when bound. This inherent flexibility allows the TADs to adapt to and bind a broad range of proteins. This entry describes TAD2 which can independently interact with Taz2 domain of the histone acetyltransferase p300. It has also been shown to bind to OB-fold domain of replication protein 70 A (RPA) as well as the pleckstrin homology (PH) domain of the p62 and Tfb1 subunits of human and yeast TFIIH.
Pfam PF16784: Putative HNHc nuclease (family)
This family is found in Gammaproteobacteria. It may be an HNH-like nucleases. The shorter matches are likely to be from phage proteins whereas the longer members are probably from the bacterial genomes.
Pfam PF03947: Ribosomal Proteins L2, C-terminal domain (domain)
This entry represents the C-terminal domain of the large ribosomal subunit protein uL2.
Ribosomal protein uL2 is one of the proteins from the large ribosomal subunit. The best conserved region is located in the C-terminal section of these proteins. In Escherichia coli, uL2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups:


 * Eubacterial uL2 (old name L2).
 * Algal and plant chloroplast uL2 (old name L2).
 * Cyanelle uL2 (old name L2).
 * Archaebacterial uL2 (old name L2).
 * Plant uL2 (old name L2).
 * Slime mold uL2 (old name L2).
 * Marchantia polymorpha mitochondrial uL2m (old name L2).
 * Paramecium tetraurelia mitochondrial uL2m (old name L2).
 * Fission yeast K5, K37 and KD4.
 * Yeast YL6.
 * Vertebrate uL2 (old name L8).

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF06942: GlpM protein (family)
This family consists of several bacterial GlpM membrane proteins. GlpM is a hydrophobic protein containing 109 amino acids. It is thought that GlpM may play a role in alginate biosynthesis in Pseudomonas aeruginosa.
Pfam PF01245: Ribosomal protein L19 (family)
This family represents the large ribosomal subunit protein bL19 found in bacteria and eukaryotes (which includes bL19c from plants (chloroplast), mitochondrial bL19m from animals, also referred to as MRLP19) . In Escherichia coli, bL19 is known to be located at the 30S-50S ribosomal subunit interface  and may play a role in the structure and function of the aminoacyl-tRNA binding site.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF17182: OSK domain (domain)
This entry represents the OSK domain defined by Jeske and colleagues. The domain is related to SGNH hydrolases but lacks the active site residues. The domain binds to RNA.
Wikipedia: Oskar may refer to:
Pfam PF11911: Protein of unknown function (DUF3429) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 147 to 245 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 PF21509: Fungal polycomb repressive complex 2, Ezh2-like, preSET CXC domain (domain)
This domain is found in a group of mostly fungal proteins, including the Polycomb repressive complex 2 (PRC2) subunit Ezh2 from Chaetomium thermophilum ([swissprot:G0SDW4]), which is responsible for methylation of histone H3 lysine 27 (H3K27) and therefore involved in epigenetic gene silencing. This entry represents the domain found N-terminal to to the SET domain ([pfam:PF00856]). It contains a Zn3Cys8His and a Zn3Cys9 cluster.
Pfam PF15887: Putative zinc-binding metallo-peptidase (family)
This family has a highly conserved HHExxH motif with a highly conserved ED pairing downstream. HExxH is indicative of a zinc-binding metallo-peptidase.
Pfam PF05048: Periplasmic copper-binding protein (NosD) (repeat)
NosD is a periplasmic protein which is thought to insert copper into the exported reductase apoenzyme (NosZ). This region forms a parallel beta helix domain.
Pfam PF19519: Family of unknown function (DUF6051) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 377 and 403 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 PF03094: Mlo family (family)
A family of plant integral membrane proteins, first discovered in barley. Mutants lacking wild-type Mlo proteins show broad spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. Thus wild-type Mlo proteins are thought to be inhibitors of cell death whose deficiency lowers the threshold required to trigger the cascade of events that result in plant cell death. Mlo proteins are localised in the plasma membrane and possess seven transmembrane regions; thus the Mlo family is the only major higher plant family to possess 7 transmembrane domains. It has been suggested that Mlo proteins function as G-protein coupled receptors in plants; however the molecular and biological functions of Mlo proteins remain to be fully determined.
Pfam PF14480: DNA polymerase III polC-type N-terminus I (family)
This is the first N-terminal domain, NI domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria.  Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding. This domain is associated with DNA_pol3_alpha [pfam:PF07733] and DNA_pol3_a_NI [pfam:PF11490].
Pfam PF18113: Rubredoxin binding C-terminal domain (domain)
This is the C-terminal domain found in rubredoxin reductase (RdxR) present in Pseudomonas aeruginosa. RdxR are important in prokaryotes as they allow for the metabolism of inert n-alkanes and RdxR is also crucial for archaea and anaerobic bacteria in the response to oxidative stress. This domain is known to recognise and bind to rubredoxin.
Pfam PF20810: Msx2-interacting protein, nuclear receptor-interacting domain (domain)
This entry represents the nuclear receptor-interacting domain (RID) from Msx2-interacting protein (MINT), a widely expressed transcription repressor that regulates key transcription effectors in several signalling pathways, including MSX2, RBP-J, and nuclear receptors. This RID segment of MINT partially overlaps the Msx2-interacting domain (MID, [pfam:PF20809]). This entry covers the C-terminal end of the RID domain described in.
Pfam PF24334: Family of unknown function (DUF7502) (family)
This entry represents a group of 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 PF08719: NADAR domain (domain)
This is a domain of unknown function, it has been named been named the NADAR (NAD and ADP-ribose) domain.
Pfam PF06736: Endosomal/lysosomal potassium channel TMEM175 (family)
This family represents the conserved region of transmembrane protein 175 which is an organelle-specific potassium channel responsible for potassium conductance in endosomes and lysosomes. It forms a potassium-permeable leak-like channel, which regulates luminal pH stability and is required for autophagosome-lysosome fusion. TMEM175 is the major lysosomal potassium conductance. It is present in eukaryotes, where TMEM175 has two repeats of 6-transmembrane-spanning segments, and also in prokaryotes in which it has one copy.
Wikipedia: Transmembrane protein 175, or TMEM175, is a transmembrane protein that is thought to be an endolysosomal potassium channel. It is predicted to have many orthologs across eukaryotes.
Pfam PF07578: Lipid A Biosynthesis N-terminal domain (repeat)
This family is found at the N-terminus of a group of Chlamydial Lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function.
Pfam PF17877: DIS3-like exonuclease 2 C terminal (domain)
This is the C-terminal S1 domain found in Dis3L2 proteins. Dis3L2 belongs to the RNase II/R 3-5 exonuclease superfamily, which includes the catalytic subunit of the RNA exosome in yeast and in humans.
Pfam PF20958: GxGYxYP third domain (domain)
This entry represents a domain that is found repeated in three copies per protein and is likely to be involved in binding the bacterial cell wall. This domain is found in association with [pfam:PF14323].
Pfam PF10862: FcoT-like thioesterase domain (domain)
Proteins in this family have a HotDog fold. This family was formerly known as domain of unknown function 2662 (DUF2662). The structure of Rv0098 from M. tuberculosis suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups. The maximal Kcat was observed for palmitoyl-CoA although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex.
Pfam PF15914: FAM193 family C-terminal (family)
This domain family is found in eukaryotes, and is approximately 60 amino acids in length. This C-terminal region of these proteins carries the most conserved residues.
Pfam PF02530: Porin subfamily (family)
This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to [pfam:PF00267]. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria.
Pfam PF22823: MrpR, C-terminal catalytic domain (domain)
This family includes the MrpR protein from Bacillus subtilis (also known as YopR), the master repressor of the lytic cycle of the temperate phage SPbeta. MrpR, a DNA-binding protein that has lost its recombinase function, shows a tyrosine recombinase fold with an N-terminal all-alpha domain ([pfam:PF22822]) and a C-terminal catalytic domain (this entry).
Pfam PF15068: FAM101 family (family)
This protein family includes the actin regulators, Refilin A and B, however the exact function of this protein family remains unknown. Refilin is thought to stabilise peri-nuclear actin filament bundles, important in fibroblasts. Refilin is important as changes in localisation and shape in the nucleus plays a role in cellular and developmental processes.
Pfam PF19328: 2,4-diaminopentanoate dehydrogenase C-terminal domain (domain)
This entry represents the C-terminal presumed domain from the 2,4-diaminopentanoic acid C 4 dehydrogenase enzyme. This enzyme is involved in the ornithine fermentation pathway. It catalyzes the oxidative deamination of (2R,4S)-2,4-diaminopentanoate (DAP) to yield 2-amino-4-ketopentanoate (AKP). The N-terminal domain has a Rossmann fold.
Pfam PF06289: Flagellar and Swarming motility proteins (family)
This family consists of several bacterial FlbD flagellar proteins. Such as SwrD of Bacillus subtilis which is necessary for swarming because it increases flagellar torque.
Pfam PF05417: Hepatitis E cysteine protease (family)
Corresponds to MEROPs family C41. This papain-like protease cleaves the viral polyprotein encoded by ORF1 of the hepatitis E virus (HEV).
Pfam PF09131: Bacillus thuringiensis delta-Endotoxin, middle domain (repeat)
Members of this family adopt a structure consisting of three four-stranded beta-sheets, each with a Greek key fold, with internal pseudo threefold symmetry. Thus they act as a receptor binding beta-prism, binding to insect-specific receptors of gut epithelial cells.
Wikipedia: Delta endotoxins (δ-endotoxins) are a family of pore-forming toxins produced by Bacillus thuringiensis species of bacteria. They are useful for their insecticidal action and are the primary toxin produced by the genetically modified (GM) Bt maize/corn and other GM crops. During spore formation the bacteria produce crystals of such proteins that are also known as parasporal bodies, next to the endospores; as a result some members are known as a parasporin. The Cyt (cytolytic) toxin group is another group of delta-endotoxins formed in the cytoplasm. VIP toxins are formed at other stages of the life cycle.
Pfam PF18675: Heparinase II C-terminal domain (domain)
Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. The C-terminal domain contains nine beta-strands packed together in a manner resembling a beta-barrel.
Pfam PF04793: BRRF1-like protein (family)
Family of herpesvirus proteins including Epstein-barr virus protein BBRF1.
Pfam PF05985: Ethanolamine ammonia-lyase light chain (EutC) (family)
This family consists of several bacterial ethanolamine ammonia-lyase light chain (EutC) [ec:4.3.1.7] sequences. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia.
Pfam PF21592: Bc2l-C, N-terminal domain (domain)
This domain is found at the N-terminal end of Lectin from Burkholderia cenocepacia (Bc2l-C) and similar bacterial sequences. Bc2l-C is a soluble lectin involved in bacterial adhesion and subsequent deadly infection to the host. It has two domains: a C-terminal domain [pfam:PF07472] and this domain, which adopts a compact jellyroll architecture composed of 11 beta-strands and a short helix. It shows specificity for fucosylated human histo-blood group epitopes H-type 1, Lewis b, and Lewis Y.
Pfam PF08474: Myelin transcription factor 1 (family)
This domain is found in the myelin transcription factor 1 (MYT1) of chordates.  MYT1 contains C2HC zinc finger domains ([pfam:PF01530]) and is expressed in developing neurons of the central nervous system where it is involved in the selection of neuronal precursor cells.
Pfam PF13474: SnoaL-like domain (domain)
This family contains a large number of proteins that share the SnoaL fold.
Pfam PF11569: Homeodomain leucine-zipper encoding, Homez (family)
Homez contains two leucine zipper-like motifs and an acidic domain and belongs to the superfamily of homeobox-containing proteins. The presence of leucine zippers suggests that Homez can function as a homo or heterodimer in the nucleus. It is thought that the first leucine zipper and homeodomain 1 (HD1)of Homez is responsible for dimerisation and HD2 has a specific DNA-binding activity. Homez is also thought to function as a transcriptional repressor due to the acidic region in its C-terminal domain. Homez is involved in a complex regulatory network.
Pfam PF15510: CENP-W protein (domain)
CENP-W is a family of vertebral kinetochore proteins that associates directly with CENP-T. CENP-W members are histone-fold proteins. The histone fold region is critical for binding to centromeric DNA. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes.