SII-SWORD/CoKE huggingface dataset:
Pfam PF00572: Ribosomal protein L13 (family)
Ribosomal protein uL13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, uL13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. uL13 proteins were previously known as L13 from bacteria, L16 from yeast and L13A from human.
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 PF18063: Beta barrel Pore-forming domain (domain)
This domain is found in Monalysin Pore-forming Toxin which is a type of beta-barrel pore-forming toxin protein found in Pseudomonas entomophila. Monalysin forms a stable doughnut-like 18-mer complex composed of two disk-shaped nonamers to form a pore. The domain is composed of a central twisted beta -sheet composed of three antiparallel beta-strands (beta 3, beta 6, and beta 8/9) and flanked by the pore-forming segment and the C-terminal region on either side. The pore-forming domain (residues 102-170) is located between strands beta 3 and beta 6, and is formed from two antiparallel beta-strands connected by three alpha-helices, alpha 3, alpha 4, and alpha 5. The C-terminal region forms a long alpha-helix followed by a small hairpin and a short alpha-helix.
Pfam PF23035: RING finger protein unkempt homolog-like, CCCH zinc finger (domain)
This entry represents the fourth CCCH-type zinc finger of human RING finger protein unkempt homolog (UNK) and similar sequences mainly found in animals. UNK is a sequence-specific RNA-binding protein which plays an important role in the establishment and maintenance of the early morphology of cortical neurons during embryonic development.
Pfam PF10343: Queuosine salvage protein (family)
Queuosine salvage proteins occur in most Eukarya as well as in a few bacteria possible via horizontal gene-transfer. Queuosine (Q) is a chemical modification found at the wobble position of tRNAs that have GUN anticodons, and it ensures faithful translation of the respective C- and U-ending codons. Most bacteria synthesize queuosine de novo, whereas eukaryotes rely solely on salvaging this essential component from the environment or the gut flora. This entry represents  queuosine salvage proteins (Qng1, also known as DUF2419) which have been identified as a queuosine nucleoside glycosylases that play an essential role in allowing eukaryotic cells to salvage Q from bacterial sources and to recycle Q from endogenous tRNAs.
Wikipedia: A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules. The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C). In order to maintain consistency of nucleic acid nomenclature, "I" is used for hypoxanthine because hypoxanthine is the nucleobase of inosine;
nomenclature otherwise follows the names of nucleobases and their corresponding nucleosides. The thermodynamic stability of a wobble base pair is comparable to that of a Watson-Crick base pair. Wobble base pairs are fundamental in RNA secondary structure and are critical for the proper translation of the genetic code.
Pfam PF24692: Family of unknown function (DUF7659) (family)
This family of uncharacterised proteins is found in bacteria and phage. Proteins in this family are typically between 128 and 147 amino acids in length. The proteins contain two subdomains separated by an alpha-helical linker.
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 PF24412: Family of unknown function (DUF7546) (family)
This entry represents a group of uncharacterised proteins found mainly in Halobacteria. These proteins are likely associated with the membrane.
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 PF23732: PH domain (domain)
This domain is found in uncharacterised proteins mainly from Trypanosomes. It has a weak sequence similarity to known PH-domains and it is predicted to adopt similar structure. It contains a conserved GTFKT sequence motif.
Pfam PF16873: Putative abortive phage resistance protein AbiGii toxin (domain)
AbiGii is a family of putative type IV toxin-antitoxin system toxins. The AbiG abortive phage resistance protein affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis. The cognate anti-toxin is found in [pfam:PF10899].
Pfam PF21698: Spo16 protein, C-terminal (domain)
This entry includes proteins related to yeast Spo16. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs. The Spo16 protein contains a C-terminal HHH motif, represented in this entry.
Pfam PF11776: Nickel/cobalt transporter regulator (family)
RcnB is a family of Proteobacteria proteins. RcnB is required for maintaining metal ion homeostasis, in conjunction with the efflux pump RcnA, family NicO, [pfam:PF03824].
Pfam PF05075: Protein of unknown function (DUF684) (family)
This family contains several uncharacterised proteins from Caenorhabditis elegans. The GO annotation suggests that the protein is involved in nematode larval development and has a positive regulation on growth rate.
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 PF17409: MoaF C-terminal domain (domain)
MoaF protein is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella. It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha. It is conserved in Proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis. This entry corresponds to the C-terminal domain.
Pfam PF13515: Fusaric acid resistance protein-like (family)
This entry represents a domain found in a group of probable integral membrane bound transporters mainly found in bacteria, including putative arylamide transporter from Mycobacterium tuberculosis (P9WL89) . It is predicted to adopt an all-Î± configuration,
Pfam PF00708: Acylphosphatase (domain)
Acylphosphatase (3.6.1.7) is an enzyme of approximately 98 amino acid residues that specifically catalyses the hydrolysis of the carboxyl-phosphate bond of acylphosphates , its substrates including 1,3-diphosphoglycerate and carbamyl phosphate . The enzyme has a mainly Î²-sheet structure with 2 short Î±-helical segments. It is distributed in a tissue-specific manner in a wide variety of species, although its physiological role is as yet unknown : it may, however, play a part in the regulation of the glycolytic pathway and pyrimidine biosynthesis . There are two known isozymes. One seems to be specific to muscular tissues, the other, called 'organ-common type', is found in many different tissues. A number of bacterial and archebacterial hypothetical proteins are highly similar to that enzyme and that probably possess the same activity.
An acylphosphatase-like domain is also found in some prokaryotic hydrogenase maturation HypF carbamoyltransferases .
Wikipedia: In enzymology, an acylphosphatase (EC 3.6.1.7) is an enzyme that catalyzes the hydrolysis of the carboxyl-phosphate bond of acylphosphates, with acylphosphate and H2O as the two substrates of this enzyme, and carboxylate and phosphate as its two products:
Pfam PF19746: Family of unknown function (DUF6233) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001973) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a  member from the fervenulin biosynthetic gene cluster from  Streptomyces hiroshimensis. This family appears to be predominantly found in Actinoabacteria.
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 PF15342: FAM212 family (family)
This domain family is found in eukaryotes, and is approximately 60 amino acids in length.
Pfam PF01913: Formylmethanofuran-tetrahydromethanopterin formyltransferase (domain)
This enzyme [ec:2.3.1.101] is involved in archaebacteria in the formation of methane from carbon dioxide. N-terminal distal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with C-terminal proximal lobe.
Wikipedia: In enzymology, a formylmethanofuran-tetrahydromethanopterin N-formyltransferase is an enzyme that catalyzes the chemical reactionformylmethanofuran + 5,6,7,8-tetrahydromethanopterin  methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin
Pfam PF00728: Glycosyl hydrolase family 20, catalytic domain (domain)
This domain has a TIM barrel fold.
Wikipedia: In molecular biology, glycoside hydrolase family 20 is a family of glycoside hydrolases.
Pfam PF19728: Family of unknown function (DUF6220) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001612) is described by MIBiG as an example of the following biosynthetic class, alkaloid. It includes a member from  the ambiguine H isonitrile biosynthetic gene cluster from  Fischerella ambigua UTEX 1903. This family appears to be  predominantly found in bacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02401: LytB protein (family)
The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway.
Pfam PF16525: Haemophore, haem-binding (domain)
MHB is a coiled-coil molecule that binds free haem in mycobacterial cytoplasm to deliver it to membrane proteins for shuttling through the membrane.
Pfam PF15751: FAAP20 FANCA interaction domain (family)
This domain is found at the N-terminus of Fanconi anemia-associated protein of 20 kDa (FAAP20), where it is responsible for interaction with Fanconi anemia group A protein (FANCA).
Pfam PF12676: Protein of unknown function (DUF3796) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 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 PF00841: Sperm histone P2 (family)
This protein also known as protamine P2 can substitute for histones in the chromatin of sperm (Swiss). The alignment contains both the sequence of the mature P2 protein and its propeptide.
Wikipedia: Protamines are small, arginine-rich, nuclear proteins that replace histones late in the haploid phase of spermatogenesis and are believed essential for sperm head condensation and DNA stabilization. They may allow for denser packaging of DNA in the spermatozoon than histones, but they must be decompressed before the genetic data can be used for protein synthesis. However, part of the sperm's genome is packaged by histones thought to bind genes that are essential for early embryonic development.
Pfam PF15743: Spermatogenesis-associated C-terminus (family)
This domain family is found in eukaryotes, and is approximately 150 amino acids in length. There is a single completely conserved residue E that may be functionally important.
Pfam PF13963: Transposase-associated domain (domain)
This entry represents a domain found in some putative transposases from plants.
Pfam PF11758: Aureocin-like type II bacteriocin (family)
This is a small family of type II bacteriocins usually encoded on a plasmid. Characteristically the members are small, cationic, rich in Lys and Try, and bring about a generalised membrane permeabilisation leading to leakage of ions. The family includes aureocin A, lacticins Q and Z, and BhtB as well as an archaeal member.
Pfam PF02257: RFX DNA-binding domain (domain)
RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD).
Pfam PF00758: Erythropoietin/thrombopoietin (domain)
Erythropoietin, a plasma glycoprotein, is the primary physiological mediator of erythropoiesis . It is involved in the regulation of the level of peripheral erythrocytes by stimulating the differentiation of erythroid progenitor cells, found in the spleen and bone marrow, into mature erythrocytes . It is primarily produced in adult kidneys and foetal liver, acting by attachment to specific binding sites on erythroid progenitor cells, stimulating their differentiation . Severe kidney dysfunction causes reduction in the plasma levels of erythropoietin, resulting in chronic anaemia - injection of purified erythropoietin into the blood stream can help to relieve this type of anaemia. Levels of erythropoietin in plasma fluctuate with varying oxygen tension of the blood, but androgens and prostaglandins also modulate the levels to some extent . Erythropoietin glycoprotein sequences are well conserved, a consequence of which is that the hormones are cross-reactive among mammals, i.e. that from one species, say human, can stimulate erythropoiesis in other species, say mouse or rat .

Thrombopoietin (TPO), a glycoprotein, is the mammalian hormone which functions as a megakaryocytic lineage specific growth and differentiation factor affecting the proliferation and maturation from their committed progenitor cells acting at a late stage of megakaryocyte development. It acts as a circulating regulator of platelet numbers.
Pfam PF06079: Apyrase (repeat)
This family consists of several eukaryotic apyrase proteins ([ec:3.6.1.5]). The salivary apyrases of blood-feeding arthropods are nucleotide hydrolysing enzymes implicated in the inhibition of host platelet aggregation through the hydrolysis of extracellular adenosine diphosphate..
Wikipedia: Apyrase is a calcium-activated plasma membrane-bound enzyme that catalyses the hydrolysis of ATP to yield AMP and inorganic phosphate. Two isoenzymes are found in commercial preparations from S. tuberosum. One with a higher ratio of substrate selectivity for ATP:ADP and another with no selectivity.
Pfam PF20238: Copper acquisition factor BIM1-like (domain)
This domain is found in fungal proteins, including copper acquisition factor BIM1 from Cryptococcus neoformans, a cell-surface bound protein that functions in the copper-accumulation pathway shared by the CUF1-dependent copper transporter CTR1. BIM1 facilitates copper acquisition in the brain of mammalian hosts and acts as a copper-dependent virulence trait in fungal meningitis. This domain has a lytic polysaccharide monooxygenase-like (LPMO, [pfam:PF03067]) fold,  which are evolutionarily related but have diverged to a different biological function.
Pfam PF12297: Ellis van Creveld protein 2 like protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism.
Pfam PF24164: Tape measure protein N-terminal (family)
This entry represents the N-terminal conserved region of the Tape measure protein PB2 and related proteins found mainly in T5-like phages. PB2 functions as a tape measure protein that serves as a base for tail tube protein polymerization and acts as a template for tail length determination. This protein fills the tail tube with its long coiled-coil domain and is expelled during the conformation changes that follow T5 binding to host FhuA receptor. The tape measure protein N-terminal region is organized within the tail tube in a three-stranded parallel alpha-helical coiled coil which makes direct contact with the genomic DNA.
Pfam PF13105: Protein of unknown function (DUF3959) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length.
Pfam PF01285: TEA/ATTS domain (domain)
The TEA domain is a DNA-binding region of about 66 to 68 amino acids that has been named after the two proteins that originally defined the domain: TEF-1 and AbaA. The TEA domain is located toward the N terminus of eukaryotic transcription factors of the TEA/ATTS family. It shows a three-helix bundle with a homeodomain fold . Two Î±-helices are nearly anti-parallel and pack on either side of the third one, which is the DNA-recognition helix of the TEA domain. Phosphorylation of one or both of the two conserved serines found on the DNA-binding surface could interfere with DNA-binding activity, by introducing electrostatic repulsion and/or steric hindrance, and help regulate the transcription factor activity of the proteins .
Pfam PF03712: Copper type II ascorbate-dependent monooxygenase, C-terminal domain (domain)
The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.
Wikipedia: In molecular biology, the copper type II ascorbate-dependent monooxygenases are a class of enzymes that require copper as a cofactor and which use ascorbate as an electron donor. This family contains two related enzymes, dopamine beta-monooxygenase EC 1.14.17.1 and peptidylglycine alpha-amidating monooxygenase EC 1.14.17.3. There are a few regions of sequence similarities between these two enzymes, two of these regions contain clusters of conserved histidine residues which are most probably involved in binding copper.
Pfam PF19554: Family of unknown function (DUF6077) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 347 and 622 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 PF10517: Electron transfer DM13 (domain)
The DM13 domain is a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins.  It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme.
Pfam PF09456: RcsC Alpha-Beta-Loop (ABL) (domain)
This domain is found in the C-terminus of the phospho-relay kinase RcsC between [pfam:PF00512] and [pfam:PF00072], and forms a discrete alpha/beta/loop structure.
Pfam PF00807: Apidaecin (family)
These antibacterial peptides are found in bees. These heat-stable, non-helical peptides are active against a wide range of plant-associated bacteria and some human pathogens. The Pfam alignment includes the propeptide and apidaecin sequence.
Pfam PF24278: HVO_0513, N-terminal (domain)
This domain is found at the N-terminal of the predicted transcription regulator HVO_0513 from Haloferax volcanii and similar archaeal proteins. This domain is predicted to adopt an alpha-beta structure. It is often found associated with [pfam:PF04967].
Pfam PF09869: DUF2096 C-terminal KH-like domain (domain)
This domain, found in various hypothetical archaeal proteins, has no known function. The domain shows structural similarity to KH domains suggesting it may have an RNA-binding function.