SII-SWORD/CoKE huggingface dataset:
Pfam PF00453: Ribosomal protein L20 (family)
This entry represents the large ribosomal subunit protein family bL20 that contains members from eubacteria, as well as their mitochondrial and plastid homologs. bL20 is an assembly protein, required for the first in vitro reconstitution step of the 50S ribosomal subunit, but does not seem to be essential for ribosome activity. bL20 has been shown to partially unfold in the absence of RNA, in regions corresponding to the RNA-binding sites. bL20 represses the translation of its own mRNA via specific binding to two distinct mRNA sites, in a manner similar to the bL20 interaction with 23S ribosomal RNA .
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 PF08035: Opioids neuropeptide (family)
This family corresponds to the conserved YGG motif that is found in a wide variety of opioid neuropeptides such as enkephalin.
Wikipedia: Pro-opiomelanocortin (POMC) is a precursor polypeptide with 241 amino acid residues. POMC is synthesized in corticotrophs of the anterior pituitary from the 267-amino-acid-long polypeptide precursor pre-pro-opiomelanocortin (pre-POMC), by the removal of a 26-amino-acid-long signal peptide sequence during translation. POMC is part of the central melanocortin system.
Pfam PF15970: HicB_like antitoxin of bacterial toxin-antitoxin system (domain)
This is a family of HicB-like antitoxins.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF04890: Family of unknown function (DUF648) (family)
Family of hypothetical Chlamydia proteins.  This family may well comprise of two domains, as some members only match the N-terminus.
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 PF02331: Apoptosis preventing protein (domain)
This viral protein functions to block the host apoptotic response  caused by infection by the virus. The apoptosis preventing protein (or early 35kD protein, P35) acts by blocking caspase protease  activity.
Pfam PF05310: Tenuivirus movement protein (family)
This family of ssRNA negative-strand crop plant tenuivirus proteins appears to combine PV2, NS2, NS3, and PV3 proteins. Plant viruses encode specific proteins known as movement proteins (MPs) to control their spread through plasmodesmata (PD) in walls between cells as well as from leaf to leaf via vascular-dependent transport.  During this movement process, the virally encoded MPs interact with viral genomes for transport from the viral replication sites to the PDs in the walls of infected cells along the cytoskeleton and/or endoplasmic reticulum (ER) network. The virus is then thought to move through the PDs in the form of MP-associated ribonucleoprotein complexes or as virions. The NS3 protein appears to function as an RNA silencing suppressor.
Pfam PF19209: Coronavirus spike glycoprotein S1, C-terminal (domain)
This entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epidemic diarrhea virus spike protein.
Pfam PF13522: Glutamine amidotransferase domain (domain)
This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes, such as asparagine synthetase and glutamine--fructose-6-phosphate transaminase.
Pfam PF22314: NPC1, middle luminal domain (domain)
NPC intracellular cholesterol transporter 1 (NPC1) is a endosomal/lysosomal membrane protein that facilitates the trafficking of cholesterol and other cargo from lysosomes and is involved in cholesterol homeostasis. Mutations in the NPC1 gene cause the rare neurodegenerative disease Niemann-Pick Type C (NPC). This entry represents the middle luminal domain (MLD) of NPC1, which contains the Ebola glycoprotein interacting site.
Pfam PF22316: A/B hydrolase-like, N-terminal domain (repeat)
This is the N-terminal domain found in a group of uncharacterised bacterial proteins, which have a Phospholipase/carboxylesterase/thioesterase domain ([pfam:PF02230]) at the C-terminal. This domain consists of ARM repeats.
Pfam PF05150: Legionella pneumophila major outer membrane protein precursor (family)
This family consists of major outer membrane protein precursors from Legionella pneumophila.
Pfam PF24766: Domain of unknown function (DUF7699) (domain)
This domain of unknown function is found in Zinc finger CCCH domain-containing protein 62 from Oryza sativa (C3H62) and similar proteins from plants. Members of this family also show a SAP domain ([pfam:PF02037]). This domain is predicted to adopt a mainly beta configuration.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10572: UPF0556 domain (domain)
This putative domain has no known function. It is found in a variety of eukaryotic species often as a single domain protein but also found at the C-terminus of a few other protein contains other domains.
Pfam PF11087: PRD1 phage membrane DNA delivery (family)
This small family of phage proteins are bound in the viral membrane and assist, along with P11 and P18 in the delivery of DNA.
Pfam PF19341: Beta-1,3-galactosyltransferase 2 N-terminus (family)
This family represents the N-terminal region of the beta-1,3- galactosyltransferase 2 which contains a short cytosolic region, a transmembrane region which indicates that this protein has a type II transmembrane topology, typical for all mammalian glycosyltransferases and a stem region with two putative N-glycosylation sites. This enzyme catalyses the synthesis of type 1 carbohydrate chains, which contain the Gal(beta 1-3) GlcNAc linkage.
Pfam PF07373: CAMP factor (Cfa) (family)
This family consists of several bacterial CAMP factor (Cfa) proteins which seem to be specific to Streptococcus species. The CAMP reaction is a synergistic lysis of erythrocytes by the interaction of an extracellular protein (CAMP factor) produced by some streptococcal species with the Staphylococcus aureus sphingomyelinase C (beta-toxin).
Pfam PF04997: RNA polymerase Rpb1, domain 1 (domain)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases).  This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pfam PF20262: Protein UNC80 C-terminal region (repeat)
This family represents the protein UNC80 found in eukaryotes, a component of the NALCN sodium channel complex. NALC is a cation voltage-independent channel activated by substance P, neurotensin, acetylcholine and noradrenaline that controls neuronal excitability. UNC80 forms a complex with UNC79 and both are key regulators of the channel and required for the proper expression and axonal localisation of NALCN. UNC80 is required for NALCN control by GPCRs and essential for its sensitivity to extracellular calcium. This protein acts as a scaffold for Src family of tyrosine kinases (SFK) and UNC-79 to mediate interaction with NALCN.
Pfam PF08901: Protein of unknown function (DUF1847) (family)
This family of proteins are functionally uncharacterised. THey contain 4 N-terminal cysteines that may form a zinc binding domain.
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 PF14881: Tubulin domain (domain)
This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Misato from Drosophila and Dml1p from fungi are descendants of an ancestral tubulin-like protein, and exhibit regions with similarity to members of a GTPase family that includes eukaryotic tubulin and prokaryotic FtsZ. Dml1p and Misato have been co-opted into a role in mtDNA inheritance in yeast, and into a cell division-related mechanism in flies, respectively. Dml1p might additionally function in the partitioning of the mitochondrial organelle itself, or in the segregation of chromosomes, thereby explaining its essential requirement. This domain subject to extensive post-translational modifications.
Pfam PF07543: Protein trafficking PGA2 (family)
A Saccharomyces cerevisiae member of this family (PGA2) is an ER protein which has been implicated in protein trafficking.
Pfam PF03576: Peptidase family S58 (family)
This group of serine peptidases belong to MEROPS peptidase family S58 (DmpA aminopeptidase family, clan PE). The protein fold of the peptidase unit for members of this family resembles that of archaean proteasome subunit B, the type example of clan PB. The type example is aminopeptidase DmpA from Ochrobactrum anthropi. This family also contains proteins that have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the family.

L-aminopeptidase D-Ala-esterase/amidase (DmpA) from O. anthropi releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide. DmpA shows structural homology to N-terminal nucleophile (Ntn) hydrolase family members, and may work by a similar catalytic mechanism, however their secondary structure elements differ significantly .
Pfam PF23192: NOMO C-terminal transthyretin-like domain (domain)
This domain is found C-terminal in the family of human Nodal modulators NOMO1, NOMO2, NOMO3 and in other related proteins. The Nodal modulators are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the membrane lipid bilayer. They play important role in the protein topogenesis and cells lacking these components show reduced multipass protein stability. The domain represented by this entry has a weak sequence similarity to Transthyretin-like domains and it is predicted to adopt similar structure that consists of seven-stranded beta-sandwich.
Pfam PF24818: TRF2/HOY1 PH-like domain (domain)
This domain is found in Pyriculol/pyriculariol biosynthesis cluster transcription factor 1 (TRF2), Homeobox protein HOY1 (HOY1) and uncharacterised proteins mainly from plants. TRF2 is a transcription regulator which negatively regulates the expression of a gene cluster responsible for the biosynthesis of pyriculol and pyriculariol. This domain has a detectable similarity to characterised PH domains and is predicted to adopt similar beta-barrel structure.
Pfam PF11303: Protein of unknown function (DUF3105) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is 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 PF24418: Family of unknown function (DUF7550) (family)
This entry represents a group of small uncharacterised archaeal proteins. They are predicted to fold into a single alpha-helix.
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 PF15110: TMEM141 protein family (family)
The function of this family of transmembrane proteins, TMEM141, has not, as yet, been determined. Members of this family remain uncharacterised. TMEM141 protein family is found in eukaryotes. Proteins in this family are typically between 103 and 124 amino acids in length. There are two completely conserved residues (C and W) that may be functionally important.
Pfam PF15699: NPR1 interacting (family)
This family of proteins interacts via a motif at the C-terminus with the regulatory protein NPR1.
Pfam PF24946: Dep-1 fourth Fn3-like domain (domain)
This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the beta-integrin subunit pat-3. It is involved in the regulation of the  cell fate during the development of the vulva and the excretory system. It is also involved indirectly in the negative regulation of let-23 signaling and vulval induction. Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem. This entry represents the fourth of them.
Pfam PF20523: Domain of unknown function (DUF6738) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in plants, and is approximately 70 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 PF20661: SutA RNAP-binding domain (domain)
This domain (previously known as DUF6813) is found in the transcriptional regulator SutA from Pseudomonas aeruginosa and similar proteins mainly from Gammaproteobacteria. In Pseudomonas aeruginosa, SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcriptional activity of an RNA polymerase (RNAP) holoenzyme. SutA interacts directly with RNAP holoenzyme and the RNAP-beta protrusion is its primary anchor site. This domain comprises an alpha-helix and a beta-strand and is responsible for interaction with RNAP-beta protrusion. It contains a conserved FLxxGG sequence motif that appears to be located near the C-terminal helix cap. The SutA-RBD alpha-helix binds to a hydrophobic groove on RNAP-beta protrusion.
Pfam PF16897: C-terminal region of MMR_HSR1 domain (family)
MMR_HSR1_Xtn is the C-terminal region of some members of the MMR_HSR1 family.
Pfam PF16786: Recombination enhancement, RecA-dependent nuclease (domain)
REF is a family of P1-like phage RecA-dependent nucleases. It does not appear to act as a positive RecA regulator. It is a new kind of enzyme, a RecA-dependent nuclease.
Pfam PF17545: Family of unknown function (DUF5461) (family)
This is a family of unknown function found in viruses.
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 PF23847: Family of unknown function (DUF7211) (conserved_site)
This entry represents a short highly motif that is found in some phage proteins, usually at the N-terminus. The function of this motif 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 PF06797: Protein of unknown function (DUF1229) (family)
This family consists of several hypothetical proteins of around 415 residues in length which seem to be specific to the bacterium Leptospira interrogans.
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 PF18866: CxC7 like cysteine cluster associated with KDZ transposases (domain)
A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain.
Pfam PF17026: Putative ribonucleoprotein zinc-finger pf C4 type (family)
This is a family of largely microsporidia-specific proteins. One member is annotated as being a ribonucleoprotein. The family carries two pairs of CxxC residues suggesting that there is DNA-binding.
Pfam PF22900: Ubiquitin carboxyl-terminal hydrolases, Ubiquitin-like 1 (domain)
This entry represents a Ubiquitin-like domain found in a family of ubiquitin carboxyl-terminal hydrolases (UCH). UCHs are thiol proteases that recognise and hydrolyse the peptide bond at the C-terminal glycine of ubiquitin.
Pfam PF18805: Leucine-rich repeat (repeat)
This Pfam entry includes some LRRs that fail to be detected with the [pfam:PF00560] model. This entry represents two repeat units.
Pfam PF21690: Uncharacterized ATP-binding protein MJ1010-like, C-terminal domain (domain)
This domain is found at the C-terminal end of a group of uncharacterised proteins that belong to the archaeal AAA+ ATPase superfamily, including MJ1010 from Methanocaldococcus jannaschii. This domain is usually found associated with [pfam:PF01637].
Pfam PF07560: Domain of Unknown Function (DUF1539) (family)
This domain is found in a small number of Chlamydia proteins of unknown function. It occurs together with IPR013044.
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 PF14606: GDSL-like Lipase/Acylhydrolase family (domain)
This entry represents the SGNH hydrolase-type esterase domain, which has a similar fold to flavoproteins, namely a three-layer Î±/Î²/Î± structure, where the Î²-sheets are composed of five parallel strands. Enzymes containing this domain act as esterases and lipases, but have little sequence homology to true lipases . Proteins containing this type of esterase domain have been found in a variety of hydrolases; those with structural information include an esterase from Streptomyces scabies ; the esterase domain of viral haemagglutinin-esterase surface glycoproteins (influenza C virus, coronaviruses and toroviruses) ; mammalian acetyl hydrolases ; fungal rhamnogalacturonan acetylesterase ; and the multifunctional enzyme thioesterase I (TAP) from Escherichia coli . SGNH hydrolase-type esterase domains contain unique hydrogen bond network that stabilises their catalytic centres; they usually contain the catalytic triad Ser/Acid/His.
Pfam PF18303: SAVED-fused 2TM effector domain (domain)
Predicted pore-forming effector domain directly fused to predicted SAVED sensor domain. Binding of a ligand via the SAVED sensor is predicted to activate the Saf-2TM and initiate a cell suicide response. Component of a class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivative.