SII-SWORD/CoKE huggingface dataset:
Pfam PF18451: Contact-dependent growth inhibition CdiA C-terminal domain (domain)
Contact-dependent growth inhibition (CDI) systems encode polymorphic toxin/immunity proteins that mediate competition between neighboring bacterial cells. CDI is mediated by the CdiB/CdiA family of two-partner secretion proteins. This domain represents the C-terminal of CdiA proteins (CdiA-CT), which contains the CDI toxin activity.  The C-terminal nuclease domain forms a stable complex with its cognate immunity protein. It is also sufficient to inhibit growth when expressed in E. coli cells, consolidating the idea that they constitute the functional CDI toxin. The CdiA-CT C-terminal domains are structurally similar to type IIS restriction endonucleases suggesting that the toxins have metal-dependent DNase activity.
Pfam PF23276: Fungal tetratrico peptide repeats (repeat)
This entry represents the predicted tetratrico peptide repeats (TPR) found in a group of fungal proteins, including [swissprot:U7PQ97] from the rose-picker's disease fungus.
Pfam PF02265: S1/P1 Nuclease (domain)
This family contains both S1 and P1 nucleases ([ec:3.1.30.1]) which cleave RNA and single stranded DNA with no base specificity.
Wikipedia: Nuclease S1 is an endonuclease enzyme that splits single-stranded DNA (ssDNA) and RNA into oligo- or mononucleotides. This enzyme catalyses the following chemical reactionEndonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Pfam PF08023: Frog antimicrobial peptide (family)
This family consists of the major classes of antimicrobial peptides secreted from the skin of frogs that  protect the frogs against invading microbes. They are typically between 10-50 amino acids long and are derived from proteolytic cleavage of larger precursors. Major classes of peptides such  esculentin, gaegurin, brevinin, rugosin and ranatuerin are included in this family.
Pfam PF15146: Fanconi anemia-associated (family)
This family of proteins plays a role in the Fanconi anemia-associated DNA damage response.
Pfam PF21211: FkbH, N-terminal domain (domain)
This domain is found at the N-terminal end of a group of bacterial predicted enzymes, including BF1531 from Bacteroides fragilis. It shows an alpha-beta structure.
Pfam PF03816: LytR_cpsA_psr family (family)
The entry represents a domain found in a number of LCP (LytR-Cps2A-Psr) family proteins. LCP family is also known as TagU  family. LCP family proteins have been reported to be required for the synthesis of anionic cell wall polymers.
Wikipedia: The LCP family or TagU family of proteins is a conserved family of phosphotransferases that are involved in the attachment of teichoic acid (TA) molecules to gram-positive cell wall or cell membrane. It was initially thought as the LytR component of a LytABC operon encoding autolysins, but the mechanism of regulation was later realized to be the production of TA molecules. It was accordingly renamed TagU.
Pfam PF04651: Poxvirus A12 protein (family)
This family represents Protein A12 from Vaccinia virus, also known as 25 kDa core protein OPG138, and similar proteins from poxvirus. A12 is a component of the virion core that undergoes proteolytic processing during the immature virion (IV) to mature virion (MV) transition. It is essential for the formation of a structurally normal core .
Pfam PF23100: DUF2096 N-terminal four-helical bundle domain (domain)
This domain, found in various hypothetical archaeal proteins, has no known function. This N-terminal domain is composed of four alpha helices.
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 PF19668: Family of unknown function (DUF6171) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 90 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 PF04560: RNA polymerase Rpb2, domain 7 (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).  Rpb2 is the second largest subunit of the RNA polymerase.  This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pfam PF12340: Protein of unknown function (DUF3638) (family)
This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG.
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 PF18639: Yeast longin domain (domain)
This is a longin domain which is found in the N-terminal region of Lst4 proteins in yeast. Lst4 is the Fnip1/2 orthologue found in mammals. Lst4 forms a complex with Lst7 and are targeted to the vacuole when the cells are starved of carbon, and to a lesser extent nitrogen. Lst4 and Fnip1/2 belong to the DENN family of proteins which comprise an N-terminal longin domain, commonly found in a variety of trafficking proteins, and a C-terminal DENN domain. This domain is made up of a core five-strand beta-sheet, with one short alpha-helix.
Pfam PF20557: Putative DnaT-like ssDNA binding protein (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 110 amino acids in length. This domain is predicted to contain a complex four helical bundle structure. The structure shows similarity to the single stranded binding protein DnaT.
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 PF05349: GATA-type transcription activator, N-terminal (family)
GATA transcription factors mediate cell differentiation in a diverse range of tissues. Mutation are often associated with certain  congenital human disorders. The six classical vertebrate GATA proteins, GATA-1 to GATA-6, are highly homologous and have two tandem zinc fingers. The classical GATA transcription factors function transcription activators. In lower metazoans GATA proteins carry a single canonical  zinc finger. This family represents the N-terminal domain of the family of  GATA transcription activators.
Pfam PF20960: Bag6, BAG-similar domain (domain)
Bag6 (BCL2-associated athanogene cochaperone 6) is part of a cytosolic protein quality control complex involved in the post- translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane, in the mislocalised protein degradation pathway and in the endoplasmic reticulum- associated degradation. The BAG-similar domain, found at the C- terminal end of this protein plays a role in the interaction with the other members of the complex, Ubl4A and TRC35. This domain shows three helices in an extended conformation that differ from the three-helix bundle fold of the canonical BAG domain ([pfam:PF02179]).
Pfam PF20100: Family of unknown function (DUF6490) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 119 and 168 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 PF19055: ABC-2 type transporter (family)
ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily which uses the hydrolysis of ATP to energise diverse biological import and export systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein (mostly in eukaryotes and bacterial exporters) or on two different ones (mostly bacterial importers) . The function of the integral inner-membrane protein is to translocate the substrate across the membrane and seems to play an important role in substrate recognition .

ABC family G is a multidrug ATP-binding cassette transporter expressed in the plasma membranes of several tissues that is involved in endogenous substrates translocation, modifies drug pharmacokinetics and acts as a protector against xenobiotics .
This domain is found in several ATP binding cassette transporters family G (ABCG).
Wikipedia: The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
Pfam PF20256: Molybdopterin cofactor-binding domain (domain)
Aldehyde oxidase (AOX 1.2.3.1) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (XDH 1.17.1.4) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (1.17.3.2) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulfhydryl groups .
The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different  centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands .

This entry represents the second molybdopterin cofactor (Mo-Co) binding domain .
Pfam PF23402: LTI65/LTI78 NYQTKV repeat (disordered)
This entry represents a disordered region found in LTI78 and LTI65 from Arabidopsis and related plant proteins. LTI78 and LTI65 are involved in responses to abiotic stress. This region consists of repeats containing the conserved sequence NYQTKV. This region is found N-terminal of the CAP160 repeat ([pfam:PF07918]).
Pfam PF12224: Putative amidoligase enzyme (family)
This family of proteins are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes).
Pfam PF16321: Sigma 54 modulation/S30EA ribosomal protein C terminus (domain)
This domain often occurs at the C-terminus of proteins containing [pfam:PF02482].
Pfam PF20428: Sey1 three-helix bundle domain (domain)
This is the three-helix bundle (3HB) domain found at the C-terminal of Sey1 from yeast and RHD3 from Arabidopsis, GTP-binding proteins involved in homotypic membrane fusion of the endoplasmic reticulum. This is a stalk-like domain composed of four 3HBs that interacts with its own GTPase domain and that of a neighbouring molecule, to undergo major conformational changes during the GTP cycle to drive membrane fusion.
Pfam PF23514: YhiY (family)
This protein family includes Protein YhiY from Escherichia coli, a 37-residues micropeptide encoded by a small open reading frame (smORF). Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms.
Pfam PF13487: HD domain (domain)
HD domains are metal dependent phosphohydrolases. This entry covers the HD-GYP domain.
Pfam PF10649: Protein of unknown function (DUF2478) (family)
This is a family of hypothetical bacterial proteins found in the vicinity of Molybdenum ABC transporter ATP-binding gene-products MobA MobB and MobC. However the function could not be confirmed. This family appears to belong to the P-loop superfamily by alignment to [pfam:PF03266]. However, the characteristic P-loop sequence motif appears to have diverged beyond recognition in this family.
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 PF01862: Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) (family)
Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organisms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterised proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. Homologues of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria.
Pfam PF05726: Pirin C-terminal cupin domain (domain)
This region is found the C-terminal half of the Pirin protein.
Pfam PF09881: Predicted membrane protein (DUF2108) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF18446: Domain of unknown function (DUF5611) (domain)
This is a domain of unknown function. Studies of the TA0095 gene product indicate that this 96-residue hypothetical protein from Thermoplasma acidophilum is a member of the COG4004 orthologous group of unknown function found in Archaea bacteria. The structure displays an alpha/beta two-layer sandwich architecture formed by three alpha-helices and five beta-strands. Furthermore, structural homologs indicate that the TA0095 structure belongs to the TBP-like fold.
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 PF13101: Protein of unknown function (DUF3945) (family)
A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This is a C-terminal repeated region.
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 PF11018: Pupal cuticle protein C1 (family)
Insect cuticles are composite structures whose mechanical properties are optimised for biological function.  The major components are the chitin filament system and the cuticular proteins, and the cuticle's properties are determined largely by the interactions between these two sets of molecules. The proteins can be ordered by species.
Pfam PF08716: Coronavirus replicase NSP7 (domain)
NSP7 (non structural protein 7) has been implicated in viral RNA replication and is predominantly alpha helical in structure. It forms a hexadecameric supercomplex with NSP8 that adopts a hollow cylinder-like structure. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase. NSP7 and NSP8 heterodimers play a role in the stabilisation of NSP12 regions involved in RNA binding and are essential for a highly active NSP12 polymerase complex.
Pfam PF15972: Unpaired protein (family)
Unpaired protein activates the JAK pathway.
Pfam PF05573: NosL (family)
NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallo-centre assembly.
Pfam PF04546: Sigma-70, non-essential region (domain)
The domain is found in the primary vegetative sigma factor.  The function of this domain is unclear and can be removed without loss of function.
Pfam PF22030: Sarcoplasmic/endoplasmic reticulum calcium ATPase regulator DWORF (family)
This family includes human Sarcoplasmic/endoplasmic reticulum calcium ATPase regulator DWORF and similar sequences from vertebrates. DWORF is a micropeptide that enhances the activity of the SERCA1 ATPase in the sarcoplasmic reticulum by displacing its inhibitors, thereby acting as a key regulator of skeletal muscle activity. It also enhances sarcoplasmic reticulum Ca2+ uptake and myocyte contractility. DWORF shows an alpha-helical topology with a kink that separates two helical domains. This adaptive configuration seems to be directly linked to its activating effect on SERCA.
Pfam PF03297: S25 ribosomal protein (family)
This entry represents eS25 ribosomal protein, found in eukaryotes and archaea, that is a component of the 40S ribosomal subunit.
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 PF09888: Uncharacterized protein conserved in archaea (DUF2115) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.