SII-SWORD/CoKE huggingface dataset:
Pfam PF24218: Family of unknown function (DUF7437) (domain)
This domain is found at the C-terminal end of a group of archaeal sequences that contain [pfam:PF01978] at the N-terminal. It is predicted to adopt an all-alpha 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 PF08252: arg-2/CPA1 leader peptide (family)
In this family there are Leaders Peptides involved in the regulation the glutaminase subunit (small subunit) of arginine-specific carbamoyl phosphate synthetase.  In Neurospora crassa it is a small upstream ORF of 24 codon above the arg-2 locus. In yeast it is the leader peptide of the CPA1 gene. The 5' region of CPA1 mRNA contains a 25 codon upstream open reading frame. The leader peptide, the product of the upstream open reading frame, plays an essential, negative role in the specific repression of CPA1 by arginine.
Pfam PF17957: Bacterial Ig domain (domain)
This entry represents a bacterial ig-like domain that is found in glycosyl hydrolase enzymes.
Pfam PF00730: HhH-GPD superfamily base excision DNA repair protein (domain)
This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, [ec:4.2.99.18] and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as [swissprot:P53397]. The methyl-CPG binding protein MBD4 [swissprot:Q9Z2D7] also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II [ec:3.2.2.21] and other members of the AlkA family.
Pfam PF22140: VipD-like, C-terminal domain (domain)
This domain is found in VipD from Legionella pneumophila (effector vacuolar protein sorting inhibitor protein D), which localises to early endosomal membranes and alters their lipid and protein composition. This process protects the pathogen from endosomal fusion. VipD adopts a two-domain fold, with a N-terminal domain homologous to patatin ([pfam:PF01734]) and a C-terminal domain (this entry) that contains ten alpha-helices and two short beta-strands. VipD localises to early endosomes via this domain.
Pfam PF17816: PDZ domain (domain)
This entry represents a PDZ domain that is found in the CPAF protein from chlamydia trachomatis.
Wikipedia: The PDZ domain is a common structural domain of 80-90 amino-acids found in the signaling proteins of bacteria, yeast, plants, viruses and animals. Proteins containing PDZ domains play a key role in anchoring receptor proteins in the membrane to cytoskeletal components. Proteins with these domains help hold together and organize signaling complexes at cellular membranes. These domains play a key role in the formation and function of signal transduction complexes. PDZ domains also play a highly significant role in the anchoring of cell surface receptors to the actin cytoskeleton via mediators like NHERF and ezrin.
Pfam PF08074: CHDCT2 (NUC038) domain (domain)
The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases.
Pfam PF09532: FDF domain (domain)
The FDF domain, so called because of the conserved FDF at its  N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.
Pfam PF10759: Bacterial proteasome activator (family)
This is a family of bacterial proteasome cofactors. The family member from Mycobacterium tuberculosis, protein Rv3780, was shown to form rings and cap proteasome core particles. It enhanced peptide and protein degradation by proteasomes in an adenosine triphosphate (ATP)-independent manner, promoting degradation of the heat shock protein repressor HspR.
Pfam PF12641: Flavodoxin domain (domain)
This family represents a flavodoxin domain.
Pfam PF01282: Ribosomal protein S24e (family)
This family contains the eS24 ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.
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 PF16824: C-terminal carbohydrate-binding module (family)
CBM_26 is a family of bacterial carbohydrate-binding modules frequently found at the C-terminus of enzymes. The combination is not unusual as the CBMs function to bring the relevant polysaccharide into close proximity to the active site.
Pfam PF20670: Domain of unknown function (DUF6816) (domain)
This presumed domain is functionally uncharacterised and it is found in bacterial (predominantly in cyanobacteria) and eukaryotic (mainly from plants) sequences. Structure prediction using AlphaFold resource, suggest that this domain may have a START-like (StAR-related lipid-transfer) fold consisting of an alpha/beta structure of a helix-grip fold, that forms cavities for hydrophobic substrates or ligands which may indicate a possible function for this 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 PF03608: PTS system enzyme II sorbitol-specific factor (family)
Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.


 * It is the only PTS family in which members possess a IID protein.
 * It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.
 * Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.


The Gut family consists only of glucitol-specific transporters, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli consists of IIA protein, a IIC protein and a IIBC protein.
Pfam PF21017: PHA01746-like protein (domain)
This entry represents a domain found in an uncharacterised protein from a sulfolobus phage. ECOD notes structural similarity to [pfam:PF08796] that includes the YkuJ protein from Bacilli.
Pfam PF22647: Deacetylase EF_0837-like composite domain (domain)
This entry includes proteins that can catalyse the deacetylation of acetyl-(R)-mandelate in vitro, but with very low efficiency, such as deacetylase Oant_2987, Atu3266 and EF_0837. This entry represents the composite domain.
Pfam PF04496: Herpesvirus UL35 family (family)
UL35 represents a true late gene which encodes a 12-kDa  capsid protein.
Pfam PF24200: Domain of unknown function (DUF7425) (domain)
This entry represents a domain of unknown function found in bacteriophage proteins. The domain is around 90-95 amino acids in length. It is found in uncharacterized proteins from phages that infect Enterobacteria such as Salmonella and Shigella species as well as Dickeya. The specific function of this domain remains unknown. Structure prediction suggests that these proteins may form a homotetramer (iPTM=0.88). The domain contains a three twisted stranded beta sheet.
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 PF19096: Family of unknown function (DUF5784) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF22108: Transcription factor IIB C-terminal module 2 (domain)
In the pathogenic trypanosome, Trypanosoma brucei, transcription factor IIB (tTFIIB) is essential for spliced leader (SL) RNA gene transcription and cell viability, but has a highly divergent primary sequence in comparison to TFIIB in other eukaryotes. Structure analysis of the C-terminal region of trypanosome TFIIB, reveals 2, closely packed helical modules followed by a C-terminal extension of 32 aa. The trypanosome-specific region comprises the second helical module and the C-terminal extension. Both helical modules contain the canonical 5-helix cyclin fold characteristic of TFIIB proteins. This domain is mostly found in Trypanosomatidae. The first helical module is represented in [pfam:PF18542].
Pfam PF21106: YtxK N-terminal helical domain (domain)
This entry represents the N-terminal helical domain found in the B. subtilis YtxK protein ([swissprot:P37876]), which is a restriction-modification system methylation subunit.
Pfam PF07793: Protein of unknown function (DUF1631) (family)
The members of this family are sequences derived from a group of hypothetical proteins expressed by certain bacterial species. The region concerned  is approximately 440 amino acid residues 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 PF13224: Domain of unknown function (DUF4032) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 170 amino acids in length. The family is found in association with [pfam:PF06293].
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 PF17353: Family of unknown function (DUF5381) (family)
This is a family of unknown function found in Bacillales.
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 PF14780: Nucleolus and neural progenitor protein, N-terminal (domain)
This domain is found at the N-terminal of nucleolus and neural progenitor protein (NEPRO) which may play a role in cortex development as part of the Notch signalling pathway. Downstream of Notch may repress the expression of proneural genes and inhibit neuronal differentiation thereby maintaining neural progenitors. NEPRO may also play a role in preimplentation embryo development. NEPRO interacts with multiple protein subunits of RMRP and is implicated in Anauxetic dysplasia 3. NEPRO is likely the human orthologue of RMP1 subunit from yeast and they share a four-helix bundle domain structure.
Pfam PF23120: Peroxisomal ATPase 6 N-terminal (domain)
This entry represents a domain found at the N-terminal of a set of PEX6 protein from fungi, including PEX6 from Colletotrichum orbiculare and Neurospora crassa. PEX 6 is involved in peroxisome biogenesis required for the import of folded proteins into the peroxisomal matrix. According to structure predictions, this domain may adopt a double-psi barrel fold.
Pfam PF15598: Immunity protein 61 (family)
A predicted immunity protein with an alpha+beta fold and a conserved arginine. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox40 family.
Pfam PF12899: Alkaline and neutral invertase (repeat)
This is a family of bacterial and plant alkaline and neutral invertases, [ec:3.2.1.26], previously known as Invertase_neut [pfam:PF04853].
Wikipedia: In molecular biology, glycoside hydrolase family 100 is a family of glycoside hydrolases.
Pfam PF02641: Uncharacterized ACR, COG1993 (domain)
UPF0166 protein family includes TM_0021 from Thermotoga maritima (Q9WXM9) and other proteins predominantly found in bacteria but also in some archaea. TM_0021 is a putative PII-like signaling protein thought to be involved in the regulation of the nitrogen status in this organism. The protein adopts a trimeric assembly. Each monomer folds into an Î±+Î² sandwich with a four-stranded antiparallel Î²-sheet packed against two antiparallel Î±-helices resembling a ferredoxin-like fold, with a short Î²-hairpin inserted before the first Î±-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 PF02689: Helicase (family)
This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle.
Pfam PF22403: Domain of unknown function (DUF6981) (domain)
This entry represents an alpha-lytic protease prodomain-like domain present in a protein of unknown function from Desulfovibrio piger. It structure has been characterized (PDB:4HLB).
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 PF23612: ZN142 C2H2 zinc finger (domain)
This entry represents C2H2 zinc finger domains found in multiple copies in Zinc finger protein 142. This protein is probably involve in transcriptional regulation.
Pfam PF17247: Family of unknown function (DUF5316) (family)
This is a family of unknown function mainly found in Firmicutes. Might contain multiple trans-membrane sequences.
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 PF02107: Flagellar L-ring protein (family)
The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body . In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament . The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive Î²-sheet structure, in keeping with other outer membrane proteins .
Pfam PF07881: L-fucose isomerase, first N-terminal domain (domain)
The members of this family are similar to L-fucose isomerase expressed by E. coli ([swissprot:P11552], [ec:5.3.1.3]). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis,  and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta-sheets with surrounding  alpha helices. Domain 1 demonstrates the beta-alpha-beta-alpha- beta Rossman fold. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting  residues, and domain 1 from the adjacent subunit contributing some other residues.
Wikipedia: In enzymology, a L-fucose isomerase is an enzyme that catalyzes the chemical reactionL-fucose  L-fuculose
Pfam PF02388: FemAB family (family)
The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan. These proteins are also considered as a factor influencing the level of methicillin resistance.
Pfam PF11071: Nucleoside 2-deoxyribosyltransferase YtoQ (family)
This entry represents a family of uncharacterised proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Wikipedia: In enzymology, a nucleoside deoxyribosyltransferase is an enzyme that catalyzes the chemical reaction2-deoxy-D-ribosyl-base1 + base2  2-deoxy-D-ribosyl-base2 + base1
Pfam PF20846: PNMA N-terminal RRM-like domain (domain)
This domain resembles an RNA-binding RRM domain in AlphaFold structure predictions. This domain is found at the N-terminus of various paraneoplastic antigen like proteins.
Pfam PF07971: Glycosyl hydrolase family 92 catalytic domain (repeat)
Members of this family are alpha-1,2-mannosidases, enzymes which remove alpha-1,2-linked mannose residues from Man(9)(GlcNAc)(2) by hydrolysis. They are critical for the maturation of N-linked oligosaccharides and ER-associated degradation.
Wikipedia: In molecular biology, glycoside hydrolase family 92 is a family of glycoside hydrolases.
Pfam PF09166: Biliverdin reductase, catalytic (domain)
Members of this family adopt a structure consisting of four alpha helices and six beta sheets, in an alpha-beta-alpha-alpha-alpha-beta-beta-beta-beta-beta arrangement. They contain a catalytic active site, capable of reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.
Wikipedia: Biliverdin reductase (BVR) is an enzyme found in all tissues under normal conditions, but especially in reticulo-macrophages of the liver and spleen. BVR facilitates the conversion of biliverdin to bilirubin via the reduction of a double bond between the second and third pyrrole ring into a single bond.
Pfam PF19001: Family of unknown function (DUF5730) (family)
A highly conserved domain of unknown function found in Platyhelminthes, in which the first 21 residues correspond to a transmembrane 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 PF06670: Microneme protein Etmic-2 (family)
This family consists of several Microneme protein Etmic-2 sequences from Eimeria tenella. Etmic-2 is a 50 kDa acidic protein, which is found within the microneme organelles of Eimeria tenella sporozoites and merozoites.