SII-SWORD/CoKE huggingface dataset:
Pfam PF11450: Protein of unknwon function (DUF3008) (family)
This is a bacterial family of uncharacterised proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15425: Domain of unknown function (DUF4627) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. There is a conserved WYK sequence motif.
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 PF22452: BF9343_1606-like, C-terminal (domain)
This domain is found at the C-terminal end of BF9343_1606 from Bacteroides fragilis. This domain, which shows an all-alpha structure, is associated with [pfam:PF12985].
Pfam PF18351: Fungal Argonaute N-terminal domain (domain)
The AGO (Argonaute) proteins have four domains: an N-terminal domain, the PAZ domain, the MID domain and the PIWI domain. This entry is for the N-terminal domain. The N-terminal domain of AGOs is the most variable domain. Compared with prokaryotic Argonautes, KpAGO (Kluyveromyces polysporus Argonaute) has numerous surface-exposed insertion segments, with a cluster of conserved insertions re-positioning the N domain, contributing to the formation of nucleic-acid-binding channel to enable full propagation of the 3' end of the guide RNA guide-target pairing. The guide strand is used by the RISC complex to specify interactions with target RNAs. If sequence complementarity between guide and target is extensive, AGO catalyses cleavage, resulting in slicing of the target RNA.
Pfam PF16112: Domain of unknown function (DUF4830) (family)
This family consists of several uncharacterized proteins around 150 residues in length and is mainly found in Clostridium, Eubacterium, and Ruminococcus species. The function of this family is unknown.
Pfam PF25026: Asd-4-like domain (domain)
This domain is found in GATA type zinc finger protein asd-4 from Neurospora crassa (Asd-4) and similar fungal proteins. Asd-4 is a transcriptional regulator that functions in sexual development. This domain is predicted to adopt an all alpha configuration.
Pfam PF00382: Transcription factor TFIIB repeat (domain)
In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II . TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB .

This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex .
Pfam PF19736: Family of unknown function (DUF6226) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850. This family appears to be predominantly found  in Actinobacteria.
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 PF24984: Elongation factor 3/GNC1 HEAT repeat (repeat)
This entry represents a block of three HEAT repeats found at the N-terminal of elongation factor 3 (EF3) from yeast, after the 5 HEAT repeats block. EF3 is a ribosome-dependent ATPase that functions in cytoplasmic translation elongation. It is required for the ATP-dependent release of deacylated tRNA from the ribosomal E-site during protein biosynthesis. This block is also found in stalled ribosome sensor GCN1, a ribosome collision sensor that plays a key role in the RNF14-RNF25 translation quality control pathway, a pathway that takes place when a ribosome has stalled during translation, and which promotes ubiquitination and degradation of translation factors on stalled ribosomes.
Pfam PF22776: K+ potassium transporter C-terminal domain (domain)
This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP), yeast (HAK), and plant (AtKT) sequences as members. This entry represents the C-terminal non-membrane domain.
Wikipedia: The potassium (K+) uptake permease (KUP) family (TC# 2.A.72) is a member of the APC superfamily of secondary carriers. Proteins of the KUP/HAK/KT family include the KUP (TrkD) protein of E. coli and homologues in both Gram-positive and Gram-negative bacteria. High affinity (20 μM) K+ uptake systems (Hak1, TC# 2.A.72.2.1) of the yeast Debaryomyces occidentalis as well as the fungus, Neurospora crassa, and several homologues in plants have been characterized. Arabidopsis thaliana and other plants possess multiple KUP family paralogues. While many plant proteins cluster tightly together, the Hak1 proteins from yeast as well as the two Gram-positive and Gram-negative bacterial proteins are distantly related on the phylogenetic tree for the KUP family. All currently classified members of the KUP family can be found in the Transporter Classification Database.
Pfam PF06141: Phage minor tail protein U (domain)
Tail fibre component U of bacteriophage.
Pfam PF06266: HrpF protein (family)
The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity.
Pfam PF11828: Protein of unknown function (DUF3348) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 244 to 323 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 PF12242: NAD(P)H binding domain of trans-2-enoyl-CoA reductase (family)
This family carries the region of the enzyme trans-2-enoyl-CoA reductase, [ec:1.3.1.44], which binds NAD(P)H. The activity of the enzyme was characterised in Euglena where an unusual fatty acid synthesis path-way in the mitochondria performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. The full enzyme catalyses the reduction of enoyl-CoA to acyl-CoA. The binding site is conserved as GA/CSpGYG, where p is any polar residue.
Pfam PF18518: TcA receptor binding domain (domain)
Tc toxin complexes are virulence factors of many bacteria such as the plague pathogen Yersinia pestis. Tc toxins are composed of TcA, TcB and TcC subunits. TcA forms a large bell-shaped pentameric structure and enters the membrane like a syringe, forming a translocation channel through which the cytotoxic domain is probably transported into the cytoplasm.  TcA has four receptor-binding domains. This domain is one of 4 receptor binding domains found in TcA. All four domains have an immunoglobulin (Ig)-like beta-sandwich fold of two sheets with antiparallel beta-strands. The domains are structurally reminiscent of the receptor-binding domains of the diphtheria and anthrax toxins.
Pfam PF14691: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster (domain)
Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds. This domain carries two Fe4-S4 clusters.
Pfam PF02733: Dak1 domain (family)
This is the kinase domain of the dihydroxyacetone kinase family [ec:2.7.1.29].
Pfam PF13734: Spi protease inhibitor (family)
This family includes the inhibitor Spi and the pro-peptides of streptopain (SpeB).  SpeB is produced as a 43 kDa pre-pro-protein, which is secreted via the recently described Sec secretory pathway Exportal. There is tight coupling between this inhibitor and its associated protease: the gene for the inhibitor Spi is located directly downstream from the gene for the streptococcal cysteine protease SpeB, and the sequence of the inhibitor is very similar to that of the SpeB propeptide. This is an example of an inhibitor molecule that is a structural homologue of the cognate propeptide, and is genetically linked to the protease gene.
Pfam PF16029: Domain of unknown function (DUF4787) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, 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 PF12037: ATPase family AAA domain-containing protein 3, N-terminal (domain)
This is the conserved N-terminal domain of ATPase family AAA domain-containing protein 3 (ATAD3) which is involved in dimerisation and interacts with the inner surface of the outer mitochondrial membrane. This domain is found associated with the AAA ATPase domain ([pfam:PF00004]). ATAD3 is essential for mitochondrial network organisation, mitochondrial metabolism and cell growth at organism and cellular level. It may also play an important role in mitochondrial protein synthesis.
Pfam PF21178: Intraflagellar transport protein 52, C-terminal domain (domain)
This domain is found in Intraflagellar transport protein 52 homolog from humans (Itf52) and similar eukaryotic proteins. Itf52 is part the IFT-B complex, which is involved in intraflagellar transport (IFT), the bidirectional movement of particles required for the assembly, maintenance and functioning of primary cilia. This entry represents the C-terminal domain of Itf52, responsible for the binding to the C-terminal domain of Ift46 and essential for the interaction between the subcomplexes. It shows an all-alpha structure.
Pfam PF04087: Domain of unknown function (DUF389) (family)
Family of hypothetical bacterial proteins with  an undetermined 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 PF03574: Peptidase family S48 (family)
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .
This group of serine peptidases, which includes HetR, are associated with heterocystous cyanobacteria and belong to MEROPS peptidase family S48 (clan S-). HetR is a DNA-binding serine-type protease required for heterocyst differentiation in heterocystous cyanobacteria under conditions of nitrogen deprivation. Mutation of HetR from of Anabaena sp. (strain PCC 7120) by site-specific mutagenesis of Ser-152 showed that this residue was one of the peptidase active site residues. It was suggested that peptidase activity might be needed for repression of HetR overproduction under conditions of nitrogen deprivation . Modification of Cys-48 prevented disulphide-bond formation and homodimerisation of HetR and DNA-binding. The homodimer of HetR binds the promoter regions of hetR, hepA, and patS, suggesting a direct control of the expression of these genes by HetR. The pentapeptide RGSGR, which is present at the C terminus of PatS, blocks heterocyst formation, inhibits the DNA binding of HetR and prevents hetR up-regulation .
Pfam PF09331: Domain of unknown function (DUF1985) (family)
Members of this family of functionally uncharacterised domains are found in a set of Arabidopsis thaliana hypothetical proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14307: Glycosyltransferase WbsX (family)
Members of this family are found in within O-antigen biosynthesis clusters in Gram negative bacteria, where they are predicted to function as glycosyltransferases.
Pfam PF11468: Aromatic prenyltransferase Orf2 (family)
In vivo Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis. In vitro, Orf2 catalyses carbon-carbon based and carbon-oxygen based prenylation of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin.
Wikipedia: The PT-barrel, is a novel protein fold that was discovered in the crystal structure of the prenyltransferase, Orf2 from Streptomyces sp. strain CL190.
Pfam PF14249: Tocopherol cyclase (family)
This family contains tocopherol cyclases. These enzymes are involved in the synthesis of tocopherols and tocotrienols (vitamin E).
Pfam PF14582: Metallophosphoesterase, calcineurin superfamily (domain)
Members of this family are part of the Calcineurin-like phosphoesterase superfamily.
Pfam PF23731: ECM29, C-terminal ARM-like repeats (repeat)
This is a region of armadillo-like repeats found at the C-terminal end of human Proteasome adapter and scaffold protein ECM29 and similar eukaryotic sequences. ECM29 binds to the 26S proteasome, motor proteins and other compartment specific proteins.
Pfam PF16072: Domain of unknown function (DUF4813) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 345 and 672 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 PF02649: Type I GTP cyclohydrolase folE2 (family)
This is a family of prokaryotic proteins with type I GTP cyclohydrolase activity. GTP cyclohydrolase I is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene; it is also the first enzyme of the biopterin (BH4) pathway in Homo sapiens. The invariate, highly conserved glutamate residue at position 216 in [swissprot:Q5F9K6] is likely to be the substrate ligand and the metal ligand is likely to be the cysteine at position 147. The enzyme is Zinc 2+ dependent.
Pfam PF23989: PilB3-like, C-terminal (domain)
This domain is found at the C-terminal of PilB3 from Haloferax volcanii and similar archaeal proteins. PilB3 is associated with the assembly of genes. This domain, normally found C-terminal to [pfam:PF00437], is predicted to show an alpha-beta structure.
Pfam PF05920: Homeobox KN domain (family)
This is a homeobox transcription factor KN domain conserved from fungi to human and plants. They were first identified as TALE homeobox genes in eukaryotes, (including KNOX and MEIS genes). They have been recently classified.
Pfam PF15668: Domain of unknown function (DUF4663) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 289 and 334 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important.
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 PF17217: UPA domain (domain)
The UPA domain is conserved in UNC5, PIDD, and Ankyrins. It has a beta sandwich structure.
Pfam PF14238: Domain of unknown function (DUF4340) (family)
This domain is found in bacteria, and is typically between 183 and 196 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 PF22500: GMC oxidoreductase, C-terminal (domain)
This domain is found in a group of GMC oxidoreductases mainly from actinomycetes, including Cholesterol oxidase from Streptomyces sp. (ChoA). ChoA is organised into two domains, an FAD-binding domain ([pfam:PF00732]) and a substrate binding domain (formed by this entry and [pfam:PF05199]). This domain consists of six beta -sheets and one alpha-helix.
Pfam PF07787: Transmembrane protein 43 (family)
This entry represents the transmembrane protein 43 family of proteins, which may function as tetraspanin-like membrane organisers.
Pfam PF24426: NDX Homeobox-like domain (domain)
This domain is found in Nodulin homeobox (NDX) from Arabidopsis thaliana and related proteins. NDX regulates COOLAIR, a set of antisense transcripts originating from the 3' end ofFLOWERING LOCUS C (FLC). This protein associates with single-stranded DNA that is part of an RNA-DNA hybrid, or R-loop, that covers the COOLAIR promoter. This domain has a detectable sequence similarity to known homeobox domains and it is predicted to adopt similar structure.
Pfam PF18366: Zic proteins zinc finger domain (domain)
This is the ZF1 (Zinc Finger 1) domain found in Zic family proteins found in Eukaryotes. In humans, there are five members of the Zic family that are involved in human congenital anomalies. One of them, ZIC3, causes X-linked heterotaxy (HTX1), which is a left-right axis disturbance that manifests as variable combinations of heart malformation, altered lung lobation, splenic abnormality and gastrointestinal malrotation. Zic faily proteins contain multiple zinc finger domains (ZFD), which are generally composed of five tandemly repeated C2H2 zinc finger (ZF) motifs. Sequence comparison analysis reveal that this N-terminal ZF (ZF1) domain of the Zic zinc finger domains is unique in that it possesses more amino acid residues (6-38 amino acids) between the two cysteine residues of the C2H2 motif compared to Gli and Glis ZF1s or any of the other ZFs (ZF2-5) in the Gli/Glis/Zic superfamily of proteins.  Mutations in cysteine 253 (C253S) or histidine 286 (H286R) in ZIC3 ZF1, which are found in heterotaxy patients, result in extranuclear localization of the mutant ZIC3 protein. Furthermore, mutations in the evolutionarily conserved amino acid residues (C253, W255, C268, H281 and H286) of ZF1 generally impair nuclear localization.
Pfam PF12073: Protein of unknown function (DUF3553) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
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.