SII-SWORD/CoKE huggingface dataset:
Pfam PF19642: Family of unknown function (DUF6145) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 110 and 124 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 PF23186: Domain of unknown function (DUF7059) (domain)
This domain is found N-terminal in a group of uncharacterised bacterial proteins. These proteins are probably distantly related to Aeronamide N-methyltransferases AerE. They share two similar domains that are predicted in the same arrangement. This domain is found N-terminal to the methyltransferase domain and has a weak sequence similarity to various HTH domains.
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 PF07970: Endoplasmic reticulum vesicle transporter (family)
This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localisation. All proteins identified biochemically as Erv41p-Erv46p interactors are localised to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi.
Pfam PF21213: Primosomal protein N'-like, winged helix (domain)
This domain is found in Primosomal protein N' from Escherichia coli  (PriA) and similar proteins predominantly found in Proteobacteria. PriA is a DNA helicase involved in the restart of stalled replication forks, which are lethal in bacteria if left unrepaired. This protein shows a modular arrangement in which its central helicase core is surrounded by several DNA-binding elements, including a circularly permuted winged helix (WH) domain (this entry), which is located towards the N-terminal of the protein and can bind DNA in isolation.
Pfam PF01915: Glycosyl hydrolase family 3 C-terminal domain (domain)
This domain is involved in catalysis and may be involved in binding beta-glucan. This domain is found associated with [pfam:PF00933].
Wikipedia: In molecular biology, glycoside hydrolase family 3 is a family of glycoside hydrolases. Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of over 100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF00157: Pou domain - N-terminal to homeobox domain (domain)
This entry represents the POU-specific subunit of the POU domain.
The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (this entry), while the C-terminal subunit is a homeobox domain (IPR001356). Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. 3D structures of complexes including both POU subdomains bound to DNA are available. The domain may also be involved in protein-protein interactions . The subdomains are connected by a flexible linker . Despite of the lack of sequence homology, the tridimensional structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family .
POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system  and the development of an organism . Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) , and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1).
Wikipedia: POU is a family of eukaryotic transcription factors that have well-conserved homeodomains. The Pou domain is a bipartite DNA binding domain found in these proteins.
Pfam PF00430: ATP synthase B/B' CF(0) (coiled_coil)
Part of the CF(0) (base unit) of the  ATP synthase. The base unit is thought to translocate protons through membrane  (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits.  This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in [pfam:PF00006]
Wikipedia: ATP synthase subunit b, mitochondrial is an enzyme that in humans is encoded by the ATP5PB gene.
Pfam PF14653: Insulin growth factor-like family (family)
This family includes the insulin growth factor-like proteins. These proteins are potential ligands for the IGFLR1 cell membrane receptor.
Pfam PF09041: Aurora-A binding (disordered)
The Aurora-A binding domain binds to two distinct sites on the Aurora kinase: the upstream residues bind at the N-terminal lobe, whilst the downstream residues bind in an alpha-helical conformation between the N- and C-terminal lobes. The two Aurora-A binding motifs are connected by a flexible linker that is variable in length and sequence across species. Binding of the domain results strong activation of Aurora-A and protection from deactivating dephosphorylation by phosphatase PP1.
Pfam PF09634: Protein of unknown function (DUF2025) (domain)
This protein is produced from gene PA1123 in Pseudomonas. It contains three alpha helices and six beta strands and is thought to be monomeric.  It appears to be present in the biofilm layer and may be a lipoprotein.
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 PF00659: POLO box duplicated region (family)
A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. They are also involved in meiosis I as regulators of kinetochore function . Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain . The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster . This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule .

The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two Î±-helices and two six-stranded Î²-sheets . The topology of one polypeptide subunit of the dimer consists of, from its N-to C terminus, an extended strand segment, five Î²-strands, one Î±-helix (A) and C-terminal Î²-strand. Î²-strands from one subunit form a contiguous antiparallel Î²-sheet with Î²-strands from the second subunit. The two Î²-sheets pack with crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with Î²-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic Î²-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface.

Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures .
Pfam PF06619: Protein of unknown function (DUF1149) (family)
This family consists of several hypothetical bacterial proteins of unknown 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 PF10107: Endonuclease related to archaeal Holliday junction resolvase (family)
This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Pfam PF08309: LVIVD repeat (repeat)
This repeat is found in bacterial and archaeal cell surface proteins, many of which are hypothetical.  The secondary structure corresponding to this repeat is predicted to comprise from 1-7 of 4-beta-strands which may associate to form a beta-propeller. The repeat copy number varies from 3-29. This repeat is sometimes found with the PKD domain [pfam:PF00801].
Pfam PF06521: PAR1 protein (family)
This family consists of several plant specific PAR1 proteins from Nicotiana tabacum and Arabidopsis thaliana. The function of this family is unknown.
Pfam PF01655: Ribosomal protein L32 (family)
This family includes ribosomal protein L32 from eukaryotes and archaebacteria.
Pfam PF19124: Family of unknown function (DUF5808) (family)
This is a family of proteins of unknown function predominantly found in Firmicutes but also in Actinobacteria and Halobacteria. Members of this family are thought to be DUF1648 domain-containing proteins as they are membrane-components.
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 PF04884: Vitamin B6 photo-protection and homoeostasis domain (domain)
In plants, this domain plays a role in auxin-transport, plant growth and development and appears to be expressed by all cells in the plant as well as in plastids. The family has been shown to play a role in vitamin B6 photo-protection and homoeostasis in plants. In line with various literature findings, these proteins likely function as transporters and may be directly involved in the transport of one or more forms of the vitamin.
Pfam PF08772: Nin one binding (NOB1) Zn-ribbon like (domain)
This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1 (Nin one binding).
Pfam PF04911: ATP synthase j chain (family)
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (7.1.2.2) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the Î±(3)Î²(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.
This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms .
Pfam PF16087: Helix-turn-helix domain (DUF4817) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in insects, but also some other eukaryotes. Proteins in this family are typically between 109 and 322 amino acids in length. This domain may be involved in DNA-binding.
Pfam PF10020: Uncharacterized protein conserved in bacteria (DUF2262) (family)
This domain, found in various hypothetical bacterial 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 PF06249: Ethanolamine utilisation protein EutQ (domain)
The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear.
Pfam PF23999: CUSTOS (family)
This entry includes CUSTOS proteins, which regulate Wnt signaling pathway during early development. It plays a role in anterior head development in zebrafish. This family might be distantly related to DUF2011 ([pfam:PF09428]), a family of uncharacterised fungal proteins (according to iterative search using Jackhmmer).
Pfam PF25005: PSF2 N-terminal domain (domain)
This domain is found N-terminal in the human DNA replication complex GINS protein PSF2 and related proteins. PSF2 is an essential component of of the GINS complex, a complex that plays an essential role in the initiation of DNA replication, and progression of DNA replication forks.
Pfam PF08081: RBM1CTR (NUC064) family (family)
This C-terminal region is found in RBM1-like RNA binding hnRNPs.
Pfam PF23850: Family of unknown function (DUF7213) (domain)
This entry represents an uncharacterized protein of approximately 70-100 amino acids found in mycobacteriophages. The function of this protein is currently unknown. It is found in phages belonging to the Gracegardnervirinae subfamily, including Cheoctovirus and Terapinvirus genera. This protein forms a confident dimer according to an AlphaFold model of [swissprot:S5Z4M5]. The dimer forms a central four stranded beta sheet with two alpha helices packed orthogonally to the direction of the beta strands on each face of the 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 PF04854: Protein of unknown function, DUF624 (family)
This family includes several uncharacterised bacterial 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 PF09510: Rtt102p-like transcription regulator protein (family)
This protein is found in fungi. The family includes Rtt102p, a transcription regulator protein which appears to be integrally associated with both the Swi-Snf and the RSC chromatin remodelling complexes,.
Pfam PF20309: Deoxyribohydrolase (DRHyd) domain of the ASK signalosome (family)
This is an uncharacterised DRHyd domain observed in ASK signalosome proteins ASK1, ASK2, and ASK3. Potentially generates nucleotide-derived signal recognized by the TPR-S domain found in the same proteins.
Pfam PF15817: Transmembrane protein 40 family (family)
TMEM40 is a family of eukaryotic membrane proteins.
Pfam PF22050: Apelin receptor early endogenous ligand (family)
This family represents Apelin receptor early endogenous ligand from Danio rerio (Protein Toddler, also known as Protein Elabela) and similar sequences from vertebrates. Toddler is a short secreted required for mesendodermal differentiation, blood vessels formation and heart morphogenesis during early development and for adult cardiovascular homeostasis.
Pfam PF00406: Adenylate kinase (domain)
Wikipedia: Adenylate kinase is a phosphotransferase enzyme that catalyzes the interconversion of the various adenosine phosphates. By constantly monitoring phosphate nucleotide levels inside the cell, ADK plays an important role in cellular energy homeostasis.
Pfam PF21753: Probable sensor domain DACNK (domain)
This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases, which is typically followed by the DAC ([pfam:PF02457]) domain. This domain is mainly found in actinobacteria and cyanobacteria; structure predictions suggest that this domain may consist of five alpha-helices and five beta-strands.
Pfam PF02709: N-terminal domain of galactosyltransferase (family)
This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases.  [ec:2.4.1.90], N-acetyllactosamine synthase; [ec:2.4.1.38], Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and [ec:2.4.1.22] Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin [ec:2.4.1.90] is the catalysed reaction.
Pfam PF01206: Sulfurtransferase TusA (domain)
This family includes the TusA sulfurtransferases.
Pfam PF02761: CBL proto-oncogene N-terminus, EF hand-like domain (domain)
Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the central EF hand domain.
Wikipedia: In molecular biology, the Cbl TKB domain, also known as the phosphotyrosine binding (PTB) domain is a conserved region found at the N-terminus of Cbl adaptor proteins. This N-terminal region is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle domain, an EF hand-like domain and a SH2-like domain, which together are known to bind to phosphorylated tyrosine residues.
Pfam PF06462: Propeller (repeat)
Tectonins I and II are two dominant proteins in the nuclei and nuclear matrix from plasmodia of Physarum polycephalum (Slime mold) and both proteins contain six tandem repeats that are each 33-37 amino acids in length. Homologous repeats are found in L-6, a bacterial lipopolysaccharide-binding lectin from horseshoe crab hemocytes. The repetitive sequences of the tectonins and L-6 are reminiscent of the WD repeats of the beta-subunit of G proteins, suggesting that they form beta-propeller domains. The tectonins may be lectins that function as part of a transmembrane signalling complex during phagocytosis. Tectonin beta-propeller repeat-containing protein 1 (TECPR1) has a critical function during autophagosome maturation and autophagosome-lysosome fusion.
Pfam PF00615: Regulator of G protein signaling domain (domain)
RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
Wikipedia: Regulators of G protein signaling (RGS) are protein structural domains or the proteins that contain these domains, that function to activate the GTPase activity of heterotrimeric G-protein α-subunits.
Pfam PF18664: CdiA C-terminal tRNase domain (domain)
This entry represents the C-terminal tRNase domain of CdiA a type II toxin/immunity protein complex which can be found in B. pseudomallei isolate E479. The C-terminal tRNase domain has an alpha/beta-fold characteristic of PD(D/E)XK nucleases. The PD(D/E)XK superfamily includes most restriction endonucleases and other enzymes involved in DNA recombination and repair.
Pfam PF20101: Family of unknown function (DUF6491) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 155 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 PF18331: PKHD-type hydroxylase C-terminal domain (domain)
This is the C-terminal domain found in PKHD-type hydroxylase enzymes. Family members are found mostly in Bacteria and carry the 2OG-Fe(II) oxygenase superfamily [pfam:PF13640].
Pfam PF06241: Castor and Pollux, part of voltage-gated ion channel (family)
This family represents a short region in the middle of largely plant proteins that belong to the TCDB:1.A.1.23.2 family of the voltage-gated ion channel superfamily, eg UniProtKB:Q5H8A6, Q5H8A5 and Q4VY51.
Pfam PF10427: Argonaute hook (family)
This region has been called the argonaute hook. It has been shown to bind to the Piwi domain [pfam:PF02171] of Argnonaute proteins.