SII-SWORD/CoKE huggingface dataset:
Pfam PF10491: NLS-binding and DNA-binding and dimerisation domains of Nrf1 (family)
In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Swiss-Prot:Q8C4C0, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity.
Pfam PF11928: Early growth response N-terminal domain (domain)
Proteins containing this domain include early growth response protein 1/2/3 (EGR1/2/3). EGR1 is a transcriptional regulator that binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. EGR2, also known as Krox20, is an E3 ligase that sumoylates its Nab coregulators. This domain has a single completely conserved residue P that may be functionally important. Furthermore, it is found associated with [pfam:PF00096].
Pfam PF14698: Argininosuccinate lyase C-terminal (domain)
This domain is found at the C-terminus of argininosuccinate lyase.
Pfam PF11831: pre-mRNA splicing factor component (family)
This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex.
Pfam PF07897: Ethylene-responsive binding factor-associated repression (family)
The EAR motif is the ethylene-responsive element binding factor-associated amphiphilic repression motif. This motif binds to the Groucho/Tup1-type co-repressor TOPLESS (TPL) and TPL-related proteins. The motif is frequently to be find at the N-terminus of NINJA, or Novel INteractor of JAZ, proteins. The EAR motif, defined by the consensus sequence patterns of either LxLxL or DLN xxP, is the most predominant form of transcriptional repression motif so far identified in plants. It is highly conserved in transcriptional regulators that are known to function as negative regulators in a broad range of developmental and physiological processes across evolutionarily diverse plant species. This family is closely related to family AUX_IAA Pam:PF02309 which also has an LxLxL signature.
Pfam PF06907: Latexin (domain)
This entry consists of several animal specific latexin proteins. Latexin is a carboxypeptidase A inhibitor and is expressed in a cell type-specific manner in both central and peripheral nervous systems in the rat. It consists of two cystatin-like domains, consisting of an alpha-helix enveloped by a curved beta-sheet. These domains packed against each other, forming an interface to which the enzyme is bound.
Wikipedia: In molecular biology, the latexin family is a family of proteins which family consists of several animal specific latexin and proteins related to latexin that belong to MEROPS proteinase inhibitor family I47, clan IH.
Pfam PF09400: Protein of unknown function (DUF2002) (domain)
This is a family of putative cytoplasmic proteins.  The structure of these proteins form an antiparallel beta and sheet and contain some alpha helical regions.
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 PF14729: Domain of unknown function with cystatin-like fold (DUF4467) (domain)
Large family of predicted lipoproteins from Gram-positive bacteria Experimentally determined structure shows a cystatitin-like fold, allowing us to classify this family in the NFT2 clan, despite lack of any detectable sequence similarity between members of this family and other families in this clan
Pfam PF23210: MROH2B-like, HEAT repeats (repeat)
This entry represents HEAT repeats from Maestro heat-like repeat -containing protein family member 2B from mouse (MROH2B), Protein SHOOT GRAVITROPISM 6 from Arabidopsis thaliana (SGR6) and similar sequences mainly found in animals and plants. SPIF (also known as MRO2B) may play a role in the process of sperm capacitation. SGR6 is involved in inflorescence stems gravitropism, by modulating vacuolar membrane (VMs) dynamics in gravity-sensing cells (e.g. endodermal cells) during the amyloplast sedimentation process.
Pfam PF22356: MACPF/perforin-like, beta-prism domain (domain)
This entry represents the C-terminal beta-prism domain of the MACPF/perforin-like protein from Photorhabdus luminescens. This domain shows structural similarity to the Multivesicular body subunit 12B MABP domain DUF2464 ([pfam:PF10240]).
Pfam PF14126: Domain of unknown function (DUF4293) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 154 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 PF12158: Domain of unknown function (DUF3592) (domain)
This entry represents a beta barrel domain found in primarily in bacteria, but also in archaea and in kinetoplastids.  Proteins in this family are typically between 150 and 242 amino acids in length.  The domain is often found in integral membrane proteins. This family contains the Tsi4 immunity protein from P. aeruginosa which acts as an immunity protein to the Tse4 toxin. AlphaFold multimer modelling shows that these two protein are likely to interact directly.
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 PF15418: Domain of unknown function (DUF4625) (family)
This family contains a likely bacterial Ig-like fold, suggesting it may be a family of lipoproteins.
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 PF19350: Family of unknown function (DUF5928) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 260 amino acids in length. The family is found to the C-terminus of [pfam:PF02485] and so is likely to have a role in carbohydrate modification.
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 PF14717: Domain of unknown function (DUF4465) (family)
A large family of uncharacterized proteins mostly from  human gut bacteroides, but also some environmental  and water bacteria (Planctomycetes) as well as  metagenomic samples Most proteins from this family are secreted or  located on the outer surface and may participate  in cell-cell interactions or cell-nutrient interactions This function is supported by a solved structure of a Bacteroides ovatus homolog, which adapts a galactose binding (jelly-roll) beta barrel structure
Pfam PF16642: Unstructured region on Potassium channel subunit alpha KvLQT2 (disordered)
KCNQ2_u3 is a region of natively unstructured sequence on potassium voltage-gated channel subfamily KQT member 2 proteins from higher eukaryotes. It lies between families KCNQ_channel, [pfam:PF03520], and KCNQC3-Ank_bd, [pfam:PF11956].  The function is not known.
Pfam PF10673: Protein of unknown function (DUF2487) (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 PF00538: linker histone H1 and H5 family (domain)
Linker histone H1 is an essential component of chromatin structure. H1  links nucleosomes into higher order structures Histone H1 is replaced  by histone H5 in some cell types.
Wikipedia: In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which DNA winds to create structural units called nucleosomes. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 9 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.
Pfam PF10304: Required for nuclear transport of RNA pol II C-terminus 2 (repeat)
This domain is found towards the C-terminus of required for the nuclear transport of RNA pol II protein (RTP1). RTP1 is required for the nuclear localisation of RNA polymerase II. This family is found in association with [pfam:PF10363].
Pfam PF22366: NDH2 C-terminal domain (domain)
This entry represent the C-terminal domain of alternative NADH:quinone oxidoreductases known as NDH2 that deliver electrons to the respiratory chain by oxidation of NADH and reduction of quinones but does not pump protons. NDH-2 have particular relevance in yeasts like Saccharomyces cerevisiae and in several prokaryotes, whose respiratory chains are devoid of complex I, in which NDH-2 keep the balance and are the main entry point of electrons into the respiratory chains. NDH2 proteins are found in bacteria, certain plant, fungal and protozoan mitochondria, but not in mammals, they have been used as a drug target for Mycoplasma tuberculosis, Plasmodium falciparum and Toxoplasma gondii.
Pfam PF14153: Spore coat protein CotO (family)
Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat.  This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly.
Pfam PF13025: Protein of unknown function (DUF3886) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important.
Pfam PF23825: Family of unknown function (DUF7195) (family)
This entry represents a family of uncharacterized bacteriophage proteins, typically around 70-80 amino acids in length. They are found in phages infecting Escherichia, Pseudomonas, Salmonella, Vibrio, and other bacterial hosts.
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 PF07907: YibE/F-like protein (family)
The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE ([swissprot:Q9CHC5]) and YibF ([swissprot:Q9CHC4]). Most of the members of this family are annotated as being putative  membrane proteins, and in fact the sequences contain  a high proportion of hydrophobic residues.
Pfam PF08550: Nitrogen regulatory protein areA, GATA-like domain (domain)
This entry represents fungal proteins containing GATA domains, including nitrogen regulatory protein areA, a transcription activator that binds the consensus DNA element 5'-CGATAG-3' and mediates nitrogen metabolite repression. This entry also contains the Negative regulator of RAS-cAMP pathway MKS1 from yeast that is thought to be a negative regulator of RAS-cAMP pathway.
Pfam PF12018: Domain of unknown function (family)
This domain of about 280 residues is found in eukaryotes. There are two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704. This domain is found FAP206 [swissprot:Q23H79], a protein associated with cilia and flagella. In the ciliate Tetrahymena, the cilium has radial spokes, each of which is a macromolecular complex essential for motility. A triplet of three radial spokes, RS1, RS2, and RS3, is repeated every 96 nm along the doublet microtubule. Each spoke has a distinct base that docks to the doublet and is linked to different inner dynein arms. Knockout of the FAP206 gene results in slow cell motility and the 96-nm repeats lack RS2 and dynein c. FAP206 is probably part of the front prong and docks RS2 and dynein c to the microtubule.
Pfam PF06027: Solute carrier family 35 (family)
This is a family of putative solute carrier proteins from eukaryotes.
Pfam PF02015: Glycosyl hydrolase family 45 (domain)
O-Glycosyl hydrolases (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 glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Glycoside hydrolase family 45 GH45 comprises enzymes with only one known activity; endoglucanase (3.2.1.4).

The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases, cellobiohydrolases (3.2.1.91) (exoglucanases), or xylanases (3.2.1.8) . Fungi and bacteria produce a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family K or as the glycosyl hydrolases family 45 . The best conserved regions in these enzymes is located in the N-terminal section. It contains an aspartic acid residue which has been shown  to act as a nucleophile in the catalytic mechanism. This also has several cysteines that are involved in forming disulphide bridges.
Wikipedia: In molecular biology, glycoside hydrolase family 45 is a family of glycoside hydrolases.
Pfam PF18533: Domain of unknown function (DUF5622) (domain)
This is a domain of unknown function found in archaea-specific ribosomal proteins such as L46a which is suggested to directly bind to rRNA in the ribosome.
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 PF03607: Doublecortin (family)
X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder . Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling . Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s).

The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain, which is ubiquitin-like. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation .

Some proteins known to contain a DC domain are listed below:


 * Doublecortin. It is required for neuronal migration . A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains .
 * Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controlling neuronal migration in the developing brain .
 * Retinitis pigmentosa 1 protein. It is required for the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 .
Wikipedia: Neuronal migration protein doublecortin, also known as doublin or lissencephalin-X is a protein that in humans is encoded by the DCX gene.
Pfam PF15680: Orofacial cleft 1 candidate gene 1 protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 125 and 276 amino acids in length.
Pfam PF09193: Cholecystokinin A receptor, N-terminal (domain)
Members of this family are found in the extracellular region of the cholecystokinin A receptor, where they adopt a tertiary structure consisting of a few helical turns and a disulphide-crosslinked loop. They are required for interaction of the cholecystokinin A receptor with it's corresponding hormonal ligand.
Wikipedia: The Cholecystokinin A receptor is a human protein, also known as CCKAR or CCK1, with CCK1 now being the IUPHAR-recommended name.
Pfam PF03505: Clostridium enterotoxin (family)
Clostridial species are one of the major causes of food poisoning/gastro-intestinal illnesses. They are Gram-positive, spore-forming rods that occur naturally in the soil . Among the family are: Clostridium botulinum, which produces one of the most potent toxins in existence; Clostridium tetani, causative agent of tetanus; and Clostridium perfringens, commonly found in wound infections and diarrhoea cases. The use of toxins to damage the host is a method deployed by many bacterial pathogens.

The major virulence factor of C. perfringens is the CPE enterotoxin, which is secreted upon invasion of the host gut, and contributes to food poisoning and other gastrointestinal illnesses . It has a molecular weight of 35.3kDa, and is responsible for the disintegration of tight junctions between endothelial cells in the gut . This mechanism is mediated by host claudins-3 and -4, situated at the tight junctions.

Two more host receptors have been characterised and expressedin vivo . Named CPE-R and RVP1, these may be utilised in the passage of Clostridial species through the gut wall, although the regulatory mechanisms have not been elucidated.
This entry also includes HA-70 from Clostridium botulinum C phage. The hemagglutinin (HA) components of the progenitor toxin protects the structural integrity of botulinum neurotoxin. The structure of HA70 from type C and D toxin (HA70/C/D) has been revealed .
Wikipedia: Clostridium enterotoxins are toxins produced by Clostridium species. Clostridial species are one of the major causes of food poisoning/gastrointestinal illnesses. They are anaerobic, gram-positive, spore-forming rods that occur naturally in the soil. Among the family are: Clostridium botulinum, which produces one of the most potent toxins in existence; Clostridium tetani, causative agent of tetanus; and Clostridium perfringens, commonly found in wound infections and diarrhea cases.
Pfam PF15022: Protein of unknown function (DUF4522) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. In human this protein is known as C4orf36.
Pfam PF19824: Small, acid-soluble spore protein Tlp (family)
This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. Although previously designated tlp (thioredoxin-like protein), the B. subtilis protein was shown to be a minor small acid-soluble spore protein SASP, unique to spores. The motif E[VIL]XDE near the C terminus probably represents at a germination protease cleavage site.
Pfam PF01654: Cytochrome bd terminal oxidase subunit I (family)
This family are the alternative oxidases found in many bacteria which oxidise ubiquinol and reduce oxygen as part of the electron transport chain. This family is the subunit I of the oxidase E. coli has two copies of the oxidase, bo and bd', both of which are represented here In some nitrogen fixing bacteria, e.g. Klebsiella pneumoniae this oxidase is responsible for removing oxygen in microaerobic conditions, making the oxidase required for nitrogen fixation. This subunit binds a single b-haem, through ligands at His186 and Met393 (using SW:P11026 numbering). In addition His19 is a ligand for the haem b found in subunit II
Pfam PF14516: AAA-like domain (family)
This family of proteins are part of the AAA superfamily.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF21871: Baseplate structural protein gp6, C-terminal domain III (domain)
Baseplate structural protein gp6 is located next to the tail tube and is an intermediate (or inner) baseplate protein involved in tail assembly. Two molecules of gp6 form a complex with gp25 and gp7 which is involved sheath contraction. This domain has been described as C-terminal domain III.