SII-SWORD/CoKE huggingface dataset:
Pfam PF01044: Vinculin family (family)
Vinculin is a eukaryotic protein that seems to be involved in the attachment of the actin-based microfilaments to the plasma membrane. Vinculin is located at the cytoplasmic side of focal contacts or adhesion plaques . In addition to actin, vinculin interacts with other structural proteins such as talin and alpha-actinins.

Vinculin is a large protein of 116kDa (about a 1000 residues). Structurally the protein consists of an acidic N-terminal domain of about 90kDa separated from a basic C-terminal domain of about 25kDa by a proline-rich region of about 50 residues. The central part of the N-terminal domain consists of a variable number (3 in vertebrates, 2 in Caenorhabditis elegans) of repeats of a 110 amino acids domain.

Alpha-catenins are proteins of about 100kDa which are evolutionary related to vinculin . Catenins are proteins that associate with the cytoplasmic domain of a variety of cadherins. The association of catenins to cadherins produces a complex which is linked to the actin filament network, and which seems to be of primary importance for cadherins cell-adhesion properties. Three different types of catenins seem to exist: alpha, beta, and gamma. In terms of their structure the most significant differences are the absence, in alpha-catenin, of the repeated domain and of the proline-rich segment.
Wikipedia: 
 
Vinculin is a eukaryotic protein that seems to be involved in the attachment of the actin-based microfilaments to the plasma membrane. Vinculin is located at the cytoplasmic side of focal contacts or adhesion plaques. In addition to actin, vinculin interacts with other structural proteins such as talin and alpha-actinins.
Pfam PF22155: Mre11 accessory DNA binding capping domain (domain)
This entry represents the accessory DNA binding 'capping' domain of Thermotoga maritima Mre11 homologue (SbcD), a subunit of the MRX protein complex involved in DNA double-strand break repair. This domain forms the nuclease module with the phosphodiesterase domain at the N-terminal.
Pfam PF23109: RTEL1 helicase, ARCH domain (domain)
This domain is found in the homologues of human DNA RTEL1 helicase which is implicated in telomere-length regulation, DNA repair and maintenance of genomic stability. RTEL1 acts as anti-recombinase and antagonises homologous recombination by promoting the disassembly of D loop recombination intermediates in a reaction dependent upon ATP hydrolysis. The ARCH domain follows the N-terminal Rad3-like domain ([pfam:PF06733]). The structure of the ARCH domain is predicted to share similarity with the ARCH domain of XPD despite low sequence similarity and to contain a four-stranded antiparallel beta-sheet with four alpha-helices packed on it. This domain contains two large insertions that are not present in XPD. The ARCH domain probably plays a key role by interacting with the DNA translocating strand. Mutation found within this domain also emphasise the importance of the RTEL1 ARCH domain.
Pfam PF16464: Domain of unknown function (DUF5045) (family)
This family consists of N-terminal of several uncharacterised proteins around 260 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown.
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 PF24920: Tricalbin-1-like, C2 domain (domain)
This domain is found in Tricalbin-1 from Saccharomyces cerevisiae (TCB1) and similar fungal proteins. TCB1 may play a role in membrane trafficking. This domain is predicted to form an eight-stranded beta-sandwich.
Pfam PF07571: TAF6 C-terminal HEAT repeat domain (repeat)
TAF6_C is the C-terminal domain of the TAF6 subunit of the general transcription factor TFIID. The crystal structure reveals the presence of five conserved HEAT repeats. This region is necessary for the complexing together of the subunits TAF5, TAF6 and TAF9.
Pfam PF01262: Alanine dehydrogenase/PNT, C-terminal domain (domain)
This family now also contains the lysine 2-oxoglutarate reductases.
Pfam PF06057: Bacterial virulence protein (VirJ) (family)
This family consists of several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium.
Pfam PF02776: Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (domain)
A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown  that some of these enzymes are structurally related. There are two different functional modules in the thiamin diphosphate-binding fold, the pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules. This represents the N-terminal TPP-binding domain that in some members has been described as the Pyr-binding module.
Pfam PF22530: Terminase Bacteriophage T7, Ribonuclease H-like domain (domain)
This entry represents the C-terminal Ribonuclease H-like domain in the terminase (large subunit) from Escherichia phage T7 (Bacteriophage T7). The terminase functions as an ATP-powered molecular motor essential for the translocation of viral DNA into empty capsids. It also acts as an endonuclease, cleaving the viral genome at a specific and precise double-stranded DNA sequence to initiate and conclude the packaging process.
Pfam PF20939: Selenoprotein methionine sulfoxide reductase A, helical domain (domain)
This domain is found in 1-Cys type selenoprotein methionine sulfoxide reductase A (MsrA) from the bacteria Clostridium oremlandii, a repair enzyme for proteins that have been inactivated by oxidation that is found both in prokaryotes and eukaryotes. MsrA catalyses the reduction of methionine sulfoxide in proteins to methionine. This enzyme is organised into a catalytic domain ([pfam:PF01625]) and a helical domain (this entry) absent in most of the known MsrA structures. It consists of five helices, interacts with the catalytic domain and is essential for the active site formation.
Pfam PF06051: Domain of Unknown Function (DUF928) (family)
Family of uncharacterised bacterial protein.
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 PF00916: Sulfate permease family (family)
This family of integral membrane proteins are known as the Sulfate Permease (SulP) family. SulP is a large family found in all domains  of life. Although sulfate is a commonly transported ion there are many other activities in this family. See the TCDB description for a  comprehensive summary.
Wikipedia: The sulfate permease (SulP) family is a member of the large APC superfamily of secondary carriers. The SulP family is a large and ubiquitous family of proteins derived from archaea, bacteria, fungi, plants and animals. Many organisms including Bacillus subtilis, Synechocystis sp, Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans possess multiple SulP family paralogues. Many of these proteins are functionally characterized, and most are inorganic anion uptake transporters or anion:anion exchange transporters. Some transport their substrate(s) with high affinities, while others transport it or them with relatively low affinities. Others may catalyze SO2−4:HCO−3 exchange, or more generally, anion:anion antiport. For example, the mouse homologue, SLC26A6, can transport sulfate, formate, oxalate, chloride and bicarbonate, exchanging any one of these anions for another. A cyanobacterial homologue can transport nitrate. Some members can function as channels. SLC26A3 and SLC26A6 can function as carriers or channels, depending on the transported anion. In these porters, mutating a glutamate, also involved in transport in the CIC family, created a channel out of the carrier. It also changed the stoichiometry from 2Cl−/HCO−3 to 1Cl−/HCO−3.
Pfam PF23349: BBS7 hairpin (domain)
This entry represents a hairpin domain found in Bardet-Biedl syndrome 7 (BBS7) proteins from animals, including human and mouse. This protein forms a part of the BBSome complex, which is required for ciliogenesis. BBS7 is the BBSome subunit responsible for the binding to SMO H8.
Pfam PF12118: SprA-related family (family)
This family of bacterial proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold. Proteins in this family are typically between 234 to 465 amino acids in length.  Most members are annotated as being SprA-related.
Pfam PF08482: ATP-dependent helicase C-terminal (family)
This domain is found near the C-terminus of bacterial ATP-dependent helicases such as HrpB.
Pfam PF22478: Family of unknown function (DUF6982) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 135 and 1024 amino acids in length. This family of proteins are structurally related to [pfam:PF03614] a family of transcriptional repressors of phase-1 flagellin genes. The family appears to contain two related subdomains.
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 PF15095: Interleukin 33 (family)
This entry represents a beta-trefoil related domain found in interleukin-33 (IL33), which that binds to and signals through IL1RL1/ST2 and its stimulation recruits MYD88, IRAK1, IRAK4, and TRAF6, followed by phosphorylation of MAPK3/ERK1 and/or MAPK1/ERK2, MAPK14, and MAPK8. It also serves as a warning signal between cells at times of injury or cell death.
Wikipedia: Interleukin 33 (IL-33) is a protein that in humans is encoded by the IL33 gene.
Pfam PF07041: Protein of unknown function (DUF1327) (family)
This family consists of several hypothetical bacterial proteins of around 115 residues in length which seem to be specific to Escherichia coli. The function of this family is unknown.
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 PF15376: Domain of unknown function (DUF4603) (family)
This protein family is a domain of unknown function. In particular, this domain lies at the C-terminal end of a protein found in eukaryotes.
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 PF22826: PL28 ulvan lyases (family)
This entry represents the PL28 family of ulvan lyases. These enzymes degrade ulvan next to either epimer of uronic acid. They adopt a beta-sandwich structure with a jelly-roll topology containing a deep positively charged cleft that defines the substrate binding site.
Pfam PF10805: Protein of unknown function (DUF2730) (coiled_coil)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF05168: HEPN domain (family)
The HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain is a region of 110 residues found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archeabacterial proteins. There are three classes of proteins with HEPN domain:


 * Single-domain HEPN proteins found in many bacteria.
 * Two-domain proteins with N-terminal nucleotidyltransferase (NT) and C- terminal HEPN domains. This N-terminal NT domain belongs to a large family of NTs, which includes several classes of enzymes that are responsible for some types of bacterial resistance to aminoglycosides. These enzymes deactivate various antibiotics by transferring a nucleotidyl group to the drug.
 * A multidomain sacsin protein in genomes of fish and mammals. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain (IPR001623).


The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C-terminal all- Î±-helical domain of kanamycin nucleotidyltransferases (KNTases). It is composed of five Î± helices, three of which form an up- and-down helical bundle, with a pair of short helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding .
Wikipedia: In molecular biology, the HEPN domain is a region of approximately 110 amino acids found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archaea proteins. There are three classes of proteins with HEPN domains:Single-domain HEPN proteins found in many bacteria.
Two-domain proteins with N-terminal nucleotidyltransferase (NT) and C- terminal HEPN domains. This N-terminal NT domain belongs to a large family of NTs, which includes several classes of enzymes that are responsible for some types of bacterial resistance to aminoglycosides. These enzymes deactivate various antibiotics by transferring a nucleotidyl group to the drug.
A multidomain sacsin protein in genomes of fish and mammals. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain. The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C-terminal all-alpha-helical domain of kanamycin nucleotidyltransferases (KNTases). It is composed of five alpha helices, three of which form an up- and-down helical bundle, with a pair of short helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding.
Pfam PF08820: Domain of unknown function (DUF1803) (domain)
This small domain is found in one or two copies in proteins from bacteria. The function of this domain is unknown.
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 PF14368: Probable lipid transfer (family)
The members of this family are probably involved in lipid transfer. The family has several highly conserved cysteines, paired in various ways.
Pfam PF06314: Acetoacetate decarboxylase (ADC) (family)
This family consists of several acetoacetate decarboxylase (ADC) proteins ([ec:4.1.1.4]).
Wikipedia: Acetoacetate decarboxylase is an enzyme involved in both the ketone body production pathway in humans and other mammals, and solventogenesis in bacteria. Acetoacetate decarboxylase plays a key role in solvent production by catalyzing the decarboxylation of acetoacetate, yielding acetone and carbon dioxide.
Pfam PF21882: Putative tail fiber protein gp53-like, C-terminal (domain)
This entry represents a domain found at the C-terminal of putative tail fiber protein from Acinetobacter phage AP22 ([swissprot:I2GUG0], gp53) and similar uncharacterised sequences from tailed bacteriophages and prophages mainly found in proteobacteria. It shows structural similarities to other phage/virus host cell-binding fibres. These domains form a trimeric arrangement.
Pfam PF09983: Wadjet protein JetD, C-terminal (domain)
This is a domain found at the C-terminal of Wadjet protein JetD from Bacillus cereus. JetD is a component of the antiplasmid transformation system Wadjet type I, composed of JetA, JetB, JetC and JetD.  Expression of Wadjet type I in B.subtilis (strain BEST7003) reduces the transformation efficiency of plasmid pHCMC05. This domain is structurally similar to DNA topoisomerases, therefore, it may be a DNA-binding domain.
Pfam PF23082: Myb-like DNA-binding domain (domain)
This is the myb DNA-binding domain found in human DnaJ homolog subfamily C member 1 (DNAJC1) and similar sequences from animals and plants. This domain adopts a three helical bundle structure.
Pfam PF00178: Ets-domain (domain)
Transcription factors are protein molecules that bind to specific DNA sequences in the genome, resulting in the induction or inhibition of gene transcription . The ets oncogene is such a factor, possessing a region of 85-90 amino acids known as the ETS (erythroblast transformation specific) domain . This domain is rich in positively-charged and aromatic residues, and binds to purine-rich segments of DNA. The ETS domain has been identified in other transcription factors such as PU.1, human erg, human elf-1, human elk-1, GA binding protein, and a number of others . It is generally localized at the C terminus of the protein, with the exception of ELF-1, ELK-1, ELK-3, ELK-4 and ERF where it is found at the N terminus.

NMR-analysis of the structure of the Ets domains revealed that it contains three Î±-helices (1-3) and four-stranded Î²-sheets (1-4) arranged in the order Î±1-Î²1-Î²2-Î±2-Î±3-Î²3-Î²4 forming a winged helix-turn-helix (wHTH) topology . The third Î±-helix is responsive to contact to the major groove of the DNA. Different members of the Ets family proteins display distinct DNA binding specificities. The Ets domains and the flanking amino acid sequences of the proteins influence the binding affinity, and the alteration of a single amino acid in the Ets domain can change its DNA binding specificities.
Wikipedia: In the field of molecular biology, the ETS family is one of the largest families of transcription factors and is unique to animals. There are 28 genes in humans, 27 in the mouse, 10 in Caenorhabditis elegans and 9 in Drosophila. The founding member of this family was identified as a gene transduced by the leukemia virus, E26. The members of the family have been implicated in the development of different tissues as well as cancer progression.
Pfam PF23644: YpeD-like (family)
This protein family includes Protein YpeD from Escherichia coli, a 29-residues long microprotein encoded by a small open reading frame (smORF).
Pfam PF07070: SpoOM protein (family)
This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH.
Pfam PF08228: RNase P subunit Pop3 (family)
This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs.          The structure of Pop3 has been assigned the L7Ae/L30e fold.        This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologs.
Pfam PF14899: Domain of unknown function (DUF4492) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. The function of these proteins is unknown.
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 PF03575: Peptidase family S51 (domain)
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 belong to MEROPS peptidase family S51 (clan PC(S)). The type example being dipeptidase E (alpha-aspartyl dipeptidase) from Escherichia coli. The family contains alpha-aspartyl dipeptidases (dipeptidase E) and cyanophycinases.

The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E has been determine at 1.2-A resolution. The structure of this 25kDa enzyme consists of two mixed Î²-sheets forming a V, flanked by six Î±-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organisation of the catalytic triad differ from those of the known serine proteases. This enzyme appears to represent a new example of convergent evolution of peptidase activity .

Alpha-aspartyl dipeptidase hydrolyses dipeptides containing N-terminal aspartate residues, asp-|-xaa. It does not act on peptides with N-terminal Glu, Asn or Gln, nor does it cleave isoaspartyl peptides. In the cyanobacteria, cyanophycinase is an exopeptidase that catalyses the hydrolytic cleavage of multi-l-arginyl-poly-l-aspartic acid (cyanophycin; a water- insoluble reserve polymer) into aspartate-arginine dipeptides.