SII-SWORD/CoKE huggingface dataset:
Pfam PF13816: Haem-containing dehydratase (domain)
This family includes aldoxime dehydratase, [ec:4.99.1.5]. This is a haem-containing enzyme, which catalyses the dehydration of aldoximes to their corresponding nitrile. It also includes phenylacetaldoxime dehydratase, [ec:4.99.1.7]. This haem-containing enzyme catalyses the dehydration of Z-phenylacetaldoxime to phenylacetonitrile. The enzyme forms an elliptic beta barrel, composed of eight beta-strands, flanked by alpha-helices.
Pfam PF01175: Urocanase Rossmann-like domain (domain)
This entry represents the central domain, with a rossmann-like fold, found in Urocanase. It is found also in S-methyl thiourocanate hydratase which cannot use urocanate or thiourocanate as substrate and catalyses the conversion of S-methyl thiourocanate, to S-methyl-thiohydantoin-5-propanoate .
Urocanase  (also known as imidazolonepropionate hydrolase or urocanate hydratase) is the enzyme that catalyses the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate:

urocanate + H2O = 4,5-dihydro-4-oxo-5-imidazolepropanoate

Urocanase is found in some bacteria (gene hutU) , in the liver of many vertebrates, and has also been found in the plant Trifolium repens (white clover). Urocanase is a protein of about 60 Kd, it binds tightly to NAD+and uses it as an electrophil cofactor. A conserved cysteine has been found to be important for the catalytic mechanism and could be involved in the binding of the NAD+.
Wikipedia: Urocanase is the enzyme that catalyzes the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate.
Pfam PF07974: EGF-like domain (domain)
This family contains EGF domains found in a variety of extracellular proteins.
Wikipedia: The EGF-like domain is an evolutionary conserved protein domain, which derives its name from the epidermal growth factor where it was first described. It comprises about 30 to 40 amino-acid residues and has been found in a large number of mostly animal proteins. Most occurrences of the EGF-like domain are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted. An exception to this is the prostaglandin-endoperoxide synthase. The EGF-like domain includes 6 cysteine residues which in the epidermal growth factor have been shown to form 3 disulfide bonds. The structures of 4-disulfide EGF-domains have been solved from the laminin and integrin proteins. The main structure of EGF-like domains is a two-stranded β-sheet followed by a loop to a short C-terminal, two-stranded β-sheet. These two β-sheets are usually denoted as the major (N-terminal) and minor (C-terminal) sheets. EGF-like domains frequently occur in numerous tandem copies in proteins: these repeats typically fold together to form a single, linear solenoid domain block as a functional unit.
Pfam PF08702: Fibrinogen alpha/beta chain family (coiled_coil)
Fibrinogen is a protein involved in platelet aggregation and is essential for the coagulation of blood.  This domain forms part of the central coiled coiled region of the protein which is formed from two sets of three non-identical chains (alpha, beta and gamma).
Wikipedia: Fibrinogen is a glycoprotein complex, produced in the liver, that circulates in the blood of all vertebrates. During tissue and vascular injury, it is converted enzymatically by thrombin to fibrin and then to a fibrin-based blood clot. Fibrin clots function primarily to occlude blood vessels to stop bleeding. Fibrin also binds and reduces the activity of thrombin. This activity, sometimes referred to as antithrombin I, limits clotting. Fibrin also mediates blood platelet and endothelial cell spreading, tissue fibroblast proliferation, capillary tube formation, and angiogenesis and thereby promotes revascularization and wound healing.
Pfam PF22474: Argonaute, middle domain (domain)
This domain is found centrally in Protein argonaute from Thermus thermophilus (Ago), a site-specific DNA-guided endoRNase organised into four domain: N ([pfam:PF22472]), PAZ ([pfam:PF18309]), Mid (this entry) and PIWI ([pfam:PF02171]). This domain contains residues that have been reported to be critical for cleavage activity. It folds into an alpha-beta three layered sandwich.
Pfam PF17967: Pullulanase N2 domain (domain)
This domain is found close to the N-terminus of the Klebsiella starch debranching pullulanase enzyme. The structure of the domain is a beta sandwich fold.
Pfam PF02954: Bacterial regulatory protein, Fis family (domain)
The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences . It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli . Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion.

In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA-binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azotobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor .

The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution . FIS is composed of four Î±-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition . Other proteins belonging to this subfamily include:


 * E. coli: atoC, hydG, ntrC, fhlA, tyrR,
 * Rhizobium spp.: ntrC, nifA, dctD
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF13584: BatD DUF11 like domain (domain)
This domain that probably has an Ig-like fold is found in three copies in BatD proteins that are involved in tolerance to oxygen in in Bacteroides spp.
Pfam PF06493: Protein of unknown function (DUF1096) (family)
This family represents the N-terminal region of several proteins found in C. elegans. The family is often found with [pfam:PF02363].
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 PF23530: YHR052C-B (family)
This protein family includes the uncharacterised protein YHR052C-B from Saccharomyces cerevisiae, a 57-residues long peptide encoded by a small open reading frame (smORF).
Pfam PF04054: CCR4-Not complex component, Not1 (repeat)
The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate  transcription factor TFIID.
Wikipedia: CCR4-NOT transcription complex subunit 1 is a protein that in humans is encoded by the CNOT1 gene.
Pfam PF12542: Pre-mRNA splicing factor (family)
This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with [pfam:PF10197]. There is a single completely conserved residue Y that may be functionally important. Cwc25 has been identified to associate with pre-mRNA splicing factor Cef1/Ntc85, a component of the Prp19-associated complex (NTC) involved in spliceosome activation. Cwc25 is neither tightly associated with NTC nor required for spliceosome activation, but is required for the first catalytic reaction.
Pfam PF01073: 3-beta hydroxysteroid dehydrogenase/isomerase family (family)
The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyses the oxidation and isomerisation of 5-ene-3 beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precursors into the corresponding 4-ene-ketosteroids necessary for the formation of all classes of steroid hormones.
Pfam PF04735: Baculovirus DNA helicase (family)
Baculovirus P143 is a DNA helicase essential for virus DNA replication . It has distinct roles during infection and contributes to host range determination .
Pfam PF07768: PVL ORF-50-like family (family)
This is a family of sequences found in both bacteria and bacteriophages. This region is approximately 130 residues long and in some cases is found as part of the PVL (Panton-Valentine leukocidin) group of genes, which encode a member of the leukocidin group of bacterial toxins that kill leukocytes by creation of pores in the cell membrane. PVL appears to be a virulence factor associated with a number of human diseases.
Pfam PF09070: PFU (PLAA family ubiquitin binding) (domain)
This domain is found N terminal to [pfam:PF08324] and binds to ubiquitin.
Pfam PF07645: Calcium-binding EGF domain (domain)
This entry represents the EGF-like domains found in Neurogenic locus notch homolog protein 1 (NOTCH1) and related proteins such as protein kinase C-binding protein NELL2, Uromodulin and others. The EGF-like domains in NOTCH1 perform multiple functions and constitute crucial elements of the Notch signalling system. They play a role in dimer formation. They also serve as a protection against proteases, including TNF-alpha converting enzyme, which prevents Notch1 from ligand-independent activation .
Wikipedia: In molecular biology, the calcium-binding EGF domain is an EGF-like domain of about forty amino-acid residues found in epidermal growth factor (EGF). This domain is present in a large number of membrane-bound and extracellular, mostly animal, proteins. Many of these proteins require calcium for their biological function and a calcium-binding site has been found at the N-terminus of some EGF-like domains. Calcium-binding may be crucial for numerous protein-protein interactions.
Pfam PF03551: Transcriptional regulator PadR-like family (domain)
Members of this family are transcriptional regulators that appear to be related to the [pfam:PF01047] family. This family includes PadR [swissprot:Q9EXE6] a protein that is involved in negative regulation of phenolic acid metabolism.
Pfam PF04406: Type IIB DNA topoisomerase (domain)
Type II DNA topoisomerases are ubiquitous enzymes that catalyse the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break.  Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases.  TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP).
Pfam PF13319: Protein of unknown function (DUF4090) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in cyanobacteria. Proteins in this family are approximately 90 amino acids in length. A member of this family, the ssr1528 gene was found to be regulated by an sRNA NsiR4. In addition the expression of that gene was repressed under conditions of nitrogen depletion suggesting it may have a role related to cellular nitrogen status.
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 PF01129: NAD:arginine ADP-ribosyltransferase (family)
Mono-ADP-ribosylation is a post-translational modification of proteins in which the ADP-ribose moiety of NAD is transferred to proteins. This process is responsible for the toxicity of some bacterial toxins (e.g., cholera and pertussis toxins). Mono (ADP-ribosyl) transferases exist in vertebrates 2.4.2.31 that transfer ADP-ribose to arginine .

NAD+ + L-arginine = nicotinamide + N2-(ADP-D-ribosyl)-L-arginine

At least five forms of the enzyme have been characterised to date, some of which are attached to the membrane via glycosylphosphatidylinositol (GPI) anchors, while others appear to be secreted. The enzymes contain ~250-300 residues, which encode putative signal sequences and carbohydrate attachment sites. In addition, the N- and C-termini are predominantly hydrophobic, a characteristic of GPI-anchored proteins .
Pfam PF03776: Septum formation topological specificity factor MinE (family)
The E. coli minicell locus was shown to code for three gene products (MinC, MinD, and MinE) whose coordinate action is required for proper placement of the division septum. The minE gene codes for a topological specificity factor that, in wild-type cells, prevents the division inhibitor from acting at internal division sites while permitting it to block septation at polar sites.
Pfam PF20533: Domain of unknown function (DUF6748) (domain)
This presumed domain family is functionally uncharacterised. This  domain is found in bacterial and eukaryotic proteins. It is around 100 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 PF23151: NuiA-like (domain)
This entry represents a group of fungal proteins that are related to the nuclease A inhibitor NuiA ([pfam:PF07924]). NuiA is known to regulate the activity of NucA, one of the most potent nucleases involved in degradation of both single- and double-stranded DNA and RNA. The NucA inhibition by NuiA involves an unusual divalent metal ion bridge that connects the nuclease with its inhibitor. A highly conserved glutamate extends into the active site, mimicking the charge of a phosphate. The functionally essential glutamate is conserved within this family. In some members, it is replaced with aspartate. Most members of this family bear a deletion affecting the second interaction site located on one of the two 'jaws' of the NuiA structure and known to contribute to the specificity and strength of the NuiA-NucA interaction. The lack of this region indicates some functional differences of this group of potential inhibitors.
Pfam PF10612: Spore coat protein Z (family)
This family has members annotated as Spore coat protein Z, otherwise known as CotZ, It is a cysteine-rich spore coat family, and along with CotY is necessary for assembly of intact exosporium.
Pfam PF12855: ECL1/2/3 zinc binding proteins (family)
This family is involved in the chronological life-span of S. cerevisiae. Over-expression leads to an extended viability of wild-type strains, indicating a role in regulation. There are four cysteine residues conserved in the N-terminal region involved in zinc binding and have been shown to be essential for protein functions. Ecl1-family proteins are essential for sexual development caused by zinc depletion in S. pombe. They are also important for cellular response to zinc limitation.
Pfam PF22090: Gins51, C-terminal domain (domain)
This domain is found at the C-terminal end of the DNA replication complex GINS family protein TK0536 from Thermococcus kodakarensis (Gins51, [swissprot:Q5JF31]). This mobile domain acts as a hook to bind the archaeal GINS-associated nuclease to form the 'CGM' unwindosome complex. It shows an alpha-beta configuration.
Pfam PF02216: B domain (domain)
This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.
Wikipedia: In molecular biology, the domain B, refers to the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Hence, it is abbreviated to SpAB.
Pfam PF23392: Domain of unknown function (DUF7101) (domain)
This is a domain found in a group on uncharacterised proteins from fungi. The function of this domain is unknown. According to structural predictions, this domain likely adopts an alpha-beta-beta-beta-beta-alpha fold. This domain is usually found associated with an alpha-helical domain at the N-terminal ([pfam:PF23391]) and a beta-propeller at the C-terminal ([pfam:PF23388]).
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 PF05578: Pestivirus NS3 polyprotein peptidase S31 (family)
These serine peptidases are involved in processing of the flavivirus polyprotein.
Pfam PF12862: Anaphase-promoting complex subunit 5 (repeat)
Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1.  Apc5, although it does not harbour a classical RNA binding domain, Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction. The N-terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC. This region of the Apc5 member proteins carries a TPR-like motif.
Pfam PF00717: Peptidase S24-like (domain)
This entry represents a structural domain superfamily found in serine peptidases belonging to MEROPS peptidase families: S24 (LexA family, clan SF); S26A (signal peptidase I), S26B (signalase) and S26C TraF peptidase. This domain has a complex fold made of several coiled Î²-sheets, which contains an SH3-like barrel structure.

The S26 family includes Escherichia coli signal peptidase, SPase, which is a membrane-bound endopeptidase with two N-terminal transmembrane segments and a C-terminal catalytic region . SPase functions to release proteins that have been translocated into the inner membrane from the cell interior, by cleaving off their signal peptides. In SPase proteins, this domain is disrupted by the insertion of an additional all-beta subdomain.

Note: This signature covers both the SH3-like barrel Î²-ribbon domain and the all-Î² subdomain inserted into it.

The S24 family includes:


 * the lambda repressor CI/C2 family and related bacterial prophage repressor proteins .
 * LexA, the diverse family of bacterial transcription factors that repress genes in the cellular SOS response to DNA damage .
 * MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage . UmuD is self-processed by its own serine protease activity during the SOS response.
 * RulA, a component of the rulAB locus that confers resistance to UV.


All of these proteins, with the possible exception of RulA, interact with RecA, which activates self cleavage either derepressing transcription in the case of CI and LexA  or activating the lesion-bypass polymerase in the case of UmuD and MucA. UmuD'2, is the homodimeric component of DNA pol V, which is produced from UmuD by RecA-facilitated self-cleavage. The first 24 N-terminal residues of UmuD are removed; UmuD'2 is a DNA lesion bypass polymerase . MucA , like UmuD, is a plasmid encoded a DNA polymerase (pol RI) which is converted into the active lesion-bypass polymerase by a self-cleavage reaction involving RecA .

This group of proteins also contains proteins not recognised as peptidases as well as those classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity.
Pfam PF19115: Family of unknown function (DUF5800) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23900: PRS2 N-terminal domain (domain)
This entry represents the N-terminal domain of bacterial Putative 26S proteasome regulatory subunit homologues (PRS2). The function of this domain is unknown and it may be found in association with an AAA-ATPase domain ([pfam:PF00004]). The 26S proteasome is a large multiprotein complex involved in the regulated degradation of ubiquitinated proteins. This complex can be divided in two sub-complexes, the core particle (CP, 20S) and the regulatory particle (RP, 19S). The RP consists of 19 subunits organised in two sub-structures, the base and lid complexes. The base consists of a ring of six AAA-ATPases. The C-termini of these ATPases dock into pockets present between the alpha-subunits of the CP.
Pfam PF04818: CID domain (repeat)
This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).
Pfam PF05065: Phage capsid family (family)
Family of bacteriophage hypothetical proteins and capsid proteins.
Pfam PF08041: PetM family of cytochrome b6f complex subunit 7 (family)
This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta hemes and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin.
Pfam PF23766: Pneumovirus matrix protein C-terminal domain (domain)
This entry represents the C-terminal domain of the pneumoviral matrix protein. The C-terminal domain of the RSV M protein (residues 140-255) consists of a flattened beta-barrel formed by two 3-stranded antiparallel beta-sheets. The regions linking the beta-sheets between strands 2 and 3, and strands 5 and 6, are largely alpha-helical. This domain contains a positively charged pocket that may serve as an interaction site. A striking planar arrangement of conserved tyrosine residues (Y163, Y197, Y215, Y229, Y236, Y237) encircles the domain, suggesting a role in membrane association. Sequence comparisons indicate the C-terminal domain is more conserved among pneumoviruses compared to the N-terminal domain. However, surface-exposed loop regions still represent areas of significant diversity, likely involved in species-specific interactions. The C-terminal domain is loosely tethered to the N-terminal domain by a flexible linker.