SII-SWORD/CoKE huggingface dataset:
Restriction endonuclease, type II, XcyI (Restrct_endonuc_II_XcyI)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry represents the restriction endonuclease XcyI, which recognises and cleaves the double-stranded sequence C^CCGGG.
Restriction endonuclease, type II, XamI (Restrct_endonuc_II_XamI)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry includes the XamI restriction endonuclease which recognises GTCGAC but cleavage site unknown.
Restriction endonuclease, type II, TaqI (Restrct_endonuc_II_TaqI)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry represents the restriction endonuclease TaqI, which recognises and cleaves the double-stranded sequence T^CGA.
Spore cortex biosynthesis protein, YabQ (YabQ)
Type: Family

This protein is predicted to span the membrane several times. It is only found in genomes of species that perform sporulation, such as Bacillus subtilis, Clostridium tetani, and other members of the Firmicutes (low-GC Gram-positive bacteria). Mutation of this sigmaE-dependent gene blocks development of the spore cortex. The length of the C-terminal region, which includes some hydrophobic regions, is variable. This entry includes the Bacillus subtilis YabQ, which is essential for formation of the spore cortex .
Sporulation lipoprotein YhcN/YlaJ-like (Spore_lipoprot_YhcN/YlaJ-like)
Type: Family

This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis . Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Capsule synthesis protein, CapA (Capsule_synth_CapA)
Type: Domain

CapA is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein .
YqaJ viral recombinase (YqaJ_viral_recombinase)
Type: Domain

Proteins containing this domain are found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit .
Uncharacterised protein family UPF0328 (UPF0328)
Type: Family

This protein is found in eukaryotic, parasitic microsporidia. Its function is unknown.
Neurogenic mastermind-like, N-terminal (Mastermind-like_N)
Type: Domain

This entry represents the N-terminal domain found in a family of neurogenic mastermind-like proteins (MAMLs), which act as critical transcriptional co-activators for Notch signaling . Notch receptors are cleaved upon ligand engagement and the intracellular domain of Notch shuttles to the nucleus. MAMLs form a functional DNA-binding complex with the cleaved Notch receptor and the transcription factor CSL, thereby regulating transcriptional events that are specific to the Notch pathway. MAML proteins may also play roles as key transcriptional co-activators in other signal transduction pathways as well, including: muscle differentiation and myopathies (MEF2C) , tumour suppressor pathway (p53) and colon carcinoma survival (beta-catenin) . MAML proteins could mediate cross-talk among the various signaling pathways and the diverse activities of the MAML proteins converge to impact normal biological processes and human diseases, including cancers.

The N-terminal domain of MAML proteins adopt an elongated kinked helix that wraps around ANK and CSL forming one of the complexes in the build-up of the Notch transcriptional complex for recruiting general transcription factors . This N-terminal domain is responsible for its interaction with the ankyrin repeat region of the Notch proteins NOTCH1 , NOTCH2 , NOTCH3 and NOTCH4. It forms a DNA-binding complex with Notch proteins and RBPSUH/RBP-J kappa/CBF1, and also binds CREBBP/CBP and CDK8 . The C-terminal region is required for transcriptional activation.
Small ribosomal subunit protein mS41, SAM domain (SAM_Ribosomal_mS41)
Type: Domain

This entry represents a SAM-like domain found in fungal mitoribosome protein mS41. The mitochondrion-specific ribosomal protein mS41 family comprises proteins that are integral components of the mitochondrial ribosome, also known as the mitoribosome . These proteins play a crucial role in the dedicated translation machinery that synthesizes mitochondrial genome-encoded proteins, which include essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are tethered to the mitochondrial inner membrane, ensuring that translation products are cotranslationally integrated into the membrane. Additionally, members of the mS41 family are implicated in the regulation of telomere length, a process essential for maintaining chromosome stability and cellular lifespan. Certain members are also required for survival upon exposure to specific environmental stressors, such as the K1 killer toxin and also in telomere length regulation .
STM1-like, N-terminal (STM1-like_N)
Type: Domain

This domain is found at the N-terminal region of the Stm1 and similar proteins. Stm1 is a G4 quadraplex and purine motif triplex nucleic acid-binding protein. It has been implicated in many biological processes including apoptosis and telomere biosynthesis. Stm1 is known to interact with Cdc13 , and is known to associate with ribosomes and nuclear telomere cap complexes . This domain is also found at the N-terminal of some 'RGG repeats nuclear RNA binding proteins' .
Mediator of RNA polymerase II transcription subunit 15, N-terminal (Med15_N)
Type: Domain

This entry represents the N-terminal domain of human Mediator of RNA polymerase II transcription subunit 15 (MED15, also known as ARC105) and similar animal proteins. This region, of approximately 70 residue, is a three-helix bundle with marked similarity to the KIX domain .

The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, MED15 is a critical transducer of gene activation signals that control early metazoan development .

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.
Conserved hypothetical protein CHP02186-related, transmembrane (CHP02186-rel_TM)
Type: Family

This entry consists of predicted transmembrane proteins of about 270 amino acids. They are found predominantly, though not exclusively, in alphaproteobacteria, generally only once in each genome.
CRISPR-associated protein, GSU0054 (Cas_GSU0054)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents a rare CRISPR-associated protein. CRISPR-associated proteins typically are found near CRISPR repeats and other CRISPR-associated proteins, have low levels of sequence identify, have sequence relationships that suggest lateral transfer, and show some sequence similarity to DNA-active proteins such as helicases and repair proteins.
CRISPR system ring nuclease SSO2081-like domain (SSO2081-like_dom)
Type: Domain

This entry represents a domain found in a Cas protein family from bacteria and archaea, including the ring nuclease SSO2081 from Saccharolobus solfataricus .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
YpkA, Rac1-binding domain (Rac1-binding_domain)
Type: Domain

The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. The N-terminal end of this domain (residues 434-615) consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end (residues 705-732) is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. The Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host .
Bacteriophage SP-beta, YorD (Phage_SP-beta_YorD)
Type: Domain

This entry includes the phage SPbeta protein YorD, the function of which is not known. It also contains the protein XkdW (

) from the Phage-like element PBSX in Bacillus subtilis. XkdW is approximately 100 residues long and contains two α helices and two β strands, and is probably monomeric. XkdW is expressed in bacteria but is probably viral in origin. Its function is unknown. PBSX, a defective prophage of B. subtilis, is a chromosomally based element which encodes a non-infectious phage-like particle with bactericidal activity. PBSX is induced by agents which elicit the SOS response .
Mediator complex, subunit Med18 (Mediator_Med18)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

Med18 is one subunit of the Mediator complex and a component of the head module that is involved in stimulating basal RNA polymerase II (PolII) transcription. Med18 consists of an eight-stranded β-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal α-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators .
YopX protein (YopX_protein)
Type: Domain

YopX is a protein of plasmid origin found in bacteria. It is of approx. 135 residues and is largely helical, with three identical chains probably complexing into a twelve-chain structure. Yop proteins are a subset of pathogenicity factors known as (Yersinia) outer proteins - Yops - which act as chaperones for other proteins such as X. They are exported by the type III secretion system (TTSS) upon bacterial infection of host cells. The TTSS is encoded on a virulence plasmid and is necessary for the survival and replication of the bacterium within host lymphoid tissues .
Mg296 protein (Mg296_protein)
Type: Domain

This protein of 129 residues is expressed in bacteria. It consists of three identical chains of five α helices. Two copies of each chain associate into a complex of six units of possible biological significance but of unknown function.
Histone chaperone domain CHZ (Histone_chaperone_domain_CHZ)
Type: Domain

This domain is highly conserved from yeasts to humans and is part of the chaperone protein HIRIP3 in vertebrates which interacts with the H3.3 chaperone HIRA, implicated in histone replacement during transcription. N- and C- termini of Chz family members are relatively divergent but do contain similar acidic stretches rich in Glu/Asp residues, characteristic of all histone chaperones .
Uncharacterised protein family PGPGW, transmembrane (Uncharacterised_PGPGW_TM)
Type: Family

This entry represents proteins that contain three predicted transmembrane helices and an unusual motif with consensus sequence PGPGW.
HMG box transcription factor BBX, domain of unknown function DUF2028 (TF_HMG_box_BBX_DUF2028)
Type: Domain

This entry represents a conserved domain found the in HMG box transcription factor BBX. This protein is necessary for cell cycle progression from the G1 to the S phase .
Aspartic peptidase, DDI1-type (Peptidase_aspartic_DDI1-type)
Type: Domain

This domain is found in eukaryotic aspartyl protease DDI1 (DNA Damage Inducible protein 1; MEROPS identifier A28.001). The remarkable structural similarity between this central domain of DDI1 and the retroviral proteases suggests that DDI1 functions proteolytically during regulated protein turnover . DDI1 has been shown to activate an endoplasmic-reticulum isoform of the transcription factor SKN-1 in Caenorhabditis elegans when the proteasome is dysfunctional . DDI1 also has an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain .
Type-F conjugative transfer system pilin assembly protein TrbC (T4SS_TrbC)
Type: Family

This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA . The N-terminal portion of these proteins is heterogeneous.
Cytochrome c oxidase caa3-type, assembly factor CtaG-related (Caa3_assmbl_CtaG-rel)
Type: Family

This entry represents the CtaG protein, required for the assembly of active caa3-type cytochrome c oxidase in Bacillus subtilis , and related proteins both from Gram-positive and Gram-negative bacteria.
Protein of unknown function DUF4870 (DUF4870)
Type: Family

This entry represents a large group of uncharacterised conserved proteins. Their function is not clear.
Uncharacterised protein family, RAQPRD (Uncharacterised_RAQPRD)
Type: Family

This entry identifies a family of proteins, around 100 amino acids in length, that include a predicted signal sequence and a perfectly conserved motif, RAQPRD, towards the C terminus. They are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae pv. tomato str. DC3000. The function of these proteins is unknown.