SII-SWORD/CoKE huggingface dataset:
Restriction endonuclease, type II, DpnII (Restrct_endonuc_II_DpnII)
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 type II restriction enzymes such as DpnII (

), which recognises the double-stranded unmethylated sequence GATC and cleave before G-1 .
Uncharacterised conserved protein UCP031578, VanZ/RDD-type (UCP031578_Vanz/RDD)
Type: Family

This entry represents an uncharacterised protein with VanZ and RDD domains.
BPI fold-containing family B member 1 (Bpifb1)
Type: Family

This entry represents long palate, lung and nasal epithelium carcinoma-associated protein 1 (Lplunc1), also known as BPI fold-containing family B member 1, which belongs to the palate, lung, and nasal epithelium clone (PLUNC) family. It is a small secreted protein expressed in the oropharynx and upper airways of humans, mice, rats, and cows . It may play a role in innate immunity in the mouth, nose and lungs and in the formation of the left-right axis in the node of the developing embryo .
Uncharacterised protein family, dehydrogenase DR0790 type, predicted (Uncharacterised_DHase_DR0790)
Type: Family

This entry represents a predicted dehydrogenase, designated as DR0790.
Ubiquinol cytochrome c reductase, cytochrome c1 subunit, predicted (Ubol_Cyt_c_Rdtase_Cyt_c_su_prd)
Type: Family

This entry contains putative Ubiquinol cytochrome c reductase, cytochrome c1 subunit proteins found in some Proteobacteria and Aquificae. They are not characterised at present.
PdxT/SNO family, conserved site (PdxT/SNO_CS)
Type: Conserved_site

The term vitamin B6 is used to refer collectively to the compound pyridoxine and its vitameric forms, pyridoxal, pyridoxamine, and their phosphorylated derivatives. Vitamin B6 is required by all organisms and plays an essential role as a co-factor for enzymatic reactions. Plants, fungi, bacteria, archaebacteria, and protists synthetize vitamin B6. Animals and some highly specialised obligate pathogens obtain it nutritionally. Vitamin B6 has two distinct biosynthetic pathways, which do not coexist in any organism. The pdxA/pdxJ pathway, that has been extensively characterised in Escherichia coli, is found in the gamma subdivision of the proteobacteria. A second pathway of vitamin B6 synthesis involving the pdxS/SNZ and pdxT/SNO protein families, which are completely unrelated in sequence to the pdxA/pdxJ proteins, is found in plants, fungi, protists, archaebacteria, and most bacteria.

PdxS/SNZ and pdxT/SNO proteins form a complex which serves as a glutamine amidotransferase to supply ammonia as a source of the ring nitrogen of vitamin B6 . PdxT/SNO and pdxS/SNZ appear to encode respectively the glutaminase subunit, which produces ammonia from glutamine, and the synthase subunit, which combines ammonia with five- and three-carbon phosphosugars to form vitamin B6 .

The pdxT/SNO family belongs to the triad glutamine aminotransferase fold, characterised by a conserved Cys-His-Glu active site . Two regions are highly conserved across all taxa, the PGGEST motif and the FHPE(LT) motif . PdxT/SNO proteins are an α/β three-layer sandwich containing a seven- stranded twisted mixed parallel β-sheet flanked by a six α-helices on the N-terminal stretch of the sheet, four on one side and two on the other .

Proteins belonging to the pdxT/SNO family include:

Bacillus subtilis glutamine amidotransferase subunit pdxT

Haemophilus influenzae glutamine amidotransferase subunit pdxT

Methanococcus jannaschii glutamine amidotransferase subunit pdxT

Yeast probable glutamine amidotransferase SNO1

Yeast probable glutamine amidotransferase SNO2

Yeast probable glutamine amidotransferase SNO3

These are hydrophilic proteins of about 19 to 25 Kd.

This entry represents a conserved site containing the PGGEST motif.
Cross-wall-targeting lipoprotein motif (Cross-wall-target_lipo_motif)
Type: Conserved_site

The N-terminal YSIRK signal domain targets proteins to the cross-wall, or septum, of dividing Gram-positive bacteria. Lipoprotein signal motifs direct a characteristic N-terminal cleavage and lipid modification for membrane anchoring. This Streptococcal-only signal peptide variant appears to be a hybrid between the two, likely directing protein targeting of nascent surface lipoproteins to the cross-wall. Nearly all members of this family have the characteristic LPXTG cell wall anchor signal at the C terminus.
Pyridoxamine 5'-phosphate oxidase, plant (Pyridox_Oxase_pln)
Type: Family

This entry represents plant-specific pyridoxine/pyridoxamine 5'-phosphate oxidase 1 (PPOX1 or PDX3) . It is involved in the salvage pathway of pyridoxal 5'-phosphate (vitamin B6) .
Cytadherence high molecular weight protein 1 N-terminal (Cytadherence_HMW-1_N)
Type: Domain

This entry describes the N-terminal region of the Mycoplasma cytadherence protein high molecular weight protein 1 (HMW1), up to but not including the first EAGR box domain. The apparent orthologs in different Mycoplasma species differ profoundly in archictecture C-terminally to the region described by this entry.
Conserved hypothetical integral membrane protein (CHIM_prot)
Type: Family

This entry represents a small clade that correlates (by both gene clustering and phyletic pattern) to the three gene system that includes

,

and

found in several Gram-positive bacteria, where

(XrtG) is distantly related to exosortases. Both this narrow clade, and the larger set of full-length homologous integral membrane proteins, have an especially well-conserved region near the C-terminal with an invariant tyrosine. This homology suggests glycosyltransferase activity .
Leader peptide, exosporium (Leader_pep_exosporium)
Type: Domain

This domain is found as a leader peptide in at least two proteins targeted to the exosporium, a structure that occurs as the outermost layer of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis spores. The exosporium consists of a basal layer and a nap of hair-like filaments. BclA, the major protein of the nap filaments, is targeted there by this leader peptide .
Apoptosis inhibitor Rv3654c-like (Rv3654c-like)
Type: Family

This family of proteins from Actinobacteria includes apoptosis inhibitor Rv3654c. Rv3654c is one of two proteins identified in Mycobacterium tuberculosis which are secreted into the host macrophage cytoplasm to suppress apoptosis by blocking the extrinsic pathway, a mechanism to avoid the host defense. Rv3654c recognizes the polypyrimidine tract binding Protein-associated Splicing Factor (PSF) and cleaves it, diminishing the availability of caspase-8 .
Muellerian-inhibiting factor (Muellerian-inhibiting_factor)
Type: Family

Muellerian-inhibiting factor, a member of the transforming growth factor beta family, is a glycoprotein hormone that is structurally related to inhibin and activin. It is expressed in male embryos, preventing formation of the Muellerian ducts . Expression levels in males remain high in early years, but decline around the time of puberty. In females the protein is not detectable until the onset of puberty, where it is expressed in the ovaries and is involved in folliculogenesis . It is also able to inhibit the growth of tumours derived from tissues of Muellerian duct origin.
Integrating conjugative element protein, PFL4711 (Integr_conj_element_PFL4711)
Type: Family

Members of this protein family are found in genomic regions associated with conjugative transfer and integrated TOL-like plasmids. The specific function is unknown.
Lantibiotic ABC transporter permease subunit, SpaE/MutE/EpiE-like (Lanti_perm_SpaE/MutE/EpiE-like)
Type: Family

represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family is largely restricted to gallidermin-family lantibiotic cassettes, but also include orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes. In most species, this subunit is paralogous to an adjacent gene. This entry represents lantibiotic ABC transporter permease subunits SpaE/MutE/EpiE-like, which are highly hydrophobic, integral membrane proteins, and part of the bacitracin ABC transport system that confers resistance to the Gram-positive bacteria in which this system operates .
MprA protease C-terminal rhombosortase-interaction domain (MprA_tail)
Type: Domain

This entry describes the Ralstonia lineage variant of the GlyGly-CTERM domain (

) . This is a predicted target for protein sorting and cleavage by rhombosortase, a member of the family of rhomboid proteases. The domain occurs in MprA proteases, which are predicted to be serine proteases.
Integrating conjugative element protein, PFL4705 (Integr_conj_element_PFL4705)
Type: Family

Proteins in this entry are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Exosporium BclB, C-terminal domain (Exosporium_BclB)
Type: Domain

This domain occurs as the C-terminal region in a number of proteins that have extensive collagen-like triple helix repeat regions. Member domains are predicted by TmHMM to have four or five transmembrane helices. Proteins in this entry are found mostly in the Firmicutes, but also in Acanthamoeba polyphaga mimivirus. This entry includes spore surface glycoprotein BclB from Bacillus anthracis, a protein of the exosporium. The exosporium is an additional outermost spore layer, lacking in Bacillus subtilis and most other spore formers, consisting of a basal layer and, above it, a nap of fine filaments.

Proteins containing this domain also include some uncharacterised virus proteins.
Sorting assembly machinery 35kDa subunit (SAM35)
Type: Family

SAM35 is a component of the mitochondrial outer membrane sorting assembly machinery (SAM) complex. It is crucial for the assembly pathway of outer membrane β-barrel proteins, such as the precursors of Tom40 and porin .
Domain of unknown function DUF2760 (DUF2760)
Type: Domain

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF2567 (DUF2567)
Type: Family

This is a bacterial family of proteins with unknown function.
Protein of unknown function DUF2568 (DUF2568)
Type: Family

One member in this family is annotated as yrdB which is part of a four gene operon however currently no function is known.
Protein of unknown function DUF2752 (DUF2752)
Type: Family

This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Protein of unknown function DUF2722 (DUF2722)
Type: Family

This eukaryotic family of proteins has no known function.
Spiroplasma phage 1-C74, Orf10 (Phage_1-C74_Orf10)
Type: Family

This entry is represented by Spiroplasma phage 1-C74, Orf10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

Members in this family of proteins are also annotated as Plectrovirus orf 10 transmembrane proteins however currently no function is known.
Protein of unknown function DUF2784 (DUF2784)
Type: Family

This is a family of uncharacterised protein. The function is not known however it is conserved in Bacteria.
Protein of unknown function DUF2703 (DUF2703)
Type: Family

This family of protein has no known function.
Protein of unknown function DUF2686 (DUF2686)
Type: Family

Some members in this family of proteins are annotated as yjfZ however currently no function is known.
Protein fil (Fil)
Type: Family

This entry represents Protein fil from Escherichia phage 186 (Bacteriophage 186). Fil is thought to cause filamentation. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function DUF2714 (DUF2714)
Type: Family

This family of proteins with unknown function appears to be restricted to Mycoplasmataceae.
Abortive phage resistance protein AbiGi (AbiGi)
Type: Family

This is a bacterial family of proteins with unknown function. AbiGi is a family of putative type IV toxin-antitoxin system antitoxins. The AbiG abortive phage resistance system affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis .
Protein of unknown function DUF2690 (DUF2690)
Type: Family

This bacterial family of proteins has no known function.
Tlde1 domain (Tlde1_dom)
Type: Domain

This domain is found in Tlde1 family of antibacterial effectors secreted by the type VI secretion system (T6SS). Tlde1 family is evolutionarily related to l, d transpeptidases which form mDAP3-mDAP3 peptidoglycan crosslinks. Tlde1 family is widespread among Proteobacteria and is divided into three subfamilies (Tlde1a, Tlde1b and Tlde1c) .
Phage gene 29 protein (Phage_gene29)
Type: Family

This entry represents a family of phage proteins related to gene 29 protein from Mycobacterium phage D29 and L5. The function of the proteins in this family is unknown. AlphaFold multimer shows that the proteins in the family adopt a confident dimeric structure. The individual proteins are not compact in isolated structure predictions.
BREX system ATP-binding protein BrxD (BrxD)
Type: Family

This is a family of proteins found in bacterial proteins associated with Bacteriophage Exclusion (BREX) system, a defense system that allows bacteriophage adsorption but blocks phage DNA replication . This family represents the ATP-binding protein BrxD .
Protein of unknown function DUF2800 (DUF2800)
Type: Family

This is a family of uncharacterised proteins found in bacteria and viruses.
Protein of unknown function DUF2810 (DUF2810)
Type: Family

This is a bacterial family of uncharacterised proteins.

This entry contains YibL (

), which comigrates with the mature 50S ribosome subunit. It either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles .
Protein of unknown function DUF2811 (DUF2811)
Type: Family

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF2735 (DUF2735)
Type: Family

Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed.
Protein of unknown function DUF2783 (DUF2783)
Type: Family

This is a bacterial family of uncharacterised protein.
Protein of unknown function DUF2827 (DUF2827)
Type: Family

This is a family of uncharacterised proteins found mostly in Burkholderia.
Protein of unknown function DUF2637 (DUF2637)
Type: Family

This family of proteins has no known function.
Uncharacterised protein family YfdX (Uncharacterised_YfdX)
Type: Family

YfdX is a protein found in Proteobacteria of unknown function. The protein coding for this gene is regulated by EvgA in Escherichia coli .
Leader peptide SpeFL (SpeFL)
Type: Family

SpeFL is a small protein (arrest peptide) encoded upstream of inducible ornithine carboxylase gene (speF) that controls expression of downstream genes (speF and patE) by nascent chain-translational arrest and transcriptional attenuation . Ornithine capture by a translating ribosome controls bacterial polyamine synthesis, inducing the expression of ornithine decarboxylase SpeF4, in a mechanism involving ribosome stalling and transcription antitermination .
Protein of unknown function DUF2620 (DUF2620)
Type: Family

This is a bacterial family of proteins with unknown function.
Protein of unknown function DUF2625 (DUF2625)
Type: Family

Some members in this family of proteins are annotated as ybfG however currently no function is known.
Protein of unknown function DUF2776 (DUF2776)
Type: Family

This bacterial family of proteins has no known function.
Peptidoglycan-binding protein, CsiV (CsiV)
Type: Family

CsiV, a small periplasmic protein (cell-shape integrity in Vibrio), is essential for growth of Vibrio cholerae in the presence of DAA, non-canonical amino-acids, the typical components of peptidoglycan side-chains in Vibrio cholerae. CsiV interacts with LpoA, the lipoprotein activator of penicillin-binding-protein1A that is necessary for mediating the assembly of peptidoglycan. CsiV acts through LpoA to promote peptidoglycan biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found .
Protein of unknown function DUF2799 (DUF2799)
Type: Family

Some members in this family of proteins are annotated as yfiL which has no known function.
Protein of unknown function DUF2804 (DUF2804)
Type: Family

This is a family of proteins with unknown function. Members are predicted to fold into a double barrel-like structure consisting of two co-join barrels predicted to be structurally similar to

, with a lipocalin fold (

) .
Protein of unknown function DUF2802 (DUF2802)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF2790 (DUF2790)
Type: Family

This family of proteins with unknown function appear to be restricted to Pseudomonadaceae.
Protein of unknown function DUF2797 (DUF2797)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF2785 (DUF2785)
Type: Family

Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family has no known function.
Protein of unknown function DUF2787 (DUF2787)
Type: Family

This family of proteins, predominantly found in Gammaproteobacteria, has no known function. The conserved hypothetical protein VC1805 from Vibrio cholerae is included in this entry. VC1805 adopts a monomeric assembly, showing an unusual topology with a flat seven-stranded anti-parallel β-sheet and two helices located on the same side of the sheet. It has some structural homology with the human protein p32 and binds to the complement protein C1q, which suggests a possible role in the adherence of the bacteria to the intestinal wall .
Protein of unknown function DUF2788 (DUF2788)
Type: Family

This bacterial family of proteins have no known function.
Protein of unknown function DUF2789 (DUF2789)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF2793 (DUF2793)
Type: Family

This family of proteins currently has no known function.
Protein of unknown function DUF2794 (DUF2794)
Type: Family

This is a bacterial family of proteins with unknown function.
Zinc-specific solute binding protein ZrgA (ZrgA-like)
Type: Family

This entry, previously known as DUF2796, represents the zinc-specific solute binding protein ZrgA homologues found predominantly in gammaproteobacteria. ZrgA is an important component of the zrgABCDE operon in Vibrio parahaemolyticus and Vibrio cholerae. It is anticipated to function as a solute binding protein (SBP) for the ZrgBC permease/ATPase transporter system as it is required for a normal growth and survival in zinc-deficient conditions .

The wild type ZrgA can bind up to 10 zinc ions with four high-affinity zinc binding sites . The structures of ZrgA from Vibrio cholerae and its homologue, protein PA4063 from Pseudomonas aeruginosa, were determined bound to zinc,

and

, respectively . These proteins adopt an α/β structure consisting of a six-stranded meander β-sheet and two α-helices packed on it with an unique topology.
Protein of unknown function DUF2806 (DUF2806)
Type: Family

This bacterial family of proteins has no known function.
Putative auto-transporter adhesin, head GIN domain (DUF2807)
Type: Domain

Proteins containing this domain show structural similarity to other pectin lyase families. Although these proteins align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In

, it is interesting to note that the polypeptide contains several well defined sequence repeats, centred around GSG motifs defining the tight β-turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two. It seems likely that proteins in this entry belongs to the superfamily of trimeric auto-transporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens . In the case of Parabacteroides distasonis, which is a component of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN).
Protein of unknown function DUF2808 (DUF2808)
Type: Family

This family of proteins with unknown function are mostly from Cyanobacteria.
Protein of unknown function DUF2809 (DUF2809)
Type: Family

Some members in this family of proteins are annotated as yjgA however currently no function for the protein is known.
Epiplasmin protein (Epiplasmin)
Type: Family

This entry represents a group of epiplasmins, which are multigene family in Paramecium. They make up a scale structure called the epiplasm under the cell .
Protein of unknown function DUF2817 (DUF2817)
Type: Family

This family of proteins has no known function.
Lipid II flippase Amj (Amj)
Type: Family

This entry includes lipid II flippase Amj, which is required for bacterial cell wall synthesis. It transports lipid-linked peptidoglycan precursors from the inner to the outer surface of the cytoplasmic membrane .