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Figure 2 | BMC Structural Biology

Figure 2

From: Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches

Figure 2

Novel PD-(D/E)XK nuclease families. Multiple sequence alignment of representative sequences from newly detected families and selected PD-(D/E)XK nuclease structures for the conserved structural core. Sequences are labeled according to gi number or PDB code and an abbreviation of the species name: Ac Azotobacter chroococcum, Ap Aeropyrum pernix, At Arabidopsis thaliana, Ba Bacillus anthracis, Bc Bacillus cereus, Bf Bacteroides fragilis, Ca Chloroflexus aurantiacus, Cs Chromohalobacter salexigens, Ct Clostridium tetani, Ec Escherichia coli, Fn Fusobacterium nucleatum, Mh Methanospirillum hungatei, Mtr Medicago truncatula, Mth Methanothermobacter thermautotrophicus, Os Oryza sativa, Pa Pyrobaculum aerophilum, Ph Pyrococcus horikoshii, Pp Pinus pinaster, Sp Sodalis phage, Ss Sulfolobus solfataricus, St Sulfolobus tokodaii, Vc Vibrio cholerae, Yp Yersinia pesti. Sequence gi numbers are colored according to taxonomy: with bacterial in black, archeal in red, eukaryotic in blue and viral in green. The first and last residues numbers are indicated before and after each sequence with total sequence length following in square bracket. The numbers of excluded residues are specified in parentheses. Residue conservation is denoted with following scheme: uncharged, highlighted in yellow; charged or polar highlighted in grey; small, letters in red. Active site PD-(D/E)XK signature residues are highlighted in black while other conserved polar/charged residues in alternative active site positions are highlighted in blue. Restriction endonuclease-like motifs (I-IV) are labeled on the top. Predicted (gi:42571125, gi:3257283, gi:15622690, gi:88603216 and gi:75241498) and observed (pdb:1hh1) secondary structure elements (E, β-strand; H, α-helix) are indicated above the sequences. Italicized sequence corresponds to domain-swapped region of 1fzr.

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