Figure 2

Multialignment of RecA from different bacteria and E. coli RecA variants characterized in the study. The sequences aligned are from the following organisms. AML00775: Escherichia coli str. K-12 substr. MG1655 RecA; WP_038923633: Dickeya dadantii strain 3937 RecA; AAG07005: Pseudomonas aeruginosa PAO1 RecA; and AAF11887: Deinococcus radiodurans R1 RecA. The three E. coli variants EcRecAV1, EcRecAV2 and EcPa were also aligned. The filled red boxes indicate strict identity between residues, and the filled yellow boxes indicate strong homology between residues. No difference is made between black and red characters in this case because this feature is applied for other usages. At the top of the first sequence, the 2D structure of E. coli RecA is shown: the squiggles represent α-helices; the arrows, β-strands; the TT letters, strict β-turns; and the star, a residue with multiple conformations revealed by crystallography. The 2D structure is from the PDB entry 4TWZ. Additionally, the different domains of RecA are indicated in boxes: in red, the N-terminal domain (NTD); in pink, the ATP binding site; in blue, the hydrolytic residue and the hydrolytic motif; in orange, site I; in cyan, site II; in yellow, the dsDNA gateway in the CTD; and in green, the C-tail and the Mg²⁺ binding sites. The first methionine is present in the alignments to allow the program to perform well. Thus, the numbering of each amino acid is shifted by one in the figure compared to the text. For example, in EcRecA, L29 is in the 30^th position in the figure. The figure was generated using the ENDscript server²⁷.