Figure 2

In silico analysis of integrase promoters. (A) Alignment of representative promoter regions of Vibrionaceae intIA homologs. Putative LexA binding sequences are boxed, whereas putative σ70 promoter elements (-35 and -10) are underlined, and the translation start site of intIA is boxed and in bold type. The multiple sequence alignment was performed using CLUSTALW with default parameters [89]. (B) Representative examples of LexA binding sites identified upstream of different integrase genes from mobile integrons, with (1-5) denoting the integrase class. The provided accessors correspond to IntI proteins from: Escherichia coli pSa (AAA92752), Providencia stuartii ABR23a (ABG21674), Serratia marcescens AK9373 (BAA08929), Vibrio cholerae 569B (AAC38424) and Vibrio salmonicida VS224 pRVS1 (CAC35342). (C) Sequence logos [100] of the profile used to search for β/γ-Proteobacteria LexA binding sites (top) and the profile emerging from the 93 distinct binding sites located (bottom). Lan = Listonella anguillarum; Lpe_CIP = L. pelagia CIP 102762T; Val_12G01 = Vibrio alginolyticus 12G01; Vch_N16961 = V. cholerae O1 biovar Eltor str. N16961; Vha_ATCC = Vibrio harveyi ATCC BAA-1116; Vha_HY01 = V. harveyi HY01; Vme = Vibrio metschnikovii; Vmi = Vibrio mimicus; Vna_CIP = Vibrio natriegens strain CIP 10319; Vpa = Vibrio parahaemolyticus; Vpa_RIMD = V. parahaemolyticus RIMD 2210633; Vsh_AK1 = Vibrio shilonii AK1; Vsp_DAT722 = Vibrio sp. DAT722; Vsp_Ex25 = Vibrio sp. Ex25; Vvu_CIP754 = Vibrio vulnificus CIP 75.4; Vvu_YJ016 = V. vulnificus YJ016 (see Additional file 11 for corresponding accession numbers).