Comparison of ICESt1 and ICESt3 regulation, conjugation and recombination modules. Location and orientation of ORFs and a truncated IS are indicated by arrowed boxes and a rectangle, respectively. ORF names beginning with "orf" are abbreviated with the corresponding letters or numbers. The pattern of the arrowed boxes depicts the relationships of each ORF deduced from functional analyses or from BLAST comparisons. White arrowed boxes correspond to unrelated ORFs of the two elements. Black arrowed box is the chromosomal fda gene. The grey areas indicate closely related sequences with the nucleotide identity percentage value. The angled arrows and the lollipops indicate the experimentally demonstrated promoters and rho-independent transcription terminators predicted from in silico analysis (black) or unpredicted (grey). The star corresponds to the putative transfer origin. Horizontal lines delimitate functional modules with their names above. Dashed lines indicate the A, B and C intergenic regions of both ICEs; their nucleotide sequence alignments are detailed below. (A) Region upstream from the orfQ gene, (B) Region upstream from the arp2 gene, (C) Parp2s region. The position of the ribosome binding sites (RBS), initiation and stop codons are annotated in bold. Coding regions are boxed. The -10 and -35 boxes of the promoters and transcriptional start sites (+1) determined by 5'RACE PCR are in boldface and underlined. Numbers indicate the nucleotide position on the ICE sequence [GenBank:AJ278471 for ICESt1 and GenBank:AJ586568 for ICESt3]. For region upstream from the orfQ gene (A), arrows indicate the rho-independent transcription terminator inverted repeats. For region upstream from the arp2 gene (B), horizontal lines below the sequences delimitate the putative stems regions and dashed lines indicate the loop part.
Carraro et al. BMC Microbiology 2011 11:238 doi:10.1186/1471-2180-11-238