BMC Genomics 2002, 3 http://www.biomedcentral.com/1471-2164/3/8 and SbcC, which implies functional connections between the encoded proteins. Evidence is presented of convergent emergence of similar SSAP-encoding operons in different lineages and of in situ non-orthologous displacement of functionally similar genes in these operons. Materials and Methods Sequence searches of the non-redundant (NR) and the un- finished genomes databases, were done using the gapped BLAST and PSI-BLAST programs [38]. Iterative PSI-BLAST searches used for in-depth sequence analysis were done with the profile inclusion cutoff expectation value (E val- ue) set at 0.1. Multiple sequence alignments were generat- ed using the T_Coffee program [39] and the output was adjusted using PSI-BLAST search results and secondary structure predictions, which were conducted using the PHD [40,41] and Jpred [42] programs. Fold predictions were done using the 3-D position specific score matrix (3DPSSM) [43] and the Hybrid fold method [44]. Phylo- genetic analysis was carried out using the neighbor-join- ing algorithm, with subsequent local rearrangements using the maximum likelihood algorithm [45]. The ro- bustness of tree topology was assessed with 10000 Resam- pling of Estimated Log Likelihoods (RELL) bootstrap replicates. The MOLPHY and Phylip software packages were used for the analyses [46,47]. Authors' contributions Author 1 (LMI) contributed to the discovery process, preparation of the manuscript and multiple sequence alignments. Author 2 (EVK) contributed to the analysis of the predicted operons encoding RecT and SSB proteins from Gram positive bacteria, Author 3 (LA) contributed to the discovery process, preparation of the manuscript and conceived the study. References Roca AI, Cox MM: RecA protein: structure, function, and role in recombinational DNA repair. 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