For construction of the ortholog group table, the complete genomes of six organisms were analyzed, E. coli (Blattner et al. 1997), Treponema pallidum (Fraser et al. 1998) and Chlamydia trachomatis (Stephens et al. 1998) from Gram-negative bacteria, Mycoplasma genitalium (Fraser et al. 1995), Ureaplasma urealyticum , and Bacillus subtilis (Kunst et al. 1997) from Gram-positive bacteria and Archaeoglobus fulgidus (Klenk et al. 1997) from archaea. The amino acid sequences and gene locations were taken from the complete genomes section of GenBank.ftp://ncbi.nlm.nih.gov/genbank/genomes/Bacteria/
The analytical procedure consisted of the following steps. (1) All possible (7X6) organism-by-organism comparisons to catalog ortholog pairs among the seven organisms were performed. (2) Known ABC transporter proteins and their paralogs from each organism were catalogued via local blast searches. (3) Using the paralogous groups of proteins in each organisms and the orthologous relations of proteins between two organisms, a sub-table of ortholog groups for the ABC transporter proteins was constructed. (4) By examining neighbor genes on both sides of the ATP-binding protein gene in the genome, additional ABC components were uncovered.
An e value of <0.001 was used for the similarity criterion. Because the e value is dependent on the database to be searched, the value may not be identical when a pair of proteins is compared between two complete genomes depending on which genome is taken as a database. In the search of the ABC transporter proteins paralogs and orthologs, the computed similarities were manually verified.
When two genes between two organisms satisfy the similarity criterion and when both exhibit the highest similarity according to the e value and the homology search against the counterpart genome, the gene pair is defined as an ortholog. When combining the paralogous relation into an ortholog group, conflicts of relations can happen. Basically, we performed the gene cluster analysis and gave the priority of the relation in order of the forming the functional related gene cluster. When constructing an ortholog group table, separate groups in one organism can sometimes be merged into a single group because of the grouping in another organism.