The 3782 annotated genes in the R. rubrum genome are sorted using three different criteria.

Genes were screened using: 1) the RPKM ratio of anaerobic:aerobic mRNA transcripts (RPKM ratio greater than 2.99); 2) closest similarity to R. ferrireducens, a RQ producing species versus R. sphaeroides, a non RQ-producing species (logRat_RrRf_to_RrRs below -5); and 3) by presence of eggNOG orthologous clusters in R. ferrireducens, but not R. sphaeroides (eggNOG_Rr-Rf-NotRs). Yellow highlighting indicates that a criterion was met. There were 45 genes that met all three criteria, and the seven highlighted in orange were selected for deletion in this study (which includes rquA, Rru_A3227). Three additional genes were selected for this study that met the first two criteria are highlighted in blue. (XLSX)