Table 4.
Functional protein CDSs that overlap t(m)RNA genes.
| Valid t(m)RNA | Question-able tRNA | Top Pfam domain of CDSs overlapping valid t(m)RNA | No. top Pfam | Settings for top Pfam | |
|---|---|---|---|---|---|
| No. t(m)RNA | 115660 | 4809 | |||
| Overlapping Pfam CDS | 828 | 1364 | |||
| Same orientation | 379 | 735 | |||
| CDS upstream | 250 | 244 | FTSW_RODA_SPOVE | 44 | All 44 are tRNAIle-CAT in Helicobacter |
| CDS downstream | 106 | 186 | Aminotran_3 | 9 | 8 are tRNALeu-CAA in Prochlorococcus |
| CDS internal | 0 | 92 | – | – | – |
| CDS spanning | 23 | 213 | GTP_EFTU | 6 | All 6 are tRNASec in Rhizobiales |
| Opposite orientation | 449 | 629 | |||
| CDS upstream | 23 | 187 | RNB (RNase R) | 4 | All 4 are tRNALeu-CAG in Burkholderiaceae |
| CDS downstream | 381 | 186 | Resolvase | 72 | Diverse settings |
| CDS internal | 0 | 83 | – | – | – |
| CDS spanning | 45 | 173 | Resolvase | 16 | Diverse settings |
Of the 6,489,445 original NCBI protein calls in the 2031 bacterial genome projects, 5,805,765 were positive for functionality with the Pfam/HMMER system (testing Pfam-A and Pfam-B) or with the CDD/RPSBLAST system, and were tested for overlap with either tmRNA genes from the tmRNA Website or tRNA genes found with a combination of tRNAscan-SE and Aragorn (see Materials and Methods for distinction between “valid” and “questionable” tRNAs).