TABLE 1.
R. typhi signal peptide predictions and PhoA assay resultsa
| Signal Peptide Analysis | Signal peptide prediction by the following algorithms:
|
Total unique proteins with predicted signal peptides | |||
|---|---|---|---|---|---|
| Phobius | LipoP 1.0 | SignalP 3.0 (NN) | SignalP 3.0 (HMM) | ||
| Proteins with predicted signal peptides | 106 | 67 | 136 | 106 | 191 |
| Signal peptides tested (′PhoA assay) | 74 | 58 | 77 | 73 | 102 |
| Positive signal peptides | 66 | 55 | 65 | 66 | 84 |
| Percent positive signal peptides of those tested | 89% | 95% | 84% | 90% | 82% |
a
For each algorithm used to identify putative R. typhi signal peptides, the predicted number of signal peptides, the number tested by PhoA fusions, and the number found to function in E. coli are listed. The consolidated results for the total number of signal peptides identified across all the programs are presented in the final column. Results stratified by all the different combinations of the algorithms are presented in Table S4 in the supplemental material.