Table 2. Results of the computational and experimental phases for the candidate proteins, positive and negative controls.
| Computational phase | Experimental phase | |||||||||||||
| Proteins | Cleavage site | PA-SUB v.2.5 | Gpos-PLoc | PSORTb v. 2.0.4 | TMHMM 2.0 (PredHel) | Phobius | TPS | SF | IEM | |||||
| Score | Position | C | E | PM | TM | SP | ||||||||
| SignalP 3.0 | Rv0200 (+) | 0.885 | between positions 23 and 24 | − | − | + | plasma membrane | cytoplasmic membrane | 3 | 3 | − | + | + | + |
| Rv1733c | 0.974 | between positions 62 and 63 | − | − | + | plasma membrane | unknown | 2 | 2 | − | − | − | NA | |
| Rv0403c | 0.974 | between positions 33 and 34 | − | − | + | plasma membrane | cytoplasmic membrane | 2 | 0 | + | + | + | + | |
| TatP 1.0 | Rv1280c (+) | 0.819 | between positions 41 and 42: ATA-GA | − | + | − | cytoplasm | unknown | 1 | 0 | + | + | − | + |
| Rv3069 | 0.853 | between positions 30 and 31: ALA-IP | − | − | + | plasma membrane | cytoplasmic membrane | 4 | 3 | + | − | − | NA | |
| Rv3630 | 0.813 | between positions 39 and 40: GTA-AA | − | − | + | plasma membrane | cytoplasmic membrane | 11 | 12 | − | + | − | + | |
| LipoP 1.0 | Rv0418 (+) | 0.954 | between positions 24–25: FLTTG-CIRWS Pos+2 = I | − | + | − | cytoplasm | extracellular | 1 | 0 | + | + | − | + |
| Rv1022 | 0.941 | between positions 23–24: LLASS-CTWQL Pos+2 = T | + | − | − | cytoplasm | unknown | 1 | 0 | + | − | + | + | |
| Rv0835 | 11.3 | between positions 22–23: IATTA-CSFQA Pos+2 = S | − | − | + | cytoplasm | cytoplasmic | 0 | 0 | + | + | + | + | |
| SecretomeP 2.0 | Rv0556 (+) | 0.829 | NA | − | − | + | plasma membrane | cytoplasmic membrane | 2 | 2 | − | + | − | + |
| Rv0361 | 0.924 | NA | − | − | + | cytoplasm | unknown | 1 | 1 | − | + | + | + | |
| Rv0178 | 0.790 | NA | − | − | + | extracellular | unknown | 1 | 1 | − | + | + | + | |
| Negative controls | Rv0126 (−) | NA | NA | + | − | − | cytoplasm | cytoplasmic | 0 | 0 | − | + | − | + |
| Rv1326c (−) | NA | NA | + | − | − | cytoplasm | cytoplasmic | 0 | 0 | − | − | − | NA | |
PredHel: number of transmembrane helices predicted by TMHMM 2.0; (+): positive control proteins, (−): negative control proteins; PA-SUB v.2.5 predictions are classified as: NA: Not applicable. C: cytoplasmic; E: extracellular; PM: plasma membrane. In Phobius predictions: TM indicates the number of predicted transmembrane segments, SP: indicates if there is a predicted signal peptide. TPS: Protein recognition by the specific immune sera in M. tuberculosis H37Rv total protein sonicate; SF: Protein recognition by the specific immune sera in M. tuberculosis H37Rv membrane and culture filtrate (for positive controls and candidate proteins) or cytoplasm (for negative controls) by subcellular fractionation. IEM: Protein recognition on the surface of intact M. tuberculosis H37Rv bacillus by immune electron microscopy. None of these proteins was part of the training data sets of any of the Machine Learning tools.