Table 1.
Examples of control proteins used to develop the scoring scheme, and a summary of the outputs from each of ReVac’s components
| General Information | |||||||
| No | ReVac Score | Score Breakdown | Organism | Gram Stain | Type | ||
| 1 | 14.853 | 15.253–0.400 | Bordetella pertussis | – | Antigen | ||
| 2 | 13.709 | 13.709–0.000 | Non-typable Hemophilus influenzae | – | Antigen | ||
| 3 | 9.049 | 9.049–0.000 | Moraxella catarrhallis | – | Antigen | ||
| 4 | 8.192 | 8.192–0.000 | Streptococcus agalactiae A909 | + | Antigen | ||
| 5 | 6.791 | 6.791–0.000 | Streptococcus pneumoniae | + | Antigen | ||
| 6 | 6.32 | 6.520–0.200 | Neisseria meningitidis LNP21362 | – | Antigen | ||
| 7 | 5.768 | 7.768–2.000 | Streptococcus pneumoniae | + | Non Antigen | ||
| 8 | 2.475 | 5.542–3.066 | Clostridium perfringens str. 13 | + | Non Antigen | ||
| Surface Exposure Predictions | |||||||
| No. | PSORTB Localization | LipoProtein | Transmembrane Helices | Signal Peptide | SPAAN adhesin ratio | HMM mapping to surface exposed database | Annotation/GO Terms |
| 1 | OuterMembrane | SignalPeptidase I | None | MNMSLSRIVKAAPLRRTTLAMALGALGAAPAAHA | None | Positive | outer membrane autotransporter barrel|GO:0009405,GO:0015474,GO:0045203,GO:0046819 |
| 2 | OuterMembrane | SignalPeptidase II | None | MNKFVKSLLVAGSVAALAACSSSNNDA | None | Positive | peptidoglycan-associated lipoprotein|GO:0009279 |
| 3 | None | SignalPeptidase II | None | MQFSKSIPLFFLFSIPFLA | None | Positive | Bacterial extracellular solute-binding protein |
| 4 | Cellwall | SignalPeptidase I | 1 | None | 0.782535 | Positive | hypothetical protein |
| 5 | Extracellular | Intracellular | None | None | None | None | Thiol-activated cytolysin family protein|GO:0015485,GO:0009405 |
| 6 | Periplasmic | SignalPeptidase II | None | MFKRSVIAMACIFALSACG | None | None | Transferrin binding family protein|GO:0016020 |
| 7 | None | Intracellular | None | None | None | None | Capsular polysaccharide synthesis family protein |
| 8 | None | Intracellular | None | None | None | None | shikimate dehydrogenase ec::1.1.1.25|GO:0004764,GO:0009423 |
| Antigenicity Predictionsa | |||||||
| No. | Antigenicity | B cell epitopes | MHC I binding | MHC II binding | MHC binding + Antigen Processing | Immunogenicity within MHC complex | Alignment to curated epitopes |
| 1 | 45.05% | 15.16% | 94.07% | 100.00% | 61.10% | 13.08% | 26.92% |
| 2 | 30.72% | 5.23% | 96.73% | 94.12% | 79.08% | 17.65% | 99.35% |
| 3 | 44.02% | 16.03% | 94.57% | 100.00% | 69.57% | 23.91% | None |
| 4 | 50.40% | 38.97% | 83.10% | 90.46% | 43.34% | 1.79% | None |
| 5 | 43.74% | 13.80% | 95.33% | 98.94% | 73.04% | 12.10% | 22.08% |
| 6 | 30.33% | 15.16% | 81.56% | 86.68% | 46.93% | 1.84% | None |
| 7 | 48.94% | 4.61% | 96.81% | 100% | 81.91% | 30.85% | None |
| 8 | 34.32% | 7.75% | 96.31% | 98.89% | 77.49% | 16.61% | None |
| Adverse Features | |||||||
| No. | Autoimmunity with humans | Repeat regions genes & copy number | Repeat regions proteins & copy number | ||||
| 1 | None | None | |APAGGAVPGG 2||PQP 3| | ||||
| 2 | None | None | None | ||||
| 3 | None | None | None | ||||
| 4 | None | None | None | ||||
| 5 | None | None | None | ||||
| 6 | None | None | |ARFRRS 2| | ||||
| 7 | None | None | None | ||||
| 8 | 3.32% | None | None | ||||
aPercents are relative to the length of the amino acid sequence