Table 4. Potential T3S proteins in representative species predicted by T3SEpre (5 with highest prediction scores were given for each species).
| Species | Protein | SVM_Value |
| Agrobacterium (NC_003062) | NP_353267.1 | 1.8262186013 |
| (Gram −; no reported T3SS) | NP_353197.1 | 1.8182696817 |
| NP_354762.2 | 1.3438005288 | |
| NP_353597.1 | 1.3053632004 | |
| NP_529196.1 | 1.1505788212 | |
| Helicobacter (NC_000915) | NP_208221.1 | 1.2728691623 |
| (Gram −; no T3SS) | NP_208270.1 | 0.81876863031 |
| NP_207400.1 | 0.79814466522 | |
| NP_207364.1 | 0.76127749423 | |
| NP_208245.1 | 0.74734863579 | |
| Mycobacterium (NC_002755) | NP_334701.1 | 2.5282200382 |
| (Gram −; no T3SS) | NP_334584.1 | 2.1134425698 |
| NP_338544.1 | 2.091326393 | |
| NP_337005.1 | 1.8061094469 | |
| NP_337833.1 | 1.7706735128 | |
| Staphylococcus (NC_013450) | YP_003281316.1 | 1.1964289751 |
| (Gram +; no T3SS) | YP_003282311.1 | 1.1653620221 |
| YP_003281905.1 | 0.99871685539 | |
| YP_003281879.1 | 0.82115720581 | |
| YP_003282635.1 | 0.70904028709 | |
| Streptococcus (NC_011900) | YP_002511184.1 | 0.86992793954 |
| (Gram +; no T3SS) | YP_002510266.1 | 0.86910627471 |
| YP_002510762.1 | 0.73099842015 | |
| YP_002511727.1 | 0.63822324187 | |
| YP_002511008.1 | 0.60030423151 | |
| Yeast (S288c; no T3SS) | DAA10219.1 | 2.9246207038 |
| DAA07267.1 | 2.9232109626 | |
| DAA10797.1 | 2.7428577459 | |
| DAA09242.1 | 2.6276802073 | |
| DAA08250.1 | 2.3665151381 |