Table 3.
Unique CDS of M. parvum strain Indiana and M. suis strain Illinois: subcellular localization and protein sorting signals (PSORTb v3.0.2), presence of signal peptide cleavage sites (SignalP), and presence of lipoproteins (LipoP).
| Software & parameters | M. parvum - unique CDS not in paralogous families | M. parvum - unique CDS in paralogous families | M. suis - unique CDS not in paralogous families | M. suis - unique CDS in paralogous families |
|---|---|---|---|---|
| PSORTb | ||||
| Subcellular localization: | ||||
| Unknown | 34 (54.0%) | 37 (57.8%) | 83 (54.2%) | 125 (66.5%) |
| Cytoplasmic Membrane | 13 (20.6%) | 3 (4.7%) | 31 (20.3%) | 12 (6.4%) |
| Cytoplasmic | 11 (17.5%) | 23 (35.9%) | 29 (18.97%) | 43 (22.9%) |
| Extracellular | 5 (7.9%) | 1 (1.6%) | 10 (6.53%) | 8 (4.2%) |
| Features: | ||||
| 1 internal helix found | 30 (47.6%) | 20 (31.25%) | 77 (50.3%) | 153 (81.4%) |
| 2 internal helices found | 0 | 0 | 7 (4.6%) | 0 |
| 3 internal helices found | 0 | 0 | 2 (1.3%) | 0 |
| Signal peptide detected | 3 (4.8%) | 1 (1.6%) | 18 (11.8%) | 31 (16.5%) |
| None | 30 (47.6%) | 43 (67.15%) | 49 (32%) | 4 (2.1%) |
| SignalP | ||||
| YES | 3 (4.8%) | 0 | 11 (7.2%) | 8 (4.2%) |
| NO | 60 (95.2%) | 64 (100%) | 142 (92.8%) | 180 (95.8%) |
| LipoP | ||||
| SpI | 8 (12.7%) | 9 (14.0%) | 36 (23.5%) | 65 (34.6%) |
| SpII | 0 | 1 (1.6%) | 1 (0.65%) | 1 (0.53%) |
| TMH | 2 (3.2%) | 3 (4.7%) | 18 (11.8%) | 29 (15.4%) |
| None | 53 (84.1%) | 51 (79.7%) | 98 (64.05%) | 93 (49.47%) |
| Total | 63 | 64 | 153 | 188 |
PSORTb: results were obtained using the output for Gram-negative bacteria without outer membrane.
SignalP: YES: signal peptide present, NO: signal peptide absent.
LipoP: SpI: signal peptide (signal peptidase I), SpII: lipoprotein signal peptide (signal peptidase II), TMH: n-terminal transmembrane helix. Note from the software: TMH is generally not a very reliable prediction and should be tested. This part of the model is mainly there to avoid transmembrane helices being falsely predicted as signal peptide.