Table 3.
Prediction of signal peptides of proteins identified in the culture supernatant
| Protein | Signal peptide probability | Maximum cleavage site probability | Predicted signal length (aa) | Predicted signal peptide | Predicted secretion system | Predicted function |
| RL0196 | 1.000 | 0.999 | 20 | MKKSLLTLFAVAAMSTTALA | GEP | basic membrane lipoprotein |
| RL0489 | 1.000 | 1.000 | 23 | MKKSVLAFGALALGVTFSAPVMA | GEP | sugar-binding protein |
| RL0518 | 1.000 | 1.000 | 32 | MSIVKSLLSRRAFTALAGAAVIATAMPAPSFA | TAT | ribose-binding protein |
| RL0778 | 1.000 | 0.956 | 23 | MKKISVLLAATALISVMATSAWS | GEP | dipeptide-binding protein |
| RL1369 | 0.999 | 0.803 | 25 | MAMHGSSLGLLALVLLAFPPVAARA | GEP | pentapeptide repeat protein |
| RL2375 | 1.000 | 0.944 | 24 | MKKLALALAATAALVLSIGSAAEA | GEP | basic membrane lipoprotein |
| RL2404 | 1.000 | 0.983 | 23 | MKLFYLAFAGVLYLASFAGDAFA | GEP | peptidyl prolyl cis-trans isomerase |
| RL2697 | 0.999 | 0.933 | 28 | MMNIAGLGRLAAATVVLSGLAFGSAVKA | GEP | COG3184 |
| RL2753 | 1.000 | 1.000 | 25 | MLNSTRIFAAASIAAMSLFAGSAMA | GEP | arginine/ornithine-binding protein |
| RL3329 | 1.000 | 0.975 | 25 | MHRSLASCSALALLFALALAGGAAA | GEP | membrane bound lytic tranglycosylase |
| RL3745 | 1.000 | 0.999 | 23 | MKKSLLSAVALTAMVAFSGNAWA | GEP | Leu/Ile/Val-binding protein (BraC) |
| RL4218 | 1.000 | 0.998 | 22 | MTLRTFLLGACSALAFAGMASA | GEP | sorbitol-binding protein |
| RL4651 | 1.000 | 1.000 | 29 | MTKLNRNFRMLSAGAALSLLMMAAPSAFA | GEP | dipeptide-binding protein |
| pRL90140 | 0.000 | 0.000 | - | - | PrsDE | parallel beta-helix repeat protein |
| pRL100309 | 0.000 | 0.000 | - | - | PrsDE | cadherin-like protein |
| pRL100451 | 0.000 | 0.000 | - | - | PrsDE | RapA2 |
| RL1580 | 0.000 | 0.000 | - | - | PrsDE | nucleoside diphosphate kinase |
| RL2412 | 0.000 | 0.000 | - | - | PrsDE | glycosyl hydrolase |
| RL2961 | 0.000 | 0.000 | - | - | PrsDE | cadherin-like protein |
| RL3024 | 0.000 | 0.000 | - | - | PrsDE | PlyB |
| RL0718 | 0.002 | 0.001 | - | - | Flagellum | flagellin |
| RL0720 | 0.012 | 0.005 | - | - | Flagellum | flagellin |
| RL0728 | 0.032 | 0.029 | - | - | Flagellum | flagellar hook |
Signal peptide prediction was done using the hidden Markov model of the SignalP 3.0 software [66]. Probabilities for the presence of a signal peptide and for the correct identification of the cleavage site are given. The TAT signal prediction software TATP 1.0 predicts the same signal peptide length for the predicted TAT substrate RL0518. The twin-arginine motif of the RL0518 protein is in bold. The prediction of the secretion system involved in the export of the identified proteins was based on signal peptide prediction (GEP and TAT), observed absence from the culture supernatant of the prsD mutant (PrsDE) and similarity to known proteins (Flagellum).