Table 2.
In silico prediction of signal peptides for LKADH
| Protein Name |
SignalP analysis
|
Philius analysis
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| n-region | h-region | c-region | Cleavage Site | C-score | Y-score | S-score | S-mean | D-score | Type confidence | |
| PPB_ECOLI | 1-4(4) | 5-15(11) | 16-21(6) | TKA-MT (21,22) | 0.393 | 0.506 | 0.868 | 0.700 | 0.597 | 0.99 |
| PHOE_ECOLI | 1-4(4) | 5-17(13) | 18-21(4) | VQA-MT (21,22) | 0.688 | 0.738 | 0.901 | 0.804 | 0.769 | 0.99 |
| OMPA_ECOLI | 1-3(3) | 4-16(13) | 17-21(5) | AQA-MT (21,22) | 0.751 | 0.794 | 0.954 | 0.861 | 0.825 | 0.99 |
| OMPF_ECOLI | 1-4(4) | 5-18(14) | 19-22(4) | ANA-MT (22,23) | 0.805 | 0.817 | 0.937 | 0.864 | 0.839 | 0.99 |
| OMPT_ECOLI | * | - | - | - | 0.307 | 0.427 | 0.808 | 0.633 | 0.524 | 0.98 |
| OMPC_ECOLI | 1-4(4) | 5-16(10) | 17-20(4) | ANA-MT (21,22) | 0.784 | 0.829 | 0.956 | 0.901 | 0.863 | 0.99 |
| ELBH_ECOLX | 1-3(3) | 4-17(14) | 18-21(4) | AHG-MT (21,22) | 0.750 | 0.734 | 0.912 | 0.746 | 0.740 | 0.99 |
| LAMB_ECOLI | 1-7(7) | 8-19(12) | 20-25(6) | AMA-MT (25,26) | 0.709 | 0.760 | 0.964 | 0.877 | 0.815 | 0.96 |
| MALE_ECOLI | 1-4(4) | 5-19(15) | 20-26(7) | ALA-MT (26,27) | 0.630 | 0.754 | 0.981 | 0.923 | 0.834 | 0.98 |
| DSBA_ECOLI | 1-3(3) | 4-14(11) | 15-19(5) | ASA-MT (19,20) | 0.565 | 0.723 | 0.959 | 0.922 | 0.816 | 0.99 |
| DGAL_ECOLI | 1-4(4) | 5-16(10) | 17-23(7) | AHA-MT (23,24) | 0.690 | 0.781 | 0.967 | 0.910 | 0.841 | 0.98 |
| TORT_ECOLI | 1-2(2) | 3-14(12) | 15-18(4) | AFS-MT (18,19) | 0.517 | 0.694 | 0.957 | 0.928 | 0.804 | 0.99 |
| TOLB_ECOLI | * | - | - | - | 0.457 | 0.469 | 0.607 | 0.474 | 0.471 | 0.99 |
| HSTI_ECOLX | 1-3(3) | 4-18(15) | 19-23(5) | AYA-MT (23, 24) | 0.820 | 0.824 | 0.956 | 0.877 | 0.849 | 0.97 |
| BLAT_ECOLX | * | - | - | - | 0.536 | 0.454 | 0.549 | 0.425 | 0.443 | 0.99 |
| ASPG2_ECOLI | 1-6(6) | 7-18(12) | 19-22(4) | ALA-MT (22,23) | 0.805 | 0.773 | 0.941 | 0.770 | 0.772 | 0.99 |
| CEXE_ECOLX | 1-3(3) | 4-14(11) | 15-19(5) | AIA-MT (19,20) | 0.639 | 0.712 | 0.943 | 0.799 | 0.753 | 0.97 |
| PTRA_ECOLI | 1-6(6) | 7-20(14) | 21-25(5) | SQA-MT (23,24) | 0.753 | 0.833 | 0.964 | 0.920 | 0.874 | 0.99 |
| FKBA_ECOLI | 1-6(6) | 7-20(14) | 21-25(5) | TFA-MT (25,26) | 0.522 | 0.607 | 0.957 | 0.819 | 0.706 | 0.99 |
| LPP_ECOLI | * | - | - | - | 0.148 | 0.251 | 0.689 | 0.497 | 0.342 | 0.99 |
| THIB_ECOLI | 1-4(4) | 5-14(10) | 15-18(4) | VFA-MT (18,19) | 0.515 | 0.656 | 0.919 | 0.845 | 0.744 | 0.99 |
| TAUA_ECOLI | 1-7(7) | 8-17(10) | 18-22(5) | AQA-MT (22,23) | 0.775 | 0.741 | 0.919 | 0.775 | 0.757 | 0.99 |
| PSPE_ECOLI | 1-4(4) | 5-15(11) | 16-19(4) | VFA-MT (19,20) | 0.850 | 0.858 | 0.952 | 0.876 | 0.866 | 0.99 |
| PPA_ECOLI | 1-2(2) | 3-13(11) | 14-22(9) | AFA-MT (22, 23) | 0.728 | 0.734 | 0.896 | 0.791 | 0.761 | 0.99 |
| OMPP_ECOLI | 1-4(4) | 5-15(11) | 16-23(8) | ASA-MT (23,24) | 0.517 | 0.577 | 0.853 | 0.724 | 0.646 | 0.95 |
| DRAA_ECOLX | 1-3(3) | 4-13(10) | 14-21(8) | AHA-MT (21,22) | 0.622 | 0.735 | 0.946 | 0.895 | 0.810 | 0.99 |
| OMPW_ECOLI | 1-3(3) | 4-13(10) | 14-21(8) | AFA-MT (21,22) | 0.759 | 0.816 | 0.949 | 0.889 | 0.850 | 0.99 |
| PBP7_ECOLI | 1-3(3) | 4-17(14) | 18-25(8) | AVA-MT (25,26) | 0.589 | 0.695 | 0.972 | 0.886 | 0.785 | 0.99 |
| NIKA_ECOLI | 1-7(7) | 8-19(12) | 20-22(3) | VHA-MT (22,23) | 0.775 | 0.804 | 0.925 | 0.861 | 0.831 | 0.99 |
| LPTA_ECOLI | 1-4(4) | 5-23(19) | 24-27(4) | AFA-MT (27,28) | 0.828 | 0.846 | 0.977 | 0.912 | 0.877 | 0.99 |
| SUBF_BACSU | 1-4(4) | 5-23(19) | 24-30(7) | AGA-MT (30,31) | 0.581 | 0.669 | 0.955 | 0.859 | 0.758 | 0.99 |
| CWBA_BACSU | 1-5(5) | 6-19(18) | 20-25(6) | SFA-MT (25,26) | 0.853 | 0.894 | 0.976 | 0.940 | 0.916 | 0.99 |
| QOX2_BACSU | * | - | - | - | 0.136 | 0.170 | 0.372 | 0.296 | 0.217 | 0.99 |
| CHIS_BACSU | * | - | - | - | 0.357 | 0.331 | 0.536 | 0.283 | 0.313 | 0.86 |
| SACB_BACAM | 1-8(8) | 9-24(16) | 25-29(5) | AFA-MT (29,30) | 0.558 | 0.596 | 0.951 | 0.772 | 0.679 | 0.97 |
| BLAC_BACSU | * | - | - | - | 0.274 | 0.302 | 0.752 | 0.504 | 0.377 | 0.95 |
| GUB_BACAM | * | - | - | - | 0.307 | 0.398 | 0.715 | 0.575 | 0.463 | 0.98 |
| CDGT_BACST | * | - - |
- - |
- | 0.130 | 0.280 | 0.706 | 0.572 | 0.388 | 0.99 |
| THER_BACST | * | - | - | - | 0.257 | 0.400 | 0.813 | 0.699 | 0.510 | 0.98 |
| BLAC_BACLI | 1-2(2) | 3-22(20) | 23-26(4) | ALA-GM (25,26) | 0.756 | 0.824 | 0.965 | 0.914 | 0.866 | 0.99 |
| AMY_BACLI | 1- 10(10) | 11-22(12) | 23-29(7) | AAA-AM (28,29) | 0.452 | 0.590 | 0.889 | 0.665 | 0.618 | 0.99 |
SignalP 4.1 outputs includes several different scores. The C-score and S-score were used for determination of cleavage sites and signal peptides positions, respectively. Y-score indicates the geometric average between the C-score and a smoothed derivative of the S-score. S-mean is arithmetic average of the S-score from the beginning to position where the Y-score is the max. D-score is the mean of the S-mean and Y-max which determines secretory and non-secretory proteins with cut-off value of 0.5. Sequences with D-score > 0.5 are considered as signal peptide.