Spreadsheet: 4d3146de-269f-4705-997c-e117547f8812
Sheet: Sheet1

Table S3.  Surface-exposed proteins of R. typhi str. [NAME] identified by LC/MS/MS.  Proteins were identified based on at least one high scoring peptide.1,2 | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10
Locus tag | Annotation | Predicted [NAME] | sequence coverage (%) | Protein identification probability | SignalP cleavage site (NN,HMM) | LipoP | Phobius | SecretomeP | Predicted localization (SOSUIGramN) | Predicted localization (pSORTb)
RT0011 | hypothetical protein4 | 41.149 | 1.68 | 0.586 | Y,Y | SpI | Y | N | P | U
RT0032 | VirB6-like protein of the type IV secretion system | 125.445 | 1.76 | 0.902 | Y,Y | CYT | Y | N | CM | CM
RT0049 | Elongation factor Ts, [NAME] | 33.916 | 13.9 | 0.9639 | N,N | CYT | N | N | C | C
RT0052 | 190 kDa antigen precursor, sca23 | 169.739 | 0.81 | 1 | Y,Y | SpI | Y | Y | E | U
RT0085 | conserved hypothetical protein | 41.492 | 1.96 | 0.99 | N,N | CYT | N | N | C | C
RT0087 | cell division protein, FtsH | 49.4253077 | 4.4 | 0.999 | Y,Y | TMH | N | N | CM | CM
RT0094 | ATP-binding ClpB chaperone | 96.276 | 0.58 | 0.999 | N,N | CYT | N | N | C | C
RT0107 | F0F1 ATP synthase subunit B, atpX | 18.233 | 7.05 | 0.902 | Y,N | CYT | N | N | C | U
RT0117 | succinate dehydrogenase flavoprotein subunit, sdhA | 65.726 | 3.69 | 0.99 | N,N | SpI | N | N | E | CM
RT0121 | elongation factor G, fusA | 77.636 | 2 | 0.993 | N,N | CYT | N | N | C | C
RT0138 | conserved hypothetical protein5 | 18.034 | 8.07 | 0.902 | N,N | CYT | N | Y | E | U
RT0146 | Multidrug resistance protein B | 56.19 | 4 | 0.9985 | N,Y | TMH | N | N | CM | CM
RT0170 | dihydrolipoamide succinyltransferase, sucB | 43.692 | 4.5 | 0.9314 | N,N | CYT | N | N | C | C
RT0171 | 2-oxoglutarate dehydrogenase E1 component, sucA | 105.127 | 22.5 | 1 | N,N | CYT | N | N | C | C
RT0176 | chaperone protein DnaK5 | 68.302 | 27.9 | 0.979 | N,N | CYT | N | Y | E | C
RT0193 | excinuclease ABC subunit B, uvrB | 75.701 | 1.66 | 0.902 | N,N | CYT | N | N | C | C
RT0198 | methionyl-tRNA formyltransferase, fmt | 33.896 | 2.97 | 0.99 | N,N | CYT | N | N | C | C
RT0212 | threonine--tRNA ligase, thrS | 72.784 | 1.57 | 0.902 | N,N | CYT | N | N | C | C
RT0222 | conserved hypothetical protein3 | 27.962 | 5.37 | 0.99 | N,N | CYT | Y | N | C | C
RT0248 | ribonuclease E, rne | 78.134 | 1.17 | 0.99 | N,N | CYT | N | N | E | C
RT0252 | pyruvate decarboxylase, pdhA | 36.888 | 2.76 | 0.855 | N,N | CYT | N | N | C | C
RT0259 | heme exporter protein B, ccmB | 25.087 | 5.94 | 0.902 | N,N | TMH | N | N | CM | CM
RT0329 | glycosyltransferase | 36.987 | 3.46 | 0.902 | N,N | CYT | N | N | U | CM
RT0362 | Sec7-domain containing protein transport protein5 | 52.423 | 4 | 0.9926 | N,N | CYT | N | N | C | C
RT0406 | conserved hypothetical protein3 | 18.838 | 7.23 | 0.852 | Y,Y | SpI | Y | N | CM | U
RT0420 | succinyl-CoA synthetase subunit beta, sucC | 41.773 | 2.8 | 0.9949 | N,N | CYT | N | N | C | C
RT0438 | cell surface antigen, sca33 | 247.734 | 0.5 | 0.9985 | Y,Y | SpI | Y | Y | E | U
RT0446 | conserved hypothetical protein | 25.873 | 4.87 | 0.902 | N,N | CYT | N | N | C | C
RT0447 | dihydrolipoamide dehydrogenase, pdhD1 | 49.433 | 4.58 | 0.98 | N,N | CYT | N | N | U | C
RT0485 | cell surface antigen sca43,5 | 113.933 | 57.1 | 1 | N,N | CYT | N | Y | C | C
RT0488 | 30S ribosomal protein S15, rpsO | 10.592 | 7.69 | 0.902 | N,N | CYT | N | N | C | C
RT0495 | tRNA delta(2)-isopentenylpyrophosphate transferase | 36.008 | 3.54 | 0.994 | N,N |  |  |  | U | C
RT0496 | [NAME] conserved hypothetical protein | 108.675 | 4.3 | 1 | N,N | CYT | N | N | E | C
RT0521 | biotin-protein ligase, birA | 29.965 | 3.44 | 0.902 | N,N | CYT | N | N | OM | C
RT0522 | conserved hypothetical protein with phospholipase A activity | 66.055 | 1.03 | 0.99 | N,N | CYT | N | N | C | E
[NAME] | 2-octaprenyl-6-methoxyphenyl hydroxylase3 | 43.807 | 7.29 | 0.999 | Y,Y | SpI | Y | N | C | U
RT0565 | protein export protein PrsA precursor3 | 32.065 | 32.2 | 1 | Y,Y | SpII | Y | Y | U | OM
RT0569 | DNA topoisomerase II subunit B, gyrB | 90.938 | 1.49 | 0.994 | N,N | CYT | N | N | C | C
RT0584 | D-alanine ligase, murF | 50.565 | 1.56 | 0.96 | N,N | CYT | Y | N | C | C
RT0593 | Peptidyl-tRNA hydrolase, pth | 20.983 | 7.57 | 0.929 | N,N | CYT | N | N | C | C
RT0603 | nitrogen regulation protein, NtrY | 67.527 | 1.66 | 0.99 | Y,Y | TMH | N | N | CM | CM
[NAME] | 60 kDa chaperonin/chaperonin GroEL | 58.884 | 20.7 | 1 | N,N | CYT | N | N | C | C
RT0638 | 30S ribosomal protein S14, rpsN5 | 11.368 | 10.9 | 0.9985 | N,N | CYT | N | Y | C | C
RT0653 | Elongation factor [NAME], tuf | 42.85 | 11.7 | 0.997 | N,N | CYT | N | N | C | C
RT0657 | Fumarase C, fumC | 50.997 | 4.56 | 0.999 | N,N | CYT | N | N | C | C
RT0666 | [NAME], [NAME] | 30.683 | 6.6 | 0.9985 | N,N | CYT | N | N | C | C
RT0669 | exodeoxyribonuclease VII large subunit, xseA | 50.937 | 2.65 | 0.902 | N,N | CYT | N | N | C | C
RT0671 | exodeoxyribonuclease III, xthA2 | 31.497 | 2.65 | 0.902 | N,N | CYT | N | N | C | C
[NAME] | methionine--tRNA ligase, [NAME] | 58.309 | 2.96 | 0.932 | N,N | CYT | N | N | C | C
RT0679 | thymidylate kinase, tmk | 23.602 | 3.94 | 0.902 | N,N | CYT | N | N | C | C
RT0698 | cytochrome c-type biogenesis protein, ccmF | 76.739 | 0.9 | 0.902 | Y,N | TMH | N | N | CM | CM
RT0699 | rickettsial outer membrane protein B, rOmpB (sca5)3 | 169.799 | 2.2 | 0.9 | Y,Y | SpI | Y | Y | E | OM
RT0728 | [NAME], glyA | 46.067 | 2.6 | 0.9949 | N,N | CYT | N | N | C | C
RT0744 | conserved hypothetical protein | 181.687 | 1.27 | 1 | N,N | CYT | N | N | OM | C
RT0749 | acyl carrier protein, acpP | 9.221 | 12.3 | 0.902 | N,N | CYT | N | N | C | C
RT0767 | conserved hypothetical protein, predicted membrane protein3 | 94.603 | 1.6 | 0.999 | Y,Y | SpI | Y | N | CM | U
RT0776 | conserved hypothetical protein | 63.166 | 1.63 | 0.902 | N,N | CYT | N | N | C | C
RT0777 | NADH dehydrogenase subunit J, nuoJ | 23.084 | 4.39 | 0.897 | N,N | TMH | N | N | CM | CM
RT0788 | F0F1 ATP synthase subunit beta, atpD | 50.963 | 8.2 | 1 | N,N | CYT | N | N | C | C
RT0790 | F0F1 ATP synthase subunit alpha, atpA | 56.115 | 2.5 | 0.9761 | N,N | CYT | N | N | C | C
RT0796 | hypothetical protein | 5.473 | 19.6 | 0.99 | N,N | CYT | N | N | U | U
RT0805 | site-specific tyrosine recombinase, [NAME] | 35.474 | 3.61 | 0.995 | N,N | CYT | N | N | C | C
RT0815 | possible outer surface protein3 | 26.629 | 5.3 | 0.9949 | Y,Y | SpI | Y | Y | OM | U
RT0817 | [NAME], fdxA | 12.763 | 6.36 | 0.902 | N,N | CYT | N | N | C | C
RT0842 | hypothetical protein | 36.316 | 5.3 | 0.999 | N,N | CYT | N | N | CM | U
RT0847 | RNA polymerase sigma factor, rpoD | 73.098 | 4.7 | 0.9999 | N,N | CYT | N | N | C | C
RT0857 | conserved hypothetical protein | 11.909 | 8.41 | 0.99 | N,N | CYT | N | N | C | U
RT0873 | proline/betaine transporter, proP7 | 46.895 | 1.89 | 0.902 | N,N | TMH | N | N | CM | CM
1Proteins shaded in blue were also identified as surface exposed in proteomic analyses of R. parkeri, A. phagocytophilum, E. chaffeensis, B. henselae, B. quintana, E. coli and L. monocytogenes [30-37, 44].
2Proteins shaded in grey have different predicted localizations reported by SOSUIGramN and pSORTb.
3PhoA positive as determined by a PhoA assay to test secretion to the periplasm [28].
4PhoA negative as determined by a PhoA assay to test secretion to the periplasm [28].
5Have a non-classical secretion signal as determined by the SecretomeP 2.0 server.
Abbreviations used by algorithms: CYT - Cytoplasmic, TMH - [NAME], SpI - Signal Peptidase I, SpII - Signal Peptidase II, OM - Outer membrane, CM - Cytoplasmic membrane, C - Cytoplasmic, P - Periplasmic, E - Extracellular, U - Unknown