Table 2.
ORFc | Gene | Annotation | Ranka |
Fold changeb | |
---|---|---|---|---|---|
In vivo | In vitro | ||||
PMI1035 | Translation initiation factor IF-3 | 9 | 3 | −1.33 | |
PMI0765 | ompF | Outer membrane porin | 13 | 3 | −1.25 |
PMI3251 | tufB | Elongation factor Tu | 13 | 6 | −1.23 |
PMI3275 | secY | Preprotein translocase SecY subunit | 23 | 20 | 1.03 |
PMI3280 | rpoA | DNA-directed RNA polymerase alpha chain | 26 | 19 | −1.32 |
PMI2792 | tufB | Elongation factor Tu | 28 | 29 | −1.16 |
PMI0856 | Conserved hypothetical protein | 29 | 36 | −1.85 | |
PMI0862 | acpP | Acyl carrier protein | 33 | 16 | −1.66 |
PMI0263 | mrpA | Major mannose-resistant/Proteus-like fimbria | 37 | 3,040 | 13,806.33 |
PMI0785 | ompA | Outer membrane protein A | 37 | 50 | 1.21 |
PMI1676 | cspC | Cold shock-like protein | 39 | 9 | −2.09 |
PMI2771 | hupA | DNA-binding protein HU-alpha (HU-2) | 52 | 60 | −1.39 |
PMI3375 | priB | Primosomal replication protein N | 52 | 34 | −1.61 |
PMI2793 | fusA | Elongation factor G (EF-G) | 52 | 80 | 1.17 |
PMI0716 | ihfB | Integration host factor beta-subunit | 57 | 53 | −1.25 |
PMI0384 | rimM | 16S rRNA processing protein | 59 | 59 | −1.28 |
PMI2284 | tsf | Elongation factor Ts | 59 | 75 | −1.00 |
PMI3059 | atpE | ATP synthase C chain | 59 | 57 | −1.47 |
PMI1213 | ahpC | Alkyl hydroperoxide reductase subunit C | 62 | 165 | 6.14 |
PMI3062 | atpA | ATP synthase alpha chain | 62 | 68 | −1.07 |
PMI3415 | secG | Protein export membrane protein | 66 | 71 | −1.05 |
PMI0073 | ahpC | Putative alkyl hydroperoxide reductase | 67 | 104 | 1.83 |
PMI3063 | atpG | ATP synthase gamma chain | 68 | 70 | −1.14 |
PMI0385 | trmD | tRNA (guanine-N1)-methyltransferase | 69 | 65 | −1.69 |
PMI0585 | pal | Peptidoglycan-associated lipoprotein | 71 | 46 | −2.60 |
PMI3060 | atpF | ATP synthase B chain | 71 | 60 | −1.39 |
PMI1504 | gapA | Glyceraldehyde 3-phosphate dehydrogenase A | 72 | 81 | 1.33 |
PMI0118 | hupB | DNA-binding protein HU-beta | 75 | 76 | −1.70 |
PMI3064 | atpD | ATP synthase beta chain | 75 | 69 | −1.18 |
PMI3065 | atpC | ATP synthase epsilon chain | 78 | 84 | −1.22 |
PMI3061 | atpH | ATP synthase delta chain | 81 | 83 | −1.15 |
PMI2544 | groS | 10-kDa chaperonin | 82 | 66 | −1.26 |
PMI3057 | atpI | ATP synthase protein I | 82 | 85 | −1.35 |
PMI3296 | Conserved hypothetical protein | 83 | 96 | −1.11 | |
PMI0418 | cspE | Putative cold shock protein | 84 | 69 | −2.52 |
PMI0861 | fabG | 3-Oxoacyl-[acyl-carrier protein] reductase | 85 | 79 | −1.67 |
PMI1039 | pheT | Phenylalanyl-tRNA synthetase beta chain | 93 | 103 | 1.06 |
PMI2784 | rpoC | DNA-directed RNA polymerase beta′ subunit | 93 | 95 | −1.15 |
PMI1898 | grcA | Autonomous glycyl radical cofactor | 95 | 788 | 19.18 |
PMI3622 | fis | DNA-binding protein Fis | 96 | 90 | −1.37 |
PMI1034 | thrS | Threonyl-tRNA synthetase | 96 | 90 | −1.27 |
PMI0114 | tig | Trigger factor | 98 | 98 | −1.15 |
PMI1828 | ptsH | Phosphotransferase system phosphocarrier protein | 100 | 683 | 16.77 |
PMI1488 | hns | DNA-binding protein (histone-like structuring protein) | 100 | 93 | −1.41 |
PMI3364 | miaA | tRNA delta(2)-isopentenylpyrophosphate transferase | 102 | 137 | −1.11 |
PMI2833 | Putative endoribonuclease | 103 | 124 | −1.02 | |
PMI0842 | TonB-dependent receptor | 104 | 913 | 17.18 | |
PMI3058 | atpB | ATP synthase A chain | 106 | 77 | −1.66 |
PMI0243 | fbaA | Fructose-bisphosphate aldolase class II | 110 | 144 | 1.61 |
PMI0691 | infA | Translation initiation factor IF-1 | 111 | 101 | −1.60 |
Median expression rank across nine microarrays (including ribosomal genes): 1 is most highly expressed, and 3,719 is most weakly expressed.
Median fold change in vivo compared to LB broth across nine microarrays.
ORF, open reading frame.