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Table 3 Genes displaying prominent differences in selection between Typhimurium and Typhi*

From: High-throughput comparison of gene fitness among related bacteria

S. Typhimurium 14028 gene symbol Gene name Gene description Best hit in S. Typhimurium strain LT2 Best hit in S. Typhi Ty2a Best hit in ECOa STM1 transposons STM1 reads STY1 transposons STY1 reads STY2 transposonsb STY2 readsb STY2 transposonsc STY2 readsc
       Percentile rank
A. Examples of genes with stronger selection in STM1 than in STY1 and STY2
STM14_0199.RJ yacC   STM0167 t0172 b0122 12 13 57 70 53 51 59 51
STM14_1028.R potF Putrescine ABC transporter putrescine-binding protein STM0877 t2019 b0854 14 15 47 63 35 24 38 32
STM14_1092   Hypothetical protein   t1967   13 10 61 59 35 42 75 66
STM14_1127 ycbL Putative metallo-beta- lactamase STM0997 t1937 b0927 13 13 30 40 27 34 23 36
STM14_1141 xisW Excisionase STM1006 t1928   11 9 72 62 53 30 43 24
STM14_1152 dnaC Putative replication protein STM1015 t1917   16 16 27 36 34 31 41 32
STM14_1548 yeaM Putative regulatory protein STM1279 t1159 b1790 14 17 50 59 36 25 44 38
STM14_1599 celG Hypothetical protein STM1317 t1196 b1733 15 17 67 75 54 46 50 48
STM14_1682 orf70 Hypothetical protein STM1388 t1256 b1675 12 11 32 71 34 27 37 29
STM14_1877 d   Putative coiled-coil protein STM1554 t1468   15 16 39 37 79 81 78 81
STM14_1977 d   Putative periplasmic binding protein STM1633 t1536   13 16 34 27 86 85 86 83
STM14_1978 d   Putative ABC transporter permease component STM1634 t1537   6 7 17 44 87 91 85 90
STM14_2116 hns Global DNA-binding transcriptional dual regulator H-NS STM1751 t1662 b1237 5 3 32 29 91 89 35 91
STM14_2119 hnr Response regulator of RpoS STM1753 t1664 b1235 1 1 63 58 69 59 48 31
STM14_2120 ychK Hypothetical protein STM1754 t1665 b1234 11 11 64 81 64 61 62 46
STM14_2140 chaB Cation transport regulator STM1770 t1679 b1217 12 11 30 29 63 60 73 49
STM14_2176 ldcA L,D-carboxypeptidase A STM1800 t1077 b1192 14 15 43 37 28 28 39 39
STM14_2186 d gsnB Putative cytoplasmic protein STM1809 t1068   18 14 39 30 43 58 59 70
STM14_2278   Hypothetical protein STM1873 t1004 b1839 14 13 37 57 48 28 54 38
STM14_2685   Putative 1,2-dioxygenase STM2178 t0677   15 18 32 33 31 29 24 32
STM14_2708.RJ   Putative DNA-binding protein STM2195 t0660   17 15 51 44 65 36 62 49
STM14_2745   Bicyclomycin/multidrug efflux system   t0634   16 14 65 47 66 43 73 68
STM14_3050 purC Phosphoribosylaminoimidazole- succinocarboxamide synthase STM2487 t0372 b2476 11 11 28 32 47 34 34 30
STM14_4596 d   Pseudogene STM3806 t0121   14 12 78 49 53 55 36 51
STM14_4883 cpxP Periplasmic repressor STM4060 t3559 b3913 16 16 27 46 38 41 43 34
STM14_5142 d   Putative cytoplasmic protein STM4276 t4182   15 13 46 28 16 49 19 47
STM14_0109 ksgA Dimethyladenosine transferase STM0090 t0093 b0051 37 28 5 5 19 13 5 5
STM14_2281 holE DNA polymerase III subunit theta STM1876 t1001 b1842 63 70 11 11 9 8 25 15
STM14_2498   Hypothetical protein STM2011.1n t0860   51 43 13 12 8 10 14 17
STM14_2665 e   Hypothetical protein STM2161 t0694 b2128 37 53 14 13 8 7 14 11
STM14_3017 eutA Reactivating factor for ethanolamine ammonia lyase STM2459 t0399 b2451 26 29 16 16 10 11 16 16
STM14_3267 e   Hypothetical protein STM2666 t2621 b2598 81 84 17 14 9 7 19 13
STM14_4041 e degS Serine endoprotease STM3349 t3265 b3235 50 34 14 14 6 7 4 4
STM14_4465 yibP Hypothetical protein STM3705 t3814 b3613 63 65 19 18 11 11 10 11
STM14_4747 yifL Putative outer membrane lipoprotein STM3946 t3351 b4558 77 65 12 12 22 17 18 16
STM14_5345 treC Trehalose-6-phosphate hydrolase STM4453 t4488 b4239 50 49 13 13 10 8 5 9
  1. * Details for all genes can be found in Additional file5: Table S2. See Table2 for notes a, b, and c. Ranks above the 20th percentile are shown in bold.
  2. d Knockout mutant has been created in STM[4].
  3. e Considered essential in STY2[3].