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. 2012 May 30;13:212. doi: 10.1186/1471-2164-13-212

Table 3.

Genes displaying prominent differences in selection between Typhimurium and Typhi*

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_1877d
 
Putative coiled-coil protein
STM1554
t1468
 
15
16
39
37
79
81
78
81
STM14_1977d
 
Putative periplasmic binding protein
STM1633
t1536
 
13
16
34
27
86
85
86
83
STM14_1978d
 
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_2186d
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_4596d
 
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_5142d
 
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_2665e
 
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_3267e
 
Hypothetical protein
STM2666
t2621
b2598
81
84
17
14
9
7
19
13
STM14_4041e
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

* Details for all genes can be found in Additional file 5: Table S2. See Table 2 for notes a, b, and c. Ranks above the 20th percentile are shown in bold.

d Knockout mutant has been created in STM [4].

e Considered essential in STY2 [3].

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