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 |