Table 2 |
||||
|
Candidate ARG boxes upstream of arginine metabolism related genes and operons |
||||
|
Genome |
Operon |
Position |
Score |
Site |
|
|
||||
|
E. coli |
argR |
-64 |
4.24 |
ttTGcATAAAAATTCATc |
|
-43 |
3.34 |
tATGcAcAAtAATgttgT |
||
|
argA |
-50 |
3.98 |
AcaGAATAAAAATaCAcT |
|
|
-39 |
3.98 |
ttcGAATAAtcATgCAaa |
||
|
argCBH |
-128 |
4.61 |
tATcAATAttcATgCAgT |
|
|
-109 |
4.61 |
tATGAATAAAAATaCAcT |
||
|
argD |
-68 |
4.01 |
AgTGAtTttttATgCATa |
|
|
-47 |
3.50 |
tgTGgtTAtAAtTTCAca |
||
|
argE |
-64 |
3.80 |
AgTGtATttttATTCATa |
|
|
-43 |
3.39 |
AcTGcATgAAtATTgATa |
||
|
argF |
-65 |
4.16 |
AATGAATAAttAcaCATa |
|
|
-44 |
4.41 |
AgTGAATtttAATTCAaT |
||
|
argG |
-210 |
4.31 |
tgTGAATgAAtATcCAgt |
|
|
-91 |
3.90 |
AtTaAATgAAAAcTCATT |
||
|
-70 |
4.51 |
ttTGcATAAAAATTCAgT |
||
|
argI |
-63 |
4.33 |
AATGAATAAtcATcCATa |
|
|
-42 |
4.49 |
AtTGAATtttAATTCATT |
||
|
carAB |
-50 |
4.36 |
tgTGAATtAAtATgCAaa |
|
|
-39 |
3.79 |
AgTGAgTgAAtaTTCtcT |
||
|
artPIQM |
-72 |
4.08 |
AtTGaATAAttATTCtgT |
|
|
artJ |
-86 |
4.36 |
AtTGcATAtAAATTCAcT |
|
|
H. influenzae |
HI1209 |
-50 |
4.27 |
AgTGAATttttATgCAaT |
|
HI0811 |
-54 |
4.52 |
tATGAATAAAtATgCAca |
|
|
HI1727 |
-64 |
3.87 |
AtaGAATttttATTCAca |
|
|
-43 |
3.75 |
AtcGAtTAtttATTCAaT |
||
|
HI1180-77 |
-50 |
4.01 |
tATGcATAAAAATgtAaT |
|
|
V. cholerae |
VC2316 |
-15 |
3.82 |
AaaGAATAAAAAgTCATT |
|
VC2390-89 |
-52 |
3.57 |
ttTGcAaAAtAATTtATT |
|
|
VC2508 |
-72 |
3.72 |
ttaaAATAtttATTCAcT |
|
|
-51 |
3.35 |
AtaGcATtttcATgCtTT |
||
|
VC2618 |
-120 |
3.83 |
AaTaAATgtAAATaCAaT |
|
|
VC2644-42 |
-76 |
3.00 |
AacacATAttAAaTCAcT |
|
|
-55 |
4.00 |
AGTGAATAAAAAaaCAaT |
||
|
VC2645 |
-79 |
3.50 |
AtTGttTttttATTCAcT |
|
|
-58 |
3.27 |
AGTGAtTtAAtATgtgTT |
||
|
VCA0757-60 |
-74 |
3.00 |
ttTtggTttttATaCATT |
|
|
-53 |
3.85 |
AtTGcATAAAAATaCgTT |
||
|
B. subtilis |
argCJBD |
-64 |
5.22 |
ATtAATTTtTATTCAT |
|
carABargF |
-55 |
4.54 |
AgGcATAaAAATTCAT |
|
|
-35 |
4.02 |
AtaAtTAatTATTCAT |
||
|
argGH |
-67 |
5.04 |
ATGtATTTtTATTaAa |
|
|
yqjN |
-31 |
4.54 |
AaGcATTTtTATTCAT |
|
|
-47 |
4.91 |
ATttATTTtTATaCAa |
||
|
rocABC |
-53 |
5.14 |
tTGcATTTtTATTCAT |
|
|
rocDEF |
-63 |
4.76 |
tTGcATTTATATaaAg |
|
|
rocR |
-193 |
4.76 |
cTttATATAAATgCAa |
|
|
yqiXYZ |
-88 |
4.21 |
tTGcATAaAAATgaga |
|
|
-51 |
4.62 |
AcGAATAaATATTCAa |
||
|
C. acetobutylicum |
414 |
-191 |
5.27 |
ATGAATAaATATTCAa |
|
491 |
-132 |
4.62 |
tTGAATAaATATTCgT |
|
|
-32 |
5.27 |
ATGAATAaAAATTCAa |
||
|
1203-4 |
-124 |
5.04 |
ATGAATATtTATaaAa |
|
|
2787-8 |
-63 |
4.79 |
tTGAATATtTATaaAg |
|
|
-43 |
4.59 |
gTGtATAatTATTCAT |
||
|
2786-2785 |
-118 |
4.59 |
ATGAATAatTATaCAc |
|
|
-98 |
4.79 |
cTttATAaATATTCAa |
||
|
3090-89 |
-181 |
4.96 |
ATGcATAaATATaaAT |
|
|
-80 |
4.91 |
ATGtATAaATATaaAa |
||
|
3533 |
-87 |
4.96 |
ATGcATAaATATaaAT |
|
|
-67 |
4.89 |
tTGAATAatTATaaAa |
||
|
4268-65 |
-194 |
5.09 |
ATGcATAaATATTaAT |
|
|
-69 |
4.62 |
gTtAATAatTATTCAT |
||
|
T. maritima |
TM0371 |
-59 |
4.21 |
tTtcATATtTATgCta |
|
TM0558-57 |
-81 |
3.92 |
tTtAATTcAAAgTaAa |
|
|
TM0593-91 |
-34 |
4.16 |
tTGtgTTatAATaaAT |
|
|
TM1780-85 |
-138 |
3.87 |
cgtAATTgATATTCAT |
|
|
TM1873 |
-91 |
4.44 |
ATttATTTAAcTTaAT |
|
|
D. radiodurans |
DR0080 |
-57 |
4.11 |
cTGtATTTcTATaCAg |
|
DR0674-78 |
-131 |
4.09 |
tTGcATAgtcATTCAT |
|
|
DR2610 |
-85 |
3.62 |
ATGgATTgAAATcCAg |
|
|
-62 |
3.69 |
cTGgATTTtAAggaAT |
||
|
C. pneumoniae |
glnPQ |
-53 |
4.26 |
tTGcATAaATATgatT |
|
-32 |
4.64 |
ATaAATAaATATgCAT |
||
|
artJ |
-112 |
3.92 |
tTtAATcaAAATTatT |
|
|
27 |
3.96 |
ATttATTTtTATaatg |
||
|
M. tuberculosis |
Rv1652-59 |
-11 |
3.91 |
tTGcATAacgATgCAa |
|
|
||||
|
Position is indicated relative to the start of translation. The score for E.coli and H. influenzae genes was computed using the profile from [27]; other scores were computed using the profile trained on B. subtilis candidate ARG boxes using the procedure from [28]. The sites used to construct the profile are shown in bold. |
||||
|
Makarova et al. Genome Biology 2001 2:research0013.1 doi:10.1186/gb-2001-2-4-research0013 |
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