A Comparative Genomics Approach to Prediction of New Members of Regulons

Table 3.

Training Set TUs Regulated by CRP

Operon Site sequence Position Score
ansB TTTTGTTACCTGCCTCTAACTT −125 10.57
araC AAGTGTGACGCCGTGCAAATAA −230 13.93
araBAD TTATTTGCACGGCGTCACACTT −131 13.93
araE AATTGGAATATCCATCACATAA −131 12.78
araFG-araH1-araH2 CGATGTGATATTGCTCTCCTAT −163 10.0
caiTABCDE TATTGTTAAGTTCCTCACCAAT −335 10.97
TATTGTTTTATGGATCACCAAT −278 10.88
AAATGTGATACCAATCACAGAA −158 20.42
crp GTATGCAAAGGACGTCACATTA −137 11.71
cyaA AGGTGTTAAATTGATCACGTTT −173 12.67
dadAX AGATGTGAGCCAGCTCACCATA −117 16.48
deoCABD TTATTTGAACCAGATCGCATTA −150 17.12
AATTGTGATGTGTATCGAAGTG −97 11.87
dsdXA TAAAGTGAACCATATCTCAATT −155 16.77
epd-pgk AAGTGTGATGTGAGTCAGATAA −213 17.30
focA-pf1B AGATATGATCTATATCAATTTC −78 10.14
fur AAATGTAAGCTGTGCCACGTTT −158 13.81
galETKM TAATTTATTCCATGTCACACTT −78 13.12
galS TGCTGTGACTCGATTCACGAAG −95 10.41
glgS AAGTGTGATCGGGGACAATATA −124 11.51
glnALG CTTTGTGATCGCTTTCACGGAG −269 9.23
glpTQ ATGTGTGCGGCAATTCACATTT −129 17.25
glpD TAATGTTATACATATCACTCTA −117 15.65
glpFK TTTTATGACGAGGCACACACAT −142 10.48
gntT TAATATGACCAACCTCTCATAA −237 13.80
lacZYA TAATGTGAGTTAGCTCACTCAT −110 18.32
malEFG TTATGTGCGCATCTCCACATTA −161 11.25
TTCTGTAACAGAGATCACACAA −132 16.06
malI TAGTGAGGCATAAATCACATTA −102 15.70
AAACGTTTTATCTGTCACATAA −42 11.14
malK-lamB-malM TTGTGTGATCTCTGTTACAGAA −255 16.06
TAATGTGGAGATGCGCACATAA −226 11.25
malS ATTTGAGAGTTGAATCTCAAAT −270 13.97
AAATGTGGGGGTTATCGCAAAA −153 11.26
malT AATTGTGACACAGTGCAAATTC −143 13.48
malXY TTATGTGACAGATAAAACGTTT −155 11.14
TAATGTGATTTATGCCTCACTA −95 15.70
nagE TTTGGTGACAAAACTCACAAAA −177 14.51
ATTTGCGATACGAATTAAATTT −143 12.59
nagBACD TTTTGTGAGTTTTGTCACCAAA −178 14.51
AAATTTAATTCGTATCGCAAAT −212 12.59
nupG AAATGTTATCCACATCACAATT −119 20.43
TTATTTGCCACAGGTAACAAAA −69 10.59
ompA ATGCCTGACGGAGTTCACACTT −188 12.84
ppiA TTTTGTGATCTGTTTAAATGTT −204 10.23
AGAGGTGATTTTGATCACGGAA −151 12.33
proP ATGTGTGAAGTTGATCACAAAT −228 20.45
ptsHI-crr TTTTGTGGCCTGCTTCAAACTT −338 14.43
rhaBAD AATTGTGAACATCATCACGTTC −127 15.16
AAATGCGGTGAGCATCACATCA −162 12.41
rhaT AGATGTGAAGCAAATCACCCAC −145 13.65
rpoS AACTGCGACCACGGTCACAGCG −270 8.77
sdhCDAB TATCGTGACCTGGATCACTGTT −314 16.41
tdcABC ATTTGTGAGTGGTCGCACATAT −82 15.0
AAATGTGACATGCCGCATTATT −384 10.83
tnaLAB GATTGTGATTCGATTCACATTT −95 19.61
tsx AACTGTGAAACGAAACATATTT −129 12.93
udp TTATGTGATTTGCATCACTTTT −145 20.62
CATGGTGATGAGTATCACGAAA −93 11.04
uhpT AAGCGTGATGCATCTCACCTTT −145 16.51
yhfa TAATGTGACGTCCTTTGCATAC −187 11.71

  • This table contains top scoring site for all 46 TUs, plus any additional sites with scores above 10 bits. Position of a CRP site is relative to the translation start of the first downstream gene. The same rule applies to all sites in Tables 3 T4 T5 T6 T7 T8.

This Article

  1. Genome Res. 11: 566-584

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