A Comparative Genomics Approach to Prediction of New Members of Regulons

Table 5.

Haemophilus influenzae TUs Predicted to Belong to the CRP Regulon

Operon Site sequence Position Score
TUs Orthologous to Training Set TUs
ansB TTATGTGATCGAGATCATAAAT −102 18.78
cyaA AATTGTGATTTATGTCACATTT −90 23.59
galR AACCGTGATCTTTGTCACAAAA −145 17.09
TTTTATGATTTAGTTCATACTT −104 13.74
galTKM TTTTGTGACAAAGATCACGGTT −85 17.09
AAGTATGAACTAAATCATAAAA −126 13.74
glpT TTTTGTGATATTGATCACAATA −186 21.10
ATTTGTGAAACACTTCACATTT −135 21.58
mtr TGATGTGAAAAATTCAATATT −319 11.14
sdaCA AAATTTTAACTTGATCACAATT −141 15.67
TTTTTTGCTTTGATTTACAATA −366 10.23
Category I
arcA AACTATGATTTAGATCACAAAA −130 17.84
argR-HI1208 TTCTATGATCTAGTTCACATTT −125 18.68
aspA AAATGTGATCTTCATCAAGTTT −71 18.39
brnQ TATTGTGACAAAATTCACATTT −96 20.49
cdd ATAAGTGATCAAGATCACAGTT −117 19.14
cmkA TTCTGTGATCCATCTCACAATC −204 20.06
cydAB AAATGTGATCTATATAGCATTT −234 17.77
CAATTTGATCTAAGTCAATTAA −298 11.86
dsbD TTTTGTGATCTAAATCATAGTT −84 17.84
fdhD TATTGTGATCTAGATCATAAAT −73 19.77
frdABCD TTTTTTGAGGTAGATCACAAAA −147 18.19
gapdH TGATTTGATATAGATCACAAAA −145 18.14
genX TTTTGTGATCTACCTCAAAAAA −57 18.19
glpABC AAATGTGAAGTGTTTCACAAAT −180 21.58
TATTGTGATCAATATCACAAAA −129 21.10
glpR ATCTGAGATCTAGATCACAGAA −96 18.12
gmk TTTTGTGATCTATATCAAATCA −278 18.14
hemX-HI0602.1-hemY AAATGTGACATAAATCACAATT −237 23.59
hslVU AAATATGATCAACTTCACATTT −129 19.07
HI0053-HI0052-HI0051 AACTGTGGCGTGGATCACAGTT −127 20.80
HI0074-HI0073 TTTTGTGATCAATATCACAATG −96 18.33
TTATTAGAAAAATATCAAATTA −150 11.87
HI0082-HI0083 TTTCTTGATCCACGTCACATTA −265 17.10
HI0145 AAATGAGAAGTTGATCACATTT −184 20.01
HI0146-HI0147 AAATGTGATCAACTTCTCATTT −188 20.01
HI0310 TAATTTGACACGCATCACAAAT −116 19.12
TAAAATGAAAAAAATCACGCTT −5 10.80
HI0432-HI0431-hupA TAACGTGAGATTTGTCACAATT −4 17.61
HI0485.1-atpBEFHAGDC AAGTGTGATTTATATAACACTT −95 18.96
HI0495-HI0494 AAATGTGAAGTTGATCATATTT −112 19.07
HI0521-HI0520 AACTGTGATCTTCCTCACGTTT −83 18.26
HI0522 AAACGTGAGGAAGATCACAGTT −152 18.26
HI0744-secB ATTTATGATCTCGATCACATAA −146 18.78
HI1010-HI1011- TTCTGTGATCTAGATCTCAGAT −85 18.12
HI1012-HI1013
HI1126 ATTTGTGACTTGTATCACATTT −86 22.72
HI1176 TTTTGTGATCTTGATCACATAT −152 22.64
HI1315 TTCTGTGATCCATCTCACAATC −76 17.91
HI1349 AACTGTGATCTTGATCACTTAT −179 19.14
HI1427 TTTTGTGATCTCGATCACAAAT −120 22.06
lctP TTCTGTGATCCATCTCACAATC −98 20.06
mdh AAATGTGAACTAGATCATAGAA −104 18.68
metR-HI1738-HI1737 AATTGTGATCTAGTTCTCAAAA −106 19.75
AATTGCTAAACGGATCAAATAT −377 11.55
AAATGTTTTGCACCGCACATTT −309 11.36
mglBAC ATTTGTGACATGGATCACAAAT −92 22.19
nhaA AAATGTGAATTTTGTCACAATA −114 20.49
nrdD CATTGTGATATTGATCACAAAA −207 18.33
TAATTTGATATTTTTCTAATAA −153 11.87
ompP2 AAATGTGATCTCGATCAGATTT −161 20.10
Operon Site sequence Position Score
pckA AAATGAGATCTACTTAACATTT −88 17.54
ATTTTTGCTCTATATCACAATA −148 16.26
pntAB TTTCGTGATCCCTATCACAATA −171 18.29
sucAB GAGTTTGAACTAGATCACAAAT −83 17.64
uspA AATTGTGATCTAGTACACAGTT −89 18.58
uxuRA TTTTGTGAGCCATATCACAAAA −5 20.80
xylAB AACTGTGATCCACGCCACAGTT −121 17.19
xylFGH AACTGTGGCGTGGATCACAGTT −135 17.19
Category IIA
artPIQM ATTCGTGTTAAAAATCTCAATT 7 10.71
citCDEF ATTAGTGAAATAATTTAAAATT −263 11.17
cspD TTTTGTGATCTACTTATCATTT −146 15.77
TATTGTAAAATGGTTCAATAAT 11 11.29
folE-HI1446 AAATTTGCAATTTTTCTCATTT −78 11.28
fucRIKUAP AAGTGCGGTCGGTTTCACACCA −170 10.52
ndh TAATGTAACATTTTTAACAATT −43 13.07
HI0017 AATTTTAATTTAGATCAAATTT −148 15.42
HI0257 AAATGAGACATAGATCATCCTT −130 13.52
HI1030-HI1029-HI1028 TAATATAAAACGAATCACATTT −44 15.46
HI1031 AAATAGGATCTAGATCACAAAA −148 14.71
HI1032 TTTTGTGATCTAGATCCTATTT −50 14.71
Hi1245 AAGTTTGCAGTTCGTCACAATT −92 13.23
HI1394 TATTGTGATGAAATTTTTATTT −188 10.35
HI1612-sfsA CTTTGTGGTCTCGCTCACTTTT −117 12.19
nifR3-fis AAATGCGAATCGGTTCATACCA −3 11.10
oppABCDF TTATTAGACACAACTCACAAAA −132 13.97
ribA AACTGAAATCCCCATCACAATT −294 14.71
rpS6 AATTGTGCCTTGCATCTCAATG −400 12.04
sodA TTTAATGATCTAAATCAATTTT −100 10.20
spr CATTGTGTAAAAGATCACAAAA −110 13.16
ung AAATTTGATCTAAATTAAAATT −132 15.42

  • Listed are predictions from categories I and IIA and TUs containing orthologs to genes in the training set.

This Article

  1. Genome Res. 11: 566-584

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