Table 2.
Top-scoring target regions
| ID | NLQ a | Start | End | Gene | Description | NtcA bs b | Putative NtcA binding site and promoter sequences c |
|---|---|---|---|---|---|---|---|
|
1203 |
8186.60 |
3561438 |
3561710 |
alr2921* |
tRNA modif. prot. |
3561528 |
GTGTGTCTTGATACAATACTTTTAAGATGACTGTTATATGCTTTCTAAG |
|
1856 |
7861.39 |
5515960 |
5516178 |
all4613 |
IlvG |
5516125 |
GAATTACTGACTACAGAATTCCCGCATTAACTTAGCTATCATCTGAGGTT |
| |
|
|
|
|
|
5516125 |
GAATT
A
CTGACTAC |
|
1152 |
7152.53 |
3427339 |
3427611 |
alr2817 |
HetC [26] |
3427445 |
GTAACATGAGATAC
ACAATAGCATTTATATTTGCTT
TAGTAT
CTCTCT
C
|
|
390 |
6288.90 |
1156154 |
1156424 |
alr0990 |
Amt4 [21] |
1156258 |
GTATTAACTAATACAGAATTAATGTTTAGGTAAATAGACAATCAATC |
|
798 |
5358.67 |
2400656 |
2400888 |
all2006 |
Unknown protein |
2400815 |
GTATATTTCAACACGAATTTGATCATTTAGATGGTGTACTGTTTATAGA |
|
931 |
4728.32 |
2807226 |
2807511 |
alr2328 |
GlnA (RNAI) [27] |
2807342 |
GTAACAAAGACTAC
AAAACTGTCTAATGTTTAGAATC
TACGAT
ATTTC
A
|
| |
|
|
|
|
GlnA (RNAII) [27] |
2807342 |
GTAACAAAGACTAC
AATCCAGACGTTC
T
|
|
1612 |
4089.39 |
4795414 |
4795682 |
asl3981 |
Unknown protein |
4795535 |
GGATTTTGTAGCTATCACTAC |
| |
|
|
|
|
|
4795535 |
GTAGCTATCACTACAATCTATAGCTTGAAAGAGGAGGAAAATAGGTTGG |
|
293 |
3663.48 |
815417 |
815662 |
alr0709 |
Fe-responsive RR [25] |
815545 |
GTATAAATTTTTAC |
|
364 |
3580.62 |
1070920 |
1071178 |
all0926
§
|
PilL |
1071039 |
GTAGCCCCTGCTAC |
|
1764 |
3570.57 |
5243203 |
5243472 |
all4376 |
SpsB [28] |
5243396 |
GTATTGAAAATTACAAAAATCTTATTTACTTATTAGTAACATTGGTGAC |
|
1165 |
3408.52 |
3463447 |
3463731 |
all2842
§
|
Unknown protein |
3463590 |
GTTACACCTGCTAC |
|
1125 |
3369.20 |
3341106 |
3341375 |
alr2743 |
Processing protease |
3341205 |
GTATAACTTGATGCGAATTTGGCGATCGTTCAGAGTTAAGATCACAAACA |
|
1530 |
3353.43 |
4573161 |
4573410 |
asl3784 |
hypothetical protein |
4573340 |
GTTAAATAGATTACAAAACTCTGGATGGACTTTGAGTATCATTTAGATA |
|
932 |
3292.44 |
2809205 |
2809466 |
asl2329 |
GifA [29] |
2809350 |
GTAGCATAAGATAC
AGAATTCTTGC
TATATT
AAATGT
G
|
|
2098 |
3220.20 |
6294152 |
6294404 |
alr5275 |
Gnd |
6294223 |
GTTGATTTGGATACAAATTAAAACTATTTATCTGTGTTACTAGTGAGCTTTTA |
| |
|
|
|
all5274 |
Hypothetical protein |
6294223 |
GTATCCAAATCAACAATTAACTTGTAAAATTTGCGA |
|
319 |
3192.18 |
902825 |
903070 |
all0778 |
Ser protease inhibitor |
902941 |
GTAGCCATGAATAC |
|
1150 |
3126.82 |
3420486 |
3420738 |
alr2811 |
AvtA |
3420576 |
GCTGAGATTGGTAC |
|
2232 |
2974.32 |
264949† |
265189† |
alr7243
§
|
Similar to ankyrin |
265067† |
GTAGCCTGTGATAC |
|
898 |
2824.47 |
2729431 |
2729698 |
all2267 |
Hypothetical protein |
2729550 |
GTATTGCTGGCTAC |
|
1858 |
2807.34 |
5523157 |
5523405 |
all4620
a
|
Na+/H+-exch. prot. |
5523288 |
GTATAAGCTGTAAC |
|
1255 |
2798.00 |
3732951 |
3733219 |
all3084 |
Hypothetical protein |
3733071 |
GTTAAAATGACGACATTTTAATAAAAAGAAGCATATACTCGATGTA |
|
260 |
2698.90 |
701137 |
701391 |
all0602 |
NtcB [30] |
701297 |
GTAACAAAATCTAC
CAAATTGGGGAGCAAAATCAGCTAACTTAATTGA
A
|
|
377 |
2641.34 |
1111093 |
1111337 |
all0956 |
Unknown protein |
1111206 |
GTAGCATAGACAAC |
| |
|
|
|
alr0957 |
FurC [31] |
1111206 |
GTAGCATAGACAAC |
|
519 |
2592.23 |
1576957 |
1577227 |
asr1328 |
Hypothetical protein |
1577115 |
GTAACATACACTACGAAACTTATGCTATGTTAGGAAGAA |
|
2149 |
2572.01 |
23295† |
23563† |
all7026
§
|
DNA binding protein |
23435† |
GTATTCGCTGATAC |
|
554 |
2517.34 |
1669629 |
1669873 |
alr1404 |
Ser acetyltransferase |
1669702 |
GTGACTGGGGATACAGAAAATTTATTTATAGTCCTGTCTACTGTATATTC |
|
1784 |
2362.05 |
5312632 |
5312908 |
all4432
§
|
EPS biosynthesis |
5312767 |
GTATCAACTGCTAC |
|
1660 |
2280.02 |
4946500 |
4946770 |
alr4105
§
|
2-comp. sensor HK |
4946621 |
GTAGCAGGTTATAC |
|
2345 |
2253.01 |
105303‡ |
105553‡ |
all7614 |
Putative porin, OprB-II |
81139‡ |
GTATGAAATAGTACAGTTTAAAATTAGTGTTTGCGTCATCATTACGAGA |
|
38 |
2141.66 |
69752 |
69991 |
asr0064 |
Hypothetical protein |
69882 |
AGTTCCGTATAGCAAAATAC |
|
1118 |
2134.47 |
3325955 |
3326229 |
alr2729* |
cox3 operon |
3326057 |
GTTACTAAAGATACAGTATTTTCTAGCTTTTAAATTTTGAATACAAAGA |
|
1283 |
2115.10 |
3807024 |
3807271 |
all3144 |
Hypothetical protein |
3807189 |
GTATCGACCATTAC |
|
94 |
2063.99 |
210284 |
210541 |
alr0194 |
Hypothetical protein |
210417 |
GTATTACCTAATAC |
| |
|
|
|
all0193 |
Haloalkane dehalogenase |
210417 |
GTATTACCTAATAC |
|
1316 |
1948.08 |
3903915 |
3904189 |
all3232 |
2-comp. RR |
3904009 |
GTAACCAAATATAC |
| |
|
|
|
alr3233 |
TrpE |
3904009 |
GTAACCAAATATAC |
|
262 |
1927.75 |
704040 |
704304 |
alr0607 |
NirA [32] |
704169 |
GTAGCTACTTATAC
TATTTTACCTGAGATCCCGACA
TAACCT
TAGA
A
|
|
729 |
1908.73 |
2158958 |
2159198 |
all1797 |
Unknown protein |
2159129 |
GTATCCTCTGCTGCTGCACTAGAAGTTTGTTCAAGGTTTAATTGTAATA |
|
1923 |
1885.93 |
5718871 |
5719130 |
alr4800 |
Anti-σ antagonist |
5718952 |
GATACGATTGATACCGAAATCCTTAGGCGTTTGTGCCTATATTGAGAAAA |
|
2111 |
1840.96 |
6328022 |
6328296 |
alr5307 |
Glycosyl transferase |
6328115 |
GTAGTTTTCGCTAC |
| |
|
|
|
all5306 |
Exodeoxyribonuclease III |
6328115 |
GTAGTTTTCGCTAC |
|
695 |
1791.79 |
2058723 |
2059007 |
alr1713* |
Hypothetical protein |
2058829 |
GTAACCTATAAGACATTTTATTTGATACCTCATACTCTAAAATCAAGTA |
| 776 | 1744.65 | 2304064 | 2304320 | alr1921 § | Biotin synthase | 2304193 | GAAGTGTGCTGTAC |
†Genomic positions within the alpha plasmid. ‡Genomic positions within the beta plasmid.
§Target regions located in internal positions of the ascribed genes. All the other target regions are upstream of the ascribed genes. The genes marked with * could be ascribed to sRNAs located in the upstream region of the indicated genes.
aNLQ: Indication of the statistical significance of the peak identifying the binding region.
bPosition in the chromosome/plasmids of the first nucleotide of the putative NtcA binding sites.
cThe putative NtcA binding sites, -10 boxes and TSPs are in italics. Those that have been previously described are indicated in bold. In some cases, the detected NtcA-binding site could be associated to two TSPs, either of the same gene or of two divergent genes.