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Name: | cbpAM |
Gene(s): | cbpM, cbpA Genome Browser M3D Gene expression COLOMBOS |
Note(s): | CbpM accumulates in late stationary phase; cbpM may be encoded in an operon together with cbpA Chae C,2004. The cbpAM operon is mainly transcribed at the transition from exponential growth to stationary phase by σS and Lrp (in the absence of leucine). The effect of Lrp on this operon could be indirect, since Lrp requires σS to activate the cbpAM operon Chenoweth MR,2008 |
Evidence: | [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process |
Reference(s): | [1] Chae C., et al., 2004 |
Promoter | |
Name: | cbpAp2 |
+1: | 1063828 |
Sigma Factor: | Sigma38 Sigmulon |
Distance from start of the gene: | 53 |
Sequence: |
tttcaataacatattctgtgttggcatatgaaattttgaggattaccctacacttataggAgttaccttacaggggttcct -35 -10 +1 |
Note(s): | The cbpA gene is transcribed by two promoters: one of them is σ38 dependent and is the most efficient; the other promoter is σ70 dependent Singh SS,2011 |
Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
Reference(s): |
[2] Huerta AM., et al., 2003 [3] Salgado H, et al., 2012 [4] Singh SS., et al., 2011 [5] Yamashino T., et al., 1994 |
Name: | cbpAM |
Gene(s): | cbpM, cbpA Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process |
Reference(s): |
[1] Chae C., et al., 2004 [5] Yamashino T., et al., 1994 |
Promoter | |
Name: | cbpAp1 |
+1: | 1063833 |
Sigma Factor: | Sigma70 Sigmulon |
Distance from start of the gene: | 58 |
Sequence: |
gatgatttcaataacatattctgtgttggcatatgaaattttgaggattaccctacacttAtaggagttaccttacagggg -35 -+1 |
Note(s): | The cbpAp1 promoter contains an unusual DNA structure (i.e, DNA curvature) Yamashino T,1994 A mutation in the -18G position, with respect to the transcriptional start site, in this promoter, causes an increasing effect on transcription. The biggest effect is seen when the G at position 18 is replaced by a T Singh SS,2011 |
Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA] [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
Reference(s): |
[2] Huerta AM., et al., 2003 [4] Singh SS., et al., 2011 [5] Yamashino T., et al., 1994 |
Name: | cbpA-cbpM | ||||||||||
Gene(s): | cbpM, cbpA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Evidence: | [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process | ||||||||||
Reference(s): | [1] Chae C., et al., 2004 | ||||||||||
Promoter | |||||||||||
Name: | cbpAp4 | ||||||||||
+1: | 1063919 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 144 | ||||||||||
Sequence: |
tggttcaactatcaaaaatcgctcaccctttttcacctgtttaaaatatgttcagcaaccCatcttgatggcgacctcctc -35 -10 +1 |
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Evidence: |
[COMP-HINF] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): | [6] Chintakayala K., et al., 2013 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | Fis | repressor | cbpAp4 | 1063927 | 1063941 | -15.0 | tttttcacctGTTTAAAATATGTTCagcaacccat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [6] |
Name: | cbpA-cbpM | ||||||||||
Gene(s): | cbpM, cbpA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Evidence: | [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process | ||||||||||
Reference(s): | [1] Chae C., et al., 2004 | ||||||||||
Promoter | |||||||||||
Name: | cbpAp6 | ||||||||||
+1: | 1064037 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 262 | ||||||||||
Sequence: |
ttccaggcctgtttcaaataattatttgcagtgcaactaattccatgtatattactacccAtatatagcgtctataaaatt -35 -10 +1 |
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Evidence: |
[COMP-HINF] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): | [6] Chintakayala K., et al., 2013 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
remote | Fis | repressor | cbpAp6 | 1063927 | 1063941 | 104.0 | tttttcacctGTTTAAAATATGTTCagcaacccat | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [6] |
Name: | cbpA-cbpM | ||||||||||
Gene(s): | cbpM, cbpA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Evidence: | [IC-ADJ-GENES-SAME-BIO-PROCESS] Products of adjacent genes in the same biological process | ||||||||||
Reference(s): | [1] Chae C., et al., 2004 | ||||||||||
Promoter | |||||||||||
Name: | cbpAp | ||||||||||
+1: | 1064037 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 262 | ||||||||||
Sequence: |
ttccaggcctgtttcaaataattatttgcagtgcaactaattccatgtatattactacccAtatatagcgtctataaaatt -35 -10 +1 |
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Evidence: |
[COMP-HINF] [EXP-IDA] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
||||||||||
Reference(s): | [6] Chintakayala K., et al., 2013 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
remote | Fis | repressor | cbpAp | 1063927 | 1063941 | 104.0 | tttttcacctGTTTAAAATATGTTCagcaacccat | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP-SITE-MUTATION], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [6] |
Reference(s) |
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