RegulonDB RegulonDB 11.1: Operon Form
   

ssb operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ssb
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: ssb
Synonym(s): OP00091
Gene(s): ssb   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Schaefer TS., et al., 1991
Promoter
Name: ssbp3
+1: 4274011
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 114
Sequence: attgacctgaatgaatatacagtattggaatgcattacccggagtgttgtgtaacaatgtCtggccaggtttgtttcccgg
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Brandsma JA., et al., 1985
[3] Huerta AM., et al., 2003
[4] Ogasawara H., et al., 2005
TF binding sites (TFBSs)
[ArcA,-] Phrase
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 ArcA-phosphorylated repressor ssbp3 4273931 4273945 -72.5 ggcgatcacaAACGGTTAATTATGAcacaaattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArcA-phosphorylated repressor ssbp3 4273994 4274008 -9.5 attacccggaGTGTTGTGTAACAATgtctggccag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote ArcA-phosphorylated repressor ssbp3 4274034 4274048 31.5 tttcccggaaCCGAGGTCACAACATagtaaaagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
remote ArcA-phosphorylated repressor ssbp3 4274077 4274091 74.5 aatggtacaaTCGCGCGTTTACACTtattcagaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
[LexA,-] Phrase
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 LexA repressor ssbp3 4273955 4273974 -46.5 acacaaattgACCTGAATGAATATACAGTAttggaatgca nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd


Transcription unit          
Name: ssb
Gene(s): ssb   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [2] Brandsma JA., et al., 1985
Promoter
Name: ssbp2
+1: 4274080
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 45
Sequence: tttgtttcccggaaccgaggtcacaacatagtaaaagcgctattggtaatggtacaatcgCgcgtttacacttattcagaa
                               -35                   -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Brandsma JA., et al., 1985
[3] Huerta AM., et al., 2003
[4] Ogasawara H., et al., 2005
TF binding sites (TFBSs)
[ArcA,-] Phrase
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 ArcA-phosphorylated repressor ssbp2 4273931 4273945 -141.5 ggcgatcacaAACGGTTAATTATGAcacaaattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArcA-phosphorylated repressor ssbp2 4273994 4274008 -78.5 attacccggaGTGTTGTGTAACAATgtctggccag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArcA-phosphorylated repressor ssbp2 4274034 4274048 -38.5 tttcccggaaCCGAGGTCACAACATagtaaaagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArcA-phosphorylated repressor ssbp2 4274077 4274091 5.5 aatggtacaaTCGCGCGTTTACACTtattcagaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Transcription unit          
Name: ssb
Gene(s): ssb   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [2] Brandsma JA., et al., 1985
Promoter
Name: ssbp1
+1: 4274092
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 33
Sequence: aaccgaggtcacaacatagtaaaagcgctattggtaatggtacaatcgcgcgtttacactTattcagaacgatttttttca
                               -35                     -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Brandsma JA., et al., 1985
[3] Huerta AM., et al., 2003
[4] Ogasawara H., et al., 2005
TF binding sites (TFBSs)
[ArcA,-] Phrase
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 ArcA-phosphorylated repressor ssbp1 4273931 4273945 -153.5 ggcgatcacaAACGGTTAATTATGAcacaaattga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArcA-phosphorylated repressor ssbp1 4273994 4274008 -90.5 attacccggaGTGTTGTGTAACAATgtctggccag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArcA-phosphorylated repressor ssbp1 4274034 4274048 -50.5 tttcccggaaCCGAGGTCACAACATagtaaaagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal ArcA-phosphorylated repressor ssbp1 4274077 4274091 -7.5 aatggtacaaTCGCGCGTTTACACTtattcagaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Schaefer TS., Hays JB., 1991, Bacteriophage P1 Bof protein is an indirect positive effector of transcription of the phage bac-1 ban gene in some circumstances and a direct negative effector in other circumstances., J Bacteriol 173(20):6469-74

 [2] Brandsma JA., Bosch D., de Ruyter M., van de Putte P., 1985, Analysis of the regulatory region of the ssb gene of Escherichia coli., Nucleic Acids Res 13(14):5095-109

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Ogasawara H., Teramoto J., Yamamoto S., Hirao K., Yamamoto K., Ishihama A., Utsumi R., 2005, Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system in Escherichia coli., FEMS Microbiol Lett 251(2):243-9

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