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Name: | puuP |
Synonym(s): | ycjJ |
Gene(s): | puuP, ymjE Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [COMP-AINF] Inferred computationally without human oversight |
Promoter | |
Name: | puuPp |
+1: | 1359373 |
Sigma Factor: | Sigma54 Sigmulon |
Distance from start of the gene: | 32 |
Sequence: |
gtaatccagacatttcccggatgtcgcgttatggagcgcgggcggcaacgggcttccgttAacgattaagactgtgacgag -24 -12 +1 |
Note(s): | This promoter was identified by microarray and ChIP assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010 We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999. |
Evidence: |
[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION] [COMP-AINF-SIMILAR-TO-CONSENSUS] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IEP] |
Reference(s): |
[1] Huerta AM., et al., 2003 [2] Reitzer L., et al., 2001 [3] Zhao K., et al., 2010 |
Name: | puuAP | ||||||||||
Gene(s): | puuP, ymjE, puuA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The transcription of puuA is induced by putrescine and overexpressed by upon deletion of puuR Kurihara S,2008. All puu genes, including puuA and puuD, may could be synchronistically regulated by PuuR and/or other regulators, such as ArcA and FNR, which repressed the expression of puuA under anaerobic conditions Kurihara S,2008. Putrescine is catabolized by products of the puu gene cluster, which that are regulated by ArcA, FNR, and PuuR to decrease the toxicity of putrescine and to utilize putrescine as both a nitrogen and carbon sources Kurihara S,2008. The puuA gene is downregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020. The curator has determined that the binding sites of PuuR may have a length of 20 nucleotides with an inverted repeated symmetry (ATGGaCAATATATTGaCCAT). The sequence proposed by Nemoto et al. in 2012 was included in these regions Nemoto N,2012. Nemoto et al. proposed binding sites that are 15 nucleotides long, with an asymmetric recognition sequence, AAAATATAATGAACA Nemoto N,2012. |
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Evidence: | [COMP-AINF] Inferred computationally without human oversight [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined |
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Reference(s): | [4] Nemoto N., et al., 2012 | ||||||||||
Promoter | |||||||||||
Name: | puuAp | ||||||||||
+1: | 1360968 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 60 | ||||||||||
Sequence: |
tcatttttgcaaactcaatttaacatttgacaaacatttagtttgcatacagattcgaatGgtggtcattatattttacgc -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [EXP-IMP] |
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Reference(s): |
[5] Gama-Castro S., et al., 2008 [6] Maciag A., et al., 2011 [4] Nemoto N., et al., 2012 |
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 | puuAp | 1361126 | 1361140 | -165.0 | cgataaccggATTGTTCATTATATTttccatgctc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
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 | FNR | repressor | puuAp | 1360933 | 1360946 | 29.0 | attttacgctTTGATAACGAGCGGaaaacaaacc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [7] |
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 | PuuR | repressor | puuAp | 1360948 | 1360967 | 11.5 | gattcgaatgGTGGTCATTATATTTTACGCtttgataacg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] | W | [4], [8], [9] |
proximal | PuuR | repressor | puuAp | 1361043 | 1361062 | -84.5 | aatgacctttATGTTCAATATTTTTTCAATctagcagtgg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] | W | [4], [8], [9] |
remote | PuuR | repressor | puuAp | 1361085 | 1361104 | -126.5 | atctcacaaaGTGGACTAAATTATCGCCATtactgcgctt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION], [IC] | C | [4], [8], [9] |
remote | PuuR | repressor | puuAp | 1361120 | 1361139 | -161.5 | gataaccggaTTGTTCATTATATTTTCCATgctcaatctc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] | W | [4], [8], [9] |
Reference(s) |
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