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Name: | frc | ||||||||||
Synonym(s): | yfdW | ||||||||||
Gene(s): | frc Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Masuda N,2003proposed a model of the regulatory network of the acid resistance genes, including evgA, ydeP, ydeO, yhiE, gadABC, and hdeAB, using a combination of microarray analysis and gene replacement techniques. With these assays, seven operons were identified as induced by EvgA overexpressed and YdeO absent; on the other hand, twelve operons were identified as induced by YdeO overexpression. To confirm these regulatory interactions, the EvgA consensus site was searched with the ALIGNACE program, and the 18-bp site found was tested by gel shift analysis with the upstream regions of the corresponding operons. As a result, just six operons are regulated by EvgA, among which the frc gene is included. Based on microarray and RT-qPCR analyses, it was determined that the asr, frc, oxc, ydeO, and yegR acid stress genes are significantly upregulated upon exposure to exogenous glutathione (GSH) Goswami M,2018 |
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Promoter | |||||||||||
Name: | frcp | ||||||||||
+1: | 2493439 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 185 | ||||||||||
Sequence: |
cacaaatgtcgcgactctctctgattaccacgaatcaatatttatcatattcttcttttcGtcctcactacttaccatgca -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[1] Huerta AM., et al., 2003 [2] Itou J., et al., 2009 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | EvgA-phosphorylated | activator | frcp | 2493506 | 2493523 | -75.5 | tcaccggcgcTTCTTACAGTTGTAAGAAtaacatcaca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [3] |
Name: | yfdX | ||||||||||
Gene(s): | yfdE, yfdV, oxc, frc, yfdX Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Masuda N,2003proposed a model of the regulatory network of the acid resistance genes, including evgA, ydeP, ydeO, yhiE, gadABC, and hdeAB, using a combination of microarray analysis and gene replacement techniques. With these assays, 7 operons were identified as induced by EvgA overexpressed and when YdeO is absent; on the other hand, 12 operons were identified as induced by YdeO overexpression. To confirm these regulatory interactions, the EvgA consensus site was searched with the ALIGNACE program, and the 18-bp site found was tested by gel shift analysis with the upstream regions of the corresponding operons. As a result, just six operons are regulated by EvgA, among which the yfdX gene is included. The yfdX-frc-oxc-yfdVE operon is required for oxalate-induced acid tolerance (AR) Fontenot EM, Ezelle KE, Gabreski LN, Giglio ER, McAfee JM, Mills AC, Qureshi MN, Salmon KM, Toyota CG,2013 |
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Evidence: | [EXP-IEP-COREGULATION] Inferred through co-regulation | ||||||||||
Reference(s): |
[4] Masuda N., et al., 2002 [3] Masuda N., et al., 2003 |
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Promoter | |||||||||||
Name: | yfdXp | ||||||||||
+1: | 2494433 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 31 | ||||||||||
Sequence: |
ttcaaaatgaccgttgctctctgatttctcatttcatgctcacccaatatgatggcggcgTtttctaaaactgttaaagaa -35 -10 +1 |
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Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[1] Huerta AM., et al., 2003 [2] Itou J., et al., 2009 |
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 | EvgA-phosphorylated | activator | yfdXp | 2494500 | 2494517 | -75.5 | cttgcgataaTAACTACAACTGTAAGATaaccctttca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2] |
remote | EvgA-phosphorylated | activator | yfdXp | 2494538 | 2494555 | -113.5 | aggaagcataTTCCTACAATTGTAAGACtaaaatactt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [2], [3] |
Name: | yfdE |
Gene(s): | yfdE Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [COMP-AINF] Inferred computationally without human oversight |
Name: | yfdV |
Gene(s): | yfdV Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [COMP-AINF] Inferred computationally without human oversight |
Name: | oxc |
Gene(s): | oxc Genome Browser M3D Gene expression COLOMBOS |
Note(s): | Based on microarray and RT-qPCR analyses, it was determined that the asr, frc, oxc, ydeO, and yegR acid stress genes are significantly upregulated upon exposure to exogenous glutathione (GSH) Goswami M,2018 |
Evidence: | [COMP-AINF] Inferred computationally without human oversight |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
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terminator | -11.1 | 2489182 | 2489213 | ttacataaatGCCGAAGTGTCTTTTCACCTTCGGCTTTTTTcaaggcataa | |
terminator | -9.3 | 2490192 | 2490224 | gccaactcatTATGCGATGGTGAGGGGACCCTTATCGGAAATactattatgc | |
terminator | -9.8 | 2491980 | 2491996 | tgatattaacGGGGGCTTCTGGCTCCcaatttataa | |
anti-terminator | -13.3 | 2489207 | 2489275 | tcacggctccCTTGTGGATTTATGTCAGTCGACTGGTTTCATAATTAATCATGTTATTGATTTTACATAAATGCCGAAgtgtcttttc |
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos" |
Reference(s) |
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