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Name: | hyaABCDEF | ||||||||||
Gene(s): | hyaA, hyaB, hyaC, hyaD, hyaE, hyaF Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The hyaABCDEF operon is induced under anaerobiosis and repressed by nitrate Richard DJ,1999 ArcA and Appy antagonize the IscR repression effect under anaerobic conditions Nesbit AD,2012 | ||||||||||
Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation |
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Reference(s): |
[1] Maciag A., et al., 2011 [2] Menon NK., et al., 1990 [3] Menon NK., et al., 1991 |
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Promoter | |||||||||||
Name: | hyaAp | ||||||||||
+1: | 1031984 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 155 | ||||||||||
Sequence: |
aaaagataaatccacacagtttgtattgttttgtgcaaaagtttcactacgctttattaaCaatactttctggcgacgtgc -35 -10 +1 |
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Note(s): | The hyaA promoter does not have much similarity to the consensus -10 and -35 promoter sequences for σ70, as shown by Richard DJ,1999. But, as reported in Atlung T,1997, a correlation with σ38 and hya operon expression has been proved under different conditions, so the promoter seems to be σ38. |
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Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [EXP-IMP] |
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Reference(s): |
[4] Atlung T., et al., 1997 [5] Huerta AM., et al., 2003 [1] Maciag A., et al., 2011 [6] Richard DJ., et al., 1999 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | ccgacgtaaaAAGACGGTAAGTATCGCTTTCAGTCTTatgaatatcg | ||||||||||
Reference(s): | [2] Menon NK., et al., 1990 |
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 | ||||||||
nd | AppY | activator | hyaAp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [11] |
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 | activator | hyaAp | 1031910 | 1031924 | -67.0 | aaaaataggtCCATTTTTATCGCTAaaagataaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [6] |
proximal | ArcA-phosphorylated | activator | hyaAp | 1031966 | 1031988 | -7.5 | gtgcaaaagtTTCACTACGCTTTATTAACAATActttctggcg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [9] |
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 | hyaAp | 1031956 | 1031970 | -21.0 | gtattgttttGTGCAAAAGTTTCACtacgctttat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [10] |
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 | IscR | repressor | hyaAp | 1031930 | 1031954 | -42.0 | cgctaaaagaTAAATCCACACAGTTTGTATTGTTTtgtgcaaaag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8] |
proximal | IscR | repressor | hyaAp | 1031933 | 1031957 | -39.0 | taaaagataaATCCACACAGTTTGTATTGTTTTGTgcaaaagttt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [9] |
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 | NarL-phosphorylated | repressor | hyaAp | 1031971 | 1031977 | -10.0 | aaagtttcacTACGCTTtattaacaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
proximal | NarL-phosphorylated | repressor | hyaAp | 1031987 | 1031993 | 7.0 | ttattaacaaTACTTTCtggcgacgtg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
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 | NarP-phosphorylated | repressor | hyaAp | 1031966 | 1031981 | -10.0 | gtgcaaaagtTTCACTACGCTTTATTaacaatactt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
proximal | NarP-phosphorylated | repressor | hyaAp | 1031982 | 1031997 | 7.0 | acgctttattAACAATACTTTCTGGCgacgtgcgcc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
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 | YdeO | activator | hyaAp | 1031912 | 1031935 | -61.0 | aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
Name: | hyaABCDEF | ||||||||||
Gene(s): | hyaA, hyaB, hyaC, hyaD, hyaE, hyaF Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The hyaABCDEF operon is induced under anaerobiosis and repressed by nitrate Richard DJ,1999 ArcA and Appy antagonize the IscR repression effect under anaerobic conditions Nesbit AD,2012 | ||||||||||
Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation |
||||||||||
Reference(s): |
[1] Maciag A., et al., 2011 [2] Menon NK., et al., 1990 [3] Menon NK., et al., 1991 |
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Promoter | |||||||||||
Name: | hyaAp2 | ||||||||||
+1: | 1031984 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 155 | ||||||||||
Sequence: |
aaaagataaatccacacagtttgtattgttttgtgcaaaagtttcactacgctttattaaCaatactttctggcgacgtgc -35 -10 +1 |
||||||||||
Note(s): | The hyaA promoter does not have much similarity to the consensus -10 and -35 promoter sequences for σ70, as shown by Richard DJ,1999. But, as reported in Atlung T,1997, a correlation with σ38 and hya operon expression has been proved under different conditions, so the promoter seems to be σ38. |
||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] [EXP-IMP] |
||||||||||
Reference(s): |
[4] Atlung T., et al., 1997 [5] Huerta AM., et al., 2003 [1] Maciag A., et al., 2011 [6] Richard DJ., et al., 1999 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | ccgacgtaaaAAGACGGTAAGTATCGCTTTCAGTCTTatgaatatcg | ||||||||||
Reference(s): | [2] Menon NK., et al., 1990 |
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 | ||||||||
nd | AppY | activator | hyaAp2 | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [11] |
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 | activator | hyaAp2 | 1031910 | 1031924 | -67.0 | aaaaataggtCCATTTTTATCGCTAaaagataaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [6] |
proximal | ArcA-phosphorylated | activator | hyaAp2 | 1031966 | 1031988 | -7.5 | gtgcaaaagtTTCACTACGCTTTATTAACAATActttctggcg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [9] |
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 | hyaAp2 | 1031956 | 1031970 | -21.0 | gtattgttttGTGCAAAAGTTTCACtacgctttat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] | W | [10] |
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 | IscR | repressor | hyaAp2 | 1031930 | 1031954 | -42.0 | cgctaaaagaTAAATCCACACAGTTTGTATTGTTTtgtgcaaaag | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [8] |
proximal | IscR | repressor | hyaAp2 | 1031933 | 1031957 | -39.0 | taaaagataaATCCACACAGTTTGTATTGTTTTGTgcaaaagttt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [9] |
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 | NarL-phosphorylated | repressor | hyaAp2 | 1031971 | 1031977 | -10.0 | aaagtttcacTACGCTTtattaacaat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
proximal | NarL-phosphorylated | repressor | hyaAp2 | 1031987 | 1031993 | 7.0 | ttattaacaaTACTTTCtggcgacgtg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
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 | NarP-phosphorylated | repressor | hyaAp2 | 1031966 | 1031981 | -10.0 | gtgcaaaagtTTCACTACGCTTTATTaacaatactt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
proximal | NarP-phosphorylated | repressor | hyaAp2 | 1031982 | 1031997 | 7.0 | acgctttattAACAATACTTTCTGGCgacgtgcgcc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | nd |
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 | YdeO | activator | hyaAp2 | 1031912 | 1031935 | -61.0 | aaataggtccATTTTTATCGCTAAAAGATAAATCcacacagttt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
Reference(s) |
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