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Name: | hypABCDE | ||||||||||
Synonym(s): | OP00209, hydBEF | ||||||||||
Gene(s): | hypA, hypB, hypC, hypD, hypE Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined [EXP-IEP-COREGULATION] Inferred through co-regulation |
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Reference(s): |
[1] Hopper S., et al., 1994 [2] Lutz S., et al., 1991 |
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Promoter | |||||||||||
Name: | hypAp | ||||||||||
+1: | 2850627 | ||||||||||
Sigma Factor: | Sigma54 Sigmulon | ||||||||||
Distance from start of the gene: | 20 | ||||||||||
Sequence: |
catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata -24 -12 +1 |
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Note(s): | Based on primer extension hypA and hypB promoters have similar activities Hopper S,1994. | ||||||||||
Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[3] Huerta AM., et al., 2003 [2] Lutz S., et al., 1991 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | atgaccttttGCACCGCTTTGCGGTGCTttcctggaag | ||||||||||
Reference(s): | [2] Lutz S., et al., 1991 |
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 | FhlA-formate | activator | hypAp | 2849869 | 2849882 | -751.5 | ctcaggtgatTGTCATTTTTGACGaaaacatgcc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [4], [5] |
remote | FhlA-formate | activator | hypAp | 2849900 | 2849913 | -720.5 | gccgatgaaaTGTCATTTTCGACActcatcgaca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [4], [5] |
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 | IHF | activator | hypAp | 2850493 | 2850505 | -127.5 | tgccaactttTAATTTATTGTTAttaaagagat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] |
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 | NsrR | repressor | hypAp | 2850526 | 2850537 | -96.0 | ttttaagctaAAGATGAATTTCgtcgccgtgt | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [6] |
Name: | hypABCDE-fhlA | ||||||||||
Gene(s): | hypA, hypB, hypC, hypD, hypE, fhlA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | It has been suggested that sometimes the downstream gene fhlA is transcribed along with the hypABCDE operon genes; however, fhlA has its own promoter (unpublished data Lutz S,1991). |
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Evidence: | [AS-NAS] Non-traceable author statement [EXP-IEP] Inferred from expression pattern |
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Reference(s): |
[2] Lutz S., et al., 1991 [7] Schlensog V., et al., 1990 |
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Promoter | |||||||||||
Name: | hypAp | ||||||||||
+1: | 2850627 | ||||||||||
Sigma Factor: | Sigma54 Sigmulon | ||||||||||
Distance from start of the gene: | 20 | ||||||||||
Sequence: |
catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata -24 -12 +1 |
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Note(s): | Based on primer extension hypA and hypB promoters have similar activities Hopper S,1994. | ||||||||||
Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
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Reference(s): |
[3] Huerta AM., et al., 2003 [2] Lutz S., et al., 1991 |
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 | FhlA-formate | activator | hypAp | 2849869 | 2849882 | -751.5 | ctcaggtgatTGTCATTTTTGACGaaaacatgcc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [4], [5] |
remote | FhlA-formate | activator | hypAp | 2849900 | 2849913 | -720.5 | gccgatgaaaTGTCATTTTCGACActcatcgaca | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1], [4], [5] |
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 | IHF | activator | hypAp | 2850493 | 2850505 | -127.5 | tgccaactttTAATTTATTGTTAttaaagagat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [1] |
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 | NsrR | repressor | hypAp | 2850526 | 2850537 | -96.0 | ttttaagctaAAGATGAATTTCgtcgccgtgt | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] | W | [6] |
Name: | hypBCDE-fhlA | ||||||||||
Gene(s): | hypB, hypC, hypD, hypE, fhlA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | It was suggested that sometimes fhlA is transcribed with the hyp operon. However, this gene is also transcribed from its own promoter (unpublished data of S. Lutz and A. Bock, cited by Lutz, 1991 Lutz S,1991). | ||||||||||
Evidence: | [AS-NAS] Non-traceable author statement [EXP-IEP] Inferred from expression pattern |
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Reference(s): |
[2] Lutz S., et al., 1991 [7] Schlensog V., et al., 1990 |
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Promoter | |||||||||||
Name: | hypBp | ||||||||||
+1: | 2850839 | ||||||||||
Distance from start of the gene: | 162 | ||||||||||
Sequence: |
gccttttgttttgatctggtttgccgcggcagcgtggcggaaggttgtaaactgcacctcGaagaacaagaggccgaatgc |
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Evidence: |
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
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Reference(s): |
[2] Lutz S., et al., 1991 [8] Salgado H, 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 | FNR | activator | hypBp | 2850683 | 2850696 | -149.5 | ggcactggaaTTGATCGAACAGCAggccgcaaaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [9] |
proximal | FNR | activator | hypBp | 2850789 | 2850802 | -43.5 | gccttttgttTTGATCTGGTTTGCcgcggcagcg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [9] |
Name: | hypBCDE | ||||||||||
Synonym(s): | hydBEF | ||||||||||
Gene(s): | hypB, hypC, hypD, hypE Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IEP-COREGULATION] Inferred through co-regulation |
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Reference(s): | [2] Lutz S., et al., 1991 | ||||||||||
Promoter | |||||||||||
Name: | hypBp | ||||||||||
+1: | 2850839 | ||||||||||
Distance from start of the gene: | 162 | ||||||||||
Sequence: |
gccttttgttttgatctggtttgccgcggcagcgtggcggaaggttgtaaactgcacctcGaagaacaagaggccgaatgc |
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Evidence: |
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
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Reference(s): |
[2] Lutz S., et al., 1991 [8] Salgado H, et al., 2012 |
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Terminator(s) | |||||||||||
Type: | rho-independent | ||||||||||
Sequence: | atgaccttttGCACCGCTTTGCGGTGCTttcctggaag | ||||||||||
Reference(s): | [2] Lutz S., et al., 1991 |
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 | FNR | activator | hypBp | 2850683 | 2850696 | -149.5 | ggcactggaaTTGATCGAACAGCAggccgcaaaa | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [9] |
proximal | FNR | activator | hypBp | 2850789 | 2850802 | -43.5 | gccttttgttTTGATCTGGTTTGCcgcggcagcg | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [9] |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Translational |
Strand: | forward |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
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terminator | -12.3 | 2854298 | 2854328 | agtcaatgacCTTTTGCACCGCTTTGCGGTGCTTTCCTGGaagaacaaaa |
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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