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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the downstream gene fhlA is transcribed along with the hypABCDE operon genes; however, fhlA has its own promoter (unpublished data Lutz S,1991). |
Evidence: | [IEP] Inferred from expression pattern [NAS] Non-traceable author statement |
Reference(s): |
[1] Lutz S., et al., 1991 [2] Schlensog V., et al., 1990 |
Promoter | |
Name: | hypAp |
+1: | 2850627 |
Sigma Factor: | Sigma54 Sigmulon |
Distance from start of the gene: | 20 |
Sequence: |
catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata -24 -12 +1 |
Note(s): | Based on primer extension hypA and hypB promoters have similar activities Hopper S,1994. |
Evidence: | [TIM] |
Reference(s): | [1] Lutz S., et al., 1991 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | FhlA-formate | activator | hypAp | 2849869 | 2849882 | -751.5 | ctcaggtgatTGTCATTTTTGACGaaaacatgcc | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [3], [4], [5] |
remote | FhlA-formate | activator | hypAp | 2849900 | 2849913 | -720.5 | gccgatgaaaTGTCATTTTCGACActcatcgaca | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [3], [4], [5] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | IHF | activator | hypAp | 2850493 | 2850505 | -127.5 | tgccaactttTAATTTATTGTTAttaaagagat | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [3] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | NsrR | repressor | hypAp | 2850526 | 2850537 | -96.0 | ttttaagctaAAGATGAATTTCgtcgccgtgt | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [6] |
Name: | hypABCDE |
Synonym(s): | OP00209, hydBEF |
Gene(s): | hypA, hypB, hypC, hypD, hypE Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [BTEI] Boundaries of transcription experimentally identified [ITC] Inferred through co-regulation [LTED] Length of transcript experimentally determined |
Reference(s): |
[3] Hopper S., et al., 1994 [1] Lutz S., et al., 1991 |
Promoter | |
Name: | hypAp |
+1: | 2850627 |
Sigma Factor: | Sigma54 Sigmulon |
Distance from start of the gene: | 20 |
Sequence: |
catcgacattattcaccgcagggataatcaacactggcacaattattgcttgtagctggcAatagttaatgggaggcgata -24 -12 +1 |
Note(s): | Based on primer extension hypA and hypB promoters have similar activities Hopper S,1994. |
Evidence: | [TIM] |
Reference(s): | [1] Lutz S., et al., 1991 |
Terminator(s) | |
Type: | rho-independent |
Sequence: | atgaccttttGCACCGCTTTGCGGTGCTttcctggaag |
Reference(s): | [1] Lutz S., et al., 1991 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | FhlA-formate | activator | hypAp | 2849869 | 2849882 | -751.5 | ctcaggtgatTGTCATTTTTGACGaaaacatgcc | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [3], [4], [5] |
remote | FhlA-formate | activator | hypAp | 2849900 | 2849913 | -720.5 | gccgatgaaaTGTCATTTTCGACActcatcgaca | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [3], [4], [5] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | IHF | activator | hypAp | 2850493 | 2850505 | -127.5 | tgccaactttTAATTTATTGTTAttaaagagat | nd | [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [3] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | NsrR | repressor | hypAp | 2850526 | 2850537 | -96.0 | ttttaagctaAAGATGAATTTCgtcgccgtgt | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [6] |
Name: | hypBCDE |
Synonym(s): | hydBEF |
Gene(s): | hypB, hypC, hypD, hypE Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [BTEI] Boundaries of transcription experimentally identified [ITC] Inferred through co-regulation |
Reference(s): | [1] Lutz S., et al., 1991 |
Promoter | |
Name: | hypBp |
+1: | 2850839 |
Distance from start of the gene: | 162 |
Sequence: |
gccttttgttttgatctggtttgccgcggcagcgtggcggaaggttgtaaactgcacctcGaagaacaagaggccgaatgc |
Note(s): | This promoter initiates within the hypA gene and is only transcribed under nonfermentative conditions, i.e., when the σ54 hypAp is silent. It facilitates the formation of hydrogenases 1 and 2 under H2 uptake conditions. It is an internal promoter. |
Evidence: |
[CV(RS-EPT-CBR)] [CV(TIM)] [RS-EPT-CBR] [TIM] |
Reference(s): |
[1] Lutz S., et al., 1991 [7] Salgado H, et al., 2012 |
Terminator(s) | |
Type: | rho-independent |
Sequence: | atgaccttttGCACCGCTTTGCGGTGCTttcctggaag |
Reference(s): | [1] Lutz S., et al., 1991 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | FNR1 | activator | hypBp | 2850683 | 2850696 | -149.5 | ggcactggaaTTGATCGAACAGCAggccgcaaaa | nd | [BPP], [GEA] | [8] |
proximal | FNR2 | activator | hypBp | 2850789 | 2850802 | -43.5 | gccttttgttTTGATCTGGTTTGCcgcggcagcg | nd | [BCE], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [8] |
Note(s): |
1FNR activates hypB transcription under anaerobiosis. 2FNR activates hypB transcription under anaerobiosis.1FNR activates hypB transcription under anaerobiosis. 2FNR activates hypB transcription under anaerobiosis. |
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: | [IEP] Inferred from expression pattern [NAS] Non-traceable author statement |
Reference(s): |
[1] Lutz S., et al., 1991 [2] Schlensog V., et al., 1990 |
Promoter | |
Name: | hypBp |
+1: | 2850839 |
Distance from start of the gene: | 162 |
Sequence: |
gccttttgttttgatctggtttgccgcggcagcgtggcggaaggttgtaaactgcacctcGaagaacaagaggccgaatgc |
Note(s): | This promoter initiates within the hypA gene and is only transcribed under nonfermentative conditions, i.e., when the σ54 hypAp is silent. It facilitates the formation of hydrogenases 1 and 2 under H2 uptake conditions. It is an internal promoter. |
Evidence: |
[CV(RS-EPT-CBR)] [CV(TIM)] [RS-EPT-CBR] [TIM] |
Reference(s): |
[1] Lutz S., et al., 1991 [7] Salgado H, et al., 2012 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
---|---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
remote | FNR1 | activator | hypBp | 2850683 | 2850696 | -149.5 | ggcactggaaTTGATCGAACAGCAggccgcaaaa | nd | [BPP], [GEA] | [8] |
proximal | FNR2 | activator | hypBp | 2850789 | 2850802 | -43.5 | gccttttgttTTGATCTGGTTTGCcgcggcagcg | nd | [BCE], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [8] |
Note(s): |
1FNR activates hypB transcription under anaerobiosis. 2FNR activates hypB transcription under anaerobiosis.1FNR activates hypB transcription under anaerobiosis. 2FNR activates hypB transcription under anaerobiosis. |
Regulation by sRNA | ![]() |
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Small RNA name (Regulator) | Regulation type | Mechanism | Function | Binding Sites | Evidence | Reference | |||
---|---|---|---|---|---|---|---|---|---|
LeftPos | RightPos | Sequence (RNA-strand) | |||||||
oxyS | antisense | translational regulation | repressor | 2854323 | 2854329 | CCTGGA | |||
oxyS | antisense | translational regulation | repressor | 2854371 | 2854379 | AAGGGTTG |
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'" |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Translational |
Strand: | forward |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
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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