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| Operon |  |
|---|---|
| Name: | pykF |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | pykF |
| Gene(s): | pykF Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | There is no evidence in the literature of pykF forming a transcription unit with the downstream lpp gene, which is in the same orientation but 311 bp downstream. The upstream gene, fumD, is oriented in the opposite direction. So, the pykF gene is defined as an isolated gene. Under nitrogen-rich growth conditions, the expression of the pykF gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011 |
| Evidence: | [BTEI] Boundaries of transcription experimentally identified |
| Reference(s): | [1] Bledig SA., et al., 1996 |
| Promoter | |
| Name: | pykFp |
| +1: | 1755467 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 231 |
| Sequence: |
atattttttgaaacgctgtttttgttttccttttggattaatttcagcgtataatgcgcgCcaattgactcttgaatggtt -35 -10 +1 |
| Note(s): | Although the evidence for the promoter is only sequence similarity, a mutation at the cis-site for the binding of FruR clearly shows repression of activity of pykF gene Ponce E, Flores N, Martinez A, Valle F, Bolívar F,1995. |
| Evidence: |
[HIPP] [ICWHO] [IHBCE] |
| Reference(s): |
[1] Bledig SA., et al., 1996 [2] Huerta AM., et al., 2003 |
| Name: | pykF |
| Gene(s): | pykF Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Under nitrogen-rich growth conditions, the expression of the pykF gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011 |
| Evidence: | [IC] Inferred by curator |
| Promoter | |
| Name: | pykFp2 |
| +1: | 1755600 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 98 |
| Sequence: |
ggctgagacacaagcacacattcctctgcacgctttttcgatgtcacctatccttagagcGaggcaccaccactttcgtaa -10 +1 |
| Evidence: |
[HTTIM] [IHBCE] [RS-EPT-CBR] |
| Reference(s): |
[3] Mendoza-Vargas A., et al., 2009 [4] Olvera L., et al., 2009 [5] Salgado H, et al., 2012 |
| Name: | pykF |
| Gene(s): | pykF Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Under nitrogen-rich growth conditions, the expression of the pykF gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011. |
| Evidence: | [IC] Inferred by curator |
| Promoter | |
| Name: | pykFp4 |
| +1: | 1755600 |
| Sigma Factor: | Sigma38 Sigmulon |
| Distance from start of the gene: | 98 |
| Sequence: |
ggctgagacacaagcacacattcctctgcacgctttttcgatgtcacctatccttagagcGaggcaccaccactttcgtaa -10 +1 |
| Evidence: |
[HTTIM] [IHBCE] [RS-EPT-CBR] |
| Reference(s): |
[3] Mendoza-Vargas A., et al., 2009 [4] Olvera L., et al., 2009 [5] Salgado H, et al., 2012 |
| Name: | pykF |
| Gene(s): | pykF Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Under nitrogen-rich growth conditions, the expression of the pykF gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011 |
| Evidence: | [IC] Inferred by curator |
| Promoter | |
| Name: | pykFp3 |
| +1: | 1755617 |
| Distance from start of the gene: | 81 |
| Sequence: |
acattcctctgcacgctttttcgatgtcacctatccttagagcgaggcaccaccactttcGtaataccggattcgctttcc |
| Evidence: | [HTTIM] |
| Reference(s): | [4] Olvera L., et al., 2009 |
| Name: | pykF |
| Gene(s): | pykF Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Under nitrogen-rich growth conditions, the expression of the pykF gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011 |
| Evidence: | [IC] Inferred by curator |
| Promoter | |
| Name: | pykFp1 |
| +1: | 1755663 |
| Sigma Factor: | Sigma70 Sigmulon |
| Distance from start of the gene: | 35 |
| Sequence: |
gcaccaccactttcgtaataccggattcgctttccggcagtgcgcccagaaagcaagtttCtcccatccttctcaacttaa -10 +1 |
| Evidence: |
[HTTIM] [IDA] [IHBCE] |
| Reference(s): |
[6] Imashimizu M., et al., 2020 [3] Mendoza-Vargas A., et al., 2009 [4] Olvera L., et al., 2009 |
| Name: | pykF |
| Gene(s): | pykF Genome Browser M3D Gene expression COLOMBOS |
| Note(s): | Under nitrogen-rich growth conditions, the expression of the pykF gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011 |
| Evidence: | [IC] Inferred by curator |
| Promoter | |
| Name: | pykFp5 |
| +1: | 1755663 |
| Sigma Factor: | Sigma38 Sigmulon |
| Distance from start of the gene: | 35 |
| Sequence: |
gcaccaccactttcgtaataccggattcgctttccggcagtgcgcccagaaagcaagtttCtcccatccttctcaacttaa -10 +1 |
| Evidence: |
[HTTIM] [IHBCE] |
| Reference(s): |
[3] Mendoza-Vargas A., et al., 2009 [4] Olvera L., et al., 2009 |
| Reference(s) |
|
|---|---|
[HIPP] Human inference of promoter position