cyoD:Gene
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| Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
| Nomenclature | Location(s) and DNA Sequence | Sequence Features | Alleles and Phenotypes | Genetic Interactions | Genetic Resources | Accessions | Links | References | Suggestions |
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
cyoD |
|---|---|
| Mnemonic |
Cytochrome o oxidase |
| Synonyms |
ECK0423, b0429, JW0419[1], JW0419 |
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Notes
Location(s) and DNA Sequence
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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.
| Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
|---|---|---|---|---|
|
MG1655 |
9.63 minutes |
MG1655: 447270..446941 |
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NC_012967: 418749..418420 |
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NC_012759: 349700..350029 |
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W3110 |
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W3110: 447270..446941 |
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DH10B: 386601..386272 |
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Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
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Notes
Alleles and Phenotypes
See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.
| Allele | Nt change(s) | AA change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
|---|---|---|---|---|---|---|---|
|
cyoD(del) (Keio:JW0419) |
deletion |
deletion |
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cyoD::Tn5KAN-2 (FB20170) |
Insertion at nt 171 in Plus orientation |
does not contain pKD46 | |||||
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cyoD(del)::kan |
deletion |
Biolog:respiration |
unable to respire L-Alanine |
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cyoD(del)::kan |
deletion |
Biolog:respiration |
unable to respire L-Asparagine |
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cyoD(del)::kan |
deletion |
Biolog:respiration |
unable to respire L-Aspartate |
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cyoD786(del)::kan |
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cyoD786(del)::FRT |
deletion |
Mutagenesis Rate |
Decrease in Stress Induced Mutagenesis (SIM). |
Parent Strain: SMR4562 Experimental Strain: SMR12574 |
The SIM was reduced significantly with a decrease in SIM by 68 to 89 percent. See table S3 for full experimental results. | ||
|
cyoD786(del)::FRT |
deletion |
Sensitivity to |
UV sensitivity |
Parent Strain: SMR4562 Experimental Strain: SMR12574 |
The mutation conferred and increase in UV sensitivity. See table S7 and S1 for a summary of experimental data. | ||
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SMR4562 cyoD786(del)::FRTKanFRT yiaG-yfp FRTcatFRT |
Deletion & Insertion |
Sigma S activity |
Decrease in SigmaS activity |
Parent Strain: SMR10582 Experimental Strain: SMR13035 |
See table S8 for full experimental results. | ||
|
CAG45114 cyoD786(del)::FRTKanFRT |
deletion |
SigmaE activity |
Decrease in SigmaE activity |
Parental Strain: CAG45114 Experimental Strain: SMR15293 |
See Table S11 for experimental calculations | ||
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Notes
Genetic Interactions
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| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
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Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW0419 |
Plasmid clone |
Status:Clone OK Primer 1:GCCAGTCATTCTACCGATCACAG Primer 2:CCGTGCATCATCATGTTGTAGTT | |
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Kohara Phage |
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|
Linked marker |
est. P1 cotransduction: 58% [9] | ||
|
Linked marker |
est. P1 cotransduction: 65% [9] | ||
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Notes
Links
| Name | URL | Comments |
|---|---|---|
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References
See Help:References for how to manage references in EcoliWiki.
- ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
- ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
- ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
- ↑ 5.0 5.1 5.2 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
- ↑ 6.0 6.1 6.2 6.3 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
- ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
- ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
- ↑ 9.0 9.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
