hdfR: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 |
hdfR |
|---|---|
| Mnemonic |
hns-dependent flhDC regulator |
| Synonyms |
ECK3756, b4480, JW5607, yifA, yifD, b3762 (obsolete), apeR?, pssR, b3763 (obsolete)[1][2] |
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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 |
85.03 minutes |
MG1655: 3945990..3945151 |
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NC_012967: 3909767..3908928 |
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NC_012759: 3834820..3835659 |
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W3110 |
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W3110: 3688714..3689553 |
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DH10B: 4044910..4044071 |
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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 |
|---|---|---|---|---|---|---|---|
|
hdfR(del) (Keio:JW5607) |
deletion |
deletion |
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hdfR785(del)::FRT |
deletion |
Mutagenesis rate |
Decrease in Stress Induced Mutagenesis (SIM) |
Paternal Strain: SMR4562 Experimental Strain: SMR12235 |
The mutation caused a significant decrease in SIM; Mutant frequency was decreased by over 90 percent. See table S3 for full experimental results. | ||
|
hdfR785(del)::FRT |
deletion |
Sensitivity to |
SDS-EDTA Sensitivity |
Paternal Strain: SMR4562 Experimental Strain: SMR12235 |
The mutation caused an increase in SDS-EDTA sensitivity. See tables S7 and S1 for a summary of experimental data. | ||
|
hdfR785(del)::FRT |
deletion |
Sensitivity to |
UV Sensitivity |
Paternal Strain: SMR4562 Experimental Strain: SMR12235 |
The mutation caused an increase in UV sensitivity. See tables S7 and S1 for a summary of experimental data. | ||
|
SMR4562 yiaG-yfp FRTcatFRT hdfR785(del)::FRTKanFRT |
deletion |
SigmaS activity |
Decrease in Sigma S activity |
Parental Strain: SMR10582 Experimental Strain: SMR14261 |
See table S8 for full experimental results. | ||
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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 |
|---|---|---|---|
|
JW5607 |
Plasmid clone |
Status:Clone OK Primer 1:GCCGATACGGAATTGTTAAAAAC Primer 2:CCATACACTTCATCCAGCACGTT | |
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Kohara Phage |
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Kohara Phage |
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Linked marker |
est. P1 cotransduction: 58% [8] | ||
|
Linked marker |
est. P1 cotransduction: 77% [8] | ||
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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)
- ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 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
- ↑ 4.0 4.1 4.2 4.3 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
- ↑ 6.0 6.1 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
- ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
- ↑ 8.0 8.1 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).
