ydiB: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 |
ydiB |
|---|---|
| Mnemonic |
Systematic nomenclature |
| Synonyms | |
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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 |
38.19 minutes |
MG1655: 1771813..1772679 |
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NC_012967: 1751055..1751921 |
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NC_012759: 1663872..1664738 |
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W3110 |
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W3110: 1775503..1776369 |
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DH10B: 1862384..1863250 |
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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 |
|---|---|---|---|---|---|---|---|
|
ΔydiB (Keio:JW1682) |
deletion |
deletion |
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ydiBT106A |
T106A |
Increases KM for quinate 2000-fold. Increases KM for shikimate 70-fold |
seeded from UniProt:P0A6D5 | ||||
|
ydiBN92A |
N92A |
Alters protein structure. Loss of activity |
seeded from UniProt:P0A6D5 | ||||
|
ydiBD107A |
D107A |
Loss of activity towards quinate. Increases KM for shikimate 20000-fold |
seeded from UniProt:P0A6D5 | ||||
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ydiBK71A |
K71A |
Increases KM for quinate 3200-fold. Increases KM for shikimate 170-fold |
seeded from UniProt:P0A6D5 | ||||
|
ydiBS67A |
S67A |
Reduces activity towards quinate about 6-fold |
seeded from UniProt:P0A6D5 | ||||
|
ΔydiB::kan |
deletion |
Biolog:respiration |
unable to respire N-Acetyl-D-glucosamine |
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ΔydiB::kan |
deletion |
Biolog:respiration |
unable to respire a-D-Glucose-1-phosphate |
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ΔydiB::kan |
deletion |
Biolog:respiration |
unable to respire a-D-Glucose-6-phosphate |
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ΔydiB::kan |
deletion |
Biolog:respiration |
unable to respire Acetate |
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ΔydiB766::kan |
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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 |
|---|---|---|---|
|
JW1682 |
Plasmid clone |
Status:Clone OK Primer 1:GCCGATGTTACCGCAAAATACGA Primer 2:CCGGCACCGAACCCCATGACCTG | |
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Kohara Phage |
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Kohara Phage |
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|
Linked marker |
est. P1 cotransduction: % [8] | ||
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zdi-925::Tn10 |
Linked marker |
est. P1 cotransduction: 84% [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 |
|---|---|---|
| edit table |
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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
- ↑ 3.0 3.1 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
- ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
- ↑ 5.0 5.1 5.2 5.3 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
- ↑ 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
- ↑ 7.0 7.1 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
- ↑ 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).
