ppdD:Gene: Difference between revisions
Data loaded by TableEdit_Loader. |
imported>Wikientrybot Bulk deleting accessions. |
||
| Line 331: | Line 331: | ||
| | | | ||
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=111 Genobase] | [http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=111 Genobase] | ||
| | |||
PMID:3038334 | |||
|- | |||
| | |||
[[:Category:Kohara_Phage:4D12|4D12]] | |||
| | |||
Kohara Phage | |||
| | |||
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=112 Genobase] | |||
| | | | ||
PMID:3038334 | PMID:3038334 | ||
| Line 352: | Line 361: | ||
| | | | ||
est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/> | est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/> | ||
|- class="tableEdit_footer" | |- class="tableEdit_footer" | ||
| Line 383: | Line 383: | ||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!|Database!!Accession!!Notes | !|Database!!Accession!!Notes | ||
|- class="tableEdit_footer" | |- class="tableEdit_footer" | ||
Revision as of 21:06, 21 September 2011
{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>
| 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 |
Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
ppdD |
|---|---|
| Mnemonic |
Prepilin peptidase-dependent |
| Synonyms |
ECK0107, b0108, JW0104[1] |
| edit table |
Notes
Location(s) and DNA Sequence
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 |
2.52 minutes |
MG1655: 117549..117109 |
||
|
NC_012967: 120353..119913 |
||||
|
NC_012759: 117108..117548 |
||||
|
W3110 |
|
W3110: 117549..117109 |
||
|
DH10B: 91653..91213 |
||||
| edit table |
Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
| edit table |
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 |
|---|---|---|---|---|---|---|---|
|
ΔppdD (Keio:JW0104) |
deletion |
deletion |
|||||
|
ΔppdD::kan |
deletion |
Biolog:respiration |
unable to respire D-Mannose |
||||
|
ΔppdD::kan |
deletion |
Biolog:respiration |
unable to respire Acetate |
||||
|
ΔppdD-726::kan |
| ||||||
| edit table |
Notes
Genetic Interactions
| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW0104 |
Plasmid clone |
Status:Clone OK Primer 1:GCCGACAAGCAACGCGGTTTTAC Primer 2:CCGTTGGCGTCATCAAAGCGGAA | |
|
Kohara Phage |
|||
|
Kohara Phage |
|||
|
leuO3051::Tn10 |
Linked marker |
est. P1 cotransduction: 26% [7] | |
|
Linked marker |
est. P1 cotransduction: 29% [7] | ||
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
<protect>
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
- ↑ 4.0 4.1 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
- ↑ 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 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).