ppdC:Gene

From EcoliWiki
Jump to: navigation, search

{{#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

<protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ppdC

Mnemonic

Prepilin peptidase-dependent

Synonyms

ECK2819, b2823, JW2791, ygdA[1], ygdA

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<protect> 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

63.81 minutes 

MG1655: 2960786..2960463
<gbrowseImage> name=NC_000913:2960463..2960786 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2857383..2857060
<gbrowseImage> name=NC_012967:2857060..2857383 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2847611..2847934
<gbrowseImage> name=NC_012759:2847611..2847934 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2961420..2961097
<gbrowseImage> name=NC_007779:2961097..2961420 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3054656..3054333
<gbrowseImage> name=NC_010473:3054333..3054656 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔppdC (Keio:JW2791)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10183[3]

ppdC::Tn5KAN-I-SceI (FB20947)

Insertion at nt 267 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20947

does not contain pKD46

ppdC::Tn5KAN-I-SceI (FB20948)

Insertion at nt 267 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20948

contains pKD46

ΔppdC748::kan

PMID:16738554[2]

CGSC:102420


<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2791

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCAGCTTCCCTGAAGAATCA

Primer 2:CCtTGACGATTCGGGCAATGCAG

3G11

Kohara Phage

Genobase

PMID:3038334[6]

5A10

Kohara Phage

Genobase

PMID:3038334[6]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: 72% [7]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: % [7]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11154

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11154

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001137

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945797

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1143

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009257

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



<protect>

References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 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. 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. 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. 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. 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).

Categories