nrfA:Gene

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Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

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Nomenclature

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

Standard name

nrfA

Mnemonic

Nitrite reductase, formate-dependent

Synonyms

ECK4063, b4070, JW4031, aidC[1]

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Notes

Location(s) and DNA Sequence

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<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

92.37 minutes 

MG1655: 4285787..4287223
<gbrowseImage> name=NC_000913:4285787..4287223 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4266697..4268133
<gbrowseImage> name=NC_012967:4266697..4268133 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4224633..4226069
<gbrowseImage> name=NC_012759:4224633..4226069 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4291354..4292790
<gbrowseImage> name=NC_007779:4291354..4292790 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4385483..4386919
<gbrowseImage> name=NC_010473:4385483..4386919 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

4285865

Edman degradation

PMID:7934939[2]


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Notes

Alleles and Phenotypes

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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

ΔnrfA (Keio:JW4031)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10899[4]

nrfAK126H,I,L

K126H,I,L

Almost complete loss of nitrite reductase activity

seeded from UniProt:P0ABK9

ΔnrfA765::kan

PMID:16738554[3]

CGSC:102116


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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

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

Resource Resource Type Source Notes/Reference

JW4031

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCACAAGGATAAAAATAAACGC

Primer 2:CCTTGGCTTAACAGACCGTTTTT

3F12

Kohara Phage

Genobase

PMID:3038334[6]

10G7

Kohara Phage

Genobase

PMID:3038334[6]

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[4]

est. P1 cotransduction: 14% [7]

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[4]

est. P1 cotransduction: 49% [7]

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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoCyc

EcoCyc:EG11781

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11781

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001715

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948571

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1729

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013342

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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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. Darwin, A et al. (1993) Regulation and sequence of the structural gene for cytochrome c552 from Escherichia coli: not a hexahaem but a 50 kDa tetrahaem nitrite reductase. Mol. Microbiol. 9 1255-65 PubMed
  3. 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. 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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).

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