yfdL:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

yfdL

Gene Synonym(s)

ECK2349, b2355, JW5384[1], JW5384

Product Desc.

putative RNA polymerase β[2]; CPS-53 (KpLE1) prophage; conserved protein[3]

Product Synonyms(s)

CPS-53 (KpLE1) prophage; conserved protein[1], B2355[2][1], YfdL[2][1] , ECK2349, JW5384, b2355

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yfdK[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Gene

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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

yfdL

Mnemonic
Synonyms

ECK2349, b2355, JW5384[1], JW5384

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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

53.23 minutes 

MG1655: 2470084..2469566
<gbrowseImage> name=NC_000913:2469566..2470084 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2477508..2476990
<gbrowseImage> name=NC_007779:2476990..2477508 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2561849..2561331
<gbrowseImage> name=NC_010473:2561331..2561849 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

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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

ΔyfdL (Keio:JW5384)

deletion

deletion

PMID:16738554

Shigen
CGSC11355[4]

ΔyfdL762::kan

PMID:16738554

CGSC:104714


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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

JW5384

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTGCAGGAGGAGCTTTGCAG

Primer 2:CCACACCCTAATGCGAAAAATGA

6F7

Kohara Phage

Genobase

PMID:3038334

3A11

Kohara Phage

Genobase

PMID:3038334

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[4]

est. P1 cotransduction: % [5]
Synonyms:zej-223::Tn10

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[4]

est. P1 cotransduction: 45% [5]
Synonyms:zfb-1::Tn10

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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:G7224

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14136

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003799

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949099

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3888

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007773

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

YfdL

Synonyms

CPS-53 (KpLE1) prophage; conserved protein[1], B2355[2][1], YfdL[2][1] , ECK2349, JW5384, b2355

Product description

putative RNA polymerase β[2]; CPS-53 (KpLE1) prophage; conserved protein[3]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc

MLQEELCSVV EASGASLEKG RHDQLLTALR ALLLSRKNPF GDIKLDGTVQ KALENLGLGE
AAKRNVGTGA NQIPDMGSFM LSASVPGYQK LPSGLIIQWG PIDVPLTSQD TVTYFPIAFP
NRCLRVFATQ DYTPGSANVG YIACAGYNQD PVKFISRAGV PGIGASFFAL GC
Length

172

Mol. Wt

18.251 kDa

pI

7.1 (calculated)

Extinction coefficient

12,950 - 13,450 (calc based on 5 Y, 1 W, and 4 C residues)


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=yfdL taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference

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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

ASAP

ASAP:ABE-0007773

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949099

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76508

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7224

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14136

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949099

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003799

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3888

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

yfdK

Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2470064..2470104 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2355 (EcoliWiki Page)

NCBI GEO profiles for yfdL

microarray

GenExpDB:b2355 (EcoliWiki Page)

Summary of data for yfdL from multiple microarray studies


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (2469982..2470139) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ06; Well:C4[6]

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Notes

Accessions Related to yfdL Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7224

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3888

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2355

EcoGene

EcoGene:EG14136

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003799

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007773

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes

PFAM (EcoliWiki Page)

PFAM:PF02413

edit table

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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

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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. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. 5.0 5.1 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).
  6. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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