yacL:On One Page

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

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Standard Name

yacL

Gene Synonym(s)

ECK0118, b0119, JW0115[1], JW0115

Product Desc.

conserved protein[2][3]

Function unknown[4]

Product Synonyms(s)

conserved protein[1], B0119[2][1], YacL[2][1] , ECK0118, JW0115, b0119

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yacL[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

yacL

Mnemonic

Systematic nomenclature

Synonyms

ECK0118, b0119, JW0115[1], JW0115

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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

2.9 minutes 

MG1655: 134388..134750
<gbrowseImage> name=NC_000913:134388..134750 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 137191..137553
<gbrowseImage> name=NC_012967:137191..137553 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 134387..134749
<gbrowseImage> name=NC_012759:134387..134749 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 134388..134750
<gbrowseImage> name=NC_007779:134388..134750 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 108492..108854
<gbrowseImage> name=NC_010473:108492..108854 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

yacL::Tn5KAN-I-SceI (FB20015)

Insertion at nt 149 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20015

contains pKD46

yacL(del) (Keio:JW0115)

deletion

deletion

PMID:16738554

Shigen

CGSC8397[5]

yacL(del)::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938

yacL106(del)::FLK2(lacZ,kan)

PMID:12142427

CGSC:86519

yacL107(del)

PMID:12142427

CGSC:86521

yacL737(del)::kan

PMID:16738554

CGSC:103458


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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

JW0115

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATTACGAATTTCTGCGCGA

Primer 2:CCCTTCTGCTGCACGAAATTGCG

4E11

Kohara Phage

Genobase

PMID:3038334

17C11

Kohara Phage

Genobase

PMID:3038334

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 9% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 61% [6]

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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:EG12605

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12605

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944809

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002328

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2489

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000414

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

YacL

Synonyms

conserved protein[1], B0119[2][1], YacL[2][1] , ECK0118, JW0115, b0119

Product description

conserved protein[2][3]

Function unknown[4]

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
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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

Protein

rapA

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

nusA

PMID:15690043

Experiment(s):EBI-879082

Protein

rplB

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

rplC

PMID:15690043

Experiment(s):EBI-879082

Protein

rplD

PMID:15690043

Experiment(s):EBI-879082

Protein

rplM

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

rplO

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

rpoA

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

rpoB

PMID:15690043

Experiment(s):EBI-879082, EBI-882523, EBI-883170

Protein

rpoC

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

rpoZ

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

rpsB

PMID:15690043

Experiment(s):EBI-879082

Protein

rpsD

PMID:15690043

Experiment(s):EBI-879082, EBI-882523

Protein

rpsM

PMID:15690043

Experiment(s):EBI-879082

Protein

arnA

PMID:15690043

Experiment(s):EBI-882523

Protein

crp

PMID:15690043

Experiment(s):EBI-882523

Protein

elaB

PMID:15690043

Experiment(s):EBI-882523

Protein

fur

PMID:15690043

Experiment(s):EBI-882523

Protein

gltA

PMID:15690043

Experiment(s):EBI-882523

Protein

hfq

PMID:15690043

Experiment(s):EBI-882523

Protein

nuoG

PMID:15690043

Experiment(s):EBI-882523

Protein

pnp

PMID:15690043

Experiment(s):EBI-882523

Protein

proV

PMID:15690043

Experiment(s):EBI-882523

Protein

rplN

PMID:15690043

Experiment(s):EBI-882523

Protein

rplP

PMID:15690043

Experiment(s):EBI-882523

Protein

rplQ

PMID:15690043

Experiment(s):EBI-882523

Protein

rplU

PMID:15690043

Experiment(s):EBI-882523

Protein

rplV

PMID:15690043

Experiment(s):EBI-882523

Protein

rpmB

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsA

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsC

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsE

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsF

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsK

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsL

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsN

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsT

PMID:15690043

Experiment(s):EBI-882523

Protein

rpsU

PMID:15690043

Experiment(s):EBI-882523

Protein

rsuA

PMID:15690043

Experiment(s):EBI-882523

Protein

slyD

PMID:15690043

Experiment(s):EBI-882523

Protein

uspG

PMID:15690043

Experiment(s):EBI-882523

Protein

yqjI

PMID:15690043

Experiment(s):EBI-882523

Protein

uspG

PMID:16606699

Experiment(s):EBI-1135630

Protein

rplN

PMID:16606699

Experiment(s):EBI-1135630

Protein

rpsL

PMID:16606699

Experiment(s):EBI-1135630

Protein

glpK

PMID:16606699

Experiment(s):EBI-1135630

Protein

ykgF

PMID:16606699

Experiment(s):EBI-1135630

Protein

glpD

PMID:16606699

Experiment(s):EBI-1135630

Protein

zwf

PMID:16606699

Experiment(s):EBI-1135630

Protein

mreB

PMID:16606699

Experiment(s):EBI-1135630

Protein

slyD

PMID:19402753

LCMS(ID Probability):99.6

Protein

gltA

PMID:19402753

LCMS(ID Probability):99.6

Protein

uspG

PMID:19402753

LCMS(ID Probability):99.6

Protein

elaB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsL

PMID:19402753

LCMS(ID Probability):99.4

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsK

PMID:19402753

LCMS(ID Probability):99.4

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6

Protein

nuoG

PMID:19402753

LCMS(ID Probability):99.6

Protein

fur

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

gapA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.5

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):15.079320

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rpsU

PMID:19402753

LCMS(ID Probability):99.5

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

kefA

PMID:19402753

LCMS(ID Probability):99.6

Protein

pnp

PMID:19402753

LCMS(ID Probability):99.6

Protein

hfq

PMID:19402753

LCMS(ID Probability):99.6

Protein

yqjI

PMID:19402753

LCMS(ID Probability):99.6

Protein

arnA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpoB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):9.731086

Protein

rpoC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):9.171032

Protein

crp

PMID:19402753

LCMS(ID Probability):99.6

Protein

nusG

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.095383

Protein

proV

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpoZ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rpoA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.255097

Protein

rsuA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rapA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):18.730389

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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 

MAQCDFGALP GAEEHTMDYE FLRDITGVVK VRMSMGHEVV GHWFNEEVKE NLALLDEVEQ
AAHALKGSER SWQRAGHEYT LWMDGEEVMV RANQLEFAGD EMEEGMNYYD EESLSLCGVE
DFLQVVAAYR NFVQQK
Length

136

Mol. Wt

15.599 kDa

pI

4.2 (calculated)

Extinction coefficient

23,950 - 24,200 (calc based on 5 Y, 3 W, and 2 C residues)

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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

Domain

1..118

PF06062 Uncharacterised protein family (UPF0231)

PMID:19920124

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<motif_map/>

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

Structures

<beststructure> gene=yacL 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

NCBI (Protein) (EcoliWiki Page)

GI:90111086

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944809

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000414

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A8E5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12605

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12605

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944809

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002328

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2489

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)

Protein

Ecoli K-12

3.867+/-0.054

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.100828729

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

1628

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

374

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1275

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

yacL

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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_000913:134368..134408 source=MG1655 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
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0119 (EcoliWiki Page)

NCBI GEO profiles for yacL

microarray

GenExpDB:b0119 (EcoliWiki Page)

Summary of data for yacL from multiple microarray studies

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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 (134120..134348) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ01; Well:A6[7]

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Notes

Accessions Related to yacL Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12605

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2489

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0119

EcoGene

EcoGene:EG12605

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002328

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000414

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

Organism Homologs (Statistics) Comments

Shigella flexneri

YACL

From SHIGELLACYC

E. coli O157

YACL

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF06062 Uncharacterised protein family (UPF0231)

EcoCyc

EcoCyc:EG12605

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12605

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002328

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2489

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000414

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. ↑ 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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).
  7. ↑ 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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