glyA: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

glyA

Gene Synonym(s)

ECK2548, b2551, JW2535[1], JW2535

Product Desc.

GlyA[2][3];

Component of glycine hydroxymethyltransferase[2][3]

Serine hydroxymethyltransferase; binds Zn(II)[4]

Product Synonyms(s)

serine hydroxymethyltransferase[1], B2551[2][1], GlyA[2][1] , ECK2548, JW2535, b2551

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): glyA[2], OP00267

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

glyA

Mnemonic

Glycine

Synonyms

ECK2548, b2551, JW2535[1], JW2535

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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

57.81 minutes 

MG1655: 2683529..2682276
<gbrowseImage> name=NC_000913:2682276..2683529 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2606206..2604953
<gbrowseImage> name=NC_012967:2604953..2606206 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2568081..2569334
<gbrowseImage> name=NC_012759:2568081..2569334 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2684163..2682910
<gbrowseImage> name=NC_007779:2682910..2684163 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2775294..2774041
<gbrowseImage> name=NC_010473:2774041..2775294 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

2682276

Edman degradation

PMID:2034230
PMID:9119048
PMID:9298646
PMID:9740056
PMID:10972807


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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

ΔglyA (Keio:JW2535)

deletion

deletion

PMID:16738554

Shigen
CGSC10018[5]

glyA6

CGSC:9647

ΔglyA41::Mu

CGSC:10749

glyA18

CGSC:11274

glyA34

CGSC:12895

glyA42::Tn5

CGSC:19321

glyA8

CGSC:72249

ΔglyA725::kan

PMID:16738554

CGSC:101220


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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

JW2535

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTAAAGCGTGAAATGAACAT

Primer 2:CCTGCGTAAACCGGGTAACGTGC

8E12

Kohara Phage

Genobase

PMID:3038334

6H2

Kohara Phage

Genobase

PMID:3038334

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 50% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 35% [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:EG10408

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10408

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000401

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947022

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0403

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008389

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

GlyA

Synonyms

serine hydroxymethyltransferase[1], B2551[2][1], GlyA[2][1] , ECK2548, JW2535, b2551

Product description

GlyA[2][3];

Component of glycine hydroxymethyltransferase[2][3]

Serine hydroxymethyltransferase; binds Zn(II)[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

GO:0004372

glycine hydroxymethyltransferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00051

F

Seeded from EcoCyc (v14.0)

complete

GO:0004372

glycine hydroxymethyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001085

F

Seeded from EcoCyc (v14.0)

complete

GO:0004372

glycine hydroxymethyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019798

F

Seeded from EcoCyc (v14.0)

complete

GO:0004372

glycine hydroxymethyltransferase activity

PMID:6190704

IMP: Inferred from Mutant Phenotype

F

complete

GO:0004372

glycine hydroxymethyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.1.2.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0004372

glycine hydroxymethyltransferase activity

PMID:3891721

IDA: Inferred from Direct Assay

F

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006730

one-carbon metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00051

P

Seeded from EcoCyc (v14.0)

complete

GO:0006730

one-carbon metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0554

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015421

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019798

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:11985624

IDA: Inferred from Direct Assay

F

complete

GO:0006564

L-serine biosynthetic process

PMID:3108237

IGI: Inferred from Genetic Interaction

EcoliWiki:serA


P

glyA serA double mutants are unable to synthesize serine by the alternate pathway (Tut cycle) and cannot grow on LRKTM:240 medium (minimal medium containing 240 mg/liter of leucine, arginine, lysine, threonine, and methionine)

complete

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

Subunits of glycine hydroxymethyltransferase

could be indirect

Protein

ymfG

PMID:16606699

Experiment(s):EBI-1143223

Protein

ymfM

PMID:16606699

Experiment(s):EBI-1143223

Protein

yghW

PMID:16606699

Experiment(s):EBI-1143223

Protein

ybaO

PMID:16606699

Experiment(s):EBI-1143223

Protein

yneF

PMID:19402753

LCMS(ID Probability):99.0

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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

MLKREMNIAD YDAELWQAME QEKVRQEEHI ELIASENYTS PRVMQAQGSQ LTNKYAEGYP
GKRYYGGCEY VDIVEQLAID RAKELFGADY ANVQPHSGSQ ANFAVYTALL EPGDTVLGMN
LAHGGHLTHG SPVNFSGKLY NIVPYGIDAT GHIDYADLEK QAKEHKPKMI IGGFSAYSGV
VDWAKMREIA DSIGAYLFVD MAHVAGLVAA GVYPNPVPHA HVVTTTTHKT LAGPRGGLIL
AKGGSEELYK KLNSAVFPGG QGGPLMHVIA GKAVALKEAM EPEFKTYQQQ VAKNAKAMVE
VFLERGYKVV SGGTDNHLFL VDLVDKNLTG KEADAALGRA NITVNKNSVP NDPKSPFVTS
GIRVGTPAIT RRGFKEAEAK ELAGWMCDVL DSINDEAVIE RIKGKVLDIC ARYPVYA
Length

417

Mol. Wt

45.316 kDa

pI

6.5 (calculated)

Extinction coefficient

46,300 - 46,675 (calc based on 20 Y, 3 W, and 3 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

Domain

8..386

PF00464 Serine hydroxymethyltransferase

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=glyA 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:16130476

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947022

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008389

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A825

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10408

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10408

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947022

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000401

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0403

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

E. coli K-12 MC4100

1.05E+04

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

1640.447+/-11.133

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

1.8741+/-0.12811

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

1.004389465

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 EMG2

3180

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: Ml6

PMID: 9298646

Protein

E. coli K-12 EMG2

300

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M92-2

PMID: 9298646

Protein

E. coli K-12 MG1655

13787

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

22684

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

12632

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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)

glyA

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_000913:2683509..2683549 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:b2551 (EcoliWiki Page)

NCBI GEO profiles for glyA

microarray

GenExpDB:b2551 (EcoliWiki Page)

Summary of data for glyA 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 (2683427..2683861) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ01; Well:E12[7]

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Notes

Accessions Related to glyA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10408

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0403

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2551

EcoGene

EcoGene:EG10408

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000401

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008389

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

Anopheles gambiae

  • ENSANGP00000000142 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G32520 (score: 1.000; bootstrap: 100%)
  • AT4G37930 (score: 0.305)
  • AT5G26780 (score: 0.279)
  • AT4G13930 (score: 0.260)
  • AT4G13890 (score: 0.233)
  • AT1G22020 (score: 0.163)
  • AT1G36370 (score: 0.159)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000022732 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00038848 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00003214 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000026966 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000000282 (score: 0.399)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000013664 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000016754 (score: 0.345)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040426-1558 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-2492 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-2493 (score: 1.000; bootstrap: 100%)
  • ZDB-EST-050302-91 (score: 0.104)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0230072 (score: 1.000; bootstrap: 100%)
  • DDB0230073 (score: 0.517)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0029823 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA15657-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000008079 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000318868 (score: 1.000; bootstrap: 100%)
  • ENSP00000333667 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000028687 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000017800 (score: 0.197)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000017113 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:98299 (score: 1.000; bootstrap: 100%)
  • MGI:1277989 (score: 0.410)

From Inparanoid:20070104

Oryza gramene

  • Q7Y1F0 (score: 1.000; bootstrap: 100%)
  • Q6TUC6 (score: 1.000; bootstrap: 100%)
  • Q8W524 (score: 0.493)
  • Q8RYY6 (score: 0.133)
  • Q75HP7 (score: 0.131)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000015094 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000008712 (score: 0.379)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000007092 (score: 1.000; bootstrap: 99%)
  • ENSRNOP00000011082 (score: 0.244)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YBR263W (score: 1.000; bootstrap: 100%)
  • YLR058C (score: 0.305)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC18G64c (score: 1.000; bootstrap: 100%)
  • SPAC24C92c (score: 0.445)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000160470 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000171194 (score: 0.659)
  • NEWSINFRUP00000150264 (score: 0.492)
  • NEWSINFRUP00000162238 (score: 0.385)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00022562001 (score: 1.000; bootstrap: 100%)
  • GSTENP00013555001 (score: 0.705)
  • GSTENP00011893001 (score: 0.401)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000020779 (score: 1.000; bootstrap: 97%)

From Inparanoid:20070104

Shigella flexneri

GLYA

From SHIGELLACYC

E. coli O157

GLYA

From ECOO157CYC


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

Superfamily (EcoliWiki Page)

SUPERFAMILY:53383

Panther (EcoliWiki Page)

PTHR11680:SF0

Pfam (EcoliWiki Page)

PF00464 Serine hydroxymethyltransferase

EcoCyc

EcoCyc:EG10408

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10408

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000401

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0403

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008389

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 1.8 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 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 3.2 3.3 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

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