murF: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

murF

Gene Synonym(s)

ECK0087, b0086, JW0084, mra[1], mra

Product Desc.

UDP- D-alanyl:D-alanine adding enzyme; UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase[2]

Product Synonyms(s)

UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase[1], B0086[3][1], Mra[3][1], MurF[3][1] , ECK0087, JW0084, mra, b0086

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ[3]

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

murF

Mnemonic

Murein

Synonyms

ECK0087, b0086, JW0084, mra[1], mra

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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

2.04 minutes 

MG1655: 94650..96008
<gbrowseImage> name=NC_000913:94650..96008 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 97454..98812
<gbrowseImage> name=NC_012967:97454..98812 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 94649..96007
<gbrowseImage> name=NC_012759:94649..96007 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 94650..96008
<gbrowseImage> name=NC_007779:94650..96008 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 68754..70112
<gbrowseImage> name=NC_010473:68754..70112 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

94650

Edman degradation

PMID:2186811


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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

murFA288T

A288T

(in murF2; temperature-sensitive mutant with low activity)

Strain variation; seeded from UniProt:P11880

murF2

CGSC:9857


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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

JW0084

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATTAGCGTAACCCTTAGCCA

Primer 2:CCACATGTCCCATTCTCCTGTAA

6C1

Kohara Phage

Genobase

PMID:3038334

6F3

Kohara Phage

Genobase

PMID:3038334

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 68% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[4]

est. P1 cotransduction: 7% [5]

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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:EG10622

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10622

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944813

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000615

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0617

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000313

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

MurF

Synonyms

UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase[1], B0086[3][1], Mra[3][1], MurF[3][1] , ECK0087, JW0084, mra, b0086

Product description

UDP- D-alanyl:D-alanine adding enzyme; UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase[2]

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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000713

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004101

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005863

F

Seeded from EcoCyc (v14.0)

complete

GO:0047480

UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity

PMID: 2186811

IDA: Inferred from Direct Assay

F

In Figure 2, the ability of the enzyme to catalyze the conversion of radiolabeled substrate (either UDP-MurNAc-tripeptide, or D-alanine) to UDP-MurNAc-pentapeptide was analyzed using HPLC.

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013221

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005863

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0007047

cellular cell wall organization

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc (v14.0)

complete

GO:0007049

cell cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0131

P

Seeded from EcoCyc (v14.0)

complete

GO:0008360

regulation of cell shape

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005863

P

Seeded from EcoCyc (v14.0)

complete

GO:0008360

regulation of cell shape

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc (v14.0)

complete

GO:0008766

UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005863

F

Seeded from EcoCyc (v14.0)

complete

GO:0009058

biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000713

P

Seeded from EcoCyc (v14.0)

complete

GO:0009058

biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004101

P

Seeded from EcoCyc (v14.0)

complete

GO:0009058

biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013221

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005863

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0573

P

Seeded from EcoCyc (v14.0)

complete

GO:0047480

UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.3.2.10

F

Seeded from EcoCyc (v14.0)

complete

GO:0051301

cell division

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005863

P

Seeded from EcoCyc (v14.0)

complete

GO:0051301

cell division

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0132

P

Seeded from EcoCyc (v14.0)

complete

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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

yceQ

PMID:15690043

Experiment(s):EBI-894104

Protein

gltD

PMID:15690043

Experiment(s):EBI-894104

Protein

mrdB

PMID:15690043

Experiment(s):EBI-894104

Protein

mukB

PMID:15690043

Experiment(s):EBI-894104

Protein

rihC

PMID:15690043

Experiment(s):EBI-894104

Protein

yedV

PMID:15690043

Experiment(s):EBI-894104

Protein

nadE

PMID:16606699

Experiment(s):EBI-1135540

Protein

dnaC

PMID:16606699

Experiment(s):EBI-1135540

Protein

iscS

PMID:16606699

Experiment(s):EBI-1135540

Protein

gltD

PMID:19402753

LCMS(ID Probability):99.0

Protein

murE

PMID:19402753

MALDI(Z-score):17.053160

Protein

yedV

PMID:19402753

LCMS(ID Probability):99.0

Protein

mrdB

PMID:19402753

LCMS(ID Probability):99.0

Protein

rihC

PMID:19402753

LCMS(ID Probability):99.0

Protein

yceQ

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

cytoplasm

From EcoCyc[6]


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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 

MISVTLSQLT DILNGELQGA DITLDAVTTD TRKLTPGCLF VALKGERFDA HDFADQAKAG
GAGALLVSRP LDIDLPQLIV KDTRLAFGEL AAWVRQQVPA RVVALTGSSG KTSVKEMTAA
ILSQCGNTLY TAGNLNNDIG VPMTLLRLTP EYDYAVIELG ANHQGEIAWT VSLTRPEAAL
VNNLAAAHLE GFGSLAGVAK AKGEIFSGLP ENGIAIMNAD NNDWLNWQSV IGSRKVWRFS
PNAANSDFTA TNIHVTSHGT EFTLQTPTGS VDVLLPLPGR HNIANALAAA ALSMSVGATL
DAIKAGLANL KAVPGRLFPI QLAENQLLLD DSYNANVGSM TAAVQVLAEM PGYRVLVVGD
MAELGAESEA CHVQVGEAAK AAGIDRVLSV GKQSHAISTA SGVGEHFADK TALITRLKLL
IAEQQVITIL VKGSRSAAME EVVRALQENG TC
Length

452

Mol. Wt

47.447 kDa

pI

5.2 (calculated)

Extinction coefficient

34,950 - 35,450 (calc based on 5 Y, 5 W, and 4 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

23..95

PF01225 Mur ligase family, catalytic domain

PMID:19920124

Domain

313..403

PF02875 Mur ligase family, glutamate ligase domain

PMID:19920124

Domain

105..293

PF08245 Mur ligase middle domain

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=murF 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:16128079

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944813

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000313

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P11880

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10622

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10622

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944813

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000615

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0617

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

1.98E+02

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

19.117+/-0.144

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.036450663

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

911

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

346

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

603

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)

mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ

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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_000913:94630..94670 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:b0086 (EcoliWiki Page)

NCBI GEO profiles for murF

microarray

GenExpDB:b0086 (EcoliWiki Page)

Summary of data for murF 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
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Notes

Accessions Related to murF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10622

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0617

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0086

EcoGene

EcoGene:EG10622

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000615

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000313

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

MURF

From SHIGELLACYC

E. coli O157

MURF

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)

PF02875 Mur ligase family, glutamate ligase domain

Pfam (EcoliWiki Page)

PF01225 Mur ligase family, catalytic domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:53244

Panther (EcoliWiki Page)

PTHR23135:SF3

Superfamily (EcoliWiki Page)

SUPERFAMILY:53623

Superfamily (EcoliWiki Page)

SUPERFAMILY:63418

Pfam (EcoliWiki Page)

PF08245 Mur ligase middle domain

EcoCyc

EcoCyc:EG10622

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10622

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000615

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0617

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000313

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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