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On One Page

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Gene |

Product(s) |

Expression|

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References |

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Standard Name	yigZ
Gene Synonym(s)	ECK3840, b3848, JW5577^[1], JW5577
Product Desc.	predicted elongation factor^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted elongation factor^[1], B3848^[2]^[1], YigZ^[2]^[1] , ECK3840, JW5577, b3848
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pepQ^[2]
Regulation/Activity
Quick Links
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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	yigZ
Mnemonic	Systematic nomenclature
Synonyms	ECK3840, b3848, JW5577^[1], JW5577
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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	86.87 minutes, 86.87 minutes	MG1655: 4030515..4031129 <gbrowseImage> name=NC_000913:4030515..4031129 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4010865..4011479 <gbrowseImage> name=NC_012967:4010865..4011479 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3920184..3920798 <gbrowseImage> name=NC_012759:3920184..3920798 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3604189..3603575 <gbrowseImage> name=NC_007779:3603575..3604189 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4129435..4130049 <gbrowseImage> name=NC_010473:4129435..4130049 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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)	Reference	Availability
ΔyigZ (Keio:JW5577)	deletion	deletion	PMID:16738554	Shigen CGSC11473^[5]
ΔyigZ788::kan			PMID:16738554	CGSC:105390
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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
JW5577	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAAAGCTGGTTAATTCCTGC Primer 2:CCTTCTTCAATCGCTAACAATTG
9B11	Kohara Phage	Genobase	PMID:3038334
16G1	Kohara Phage	Genobase	PMID:3038334
fad-751::Tn10	Linked marker	CAG18496 = CGSC7465^[5]	est. P1 cotransduction: 90% ^[6] Synonyms:fadAB101::Tn10
zih-35::Tn10	Linked marker	CAG18495 = CGSC7467^[5]	est. P1 cotransduction: 26% ^[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:EG11484	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11484	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001440	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948334	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1447	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012571	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	YigZ
Synonyms	predicted elongation factor^[1], B3848^[2]^[1], YigZ^[2]^[1] , ECK3840, JW5577, b3848
Product description	predicted elongation factor^[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
	GO:0005525	GTP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000640	F	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	References	Evidence
Protein	typA	PMID:15690043	Experiment(s):EBI-884404
Protein	topA	PMID:15690043	Experiment(s):EBI-891340
Protein	topA	PMID:19402753	LCMS(ID Probability):99.6
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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 MMESWLIPAA PVTVVEEIKK SRFITMLAHT DGVEAAKAFV ESVRAEHPDA RHHCVAWVAG APDDSQQLGF SDDGEPAGTA GKPMLAQLMG SGVGEITAVV VRYYGGILLG TGGLVKAYGG GVNQALRQLT TQRKTPLTEY TLQCEYHQLT GIEALLGQCD GKIINSDYQA FVLLRVALPA AKVAEFSAKL ADFSRGSLQL LAIEE
Length	205
Mol. Wt	21.887 kDa
pI	5.4 (calculated)
Extinction coefficient	19,940 - 20,315 (calc based on 6 Y, 2 W, and 3 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	References
Domain	17..126	PF01205 Uncharacterized protein family UPF0029	PMID:19920124
Domain	141..196	PF09186 Domain of unknown function (DUF1949)	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=yigZ 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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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:90111654	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948334	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012571	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P27862	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11484	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11484	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948334	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001440	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1447	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	5.899+/-0.035	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.039087948	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	207	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	77	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	78^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
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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)
pepQ
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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_000913:4030495..4030535 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:b3848 (EcoliWiki Page)	NCBI GEO profiles for yigZ
microarray	GenExpDB:b3848 (EcoliWiki Page)	Summary of data for yigZ 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 yigZ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11484	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1447	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3848
EcoGene	EcoGene:EG11484	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001440	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012571	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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
Arabidopsis thaliana	AT4G38090 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6ZJC5 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YIGZ	From SHIGELLACYC
E. coli O157	YIGZ	From ECOO157CYC
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Do-It-Yourself Web Tools

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:54211
Superfamily (EcoliWiki Page)	SUPERFAMILY:54980
Pfam (EcoliWiki Page)	PF01205 Uncharacterized protein family UPF0029
Pfam (EcoliWiki Page)	PF09186 Domain of unknown function (DUF1949)
EcoCyc	EcoCyc:EG11484	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11484	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001440	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1447	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012571	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.0 ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).

yigZ:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to yigZ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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