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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	yodD
Gene Synonym(s)	ECK1951, b1953, JW5317^[1], JW5317
Product Desc.	predicted protein^[2]^[3]
Product Synonyms(s)	predicted protein^[1], B1953^[2]^[1], YodD^[2]^[1] , ECK1951, JW5317, b1953
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yodD^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

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	yodD
Mnemonic	Systematic nomenclature
Synonyms	ECK1951, b1953, JW5317^[1], JW5317
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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	43.6 minutes	MG1655: 2023010..2023237 <gbrowseImage> name=NC_000913:2023010..2023237 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1915493..1915720 <gbrowseImage> name=NC_012759:1915493..1915720 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2027123..2027350 <gbrowseImage> name=NC_007779:2027123..2027350 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2114018..2114245 <gbrowseImage> name=NC_010473:2114018..2114245 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
ΔyodD (Keio:JW5317)	deletion	deletion	PMID:16738554	Shigen CGSC11318^[4]
ΔyodD728::kan			PMID:16738554	CGSC:105878
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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
JW5317	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAACCGCAAAAGAGTACAG Primer 2:CCACGATTCACTTCAGAGACGCT
3B3	Kohara Phage	Genobase	PMID:3038334
25D8	Kohara Phage	Genobase	PMID:3038334
uvrC279::Tn10	Linked marker	CAG12156 = CGSC7394^[4]	est. P1 cotransduction: 27% ^[5]
zed-3069::Tn10	Linked marker	CAG18451 = CGSC7395^[4]	est. P1 cotransduction: 62% ^[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:G7046	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14387	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003632	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946469	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4130	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006488	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	YodD
Synonyms	predicted protein^[1], B1953^[2]^[1], YodD^[2]^[1] , ECK1951, JW5317, b1953
Product description	predicted protein^[2]^[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	Aspect	Notes	Status
	GO:0044011	single-species biofilm formation on inanimate substrate	PMID:19919618	IMP: Inferred from Mutant Phenotype	P	Seeded from EcoCyc (v14.0)	complete
	GO:0070301	cellular response to hydrogen peroxide	PMID:19919618	IMP: Inferred from Mutant Phenotype	P	Seeded from EcoCyc (v14.0)	complete
	GO:0071468	cellular response to acidity	PMID:19919618	IMP: Inferred from Mutant Phenotype	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	References	Evidence
Protein	rplD	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsP	PMID:19402753	LCMS(ID Probability):99.6
Protein	wcaI	PMID:19402753	LCMS(ID Probability):99.6
Protein	hns	PMID:19402753	LCMS(ID Probability):99.6
Protein	yebR	PMID:19402753	LCMS(ID Probability):99.6
Protein	kdgR	PMID:19402753	LCMS(ID Probability):99.6
Protein	yebV	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 MRGKMMKTAK EYSDTAKREV SVDVDALLAA INEISESEVH RSQNDSEHVS VDGREYHTWR ELADAFELDI HDFSVSEVNR
Length	80
Mol. Wt	9.182 kDa
pI	4.7 (calculated)
Extinction coefficient	8,480 (calc based on 2 Y, 1 W, and 0 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	18..75	PF10733 Protein of unknown function (DUF2525)		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=yodD 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:90111359	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946469	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006488	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P64519	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7046	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14387	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946469	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003632	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4130	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	E. coli K-12 MG1655	18^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	424	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	20^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)
yodD
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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_000913:2022990..2023030 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:b1953 (EcoliWiki Page)	NCBI GEO profiles for yodD
microarray	GenExpDB:b1953 (EcoliWiki Page)	Summary of data for yodD 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 yodD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7046	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4130	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1953
EcoGene	EcoGene:EG14387	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003632	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006488	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
Shigella flexneri	S2092	From SHIGELLACYC
E. coli O157	Z3043	From ECOO157CYC
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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
Pfam (EcoliWiki Page)	PF10733 Protein of unknown function (DUF2525)
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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 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^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).

yodD: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 yodD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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