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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	ybdD
Gene Synonym(s)	ECK0592, b4512, JW0591^[1], JW0591
Product Desc.	conserved protein^[2]^[3] Function unknown^[4]
Product Synonyms(s)	conserved protein^[1], YbdD^[2]^[1], B4512^[2]^[1] , ECK0592, JW0591, b4512
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybdD^[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	ybdD
Mnemonic	Systematic nomenclature
Synonyms	ECK0592, b4512, JW0591^[1], JW0591
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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	13.61 minutes	MG1655: 631405..631602 <gbrowseImage> name=NC_000913:631405..631602 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 614879..615076 <gbrowseImage> name=NC_012967:614879..615076 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 534165..534362 <gbrowseImage> name=NC_012759:534165..534362 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 631405..631602 <gbrowseImage> name=NC_007779:631405..631602 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 570737..570934 <gbrowseImage> name=NC_010473:570737..570934 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 683997..684194 <gbrowseImage> name=NC_010473:683997..684194 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
ΔybdD (Keio:JW0591)	deletion	deletion	PMID:16738554	Shigen CGSC8707^[5]
ΔybdD737::kan			PMID:16738554	CGSC:103706
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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
JW0591	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTTGATTCACTGGCAAAAGC Primer 2:CCGCAGCAGCGCGCGCCGCCTTT
25A7	Kohara Phage	Genobase	PMID:3038334
4A5	Kohara Phage	Genobase	PMID:3038334
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: % ^[6] Synonyms:purE79::Tn10
dsbG601::Tn10	Linked marker	CAG12149 = CGSC7346^[5]	est. P1 cotransduction: 87% ^[6] Synonyms:zbd-601::Tn10, zbe-601::Tn10
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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:G0-10438	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11107	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120016290	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949021	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1098	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0285033	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	YbdD
Synonyms	conserved protein^[1], YbdD^[2]^[1], B4512^[2]^[1] , ECK0592, JW0591, b4512
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	References	Evidence
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1137323
Protein	nadE	PMID:16606699	Experiment(s):EBI-1137323
Protein	glpD	PMID:16606699	Experiment(s):EBI-1137323
Protein	rspA	PMID:16606699	Experiment(s):EBI-1137323
Protein	zwf	PMID:16606699	Experiment(s):EBI-1137323
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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	MRITIILVAP ARAENIGAAA RAMKTMGFSD LRIVDSQAHL EPATRWVAHG SGDIIDNIKV FPTLAESLHD VDFTVATTAR SRAKYHYYAT PVELVPLLEE KSSWMSHAAL VFGREDSGLT NEELALADVL TGVPMVADYP SLNLGQAVMV YCYQLATLIQ QPAKSDATAD QHQLQALRER AMTLLTTLAV ADDIKLVDWL QQRLGLLEQR DTAMLHRLLH DIEKNITK
Length	228
Mol. Wt	25.259 kDa
pI	5.9 (calculated)
Extinction coefficient	25,440 - 25,565 (calc based on 6 Y, 3 W, and 1 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..65	PF04328 Protein of unknown function (DUF466)		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=ybdD 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:94541100	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949021	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0285033	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AAS9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G0-10438	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11107	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949021	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120016290	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1098	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	147	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	262	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	63^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)
ybdD
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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_000913:631385..631425 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
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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 ybdD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G0-10438	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1098	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11107	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120016290	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0285033	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF02554
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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)	PF04328 Protein of unknown function (DUF466)
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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).

ybdD: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 ybdD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Families

Notes

Links

References

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