{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	ydhB
Gene Synonym(s)	ECK1655, b1659, JW1651^[1], JW1651
Product Desc.	protein with similarity to transcriptional regulators^[2]^[3] Function unknown, LysR family of transcriptional regulators^[4]
Product Synonyms(s)	predicted DNA-binding transcriptional regulator^[1], B1659^[2]^[1], YdhB^[2]^[1] , ECK1655, JW1651, b1659
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydhB^[2]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	ydhB
Mnemonic	Systematic nomenclature
Synonyms	ECK1655, b1659, JW1651^[1], JW1651
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	37.44 minutes	MG1655: 1737822..1736890 <gbrowseImage> name=NC_000913:1736890..1737822 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1717065..1716133 <gbrowseImage> name=NC_012967:1716133..1717065 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1628949..1629881 <gbrowseImage> name=NC_012759:1628949..1629881 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1741512..1740580 <gbrowseImage> name=NC_007779:1740580..1741512 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1828393..1827461 <gbrowseImage> name=NC_010473:1827461..1828393 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
ΔydhB (Keio:JW1651)	deletion	deletion	PMID:16738554	Shigen CGSC9405^[5]
ydhB::Tn5KAN-I-SceI (FB20412)	Insertion at nt 846 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20412	does not contain pKD46
ydhB::Tn5KAN-I-SceI (FB20413)	Insertion at nt 846 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20413	contains pKD46
ΔydhB737::kan			PMID:16738554	CGSC:104280
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1651	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTGGTCAGAATATTCACTCGA Primer 2:CCATCACCCGTTGCGGGAGTCTC
4H6	Kohara Phage	Genobase	PMID:3038334
13H4	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: % ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: 18% ^[6] Synonyms:zdh-925::Tn10
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12140	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12140	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002041	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945208	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2061	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005547	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name	YdhB
Synonyms	predicted DNA-binding transcriptional regulator^[1], B1659^[2]^[1], YdhB^[2]^[1] , ECK1655, JW1651, b1659
Product description	protein with similarity to transcriptional regulators^[2]^[3] Function unknown, LysR family of transcriptional regulators^[4]
EC number (for enzymes)
edit table

Notes

Function

[back to top]

<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:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	P	Seeded from EcoCyc (v14.0)	complete
edit table

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	ade	PMID:16606699	Experiment(s):EBI-1140400
Protein	dusB	PMID:16606699	Experiment(s):EBI-1140400
Protein	groL	PMID:16606699	Experiment(s):EBI-1140400
Protein	ybiT	PMID:16606699	Experiment(s):EBI-1140400
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MWSEYSLEVV DAVARNGSFS AAAQELHRVP SAVSYTVRQL EEWLAVPLFE RRHRDVELTA AGAWFLKEGR SVVKKMQITR QQCQQIANGW RGQLAIAVDN IVRPERTRQM IVDFYRHFDD VELLVFQEVF NGVWDALSDG RVELAIGATR AIPVGGRYAF RDMGMLSWSC VVASHHPLAL MDGPFSDDTL RNWPSLVRED TSRTLPKRIT WLLDNQKRVV VPDWESSATC ISAGLCIGMV PTHFAKPWLN EGKWVALELE NPFPDSACCL TWQQNDMSPA LTWLLEYLGD SETLNKEWLR EPEETPATGD
Length	310
Mol. Wt	35.249 kDa
pI	5.0 (calculated)
Extinction coefficient	84,450 - 85,200 (calc based on 5 Y, 14 W, and 6 C residues)
edit table

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	87..292	PF03466 LysR substrate binding domain	PMID:19920124
Domain	5..63	PF00126 Bacterial regulatory helix-turn-helix protein, lysR family	PMID:19920124
edit table

<motif_map/>

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

Structures

<beststructure> gene=ydhB taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129617	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945208	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005547	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACR2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12140	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12140	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945208	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002041	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2061	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	114	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	43	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	73	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
ydhB
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:1737802..1737842 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1659 (EcoliWiki Page)	NCBI GEO profiles for ydhB
microarray	GenExpDB:b1659 (EcoliWiki Page)	Summary of data for ydhB from multiple microarray studies
edit table

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 (1737730..1738007) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ16; Well:D3^[7]
edit table

Notes

Accessions Related to ydhB Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12140	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2061	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1659
EcoGene	EcoGene:EG12140	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002041	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005547	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

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

Organism	Homologs (Statistics)	Comments
Xenopus tropicalis	ENSXETP00000050565 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YDHB	From SHIGELLACYC
E. coli O157	YDHB	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
Pfam (EcoliWiki Page)	PF03466 LysR substrate binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:46785
Superfamily (EcoliWiki Page)	SUPERFAMILY:53850
EcoCyc	EcoCyc:EG12140	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12140	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002041	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2061	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005547	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ydhB:On One Page

Quickview

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 ydhB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search