{{#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	ydgA
Gene Synonym(s)	ECK1609, b1614, JW1606^[1], JW1606
Product Desc.	conserved protein^[2]^[3] Required for swarming phenotype, function unknown; slightly upregulated by beryllium^[4]
Product Synonyms(s)	conserved protein^[1], B1614^[2]^[1], YdgA^[2]^[1] , ECK1609, JW1606, b1614
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydgA^[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]

HT_Cmplx48_Mem: SecA+YdgA+YjiY.^[4]

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	ydgA
Mnemonic	Systematic nomenclature
Synonyms	ECK1609, b1614, JW1606^[1], JW1606
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	36.38 minutes	MG1655: 1687876..1689384 <gbrowseImage> name=NC_000913:1687876..1689384 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1667047..1668555 <gbrowseImage> name=NC_012967:1667047..1668555 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1579935..1581443 <gbrowseImage> name=NC_012759:1579935..1581443 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1691566..1693074 <gbrowseImage> name=NC_007779:1691566..1693074 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1778837..1780345 <gbrowseImage> name=NC_010473:1778837..1780345 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
ΔydgA (Keio:JW1606)	deletion	deletion	PMID:16738554	Shigen CGSC9367^[5]
ΔydgA762::kan			PMID:16738554	CGSC:104264
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
JW1606	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATAAATCGCTGGTAGCGGT Primer 2:CCtTGCTGCGGAATTGCCGGTAC
6A3	Kohara Phage	Genobase	PMID:3038334
6A5	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: % ^[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:G6865	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12457	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003454	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946172	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2351	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005402	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	YdgA
Synonyms	conserved protein^[1], B1614^[2]^[1], YdgA^[2]^[1] , ECK1609, JW1606, b1614
Product description	conserved protein^[2]^[3] Required for swarming phenotype, function unknown; slightly upregulated by beryllium^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	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	dusC	PMID:16606699	Experiment(s):EBI-1140280
Protein	nohB	PMID:16606699	Experiment(s):EBI-1140280
Protein	fusA	PMID:16606699	Experiment(s):EBI-1140280
Protein	sdhA	PMID:16606699	Experiment(s):EBI-1140280
Protein	nrdB	PMID:16606699	Experiment(s):EBI-1140280
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 MNKSLVAVGV IVALGVVWTG GAWYTGKKIE THLEDMVAQA NAQLKLTAPE SNLEVSYQNY HRGVFSSQLQ LLVKPIAGKE NPWIKSGQSV IFNESVDHGP FPLAQLKKLN LIPSMASIQT TLVNNEVSKP LFDMAKGETP FEINSRIGYS GDSSSDISLK PLNYEQKDEK VAFSGGEFQL NADRDGKAIS LSGEAQSGRI DAVNEYNQKV QLTFNNLKTD GSSTLASFGE RVGNQKLSLE KMTISVEGKE LALLEGMEIS GKSDLVNDGK TINSQLDYSL NSLKVQNQDL GSGKLTLKVG QIDGEAWHQF SQQYNAQTQA LLAQPEIANN PELYQEKVTE AFFSALPLML KGDPVITIAP LSWKNSQGES ALNLSLFLKD PATTKEAPQT LAQEVDRSVK SLDAKLTIPV DMATEFMTQV AKLEGYQEDQ AKKLAKQQVE GASAMGQMFR LTTLQDNTIT TSLQYANGQI TLNGQKMSLE DFVGMFAMPA LNVPAVPAIP QQ
Length	502
Mol. Wt	54.689 kDa
pI	4.9 (calculated)
Extinction coefficient	43,890 (calc based on 11 Y, 5 W, and 0 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	Notes	References
motif	1-19	UniProt Manual:Signal Peptides	UniProt:P77804
Domain	1..482	PF06097 Bacterial protein of unknown function (DUF945)		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=ydgA 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:16129572	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946172	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005402	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77804	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6865	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12457	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946172	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003454	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2351	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 MC4100	4.01E+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	E. coli K-12 MG1655	1875	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	871	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	1163	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)
ydgA
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_000913:1687856..1687896 source=MG1655 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:b1614 (EcoliWiki Page)	NCBI GEO profiles for ydgA
microarray	GenExpDB:b1614 (EcoliWiki Page)	Summary of data for ydgA 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 (1687702..1687936) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ15; Well:F5^[7]
edit table

Notes

Accessions Related to ydgA Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6865	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2351	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1614
EcoGene	EcoGene:EG12457	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003454	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005402	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
Shigella flexneri	YDGA	From SHIGELLACYC
E. coli O157	YDGA	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)	PF06097 Bacterial protein of unknown function (DUF945)
EcoCyc	EcoCyc:G6865	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12457	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003454	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2351	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005402	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 ^4.2 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

ydgA: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 ydgA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search