Latest revision as of 05:20, 29 July 2007

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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	djlA
Gene Synonym(s)	ECK0056, b0055, JW0054, yabH^[1], yabH
Product Desc.	chaperone with DnaK^[2]^[3] DnaK co-chaperone; membrane-asssociated protein with single transmembrane domain and a C-terminal J-like domain; mutants rapidly accumulate suppressors^[4]
Product Synonyms(s)	DnaJ-like protein, membrane anchored^[1], B0055^[2]^[1], YabH^[2]^[1], DjlA^[2]^[1] , ECK0056, JW0054, yabH, b0055
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): djlA^[2]
Regulation/Activity
Quick Links
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Notes

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DjlA overproduction activates RcsBC and Cps synthesis and causes mucoidy. Normal levels of DjlA act as an Rcs negative regulator. The DjlA transmembrane domain is a dimerization domain.^[4]

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	djlA
Mnemonic	DnaJ-like
Synonyms	ECK0056, b0055, JW0054, yabH^[1], yabH
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Notes

Location(s) and DNA Sequence

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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	1.24 minutes	MG1655: 57364..58179 <gbrowseImage> name=NC_000913:57364..58179 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 61559..62374 <gbrowseImage> name=NC_012967:61559..62374 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 57364..58179 <gbrowseImage> name=NC_012759:57364..58179 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 57364..58179 <gbrowseImage> name=NC_007779:57364..58179 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 57364..58179 <gbrowseImage> name=NC_010473:57364..58179 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
djlAL15R		L15R		Loss of activation of rcs			seeded from UniProt:P31680
djlAM16R		M16R		Only partial activation of rcs			seeded from UniProt:P31680
djlAH233Q		H233Q		Loss of activity			seeded from UniProt:P31680
djlA(del) (Keio:JW0054)	deletion	deletion			PMID:16738554	Shigen CGSC8363^[5]
djlA(del)::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
djlA766(del)::kan					PMID:16738554	CGSC:100612
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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
JW0054	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAGTATTGGGGAAAAATCAT Primer 2:CCTTTAAACCCTTTCTGCTGCTT
8D2	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 39% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 37% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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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:EG11570	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11570	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001522	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948992	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1530	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000187	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	DjlA
Synonyms	DnaJ-like protein, membrane anchored^[1], B0055^[2]^[1], YabH^[2]^[1], DjlA^[2]^[1] , ECK0056, JW0054, yabH, b0055
Product description	chaperone with DnaK^[2]^[3] DnaK co-chaperone; membrane-asssociated protein with single transmembrane domain and a C-terminal J-like domain; mutants rapidly accumulate suppressors^[4]
EC number (for enzymes)
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Notes

Function

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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:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01153	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-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
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9907	C	Seeded from EcoCyc (v14.0)	complete
	GO:0031072	heat shock protein binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001623	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	Notes	References	Evidence
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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
plasma membrane
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Notes

Structure and Physical Properties

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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 MQYWGKIIGV AVALLMGGGF WGVVLGLLIG HMFDKARSRK MAWFANQRER QALFFATTFE VMGHLTKSKG RVTEADIHIA SQLMDRMNLH GASRTAAQNA FRVGKSDNYP LREKMRQFRS VCFGRFDLIR MFLEIQIQAA FADGSLHPNE RAVLYVIAEE LGISRAQFDQ FLRMMQGGAQ FGGGYQQQTG GGNWQQAQRG PTLEDACNVL GVKPTDDATT IKRAYRKLMS EHHPDKLVAK GLPPEMMEMA KQKAQEIQQA YELIKQQKGF K
Length	271
Mol. Wt	30.579 kDa
pI	10.1 (calculated)
Extinction coefficient	30,940 - 31,190 (calc based on 6 Y, 4 W, and 2 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	205..269	PF00226 DnaJ domain	PMID:19920124^[7]
Domain	32..173	PF05099 Tellurite resistance protein TerB	PMID:19920124^[7]
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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=djlA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

Gene Product Resources

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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:16128049	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948992	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000187	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31680	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11570	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11570	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948992	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001522	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1530	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	Reference(s)
Protein	E. coli K-12 MC4100	1.67E+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	762	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	137	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	341	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	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)
djlA
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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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<gbrowseImage> name=NC_000913:57344..57384 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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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:b0055 (EcoliWiki Page)	NCBI GEO profiles for djlA
microarray	GenExpDB:b0055 (EcoliWiki Page)	Summary of data for djlA 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 djlA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11570	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1530	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0055
EcoGene	EcoGene:EG11570	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001522	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000187	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
Anopheles gambiae	ENSANGP00000014657 (score: 1.000; bootstrap: 100%) ENSANGP00000019419 (score: 0.078) ENSANGP00000010200 (score: 0.063)	From Inparanoid:20070104
Shigella flexneri	YABH	From SHIGELLACYC
E. coli O157	YABH	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
Pfam (EcoliWiki Page)	PF00226 DnaJ domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:46565
Pfam (EcoliWiki Page)	PF05099 Tellurite resistance protein TerB
EcoCyc	EcoCyc:EG11570	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11570	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001522	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1530	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000187	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 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 ^2.7 ^2.8 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).
↑ ^7.0 ^7.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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djlA:On One Page: Difference between revisions

Latest revision as of 05:20, 29 July 2007

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 djlA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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