hdeD:On One Page
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Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
Quickview | | Gene | | Product(s) | | Expression| | Evolution | | References | |
Quickview
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Standard Name |
hdeD |
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Gene Synonym(s) |
ECK3495, b3511, JW3479, yhiA[1], yhiA |
Product Desc. |
acid-resistance membrane protein[2][3] Putative membrane transporter, H-NS repressed[4] |
Product Synonyms(s) |
acid-resistance membrane protein[1], B3511[2][1], YhiA[2][1], HdeD[2][1] , ECK3495, JW3479, yhiA, b3511 |
Function from GO |
<GO_nr /> |
Knock-Out Phenotype | |
Regulation/Expression | |
Regulation/Activity | |
Quick Links | |
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>
Notes
EvgAS regulon. RpoS regulon. Six TM helices predicted.[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
Standard name |
hdeD |
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Mnemonic |
H-NS-determined expression |
Synonyms |
ECK3495, b3511, JW3479, yhiA[1], yhiA |
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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 |
78.78 minutes |
MG1655: 3655018..3655590 |
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NC_012967: 3586486..3587058 |
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NC_012759: 3543512..3544084 |
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W3110 |
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W3110: 3983420..3982848 |
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DH10B: 3752763..3753335 |
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Notes
Sequence Features
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
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 |
---|---|---|---|---|---|---|---|
ΔhdeD (Keio:JW3479) |
deletion |
deletion |
PMID:16738554 |
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ΔhdeD766::kan |
PMID:16738554 |
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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
See Help:Gene_resources for help entering information into the Genetic Resources table.
Resource | Resource Type | Source | Notes/Reference |
---|---|---|---|
JW3479 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCTTATATATAGATAAGGCAAC Primer 2:CCTTGCTGCTTAACGAACAAACT | |
Kohara Phage |
PMID:3038334 | ||
zhg-50::Tn10 |
Linked marker |
est. P1 cotransduction: 3% [6] | |
zic-4901::Tn10 |
Linked marker |
est. P1 cotransduction: % [6] | |
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:EG11495 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG11495 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120001451 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EchoBASE:EB1458 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0011467 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
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 |
HdeD |
---|---|
Synonyms |
acid-resistance membrane protein[1], B3511[2][1], YhiA[2][1], HdeD[2][1] , ECK3495, JW3479, yhiA, b3511 |
Product description |
acid-resistance membrane protein[2][3] Putative membrane transporter, H-NS repressed[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:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0997 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0005886 |
plasma membrane |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-1003 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016020 |
membrane |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0472 |
C |
Seeded from EcoCyc (v14.0) |
complete | |
GO:0016021 |
integral to membrane |
GOA:spkw |
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-9909 |
C |
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 |
C-terminus localized in the cytoplasm with 6 predicted transmembrane domains |
Daley et al. (2005) [7] |
| |
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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 |
MLYIDKATIL KFDLEMLKKH RRAIQFIAVL LFIVGLLCIS FPFVSGDILS TVVGALLICS GIALIVGLFS NRSHNFWPVL SGFLVAVAYL LIGYFFIRAP ELGIFAIAAF IAGLFCVAGV IRLMSWYRQR SMKGSWLQLV IGVLDIVIAW IFLGATPMVS VTLVSTLVGI ELIFSAASLF SFASLFVKQQ |
Length |
190 |
Mol. Wt |
20.904 kDa |
pI |
9.7 (calculated) |
Extinction coefficient |
27,960 - 28,335 (calc based on 4 Y, 4 W, and 3 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.
|
<motif_map/> |
Structure
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Structure figures<protect> | ||||||
Notes
Gene Product Resources
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
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
Escherichia coli str. K-12 substr. MG1655 | ||
Escherichia coli str. K-12 substr. MG1655 | ||
ASAP:ABE-0011467 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
EcoCyc:EG11495 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG11495 |
Escherichia coli str. K-12 substr. MG1655 | |
Escherichia coli str. K-12 substr. MG1655 | ||
RegulonDB:ECK120001451 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB1458 |
Escherichia coli str. K-12 substr. MG1655 | |
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Notes
Links
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
Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
---|---|---|---|---|---|---|---|
Protein |
E. coli K-12 MG1655 |
88 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
Protein |
E. coli K-12 MG1655 |
1108 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
Protein |
E. coli K-12 MG1655 |
27a |
molecules/cell/generation |
|
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.
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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
<protect><gbrowseImage>
name=NC_000913:3654998..3655038
source=MG1655
type=Gene+DNA_+Protein
preset=Nterminus
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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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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 |
NCBI GEO profiles for hdeD | |
microarray |
Summary of data for hdeD 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 |
---|---|---|---|---|
GFP Fusion |
Intergenic region (3654287..3654704) fused to gfpmut2. |
GFP fusion described in Zaslaver, et al. | ||
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Notes
Accessions Related to hdeD Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
Database | Accession | Notes |
---|---|---|
EcoCyc:EG11495 |
Escherichia coli str. K-12 substr. MG1655 | |
EchoBASE:EB1458 |
Escherichia coli str. K-12 substr. MG1655 | |
EcoGene:EG11495 |
Escherichia coli str. K-12 substr. MG1655 | |
RegulonDB:ECK120001451 |
Escherichia coli str. K-12 substr. MG1655 | |
ASAP:ABE-0011467 |
Escherichia coli str. K-12 substr. MG1655 | |
edit table |
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Notes
Links
Name | URL | Comments |
---|---|---|
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Evolution
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Homologs in Other Organisms
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.
Organism | Homologs (Statistics) | Comments |
---|---|---|
Shigella flexneri |
HDED |
From SHIGELLACYC |
E. coli O157 |
HDED |
From ECOO157CYC |
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Notes
Families
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See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.
Database | Accession | Notes |
---|---|---|
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Notes
Links
Name | URL | Comments |
---|---|---|
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References
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 1.8 1.9 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).
- ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
- ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed
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