garR: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 |
garR |
|---|---|
| Gene Synonym(s) |
ECK3113, b3125, JW5526, yhaE[1], yhaE |
| Product Desc. |
TSA- Tartronate semialdehyde reductase, glycerate- or galactarate-inducible[2] |
| Product Synonyms(s) |
tartronate semialdehyde reductase[1], B3125[3][1], YhaE[3][1], GarR[3][1] , ECK3113, JW5526, yhaE, b3125 |
| Function from GO |
<GO_nr /> |
| Knock-Out Phenotype | |
| Regulation/Expression |
transcription unit(s): garPLRK-rnpB[3], yhaUFED-rnpB |
| Regulation/Activity | |
| Quick Links |
|
| edit table |
</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>
Notes
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
garR |
|---|---|
| Mnemonic |
Galactarate |
| Synonyms |
ECK3113, b3125, JW5526, yhaE[1], yhaE |
| edit table |
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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 |
70.48 minutes, 70.48 minutes |
MG1655: 3270779..3269889 |
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|
NC_012967: 3205686..3204796 |
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|
NC_012759: 3157037..3157921 |
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|
W3110 |
|
W3110: 3272612..3271722 |
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|
DH10B: 3368524..3367634 |
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| edit table |
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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 |
|---|---|---|---|---|---|
| edit table |
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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 |
|---|---|---|---|---|---|---|---|
|
ΔgarR (Keio:JW5526) |
deletion |
deletion |
PMID:16738554 |
||||
|
ΔgarR739::kan |
PMID:16738554 |
| |||||
| edit table |
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Notes
Genetic Interactions
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| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
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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 |
|---|---|---|---|
|
JW5526 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCACTATGAAAGTTGGTTTTAT Primer 2:CCACGAGTAACTTCGACTTTCGC | |
|
Kohara Phage |
PMID:3038334 | ||
|
Kohara Phage |
PMID:3038334 | ||
|
Linked marker |
est. P1 cotransduction: 7% [5] | ||
|
Linked marker |
est. P1 cotransduction: 4% [5] | ||
| edit table |
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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:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001158 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EchoBASE:EB1163 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010273 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Product(s)
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Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
| Standard name |
GarR |
|---|---|
| Synonyms |
tartronate semialdehyde reductase[1], B3125[3][1], YhaE[3][1], GarR[3][1] , ECK3113, JW5526, yhaE, b3125 |
| Product description |
TSA- Tartronate semialdehyde reductase, glycerate- or galactarate-inducible[2] |
| EC number (for enzymes) | |
| edit table |
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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:0005737 |
cytoplasm |
C |
Seeded from Riley et al 2006 [1]. |
Missing: evidence, reference | ||||
|
GO:0004616 |
phosphogluconate dehydrogenase (decarboxylating) activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006115 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0004616 |
phosphogluconate dehydrogenase (decarboxylating) activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006183 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0005488 |
binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR016040 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006098 |
pentose-phosphate shunt |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006115 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006098 |
pentose-phosphate shunt |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006183 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0006573 |
valine metabolic process |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR002204 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0008442 |
3-hydroxyisobutyrate dehydrogenase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR002204 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0008679 |
2-hydroxy-3-oxopropionate reductase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006398 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0008679 |
2-hydroxy-3-oxopropionate reductase activity |
GOA:spec |
IEA: Inferred from Electronic Annotation |
EC:1.1.1.60 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0046487 |
glyoxylate metabolic process |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006398 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0050662 |
coenzyme binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR013328 |
F |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0055114 |
oxidation reduction |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR002204 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0055114 |
oxidation reduction |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006115 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0055114 |
oxidation reduction |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006183 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0055114 |
oxidation reduction |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
InterPro:IPR006398 |
P |
Seeded from EcoCyc (v14.0) |
complete | |
|
GO:0055114 |
oxidation reduction |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
SP_KW:KW-0560 |
P |
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 |
|---|---|---|---|---|
| edit table |
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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 |
|---|---|---|---|---|
| edit table |
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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 |
MIDMTMKVGF IGLGIMGKPM SKNLLKAGYS LVVADRNPEA IADVIAAGAE TASTAKAIAE QCDVIITMLP NSPHVKEVAL GENGIIEGAK PGTVLIDMSS IAPLASREIS EALKAKGIDM LDAPVSGGEP KAIDGTLSVM VGGDKAIFDK YYDLMKAMAG SVVHTGEIGA GNVTKLANQV IVALNIAAMS EALTLATKAG VNPDLVYQAI RGGLAGSTVL DAKAPMVMDR NFKPGFRIDL HIKDLANALD TSHGVGAQLP LTAAVMEMMQ ALRADGLGTA DHSALACYYE KLAKVEVTR |
| Length |
299 |
| Mol. Wt |
31.019 kDa |
| pI |
5.4 (calculated) |
| Extinction coefficient |
8,940 - 9,190 (calc based on 6 Y, 0 W, and 2 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
| </protect>
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 |
|---|---|---|
| edit table |
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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-0010273 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EcoCyc:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120001158 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1163 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
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Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
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 |
127 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
83 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
68 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
| edit table |
Notes
Transcription and Transcriptional Regulation
<protect>
|
See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
|
 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
<protect><gbrowseImage>
name=NC_000913:3270759..3270799
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
<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 |
NCBI GEO profiles for garR | |
|
microarray |
Summary of data for garR 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 |
|---|---|---|---|---|
| edit table |
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Notes
Accessions Related to garR Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1163 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001158 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010273 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
<protect></protect>
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
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 |
|---|---|---|
|
Apis mellifera |
|
From Inparanoid:20070104 |
|
Arabidopsis thaliana |
|
From Inparanoid:20070104 |
|
Bos taurus |
|
From Inparanoid:20070104 |
|
Caenorhabditis briggsae |
|
From Inparanoid:20070104 |
|
Caenorhabditis elegans |
|
From Inparanoid:20070104 |
|
Canis familiaris |
|
From Inparanoid:20070104 |
|
Ciona intestinalis |
|
From Inparanoid:20070104 |
|
Danio rerio |
|
From Inparanoid:20070104 |
|
Dictyostelium discoideum |
|
From Inparanoid:20070104 |
|
Drosophila melanogaster |
|
From Inparanoid:20070104 |
|
Gallus gallus |
|
From Inparanoid:20070104 |
|
Homo sapiens |
|
From Inparanoid:20070104 |
|
Macaca mulatta |
|
From Inparanoid:20070104 |
|
Monodelphis domestica |
|
From Inparanoid:20070104 |
|
Mus musculus |
|
From Inparanoid:20070104 |
|
Oryza gramene |
|
From Inparanoid:20070104 |
|
Pan troglodytes |
|
From Inparanoid:20070104 |
|
Rattus norvegicus |
|
From Inparanoid:20070104 |
|
Takifugu rubripes |
|
From Inparanoid:20070104 |
|
Tetraodon nigroviridis |
|
From Inparanoid:20070104 |
|
Xenopus tropicalis |
|
From Inparanoid:20070104 |
|
Shigella flexneri |
YHAE |
From SHIGELLACYC |
|
E. coli O157 |
YHAE |
From ECOO157CYC |
| edit table |
Do-It-Yourself Web Tools
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Notes
Families
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase |
||
|
EcoCyc:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11176 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001158 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1163 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010273 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
<protect></protect>
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
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 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
- ↑ 5.0 5.1 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).
Categories
- Genes with homologs in Apis mellifera
- Genes with homologs in Arabidopsis thaliana
- Genes with homologs in Bos taurus
- Genes with homologs in Caenorhabditis briggsae
- Genes with homologs in Caenorhabditis elegans
- Genes with homologs in Canis familiaris
- Genes with homologs in Ciona intestinalis
- Genes with homologs in Danio rerio
- Genes with homologs in Dictyostelium discoideum
- Genes with homologs in Drosophila melanogaster
- Genes with homologs in Gallus gallus
- Genes with homologs in Homo sapiens
- Genes with homologs in Macaca mulatta
- Genes with homologs in Monodelphis domestica
- Genes with homologs in Mus musculus
- Genes with homologs in Oryza gramene
- Genes with homologs in Pan troglodytes
- Genes with homologs in Rattus norvegicus
- Genes with homologs in Takifugu rubripes
- Genes with homologs in Tetraodon nigroviridis
- Genes with homologs in Xenopus tropicalis
- Genes with homologs in Shigella flexneri
- Genes with homologs in E. coli O157
