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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	glxR
Gene Synonym(s)	ECK0502, b0509, JW0497, ybbQ, glxB1^[1], glxB1
Product Desc.	tartronate semialdehyde reductase 2^[2]^[3] Tartronate semialdehyde reductase, glyoxylate-inducible, NADH-dependent^[4]
Product Synonyms(s)	tartronate semialdehyde reductase, NADH-dependent^[1], B0509^[2]^[1], YbbQ^[2]^[1], GlxR^[2]^[1], TSA reductase 2^[2]^[1] , ECK0502, glxB1, JW0497, ybbQ, b0509
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gcl-hyi-glxR-ybbVW-allB-ybbY-glxK^[2]
Regulation/Activity
Quick Links
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Notes

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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	glxR
Mnemonic	Glyoxylate
Synonyms	ECK0502, b0509, JW0497, ybbQ, glxB1^[1], glxB1
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Notes

Location(s) and DNA Sequence

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<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	11.55 minutes	MG1655: 535810..536688 <gbrowseImage> name=NC_000913:535810..536688 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 508752..509630 <gbrowseImage> name=NC_012967:508752..509630 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 438569..439447 <gbrowseImage> name=NC_012759:438569..439447 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 535810..536688 <gbrowseImage> name=NC_007779:535810..536688 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 475141..476019 <gbrowseImage> name=NC_010473:475141..476019 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
glxR(del) (Keio:JW0497)	deletion	deletion			PMID:16738554	Shigen CGSC8642^[5]
ybbQ(del)::kan	deletion		Biolog:respiration	unable to respire N-Acetyl-D-glucosamine	PMID:16095938
ybbQ(del)::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
glxR721(del)::kan					PMID:16738554	CGSC:101218
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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
JW0497	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACTGGGATTTATTGGCTT Primer 2:CCGGCCAGTTTATGGTTAGCCAT
9E5	Kohara Phage	Genobase	PMID:3038334
gsk-3055::Tn10	Linked marker	CAG12154 = CGSC7341^[5]	est. P1 cotransduction: 25% ^[6] Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: 56% ^[6] Synonyms:purE79::Tn10
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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:G6278	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13265	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002886	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945146	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3052	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001759	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	GlxR
Synonyms	tartronate semialdehyde reductase, NADH-dependent^[1], B0509^[2]^[1], YbbQ^[2]^[1], GlxR^[2]^[1], TSA reductase 2^[2]^[1] , ECK0502, glxB1, JW0497, ybbQ, b0509
Product description	tartronate semialdehyde reductase 2^[2]^[3] Tartronate semialdehyde reductase, glyoxylate-inducible, NADH-dependent^[4]
EC number (for enzymes)	1.1.1.60^[1]
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Notes

Function

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<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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0004616	phosphogluconate dehydrogenase (decarboxylating) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006115	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004616	phosphogluconate dehydrogenase (decarboxylating) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006183	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006098	pentose-phosphate shunt	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006115	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006098	pentose-phosphate shunt	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006183	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006573	valine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002204	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008442	3-hydroxyisobutyrate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002204	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008679	2-hydroxy-3-oxopropionate reductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006398	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008679	2-hydroxy-3-oxopropionate reductase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.60	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050662	coenzyme binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013328	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002204	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006115	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006183	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006398	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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	References	Evidence
Protein	sdhA	PMID:16606699	Experiment(s):EBI-1136971
Protein	yhhW	PMID:16606699	Experiment(s):EBI-1136971
Protein	nadE	PMID:16606699	Experiment(s):EBI-1136971
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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
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Notes

Structure and Physical Properties

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<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 MKLGFIGLGI MGTPMAINLA RAGHQLHVTT IGPVADELLS LGAVSVETAR QVTEASDIIF IMVPDTPQVE EVLFGENGCT KASLKGKTIV DMSSISPIET KRFARQVNEL GGDYLDAPVS GGEIGAREGT LSIMVGGDEA VFERVKPLFE LLGKNITLVG GNGDGQTCKV ANQIIVALNI EAVSEALLFA SKAGADPVRV RQALMGGFAS SRILEVHGER MIKRTFNPGF KIALHQKDLN LALQSAKALA LNLPNTATCQ ELFNTCAANG GSQLDHSALV QALELMANHK LA
Length	292
Mol. Wt	30.8 kDa
pI	6.0 (calculated)
Extinction coefficient	1,490 - 1,990 (calc based on 1 Y, 0 W, and 4 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	Notes	References
Domain	1..162	PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase		PMID:19920124
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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=glxR taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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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

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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:16128493	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945146	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001759	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77161	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6278	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13265	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945146	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002886	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3052	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	Notes	Reference(s)
Protein	E. coli K-12 MG1655	16	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	10	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	10^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	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.

Transcription unit(s)
gcl-hyi-glxR-ybbVW-allB-ybbY-glxK
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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

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<protect><gbrowseImage> name=NC_000913:535790..535830 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

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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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<protect> 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:b0509 (EcoliWiki Page)	NCBI GEO profiles for glxR
microarray	GenExpDB:b0509 (EcoliWiki Page)	Summary of data for glxR 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 glxR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6278	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3052	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0509
EcoGene	EcoGene:EG13265	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002886	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001759	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
Apis mellifera	ENSAPMP00000005689 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G29120 (score: 1.000; bootstrap: 81%) AT1G71180 (score: 0.220) AT1G71170 (score: 0.207)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000001374 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00028013 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007122 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029344 (score: 1.000; bootstrap: 77%) ENSCAFP00000004423 (score: 0.947)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000012462 (score: 1.000; bootstrap: 82%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040801-264 (score: 1.000; bootstrap: 88%) ZDB-CDNA-040801-283 (score: 1.000; bootstrap: 87%) ZDB-CDNA-040425-2516 (score: 0.777) ZDB-GENE-040426-1582 (score: 0.777)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0216217 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0034390 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000018063 (score: 1.000; bootstrap: 87%)	From Inparanoid:20070104
Homo sapiens	ENSP00000265395 (score: 1.000; bootstrap: 80%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000030452 (score: 1.000; bootstrap: 90%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000000404 (score: 1.000; bootstrap: 71%)	From Inparanoid:20070104
Mus musculus	MGI:1889802 (score: 1.000; bootstrap: 85%)	From Inparanoid:20070104
Oryza gramene	Q656T5 (score: 1.000; bootstrap: 95%) Q84VC8 (score: 0.316)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000013200 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000011069 (score: 1.000; bootstrap: 81%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000159095 (score: 1.000; bootstrap: 88%) NEWSINFRUP00000178935 (score: 0.391)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00034120001 (score: 1.000; bootstrap: 94%) GSTENP00017474001 (score: 0.580)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000032406 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
E. coli O157	YBBQ	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)	PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:48179
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
EcoCyc	EcoCyc:G6278	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13265	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002886	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3052	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001759	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 ^1.10 ^1.11 ^1.12 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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).

glxR:On One Page

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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 glxR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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