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Standard Name	ghrA
Gene Synonym(s)	ycdW, ECK1019, b1033, JW5146^[1]^[2], JW5146
Product Desc.	G6539^[2]^[3] Glyoxylate/hydroxypyruvate reductase; activity higher on glyoxylate than hydroxypyruvate^[4]
Product Synonyms(s)	2-ketoacid reductase^[1], B1033^[2]^[1], GhrA^[2]^[1], YcdW^[2]^[1] , ECK1019, JW5146, ycdW, b1033
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycdW^[2]
Regulation/Activity
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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	ghrA
Mnemonic	Glyoxylate/Hydroxypyruvate Reductase
Synonyms	ycdW, ECK1019, b1033, JW5146^[1]^[2], JW5146
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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	23.65 minutes	MG1655: 1097109..1098047 <gbrowseImage> name=NC_000913:1097109..1098047 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1112455..1113393 <gbrowseImage> name=NC_012967:1112455..1113393 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1001034..1001972 <gbrowseImage> name=NC_012759:1001034..1001972 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1098127..1099065 <gbrowseImage> name=NC_007779:1098127..1099065 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
Coding Start (SO:0000323)	MG1655	1097109	Edman degradation	PMID:11237876
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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
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
9G7	Kohara Phage	Genobase	PMID:3038334
1C7	Kohara Phage	Genobase	PMID:3038334
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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:G6539	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13869	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003135	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946431	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3628	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003503	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	YcdW
Synonyms	2-ketoacid reductase^[1], B1033^[2]^[1], GhrA^[2]^[1], YcdW^[2]^[1] , ECK1019, JW5146, ycdW, b1033
Product description	G6539^[2]^[3] Glyoxylate/hydroxypyruvate reductase; activity higher on glyoxylate than hydroxypyruvate^[4]
EC number (for enzymes)	1.1.1.79^[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:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01666	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016618	hydroxypyruvate reductase activity	EcoCyc_REF:BiochemJ354-707	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016618	hydroxypyruvate reductase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01666	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016618	hydroxypyruvate reductase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.81	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030267	glyoxylate reductase (NADP) activity	EcoCyc_REF:BiochemJ354-707	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0030267	glyoxylate reductase (NADP) activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01666	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030267	glyoxylate reductase (NADP) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.79	F	Seeded from EcoCyc (v14.0)	complete
	GO:0033554	cellular response to stress	PMID:19767843	IEP: Inferred from Expression Pattern		P	Seeded from EcoCyc (v14.0)	complete
	GO:0048037	cofactor binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006140	F	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
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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
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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 MRINFAQRFS GVSMDIIFYH PTFDTQWWIE ALRKAIPQAR VRAWKSGDND SADYALVWHP PVEMLAGRDL KAVFALGAGV DSILSKLQAH PEMLNPSVPL FRLEDTGMGE QMQEYAVSQV LHWFRRFDDY RIQQNSSHWQ PLPEYHREDF TIGILGAGVL GSKVAQSLQT WRFPLRCWSR TRKSWPGVQS FAGREELSAF LSQCRVLINL LPNTPETVGI INQQLLEKLP DGAYLLNLAR GVHVVEDDLL AALDSGKVKG AMLDVFNREP LPPESPLWQH PRVTITPHVA AITRPAEAVE YISRTIAQLE KGERVCGQVD RARGY
Length	325
Mol. Wt	36.837 kDa
pI	7.3 (calculated)
Extinction coefficient	66,920 - 67,295 (calc based on 8 Y, 10 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.

Type	Residues	Description	Notes	References
Domain	104..277	PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain		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=ghrA 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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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:90111205	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946431	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003503	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75913	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6539	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13869	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946431	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003135	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3628	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	Ecoli K-12	13.396+/-0.27	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.051705757	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	561	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	825	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	600	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)
ycdW
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Figure courtesy of RegulonDB

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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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<protect><gbrowseImage> name=NC_000913:1097089..1097129 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> 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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<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:b1033 (EcoliWiki Page)	NCBI GEO profiles for ghrA
microarray	GenExpDB:b1033 (EcoliWiki Page)	Summary of data for ghrA 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 (925121..1097149) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:A7^[5]
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Notes

Accessions Related to ghrA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6539	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3628	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1033
EcoGene	EcoGene:EG13869	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003135	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003503	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	ENSAPMP00000000459 (score: 1.000; bootstrap: 85%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000012659 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	YCDW	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)	PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Panther (EcoliWiki Page)	PTHR10996:SF3
EcoCyc	EcoCyc:G6539	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13869	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003135	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3628	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003503	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 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.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ghrA: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 ghrA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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