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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	glcD
Gene Synonym(s)	ECK2974, b2979, JW2946, gox, yghM^[1], yghM
Product Desc.	glycolate oxidase subunit, FAD-linked^[2]; glycolate oxidase, predicted FAD-linked subunit^[3]; Component of glycolate oxidase^[3] Glycolate oxidase subunit^[4]
Product Synonyms(s)	glycolate oxidase subunit, FAD-linked^[1], B2979^[2]^[1], YghM^[2]^[1], Gox^[2]^[1], GlcD^[2]^[1] , ECK2974, gox, JW2946, yghM, b2979
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): glcDEFGBA^[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	glcD
Mnemonic	Glycolate
Synonyms	ECK2974, b2979, JW2946, gox, yghM^[1], yghM
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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	67.34 minutes	MG1655: 3126043..3124544 <gbrowseImage> name=NC_000913:3124544..3126043 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3054913..3053414 <gbrowseImage> name=NC_012967:3053414..3054913 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3011692..3013191 <gbrowseImage> name=NC_012759:3011692..3013191 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3126677..3125178 <gbrowseImage> name=NC_007779:3125178..3126677 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3223788..3222289 <gbrowseImage> name=NC_010473:3222289..3223788 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)	Reference	Availability	Comments
ΔglcD (Keio:JW2946)	deletion	deletion	PMID:16738554	Shigen CGSC10273^[5]
glcD::Tn5KAN-I-SceI (FB20998)	Insertion at nt 1106 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20998	contains pKD46
glcD::Tn5KAN-I-SceI (FB20999)	Insertion at nt 1106 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20999	does not contain pKD46
ΔglcD753::kan			PMID:16738554	CGSC:101134
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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
JW2946	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCATCTTGTACGAAGAGCG Primer 2:CCGAAACGCTCCAGTTCAGGGAA
1G7	Kohara Phage	Genobase	PMID:3038334
12F3	Kohara Phage	Genobase	PMID:3038334
2F9	Kohara Phage	Genobase	PMID:3038334
nupG511::Tn10	Linked marker	CAG18472 = CGSC7433^[5]	est. P1 cotransduction: 47% ^[6]
metC162::Tn10	Linked marker	CAG18475 = CGSC7435^[5]	est. P1 cotransduction: 38% ^[6]
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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:G7545	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12997	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004105	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947353	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2820	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009773	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	GlcD
Synonyms	glycolate oxidase subunit, FAD-linked^[1], B2979^[2]^[1], YghM^[2]^[1], Gox^[2]^[1], GlcD^[2]^[1] , ECK2974, gox, JW2946, yghM, b2979
Product description	glycolate oxidase subunit, FAD-linked^[2]; glycolate oxidase, predicted FAD-linked subunit^[3]; Component of glycolate oxidase^[3] Glycolate oxidase subunit^[4]
EC number (for enzymes)
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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:0008891	glycolate oxidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004490	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009339	glycolate oxidase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004490	C	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004113	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006094	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016164	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016166	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016167	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
	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	Notes	References	Evidence
Protein	Subunits of glycolate oxidase	could be indirect
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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 MSILYEERLD GALPDVDRTS VLMALREHVP GLEILHTDEE IIPYECDGLS AYRTRPLLVV LPKQMEQVTA ILAVCHRLRV PVVTRGAGTG LSGGALPLEK GVLLVMARFK EILDINPVGR RARVQPGVRN LAISQAVAPH NLYYAPDPSS QIACSIGGNV AENAGGVHCL KYGLTVHNLL KIEVQTLDGE ALTLGSDALD SPGFDLLALF TGSEGMLGVT TEVTVKLLPK PPVARVLLAS FDSVEKAGLA VGDIIANGII PGGLEMMDNL SIRAAEDFIH AGYPVDAEAI LLCELDGVES DVQEDCERVN DILLKAGATD VRLAQDEAER VRFWAGRKNA FPAVGRISPD YYCMDGTIPR RALPGVLEGI ARLSQQYDLR VANVFHAGDG NMHPLILFDA NEPGEFARAE ELGGKILELC VEVGGSISGE HGIGREKINQ MCAQFNSDEI TTFHAVKAAF DPDGLLNPGK NIPTLHRCAE FGAMHVHHGH LPFPELERF
Length	499
Mol. Wt	53.811 kDa
pI	5.0 (calculated)
Extinction coefficient	20,400 - 21,650 (calc based on 10 Y, 1 W, and 10 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	230..471	PF02913 FAD linked oxidases, C-terminal domain	PMID:19920124
Domain	56..195	PF01565 FAD 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=glcD 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:16130879	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947353	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009773	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AEP9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7545	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12997	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947353	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004105	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2820	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	1^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	11	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	0^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)
glcDEFGBA
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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_000913:3126023..3126063 source=MG1655 flip=1 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:b2979 (EcoliWiki Page)	NCBI GEO profiles for glcD
microarray	GenExpDB:b2979 (EcoliWiki Page)	Summary of data for glcD 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 glcD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7545	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2820	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2979
EcoGene	EcoGene:EG12997	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004105	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009773	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	ENSANGP00000012910 (score: 1.000; bootstrap: 87%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000010393 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G06580 (score: 1.000; bootstrap: 82%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000008924 (score: 1.000; bootstrap: 83%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00031263 (score: 1.000; bootstrap: 87%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00009334 (score: 1.000; bootstrap: 85%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000029772 (score: 1.000; bootstrap: 64%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000008252 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030131-6140 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-1443 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0202037 (score: 1.000; bootstrap: 83%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0023507 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA17719-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000010244 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000300051 (score: 1.000; bootstrap: 70%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000029029 (score: 1.000; bootstrap: 87%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000018339 (score: 1.000; bootstrap: 80%)	From Inparanoid:20070104
Mus musculus	MGI:106428 (score: 1.000; bootstrap: 81%)	From Inparanoid:20070104
Oryza gramene	Q7XI14 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000014264 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000046399 (score: 1.000; bootstrap: 53%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDL178W (score: 1.000; bootstrap: 100%) YEL071W (score: 0.533)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC7133 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000129731 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00006177001 (score: 1.000; bootstrap: 52%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000015277 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
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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)	PF01565 FAD binding domain
Pfam (EcoliWiki Page)	PF02913 FAD linked oxidases, C-terminal domain
Panther (EcoliWiki Page)	PTHR11748:SF35
Superfamily (EcoliWiki Page)	SUPERFAMILY:55103
Superfamily (EcoliWiki Page)	SUPERFAMILY:56176
PFAM (EcoliWiki Page)	PFAM:PF01565
EcoCyc	EcoCyc:G7545	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12997	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004105	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2820	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009773	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 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 ^3.2 ^3.3 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).

glcD: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 glcD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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