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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	gmd
Gene Synonym(s)	ECK2047, b2053, JW2038, yefA, yefN^[1], yefN
Product Desc.	GDP-mannose 4,6-dehydratase^[2]^[3]; Component of GDP-mannose 4,6-dehydratase^[2]^[3] Fucose biosynthesis; GDP-D-mannose 4,6-dehydratase^[4]
Product Synonyms(s)	GDP-D-mannose dehydratase, NAD(P)-binding^[1], B2053^[2]^[1], YefN^[2]^[1], YefA^[2]^[1], Gmd^[2]^[1] , ECK2047, JW2038, yefA, yefN, b2053
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): wzxC^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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HT_Cmplx41_Mem: Gnd+PepD.^[4]

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	gmd
Mnemonic	GDP-D-mannose dehydratase
Synonyms	ECK2047, b2053, JW2038, yefA, yefN^[1], yefN
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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	45.81 minutes	MG1655: 2126338..2125217 <gbrowseImage> name=NC_000913:2125217..2126338 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2061519..2060398 <gbrowseImage> name=NC_012967:2060398..2061519 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2017700..2018821 <gbrowseImage> name=NC_012759:2017700..2018821 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2130451..2129330 <gbrowseImage> name=NC_007779:2129330..2130451 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2217346..2216225 <gbrowseImage> name=NC_010473:2216225..2217346 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: Description	Reference	Availability	Comments
Δgmd (Keio:JW2038)	deletion	deletion		PMID:16738554	Shigen CGSC9674^[5]
gmd::Tn5KAN-I-SceI (FB20601)	Insertion at nt 211 in Plus orientation			PMID:15262929	E. coli Genome Project:FB20601	contains pKD46
gmdT133V		T133V	Strongly reduces activity			seeded from UniProt:P0AC88
gmdE135Q		E135Q	Strongly reduces activity			seeded from UniProt:P0AC88
gmdY157F		Y157F	Strongly reduces activity			seeded from UniProt:P0AC88
gmdK161A		K161A	Strongly reduces activity			seeded from UniProt:P0AC88
Δgmd-751::kan				PMID:16738554	CGSC:101224
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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
JW2038	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCAAAAGTCGCTCTCATCAC Primer 2:CCTGACTCCAGCGCGATCGCCAC
10A9	Kohara Phage	Genobase	PMID:3038334
7A3	Kohara Phage	Genobase	PMID:3038334
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 16% ^[6] Synonyms:zee-3129::Tn10
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: 9% ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::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:EG11787	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11787	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001721	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946562	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1735	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006803	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	Gmd
Synonyms	GDP-D-mannose dehydratase, NAD(P)-binding^[1], B2053^[2]^[1], YefN^[2]^[1], YefA^[2]^[1], Gmd^[2]^[1] , ECK2047, JW2038, yefA, yefN, b2053
Product description	GDP-mannose 4,6-dehydratase^[2]^[3]; Component of GDP-mannose 4,6-dehydratase^[2]^[3] Fucose biosynthesis; GDP-D-mannose 4,6-dehydratase^[4]
EC number (for enzymes)	4.2.1.47^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001509	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	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:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006368	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:0008446	GDP-mannose 4,6-dehydratase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006368	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008446	GDP-mannose 4,6-dehydratase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.47	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009103	lipopolysaccharide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0448	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019673	GDP-mannose metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006368	P	Seeded from EcoCyc (v14.0)	complete
	GO:0044237	cellular metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001509	P	Seeded from EcoCyc (v14.0)	complete
	GO:0050662	coenzyme binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001509	F	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
Protein	Subunits of GDP-mannose 4,6-dehydratase	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1141782
Protein	glnD		PMID:16606699	Experiment(s):EBI-1141782
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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 MSKVALITGV TGQDGSYLAE FLLEKGYEVH GIKRRASSFN TERVDHIYQD PHTCNPKFHL HYGDLSDTSN LTRILREVQP DEVYNLGAMS HVAVSFESPE YTADVDAMGT LRLLEAIRFL GLEKKTRFYQ ASTSELYGLV QEIPQKETTP FYPRSPYAVA KLYAYWITVN YRESYGMYAC NGILFNHESP RRGETFVTRK ITRAIANIAQ GLESCLYLGN MDSLRDWGHA KDYVKMQWMM LQQEQPEDFV IATGVQYSVR QFVEMAAAQL GIKLRFEGTG VEEKGIVVSV TGHDAPGVKP GDVIIAVDPR YFRPAEVETL LGDPTKAHEK LGWKPEITLR EMVSEMVAND LEAAKKHSLL KSHGYDVAIA LES
Length	373
Mol. Wt	42.046 kDa
pI	5.7 (calculated)
Extinction coefficient	51,800 - 52,175 (calc based on 20 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.

Type	Residues	Description	Notes	References
Domain	5..252	PF01370 NAD dependent epimerase/dehydratase family		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=gmd 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:16129993	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946562	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006803	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AC88	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11787	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11787	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946562	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001721	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1735	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	13	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	17	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	9^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)
wzxC
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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_000913:2126318..2126358 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

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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:b2053 (EcoliWiki Page)	NCBI GEO profiles for gmd
microarray	GenExpDB:b2053 (EcoliWiki Page)	Summary of data for gmd 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 gmd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11787	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1735	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2053
EcoGene	EcoGene:EG11787	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001721	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006803	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	ENSANGP00000020185 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000035416 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G66280 (score: 1.000; bootstrap: 100%) AT3G51160 (score: 0.823)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000015992 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00040436 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00010166 (score: 1.000; bootstrap: 100%) WBGene00008276 (score: 0.744)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000013548 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000010271 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1258 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231676 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0031661 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21394-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000020915 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000324262 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000007628 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000010263 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1891112 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5VPH2 (score: 1.000; bootstrap: 100%) Q9M7I6 (score: 0.690)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000030171 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000023691 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000131355 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000159225 (score: 0.233)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00015672001 (score: 1.000; bootstrap: 100%) GSTENP00016215001 (score: 0.238)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000001321 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	GMD	From SHIGELLACYC
E. coli O157	GMD	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)	PF01370 NAD dependent epimerase/dehydratase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Panther (EcoliWiki Page)	PTHR10366:SF32
EcoCyc	EcoCyc:EG11787	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11787	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001721	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1735	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006803	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 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 ^2.11 ^2.12 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 ^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).

gmd:On One Page

Quickview

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 gmd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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