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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	ugd
Gene Synonym(s)	ECK2023, b2028, JW2010, UDG8, yefA, udg, pmrE^[1]^[2], pagA, pmrE
Product Desc.	UGD^[2]^[3] Probable UDP-glucose 6-dehydrogenase^[4]
Product Synonyms(s)	UDP-glucose 6-dehydrogenase^[1], B2028^[2]^[1], Udg^[2]^[1], YefA^[2]^[1], Ugd^[2]^[1], PmrE^[2]^[1] , ECK2023, JW2010, pagA, pmrE, udg, yefA, b2028
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ugd^[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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Salmonella Ugd ortholog is pmrA(basR)-regulated, phoP-regulated, and required for polymyxin resistance and growth in low Mg on solid media.^[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	ugd
Mnemonic	UDP-glucose 6-dehydrogenase
Synonyms	ECK2023, b2028, JW2010, UDG8, yefA, udg, pmrE^[1]^[2], pagA, pmrE
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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	45.19 minutes	MG1655: 2097637..2096471 <gbrowseImage> name=NC_000913:2096471..2097637 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2029615..2028449 <gbrowseImage> name=NC_012967:2028449..2029615 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1988954..1990120 <gbrowseImage> name=NC_012759:1988954..1990120 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2101750..2100584 <gbrowseImage> name=NC_007779:2100584..2101750 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2188645..2187479 <gbrowseImage> name=NC_010473:2187479..2188645 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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</protect>

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
Δugd (Keio:JW2010)	deletion	deletion	PMID:16738554	Shigen CGSC9655^[5]
Δugd-726::kan			PMID:16738554	CGSC:103278
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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
JW2010	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAATCACCATTTCCGGTAC Primer 2:CCGTCGCTGCCAAAGAGATCGCG
6D9	Kohara Phage	Genobase	PMID:3038334
21H10	Kohara Phage	Genobase	PMID:3038334
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 63% ^[6] Synonyms:zee-3129::Tn10
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: % ^[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:G7091	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13407	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003677	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946571	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3183	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006734	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	Ugd
Synonyms	UDP-glucose 6-dehydrogenase^[1], B2028^[2]^[1], Udg^[2]^[1], YefA^[2]^[1], Ugd^[2]^[1], PmrE^[2]^[1] , ECK2023, JW2010, pagA, pmrE, udg, yefA, b2028
Product description	UGD^[2]^[3] Probable UDP-glucose 6-dehydrogenase^[4]
EC number (for enzymes)	1.1.1.22^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003979	UDP-glucose 6-dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.22	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:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008927	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001732	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014026	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014027	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014028	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001732	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014026	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014027	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014028	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001732	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014026	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014027	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014028	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:0003979	UDP-glucose 6-dehydrogenase activity	PMID:12775214	IMP: Inferred from Mutant Phenotype		F		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	groL	PMID:16606699	Experiment(s):EBI-1141678
Protein	ydcS	PMID:16606699	Experiment(s):EBI-1141678
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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 MKITISGTGY VGLSNGLLIA QNHEVVALDI LPSRVAMLND RISPIVDKEI QQFLQSDKIH FNATLDKNEA YRDADYVIIA TPTDYDPKTN YFNTSSVESV IKDVVEINPY AVMVIKSTVP VGFTAAMHKK YRTENIIFSP EFLREGKALY DNLHPSRIVI GERSERAERF AALLQEGAIK QNIPMLFTDS TEAEAIKLFA NTYLAMRVAY FNELDSYAES LGLNSRQIIE GVCLDPRIGN HYNNPSFGYG GYCLPKDTKQ LLANYQSVPN NLISAIVDAN RTRKDFIADA ILSRKPQVVG IYRLIMKSGS DNFRASSIQG IMKRIKAKGV EVIIYEPVMK EDSFFNSRLE RDLATFKQQA DVIISNRMAE ELKDVADKVY TRDLFGSD
Length	388
Mol. Wt	43.658 kDa
pI	6.4 (calculated)
Extinction coefficient	26,820 - 27,070 (calc based on 18 Y, 0 W, and 2 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	190..283	PF00984 UDP-glucose/GDP-mannose dehydrogenase family, central domain	PMID:19920124
Domain	300..384	PF03720 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain	PMID:19920124
Domain	1..175	PF03721 UDP-glucose/GDP-mannose dehydrogenase family, 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=ugd taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16129969	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946571	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006734	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76373	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7091	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13407	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946571	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003677	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3183	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	26	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	49	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)
ugd
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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_000913:2097617..2097657 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

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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:b2028 (EcoliWiki Page)	NCBI GEO profiles for ugd
microarray	GenExpDB:b2028 (EcoliWiki Page)	Summary of data for ugd 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 (2097560..2097958) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:C1^[7]
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Notes

Accessions Related to ugd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7091	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3183	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2028
EcoGene	EcoGene:EG13407	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003677	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006734	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	ENSANGP00000014609 (score: 1.000; bootstrap: 100%) ENSANGP00000002547 (score: 0.067)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000019302 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000023536 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-011022-1 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0010851 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000023101 (score: 1.000; bootstrap: 100%) ENSGALP00000015364 (score: 0.202)	From Inparanoid:20070104
Homo sapiens	ENSP00000319501 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000002518 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000025708 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1306785 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q40728 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000027531 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000003691 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000142425 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00010193001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000033379 (score: 1.000; bootstrap: 100%) ENSXETP00000028075 (score: 0.122) ENSXETP00000036025 (score: 0.098)	From Inparanoid:20070104
E. coli O157	UGD	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:48179
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Superfamily (EcoliWiki Page)	SUPERFAMILY:52413
Panther (EcoliWiki Page)	PTHR11374:SF18
Pfam (EcoliWiki Page)	PF00984 UDP-glucose/GDP-mannose dehydrogenase family, central domain
Pfam (EcoliWiki Page)	PF03720 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
Pfam (EcoliWiki Page)	PF03721 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
EcoCyc	EcoCyc:G7091	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13407	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003677	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3183	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006734	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 ^1.14 ^1.15 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 ^2.13 ^2.14 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 ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ugd: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 ugd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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