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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	dgoD
Gene Synonym(s)	ECK3684, b4478, JW5629, yidU, b3692 (obsolete)^[1]^[2]
Product Desc.	GALACTONATE-
Product Synonyms(s)	galactonate dehydratase^[1], B4478^[2]^[1], YidU^[2]^[1], DgoD^[2]^[1] , ECK3684, JW5629, yidU, b4478
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dgoT^[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	dgoD
Mnemonic	D-Galactonate
Synonyms	ECK3684, b4478, JW5629, yidU, b3692 (obsolete)^[1]^[2]
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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	83.41 minutes	MG1655: 3871021..3869873 <gbrowseImage> name=NC_000913:3869873..3871021 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3833359..3832211 <gbrowseImage> name=NC_012967:3832211..3833359 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3758206..3759354 <gbrowseImage> name=NC_012759:3758206..3759354 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3767417..3768565 <gbrowseImage> name=NC_007779:3767417..3768565 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3968605..3967457 <gbrowseImage> name=NC_010473:3967457..3968605 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
Coding Start (SO:0000323)	MG1655	3869873	Edman degradation	PMID:7855594
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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
dgoDH185N,Q		H185N,Q	Loss of activity			seeded from UniProt:Q6BF17
dgoDH285N		H285N	Loss of activity			seeded from UniProt:Q6BF17
dgoDE310Q		E310Q	Loss of activity			seeded from UniProt:Q6BF17
ΔdgoD (Keio:JW5629)	deletion	deletion		PMID:16738554	Shigen CGSC8318^[3]
dgoD2					CGSC:6765
ΔdgoD728::kan				PMID:16738554	CGSC:99772
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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
JW5629	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAATCACCAAAATTACCAC Primer 2:CCCCACTCTGCTACGCTGTTATC
3C10	Kohara Phage	Genobase	PMID:3038334
3D1	Kohara Phage	Genobase	PMID:3038334
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[3]	est. P1 cotransduction: 16% ^[4]
zid-501::Tn10	Linked marker	CAG18499 = CGSC7458^[3]	est. P1 cotransduction: 87% ^[4]
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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:GB4478	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG20050	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004465	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:2847765	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4309	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0174106	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	DgoD
Synonyms	galactonate dehydratase^[1], B4478^[2]^[1], YidU^[2]^[1], DgoD^[2]^[1] , ECK3684, JW5629, yidU, b4478
Product description	GALACTONATE-
EC number (for enzymes)	4.2.1.6^[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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008869	galactonate dehydratase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01289	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008869	galactonate dehydratase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.6	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009063	cellular amino acid catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018110	P	Seeded from EcoCyc (v14.0)	complete
	GO:0034194	D-galactonate catabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01289	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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
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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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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 MKITKITTYR LPPRWMFLKI ETDEGVVGWG EPVIEGRART VEAAVHELGD YLIGQDPSRI NDLWQVMYRA GFYRGGPILM SAIAGIDQAL WDIKGKVLNA PVWQLMGGLV RDKIKAYSWV GGDRPADVID GIKTLREIGF DTFKLNGCEE LGLIDNSRAV DAAVNTVAQI REAFGNQIEF GLDFHGRVSA PMAKVLIKEL EPYRPLFIEE PVLAEQAEYY PKLAAQTHIP LAAGERMFSR FDFKRVLEAG GISILQPDLS HAGGITECYK IAGMAEAYDV TLAPHCPLGP IALAACLHID FVSYNAVLQE QSMGIHYNKG AELLDFVKNK EDFSMVGGFF KPLTKPGLGV EIDEAKVIEF SKNAPDWRNP LWRHEDNSVA EW
Length	382
Mol. Wt	42.523 kDa
pI	5.2 (calculated)
Extinction coefficient	67,380 - 67,880 (calc based on 12 Y, 9 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	References
Domain	125..230	PF01188 Mandelate racemase / muconate lactonizing enzyme, C-terminal domain	PMID:19920124
Domain	4..107	PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal 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=dgoD 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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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:49176390	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:2847765	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0174106	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q6BF17	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:GB4478	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG20050	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:2847765	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004465	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4309	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	18	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	6^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)
dgoT
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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_000913:3871001..3871041 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:b3692 (EcoliWiki Page)	NCBI GEO profiles for dgoD
microarray	GenExpDB:b3692 (EcoliWiki Page)	Summary of data for dgoD 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 dgoD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:GB4478	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4309	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3692
EcoGene	EcoGene:EG20050	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004465	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0174106	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF01188 Mandelate racemase / muconate lactonizing enzyme, C-terminal domain
Pfam (EcoliWiki Page)	PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51604
Panther (EcoliWiki Page)	PTHR13794:SF4
Superfamily (EcoliWiki Page)	SUPERFAMILY:54826
EcoCyc	EcoCyc:GB4478	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG20050	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004465	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4309	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0174106	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)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 CGSC: The Coli Genetics Stock Center
↑ ^4.0 ^4.1 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).

dgoD:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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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 dgoD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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