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Expression|

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Standard Name	ygiD
Gene Synonym(s)	ECK3030, b3039, JW3007, ygiE^[1]^[2]
Product Desc.	predicted dioxygenase^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted dioxygenase^[1], B3039^[2]^[1], YgiD^[2]^[1] , ECK3030, JW3007, b3039
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ygiD^[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	ygiD
Mnemonic	Systematic nomenclature
Synonyms	ECK3030, b3039, JW3007, ygiE^[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	68.53 minutes	MG1655: 3180456..3179641 <gbrowseImage> name=NC_000913:3179641..3180456 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3116606..3115791 <gbrowseImage> name=NC_012967:3115791..3116606 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3066789..3067604 <gbrowseImage> name=NC_012759:3066789..3067604 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3181090..3180275 <gbrowseImage> name=NC_007779:3180275..3181090 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3278174..3277386 <gbrowseImage> name=NC_010473:3277386..3278174 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: 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:

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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:EG11166	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11166	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001149	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946447	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1154	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009973	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	ZupT
Synonyms	predicted dioxygenase^[1], B3039^[2]^[1], YgiD^[2]^[1] , ECK3030, JW3007, b3039
Product description	predicted dioxygenase^[2]^[3] Function unknown^[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:0006725	cellular aromatic compound metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004183	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008198	ferrous iron binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004183	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014436	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004183	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:0016701	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014436	F	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
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014436	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
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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	dnaC	PMID:16606699	Experiment(s):EBI-1144634
Protein	hyfF	PMID:16606699	Experiment(s):EBI-1144634
Protein	groL	PMID:16606699	Experiment(s):EBI-1144634
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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 MTPLVKDIIM SSTRMPALFL GHGSPMNVLE DNLYTRSWQK LGMTLPRPQA IVVVSAHWFT RGTGVTAMET PPTIHDFGGF PQALYDTHYP APGSPALAQR LVELLAPIPV TLDKEAWGFD HGSWGVLIKM YPDADIPMVQ LSIDSSKPAA WHFEMGRKLA ALRDEGIMLV ASGNVVHNLR TVKWHGDSSP YPWATSFNEY VKANLTWQGP VEQHPLVNYL DHEGGTLSNP TPEHYLPLLY VLGAWDGQEP ITIPVEGIEM GSLSMLSVQI G
Length	271
Mol. Wt	29.903 kDa
pI	5.8 (calculated)
Extinction coefficient	62,910 (calc based on 9 Y, 9 W, and 0 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	16..271	PF02900 Catalytic LigB subunit of aromatic ring-opening dioxygenase		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=ygiD 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:226524747	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946447	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009973	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P24197	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11166	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11166	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946447	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001149	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1154	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	31	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	22	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	26^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)
ygiD
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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_000913:3180436..3180476 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:b3039 (EcoliWiki Page)	NCBI GEO profiles for ygiD
microarray	GenExpDB:b3039 (EcoliWiki Page)	Summary of data for ygiD 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 (3180369..3180600) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:D11^[5]
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Notes

Accessions Related to ygiD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11166	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1154	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3039
EcoGene	EcoGene:EG11166	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001149	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009973	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	ENSANGP00000027107 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G15093 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0206323 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC17096c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000041011 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGID	From SHIGELLACYC
E. coli O157	YGID	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)	PF02900 Catalytic LigB subunit of aromatic ring-opening dioxygenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:53213
EcoCyc	EcoCyc:EG11166	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11166	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001149	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1154	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009973	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 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 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

ygiD: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 ygiD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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