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On One Page

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Product(s) |

Expression|

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Standard Name	ydgJ
Gene Synonym(s)	ECK1619, b1624, JW5265^[1], JW5265
Product Desc.	G6868^[2]^[3] Putative oxidoreductase; yhhX paralog^[4]
Product Synonyms(s)	predicted oxidoreductase^[1], YdgJ^[2]^[1], B1624^[2]^[1] , ECK1619, JW5265, b1624
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydgJ^[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	ydgJ
Mnemonic	Systematic nomenclature
Synonyms	ECK1619, b1624, JW5265^[1], JW5265
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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	36.67 minutes	MG1655: 1702332..1701292 <gbrowseImage> name=NC_000913:1701292..1702332 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1681502..1680462 <gbrowseImage> name=NC_012967:1680462..1681502 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1593351..1594391 <gbrowseImage> name=NC_012759:1593351..1594391 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1706022..1704982 <gbrowseImage> name=NC_007779:1704982..1706022 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1793293..1792253 <gbrowseImage> name=NC_010473:1792253..1793293 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
ΔydgJ (Keio:JW5265)	deletion	deletion	PMID:16738554	Shigen CGSC11280^[5]
ΔydgJ772::kan			PMID:16738554	CGSC:104274
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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
JW5265	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGACAACATCCGTGTTGG Primer 2:CCTGCAAGGCACAAAGTCGCGCG
6A5	Kohara Phage	Genobase	PMID:3038334
9A1	Kohara Phage	Genobase	PMID:3038334
20B5	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: % ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: 1% ^[6] Synonyms:zdh-925::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:G6868	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13931	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003457	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947164	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3690	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005437	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	YdgJ
Synonyms	predicted oxidoreductase^[1], YdgJ^[2]^[1], B1624^[2]^[1] , ECK1619, JW5265, b1624
Product description	G6868^[2]^[3] Putative oxidoreductase; yhhX paralog^[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:0003824	catalytic activity	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:IPR004104	P	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:IPR000683	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004104	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:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004104	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	prsA	PMID:15690043	Experiment(s):EBI-889052
Protein	npdA	PMID:15690043	Experiment(s):EBI-894134
Protein	cobB	PMID:19402753	LCMS(ID Probability):99.6
Protein	prs	PMID:19402753	MALDI(Z-score):38.813813
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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 MSNSHHTSMR GNDMSDNIRV GLIGYGYASK TFHAPLIAGT PGQELAVISS SDETKVKADW PTVTVVSEPK HLFNDPNIDL IVIPTPNDTH FPLAKAALEA GKHVVVDKPF TVTLSQAREL DALAKSLGRV LSVFHNRRWD SDFLTLKGLL AEGVLGEVAY FESHFDRFRP QVRDRWREQG GPGSGIWYDL APHLLDQAIT LFGLPVSMTV DLAQLRPGAQ STDYFHAILS YPQRRVILHG TMLAAAESAR YIVHGSRGSY VKYGLDPQEE RLKNGERLPQ EDWGYDMRDG VLTRVEGEER VEETLLTVPG NYPAYYAAIR DALNGDGENP VPASQAIQVM ELIELGIESA KHRATLCLA
Length	359
Mol. Wt	39.712 kDa
pI	5.9 (calculated)
Extinction coefficient	46,870 - 46,995 (calc based on 13 Y, 5 W, and 1 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	5..122	PF01408 Oxidoreductase family, NAD-binding Rossmann fold	PMID:19920124
Domain	134..241	PF02894 Oxidoreductase family, C-terminal alpha/beta 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=ydgJ 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:90111307	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947164	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005437	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77376	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6868	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13931	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947164	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003457	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3690	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	Reference(s)
Protein	E. coli K-12 MG1655	344	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	468	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	276	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	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)
ydgJ
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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_000913:1702312..1702352 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:b1624 (EcoliWiki Page)	NCBI GEO profiles for ydgJ
microarray	GenExpDB:b1624 (EcoliWiki Page)	Summary of data for ydgJ 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 ydgJ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6868	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3690	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1624
EcoGene	EcoGene:EG13931	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003457	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005437	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	ENSANGP00000003307 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YMR315W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC1153 (score: 1.000; bootstrap: 100%) SPAC26H59c (score: 0.559)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000013496 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	S1781	From SHIGELLACYC
E. coli O157	Z2629	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)	PF02894 Oxidoreductase family, C-terminal alpha/beta domain
Pfam (EcoliWiki Page)	PF01408 Oxidoreductase family, NAD-binding Rossmann fold
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Panther (EcoliWiki Page)	PTHR22604:SF51
Superfamily (EcoliWiki Page)	SUPERFAMILY:55347
PFAM (EcoliWiki Page)	PFAM:PF01408
EcoCyc	EcoCyc:G6868	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13931	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003457	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3690	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005437	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 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.
↑ ^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).

ydgJ: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 ydgJ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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