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Product(s) |

Expression|

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Standard Name	ydiJ
Gene Synonym(s)	ECK1684, b1687, JW1677^[1], JW1677
Product Desc.	predicted FAD-linked oxidoreductase^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted FAD-linked oxidoreductase^[1], B1687^[2]^[1], YdiJ^[2]^[1] , ECK1684, JW1677, b1687
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydiH^[2]
Regulation/Activity
Quick Links
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Notes

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Overexpression causes abnormal biofilm architecture, increased crystal violet staining, and reduced motility. YdiJ is homologous to glycolate oxidase. P. putida ydiJ mutant is unaffected for growth and survival.^[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	ydiJ
Mnemonic	Systematic nomenclature
Synonyms	ECK1684, b1687, JW1677^[1], JW1677
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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	38.01 minutes	MG1655: 1766709..1763653 <gbrowseImage> name=NC_000913:1763653..1766709 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1745952..1742896 <gbrowseImage> name=NC_012967:1742896..1745952 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1655712..1658768 <gbrowseImage> name=NC_012759:1655712..1658768 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1770399..1767343 <gbrowseImage> name=NC_007779:1767343..1770399 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1857280..1854224 <gbrowseImage> name=NC_010473:1854224..1857280 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
ΔydiJ (Keio:JW1677)	deletion	deletion			PMID:16738554	Shigen CGSC9423^[5]
ΔydiJ::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
ΔydiJ::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
ΔydiJ762::kan					PMID:16738554	CGSC:104322
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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
JW1677	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTCCACAGATTTCCCAGGC Primer 2:CCTTTAATAATCTCCAGTAAAGC
15G10	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: 63% ^[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:G6913	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13969	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003501	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946189	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3726	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005632	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	YdiJ
Synonyms	predicted FAD-linked oxidoreductase^[1], B1687^[2]^[1], YdiJ^[2]^[1] , ECK1684, JW1677, b1687
Product description	predicted FAD-linked oxidoreductase^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004113	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016164	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016166	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016167	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006094	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004113	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006094	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016164	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016166	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016167	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	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	ydfG		PMID:19402753	MALDI(Z-score):21.453935
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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 MIPQISQAPG VVQLVLNFLQ ELEQQGFTGD TATSYADRLT MSTDNSIYQL LPDAVVFPRS TADVALIARL AAQERYSSLI FTPRGGGTGT NGQALNQGII VDMSRHMNRI IEINPEEGWV RVEAGVIKDQ LNQYLKPFGY FFAPELSTSN RATLGGMINT DASGQGSLVY GKTSDHVLGV RAVLLGGDIL DTQPLPVELA ETLGKSNTTI GRIYNTVYQR CRQQRQLIID NFPKLNRFLT GYDLRHVFND EMTEFDLTRI LTGSEGTLAF ITEARLDITR LPKVRRLVNV KYDSFDSALR NAPFMVEARA LSVETVDSKV LNLAREDIVW HSVSELITDV PDQEMLGLNI VEFAGDDEAL IDERVNALCA RLDELIASHQ AGVIGWQVCR ELAGVERIYA MRKKAVGLLG NAKGAAKPIP FAEDTCVPPE HLADYIAEFR ALLDSHGLSY GMFGHVDAGV LHVRPALDMC DPQQEILMKQ ISDDVVALTA KYGGLLWGEH GKGFRAEYSP AFFGEELFAE LRKVKAAFDP HNRLNPGKIC PPEGLDAPMM KVDAVKRGTF DRQIPIAVRQ QWRGAMECNG NGLCFNFDAR SPMCPSMKIT QNRIHSPKGR ATLVREWLRL LADRGVDPLK LEQELPESGV SLRTLIARTR NSWHANKGEY DFSHEVKEAM SGCLACKACS TQCPIKIDVP EFRSRFLQLY HTRYLRPLRD HLVATVESYA PLMARAPKTF NFFINQPLVR KLSEKHIGMV DLPLLSVPSL QQQMVGHRSA NMTLEQLESL NAEQKARTVL VVQDPFTSYY DAQVVADFVR LVEKLGFQPV LLPFSPNGKA QHIKGFLNRF AKTAKKTADF LNRMAKLGMP MVGVDPALVL CYRDEYKLAL GEERGEFNVL LANEWLASAL ESQPVATVSG ESWYFFGHCT EVTALPGAPA QWAAIFARFG AKLENVSVGC CGMAGTYGHE AKNHENSLGI YELSWHQAMQ RLPRNRCLAT GYSCRSQVKR VEGTGVRHPV QALLEIIK
Length	1,018
Mol. Wt	113.249 kDa
pI	7.1 (calculated)
Extinction coefficient	100,730 - 103,105 (calc based on 27 Y, 11 W, and 19 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	281..539	PF02913 FAD linked oxidases, C-terminal domain	PMID:19920124
Domain	52..193	PF01565 FAD 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=ydiJ 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:16129643	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946189	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005632	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77748	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6913	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13969	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946189	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003501	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3726	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	Ecoli K-12	6.558+/-0.137	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.073134817	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	728	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	897	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	620	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)
ydiH
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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_000913:1766689..1766729 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:b1687 (EcoliWiki Page)	NCBI GEO profiles for ydiJ
microarray	GenExpDB:b1687 (EcoliWiki Page)	Summary of data for ydiJ 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 ydiJ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6913	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3726	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1687
EcoGene	EcoGene:EG13969	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003501	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005632	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
Shigella flexneri	YDIJ	From SHIGELLACYC
E. coli O157	YDIJ	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)	PF01565 FAD binding domain
Pfam (EcoliWiki Page)	PF02913 FAD linked oxidases, C-terminal domain
Panther (EcoliWiki Page)	PTHR11748:SF4
Superfamily (EcoliWiki Page)	SUPERFAMILY:55103
Superfamily (EcoliWiki Page)	SUPERFAMILY:56176
EcoCyc	EcoCyc:G6913	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13969	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003501	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3726	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005632	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 ^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).

ydiJ: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 ydiJ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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