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Expression|

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Standard Name	ydeP
Gene Synonym(s)	ECK1494, b1501, JW1495^[1], JW1495
Product Desc.	acid resistance protein^[2]^[3] Required for acid resistance conferred by EvgA overexpression; oxidoreductase homolog^[4]
Product Synonyms(s)	predicted oxidoreductase^[1], B1501^[2]^[1], YdeP^[2]^[1] , ECK1494, JW1495, b1501
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydeP^[2]
Regulation/Activity
Quick Links
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Notes

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EvgAS regulon. AFMB Structural Genomics target No. 88 (http://afmb.cnrs-mrs.fr/article171.html). YdeO and YdeP repress the type III secretion system (TTSS) of EPEC E. coli (Nadler, 2006).^[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	ydeP
Mnemonic	Systematic nomenclature
Synonyms	ECK1494, b1501, JW1495^[1], JW1495
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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	34.1 minutes	MG1655: 1584510..1582231 <gbrowseImage> name=NC_000913:1582231..1584510 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1560437..1558158 <gbrowseImage> name=NC_012967:1558158..1560437 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1474290..1476569 <gbrowseImage> name=NC_012759:1474290..1476569 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1588200..1585921 <gbrowseImage> name=NC_007779:1585921..1588200 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1675105..1672826 <gbrowseImage> name=NC_010473:1672826..1675105 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
ΔydeP (Keio:JW1495)	deletion	deletion			PMID:16738554	Shigen
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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
JW1495	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGAAAAAAATTGAATCCTA Primer 2:CCATTTGATGGTTCTAATTCAAC
6E8	Kohara Phage	Genobase	PMID:3038334
2A9	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: 12% ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: % ^[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:G6791	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13798	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003380	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946055	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3559	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005001	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	YdeP
Synonyms	predicted oxidoreductase^[1], B1501^[2]^[1], YdeP^[2]^[1] , ECK1494, JW1495, b1501
Product description	acid resistance protein^[2]^[3] Required for acid resistance conferred by EvgA overexpression; oxidoreductase homolog^[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:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008863	formate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010046	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006656	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006657	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:0030151	molybdenum ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006657	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030151	molybdenum ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010046	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030151	molybdenum ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0500	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:0051536	iron-sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0411	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010046	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0004	F	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	Notes	References	Evidence
Protein	mdtP		PMID:16606699	Experiment(s):EBI-1139988
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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 MKKKIESYQG AAGGWGAVKS VANAVRKQMD IRQDVIAMFD MNKPEGFDCP GCAWPDPKHS ASFDICENGA KAIAWEVTDK QVNASFFAEN TVQSLLTWGD HELEAAGRLT QPLKYDAVSD CYKPLSWQQA FDEIGARLQS YSDPNQVEFY TSGRTSNEAA FLYQLFAREY GSNNFPDCSN MCHEPTSVGL AASIGVGKGT VLLEDFEKCD LVICIGHNPG TNHPRMLTSL RALVKRGAKM IAINPLQERG LERFTAPQNP FEMLTNSETQ LASAYYNVRI GGDMALLKGM MRLLIERDDA ASAAGRPSLL DDEFIQTHTV GFDELRRDVL NSEWKDIERI SGLSQTQIAE LADAYAAAER TIICYGMGIT QHEHGTQNVQ QLVNLLLMKG NIGKPGAGIC PLRGHSNVQG DRTVGITEKP SAEFLARLGE RYGFTPPHAP GHAAIASMQA ICTGQARALI CMGGNFALAM PDREASAVPL TQLDLAVHVA TKLNRSHLLT ARHSYILPVL GRSEIDMQKN GAQAVTVEDS MSMIHASRGV LKPAGVMLKS ECAVVAGIAQ AALPQSVVAW EYLVEDYDRI RNDIEAVLPE FADYNQRIRH PGGFHLINAA AERRWMTPSG KANFITSKGL LEDPSSAFNS KLVMATVRSH DQYNTTIYGM DDRYRGVFGQ RDVVFMSAKQ AKICRVKNGE RVNLIALTPD GKRSSRRMDR LKVVIYPMAD RSLVTYFPES NHMLTLDNHD PLSGIPGYKS IPVELEPSN
Length	759
Mol. Wt	83.495 kDa
pI	6.8 (calculated)
Extinction coefficient	76,780 - 78,530 (calc based on 22 Y, 8 W, and 14 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	108..501	PF00384 Molybdopterin oxidoreductase	PMID:19920124
Domain	642..752	PF01568 Molydopterin dinucleotide 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=ydeP 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:16129460	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946055	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005001	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77561	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6791	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13798	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946055	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003380	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3559	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 MC4100	1.02E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	E. coli K-12 MG1655	22	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	23	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	10^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)
ydeP
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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_000913:1584490..1584530 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:b1501 (EcoliWiki Page)	NCBI GEO profiles for ydeP
microarray	GenExpDB:b1501 (EcoliWiki Page)	Summary of data for ydeP 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 (1584428..1584872) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ12; Well:C5^[7]
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Notes

Accessions Related to ydeP Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6791	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3559	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1501
EcoGene	EcoGene:EG13798	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003380	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005001	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	S1656	From SHIGELLACYC
E. coli O157	Z2207	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)	PF01568 Molydopterin dinucleotide binding domain
Pfam (EcoliWiki Page)	PF00384 Molybdopterin oxidoreductase
Superfamily (EcoliWiki Page)	SUPERFAMILY:50692
Superfamily (EcoliWiki Page)	SUPERFAMILY:53706
EcoCyc	EcoCyc:G6791	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13798	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003380	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3559	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005001	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 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

ydeP: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 ydeP Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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