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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	ycdY
Gene Synonym(s)	ECK1021, b1035, JW1018^[1], JW1018
Product Desc.	conserved protein^[2]; putative oxidoreductase component^[3] Putative redox enzyme maturation protein (REMP), function unknown; putative TAT signal peptide binding protein and co-factor insertion chaperone; required for swarming phenotype^[4]
Product Synonyms(s)	conserved protein^[1], B1035^[2]^[1], YcdY^[2]^[1] , ECK1021, JW1018, b1035
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycdX^[2]
Regulation/Activity
Quick Links
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Notes

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torD, dmsD and ycdY are paralogs. Overexpressed YdcY and DmsD interfere with apoTorA maturation by TorD, independent of the TorA signal peptide (Ilbert, 2004).^[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	ycdY
Mnemonic	Systematic nomenclature
Synonyms	ECK1021, b1035, JW1018^[1], JW1018
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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	23.68 minutes	MG1655: 1098863..1099417 <gbrowseImage> name=NC_000913:1098863..1099417 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1114209..1114763 <gbrowseImage> name=NC_012967:1114209..1114763 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1002788..1003342 <gbrowseImage> name=NC_012759:1002788..1003342 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1099881..1100435 <gbrowseImage> name=NC_007779:1099881..1100435 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1154308..1154862 <gbrowseImage> name=NC_010473:1154308..1154862 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: Description	Reference	Availability	Comments
Strain DH10B		C144Y	Nonsynonomous mutation	PMID:18245285	ASAP	This is a SNP in E. coli K-12 Strain DH10B
ycdY(del) (Keio:JW1018)	deletion	deletion		PMID:16738554	Shigen CGSC8991^[5]
ycdY776(del)::kan				PMID:16738554	CGSC:103974
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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
JW1018	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACGAGTTTTCTATCCTCTG Primer 2:CCTTCTTCAGAATCTTCTTCCAG
9G7	Kohara Phage	Genobase	PMID:3038334
1C7	Kohara Phage	Genobase	PMID:3038334
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[5]	est. P1 cotransduction: 22% ^[6]
zce-726::Tn10	Linked marker	CAG12078 = CGSC7361^[5]	est. P1 cotransduction: 6% ^[6]
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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:G6541	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13871	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003137	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945609	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3630	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003511	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	YcdY
Synonyms	conserved protein^[1], B1035^[2]^[1], YcdY^[2]^[1] , ECK1021, JW1018, b1035
Product description	conserved protein^[2]; putative oxidoreductase component^[3] Putative redox enzyme maturation protein (REMP), function unknown; putative TAT signal peptide binding protein and co-factor insertion chaperone; required for swarming phenotype^[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:0008940	nitrate reductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009325	nitrate reductase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	C	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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	rplQ	PMID:16606699	Experiment(s):EBI-1138675
Protein	ycgE	PMID:16606699	Experiment(s):EBI-1138675
Protein	ftsL	PMID:16606699	Experiment(s):EBI-1138675
Protein	crl	PMID:16606699	Experiment(s):EBI-1138675
Protein	uspG	PMID:16606699	Experiment(s):EBI-1138675
Protein	rplB	PMID:16606699	Experiment(s):EBI-1138675
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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 MNEFSILCRV LGSLYYRQPQ DPLLVPLFTL IREGKLAANW PLEQDELLTR LQKSCDMTQV SADYNALFIG DECAVPPYRS AWVEGATEAE VRAFLSERGM PLADTPADHI GTLLLAASWL EDQSTEDESE ALETLFSEYL LPWCGAFLGK VEAHATTPFW RTMAPLTRDA ISAMWDELEE DSEE
Length	184
Mol. Wt	20.724 kDa
pI	4.0 (calculated)
Extinction coefficient	40,450 - 40,950 (calc based on 5 Y, 6 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	Notes	References
Domain	29..151	PF02613 Nitrate reductase delta subunit		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=ycdY 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:16128998	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945609	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003511	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75915	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6541	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13871	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945609	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003137	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3630	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 MC4100	5.18E+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	2564	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	1195	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	1504	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)
ycdX
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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_000913:1098843..1098883 source=MG1655 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:b1035 (EcoliWiki Page)	NCBI GEO profiles for ycdY
microarray	GenExpDB:b1035 (EcoliWiki Page)	Summary of data for ycdY 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 ycdY Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6541	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3630	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1035
EcoGene	EcoGene:EG13871	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003137	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003511	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	YCDY	From SHIGELLACYC
E. coli O157	YCDY	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)	PF02613 Nitrate reductase delta subunit
Superfamily (EcoliWiki Page)	SUPERFAMILY:89155
EcoCyc	EcoCyc:G6541	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13871	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003137	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3630	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003511	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).

ycdY: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 ycdY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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