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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	cydD
Gene Synonym(s)	ECK0878, b0887, JW0870, htrD^[1], htrD
Product Desc.	CydD^[2]^[3]; Component of cydDC glutathione ABC transporter^[2]^[3] Cysteine exporter CydDC; ABC transporter exports cysteine to periplasm as required for cytochrome assembly; N-terminal permease domain and C-terminal cytoplasmic ATP-binding domain^[4]
Product Synonyms(s)	fused cysteine transporter subunits of ABC superfamily: membrane component^[1], ATP-binding component^[1], B0887^[2]^[1], HtrD^[2]^[1], CydD^[2]^[1] , ECK0878, htrD, JW0870, b0887
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cydDC^[2]
Regulation/Activity
Quick Links
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Notes

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Translation start site verified by start codon mutagenesis (Cruz-Ramos, 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	cydD
Mnemonic	Cytochrome d
Synonyms	ECK0878, b0887, JW0870, htrD^[1], htrD
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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	20.01 minutes	MG1655: 930185..928419 <gbrowseImage> name=NC_000913:928419..930185 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 948020..946254 <gbrowseImage> name=NC_012967:946254..948020 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 831387..833153 <gbrowseImage> name=NC_012759:831387..833153 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 931384..929618 <gbrowseImage> name=NC_007779:929618..931384 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 984113..982347 <gbrowseImage> name=NC_010473:982347..984113 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
ΔcydD (Keio:JW0870)	deletion	deletion	PMID:16738554	Shigen
cydD100			PMID:2559153	CGSC:65218
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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
JW0870	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATAAATCTCGTCAAAAAGA Primer 2:CCAATCTCCTCCTGACGATGGGC
1H1	Kohara Phage	Genobase	PMID:3038334
1F10	Kohara Phage	Genobase	PMID:3038334
E6H3	Kohara Phage	Genobase	PMID:3038334
zbh-29::Tn10	Linked marker	CAG18493 = CGSC7353^[5]	est. P1 cotransduction: % ^[6] Synonyms:zbi-29::Tn10
zca-1230::Tn10	Linked marker	CAG18478 = CGSC7356^[5]	est. P1 cotransduction: 52% ^[6] Synonyms:zbj-1230::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:EG11405	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11405	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001371	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949052	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1377	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003015	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	CydD
Synonyms	fused cysteine transporter subunits of ABC superfamily: membrane component^[1], ATP-binding component^[1], B0887^[2]^[1], HtrD^[2]^[1], CydD^[2]^[1] , ECK0878, htrD, JW0870, b0887
Product description	CydD^[2]^[3]; Component of cydDC glutathione ABC transporter^[2]^[3] Cysteine exporter CydDC; ABC transporter exports cysteine to periplasm as required for cytochrome assembly; N-terminal permease domain and C-terminal cytoplasmic ATP-binding domain^[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:0000166	nucleotide binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001140	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003439	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011527	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014216	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017871	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001140	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011527	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014216	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR014216	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001140	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011527	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016887	ATPase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003439	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016887	ATPase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017871	F	Seeded from EcoCyc (v14.0)	complete
	GO:0017111	nucleoside-triphosphatase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042626	ATPase activity, coupled to transmembrane movement of substances	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001140	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042626	ATPase activity, coupled to transmembrane movement of substances	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011527	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055085	transmembrane transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001140	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055085	transmembrane transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011527	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	Subunits of cydDC glutathione ABC transporter	could be indirect
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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
plasma membrane	C-terminus localized in the cytoplasm with 6 predicted transmembrane domains	Daley et al. (2005) ^[7]
plasma membrane			From EcoCyc^[3]
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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 MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLLV LTFVLRAWVV WLRERVGYHA GQHIRFAIRR QVLDRLQQAG PAWIQGKPAG SWATLVLEQI DDMHDYYARY LPQMALAVSV PLLIVVAIFP SNWAAALILL GTAPLIPLFM ALVGMGAADA NRRNFLALAR LSGHFLDRLR GMETLRIFGR GEAEIESIRS ASEDFRQRTM EVLRLAFLSS GILEFFTSLS IALVAVYFGF SYLGELDFGH YDTGVTLAAG FLALILAPEF FQPLRDLGTF YHAKAQAVGA ADSLKTFMET PLAHPQRGEA ELASTDPVTI EAEELFITSP EGKTLAGPLN FTLPAGQRAV LVGRSGSGKS SLLNALSGFL SYQGSLRING IELRDLSPES WRKHLSWVGQ NPQLPAATLR DNVLLARPDA SEQELQAALD NAWVSEFLPL LPQGVDTPVG DQAARLSVGQ AQRVAVARAL LNPCSLLLLD EPAASLDAHS EQRVMEALNA ASLRQTTLMV THQLEDLADW DVIWVMQDGR IIEQGRYAEL SVAGGPFATL LAHRQEEI
Length	588
Mol. Wt	65.058 kDa
pI	6.4 (calculated)
Extinction coefficient	86,400 - 86,525 (calc based on 10 Y, 13 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	24..296	PF00664 ABC transporter transmembrane region	PMID:19920124
Domain	390..514	PF00005 ABC transporter	PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=cydD taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16128854	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949052	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003015	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P29018	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11405	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11405	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949052	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001371	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1377	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	15.779+/-0.24	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.013306908	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	467	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	158	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	216	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)
cydDC
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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_000913:930165..930205 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:b0887 (EcoliWiki Page)	NCBI GEO profiles for cydD
microarray	GenExpDB:b0887 (EcoliWiki Page)	Summary of data for cydD 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 (930092..930347) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ14; Well:C8^[8]
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Notes

Accessions Related to cydD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11405	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1377	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0887
EcoGene	EcoGene:EG11405	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001371	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003015	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	ENSANGP00000029662 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	CYDD	From SHIGELLACYC
E. coli O157	CYDD	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)	PF00664 ABC transporter transmembrane region
Pfam (EcoliWiki Page)	PF00005 ABC transporter
Panther (EcoliWiki Page)	PTHR24223:SF209
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Superfamily (EcoliWiki Page)	SUPERFAMILY:90123
EcoCyc	EcoCyc:EG11405	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11405	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001371	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1377	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003015	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

cydD: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 cydD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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