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cydA:On One Page

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Standard Name

cydA

Gene Synonym(s)

ECK0721, b0733, JW0722, cyd-1[1]

Product Desc.

cytochrome bd-I terminal oxidase subunit I[2][3];

Component of cytochrome bd-I terminal oxidase[2][3]

Cytochrome d (bd-I) terminal oxidase subunit I; upregulated in biofilms and microaerobic conditions; aerobically repressed by H-NS; anaerobically repressed by Fnr[4]

Product Synonyms(s)

cytochrome d terminal oxidase, subunit I[1], B0733[2][1], CydA[2][1]

Function from GO

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): cydAB[2], OP00140

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(cydA)    Textpresso(cydA)

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Notes

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H-NS, Fnr and ArcA regulons. ArcA-P antagonizes H-NS repression of cydAB in response to limiting oxygen. Biofilm microarray result was validated with RT-PCR. HT_Cmplx29_Mem: AppC+CydA.[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

cydA

Mnemonic

Cytochrome d

Synonyms

ECK0721, b0733, JW0722, cyd-1[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

16.61 minutes 

MG1655: 770681..772249
gbrowse_img.php?coord=770681..772249&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 752340..753908
gbrowse_img.php?coord=752340..753908&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 771880..773448
gbrowse_img.php?coord=771880..773448&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 823273..824841
gbrowse_img.php?coord=823273..824841&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 673441..675009
gbrowse_img.php?coord=673441..675009&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

cydA

PMID:12519969

ASAP

At position 568 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20228

cydA85

PMID:15028700

CGSC:85756

cydA2

CGSC:10372


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW0722

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTAGATATAGTCGAACTGTC

Primer 2:CCGCGTGCCGGCTGAGTAGTCGT

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[5]

est. P1 cotransduction: 1% [6]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[5]

est. P1 cotransduction: 74% [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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10173

EchoBASE (EcoliWiki Page)

EchoBASE:EB0170

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0733

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0811

EcoGene (EcoliWiki Page)

EcoGene:EG10173

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CYDA

CGSC (EcoliWiki Page)

CGSC:10369

ASAP (EcoliWikiPage)

ASAP:ABE-0002499


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Notes

Links

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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

CydA

Synonyms

cytochrome d terminal oxidase, subunit I[1], B0733[2][1], CydA[2][1]

Product description

cytochrome bd-I terminal oxidase subunit I[2][3];

Component of cytochrome bd-I terminal oxidase[2][3]

Cytochrome d (bd-I) terminal oxidase subunit I; upregulated in biofilms and microaerobic conditions; aerobically repressed by H-NS; anaerobically repressed by Fnr[4]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005506

iron ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc [7]

complete

GO:0006810

transport

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc [7]

complete

GO:0016491

oxidoreductase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR002585
SP_KW:KW-0560

F

Seeded from EcoCyc [7]

complete

GO:0031224

intrinsic to membrane

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc [7]

complete

GO:0009055

electron carrier activity

PMID:16299377

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0016679

oxidoreductase activity, acting on diphenols and related substances as donors

PMID:6321507

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc [7]

complete

GO:0017004

cytochrome complex assembly

PMID:2856143

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc [7]

complete

GO:0020037

heme binding

PMID:8516338

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc [7]

complete

GO:0005886

plasma membrane

GO_REF:0000004
GO_REF:0000004
GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997
SP_KW:KW-1003
SP_SL:SL-0037

C

Seeded from EcoCyc [7]

complete

GO:0016020

membrane

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR002585
SP_KW:KW-0472

C

Seeded from EcoCyc [7]

complete

GO:0022900

electron transport chain

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0249

P

Seeded from EcoCyc [7]

complete

GO:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [7]

complete

GO:0055114

oxidation reduction

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc [7]

complete

GO:0009054

electron acceptor activity

F

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

Subunits of [[:Category:Complex:cytochrome bd-I terminal oxidase|cytochrome bd-I terminal oxidase]]

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.

CompartmentDescriptionEvidenceSourceNotes

plasma membrane

C-terminus localized in the cytoplasm with 9 predicted transmembrane domains

Daley et al. (2005) [9]


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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MMLDIVELSR LQFALTAMYH FLFVPLTLGM AFLLAIMETV YVLSGKQIYK DMTKFWGKLF
GINFALGVAT GLTMEFQFGT NWSYYSHYVG DIFGAPLAIE GLMAFFLEST FVGLFFFGWD
RLGKVQHMCV TWLVALGSNL SALWILVANG WMQNPIASDF NFETMRMEMV SFSELVLNPV
AQVKFVHTVA SGYVTGAMFI LGISAWYMLK GRDFAFAKRS FAIAASFGMA AVLSVIVLGD
ESGYEMGDVQ KTKLAAIEAE WETQPAPAAF TLFGIPDQEE ETNKFAIQIP YALGIIATRS
VDTPVIGLKE LMVQHEERIR NGMKAYSLLE QLRSGSTDQA VRDQFNSMKK DLGYGLLLKR
YTPNVADATE AQIQQATKDS IPRVAPLYFA FRIMVACGFL LLAIIALSFW SVIRNRIGEK
KWLLRAALYG IPLPWIAVEA GWFVAEYGRQ PWAIGEVLPT AVANSSLTAG DLIFSMVLIC
GLYTLFLVAE LFLMFKFARL GPSSLKTGRY HFEQSSTTTQ PAR
Length

523

Mol. Wt

58.338 kDa

pI

6.8 (calculated)

Extinction coefficient

98,320 - 98,695 (calc based on 18 Y, 13 W, and 3 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.

TypeResiduesDescriptionNotesReferences
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tmhmm.php?gene=cydA&show=pic&.jpg
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
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:CYDA-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0ABJ9

PFAM (EcoliWiki Page)

PFAM:PF01654

RefSeq (EcoliWiki Page)

RefSeq:NP_415261

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CYDA-MONOMER


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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)

cydAB

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=770661..770701&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b0733 (EcoliWiki Page)

NCBI GEO profiles for cydA

microarray

GenExpDB:b0733 (EcoliWiki Page)

Summary of data for cydA 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to cydA Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10173

EchoBASE (EcoliWiki Page)

EchoBASE:EB0170

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0733

EcoGene (EcoliWiki Page)

EcoGene:EG10173


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Notes

Links

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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.

OrganismHomologs (Statistics)Comments

Xenopus tropicalis

  • ENSXETP00000040513 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

CYDA

From SHIGELLACYC

E. coli O157

CYDA

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01654


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page

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