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Product(s) |

Expression|

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Standard Name	cydB
Gene Synonym(s)	ECK0722, b0734, JW0723, cyd-2^[1]
Product Desc.	cytochrome bd-I terminal oxidase subunit II^[2]^[3]; Component of cytochrome bd-I terminal oxidase^[2]^[3] Cytochrome d (bd-I) terminal oxidase subunit II; upregulated in biofilms and microaerobic conditions; aerobically repressed by H-NS; anaerobically repressed by Fnr^[4]
Product Synonyms(s)	cytochrome d terminal oxidase, subunit II^[1], B0734^[2]^[1], CydB^[2]^[1] , ECK0722, JW0723, b0734
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cydAB^[2], OP00140
Regulation/Activity
Quick Links
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Notes

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Fnr and ArcA regulons. ArcA-P antagonizes H-NS repression of cydAB in response to limiting oxygen.^[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	cydB
Mnemonic	Cytochrome d
Synonyms	ECK0722, b0734, JW0723, cyd-2^[1]
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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	16.64 minutes	MG1655: 772265..773404 <gbrowseImage> name=NC_000913:772265..773404 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 753924..755063 <gbrowseImage> name=NC_012967:753924..755063 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 675025..676164 <gbrowseImage> name=NC_012759:675025..676164 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 773464..774603 <gbrowseImage> name=NC_007779:773464..774603 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 824857..825996 <gbrowseImage> name=NC_010473:824857..825996 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
cydB(del) (Keio:JW0723)	deletion	deletion			PMID:16738554	Shigen CGSC8790^[5]
cydB(del)::kan	deletion		Biolog:respiration	unable to respire a-Hydroxybutyrate	PMID:16095938
cydB(del)::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
cydB3						CGSC:9473
cydB782(del)::kan					PMID:16738554	CGSC:100464
CydAB (del), cyoABCD (del), cbdAB (del), ygiN (del)	deletion	deletion		deletion of all genes decreased oxygen uptake by 98% via activation of arcA, table 1.	PMID:20709841
CydAB(del), cyoABCD(del), cbdAB(del), ygiN(del)	deletion	deletion	Growth Phenotype	Mutaiton causes decreased growth rate via inhibition of arcA, table 1.	PMID:20709841
CydAB(del), cyoABCD(del), cbdAB(del), ygiN(del)	deletion	deletion		Increase in glucose uptake rate increase in lactate secretion rate Decrease in acetate secretion rate	PMID:20709841
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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
JW0723	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATCGATTATGAAGTATTGCG Primer 2:CCGTACAGAGAGTGGGTGTTACG
18F11	Kohara Phage	Genobase	PMID:3038334
10G5	Kohara Phage	Genobase	PMID:3038334
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: 78% ^[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:EG10174	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10174	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000169	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945347	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0171	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002501	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	CydB
Synonyms	cytochrome d terminal oxidase, subunit II^[1], B0734^[2]^[1], CydB^[2]^[1] , ECK0722, JW0723, b0734
Product description	cytochrome bd-I terminal oxidase subunit II^[2]^[3]; Component of cytochrome bd-I terminal oxidase^[2]^[3] Cytochrome d (bd-I) terminal oxidase subunit II; upregulated in biofilms and microaerobic conditions; aerobically repressed by H-NS; anaerobically repressed by Fnr^[4]
EC number (for enzymes)	1.9.3.-^[1]
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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	PMID:10393326	IDA: Inferred from Direct Assay		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:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	PMID:16299377	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003317	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: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:0016682	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor	PMID:6321507	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0017004	cytochrome complex assembly	PMID:2856143	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0020037	heme binding	PMID:8516338	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	Seeded from EcoCyc (v14.0)	complete
	GO:0031224	intrinsic to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	C	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003317	P	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	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.

Compartment	Description	Evidence	Reference/Source	Notes
plasma membrane	C-terminus localized in the cytoplasm with 8 predicted transmembrane domains	Daley et al. (2005) ^[7]
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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 MIDYEVLRFI WWLLVGVLLI GFAVTDGFDM GVGMLTRFLG RNDTERRIMI NSIAPHWDGN QVWLITAGGA LFAAWPMVYA AAFSGFYVAM ILVLASLFFR PVGFDYRSKI EETRWRNMWD WGIFIGSFVP PLVIGVAFGN LLQGVPFNVD EYLRLYYTGN FFQLLNPFGL LAGVVSVGMI ITQGATYLQM RTVGELHLRT RATAQVAALV TLVCFALAGV WVMYGIDGYV VKSTMDHYAA SNPLNKEVVR EAGAWLVNFN NTPILWAIPA LGVVLPLLTI LTARMDKAAW AFVFSSLTLA CIILTAGIAM FPFVMPSSTM MNASLTMWDA TSSQLTLNVM TWVAVVLVPI ILLYTAWCYW KMFGRITKED IERNTHSLY
Length	379
Mol. Wt	42.453 kDa
pI	7.2 (calculated)
Extinction coefficient	108,860 - 109,235 (calc based on 14 Y, 16 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.

Type	Residues	Description	Notes	References
Domain	6..363	PF02322 Cytochrome oxidase subunit II		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=cydB 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:16128709	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945347	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002501	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABK2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10174	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10174	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945347	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000169	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0171	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	6.13E+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	1735	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	445	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	1092	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)
cydAB
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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_000913:772245..772285 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:b0734 (EcoliWiki Page)	NCBI GEO profiles for cydB
microarray	GenExpDB:b0734 (EcoliWiki Page)	Summary of data for cydB 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 cydB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10174	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0171	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0734
EcoGene	EcoGene:EG10174	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000169	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002501	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	CYDB	From SHIGELLACYC
E. coli O157	CYDB	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)	PF02322 Cytochrome oxidase subunit II
EcoCyc	EcoCyc:EG10174	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10174	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000169	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0171	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002501	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 ^1.8 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 ^2.7 ^2.8 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 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

cydB: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 cydB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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