RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

cyoD gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	cyoD
Synonym(s):	ECK0423, EG10181, b0429
Genome position(nucleotides):	447717 <-- 448046 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.7
External database links:

ASAP:	ABE-0001487
CGSC:	31008
ECHOBASE:	EB0178
OU-MICROARRAY:	b0429
PortEco:	cyoD
STRING:	511145.b0429
COLOMBOS:	cyoD

Product

Name:

cytochrome bo₃ ubiquinol oxidase subunit 4

Synonym(s):

CyoD, cytochrome bo₃ terminal oxidase subunit IV, cytochrome bo₃ ubiquinol oxidase subunit IV, cytochrome o ubiquinol oxidase subunit IV

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

12.029

Isoelectric point:

7.161

Motif(s):

Type	Positions	Sequence
	1 -> 33	MSHSTDHSGASHGSVKTYMTGFILSIILTVIPF
	42 -> 68	SPAVILGTILAMAVVQVLVHLVCFLHM
	46 -> 64	ILGTILAMAVVQVLVHLVC
	72 -> 106	SDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNM
	18 -> 36	YMTGFILSIILTVIPFWMV

Classification:

Multifun Terms (GenProtEC)
		1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.6 - aerobic respiration
		1 - metabolism --> 1.4 - energy production/transport --> 1.4.2 - electron acceptors
		6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)
	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0005887 - integral component of plasma membrane GO:0016021 - integral component of membrane GO:0009319 - cytochrome o ubiquinol oxidase complex
	molecular_function	GO:0005515 - protein binding GO:0009055 - electron transfer activity GO:0015453 - oxidoreduction-driven active transmembrane transporter activity GO:0016491 - oxidoreductase activity GO:0015078 - proton transmembrane transporter activity GO:0008827 - cytochrome o ubiquinol oxidase activity GO:0009486 - cytochrome bo3 ubiquinol oxidase activity
	biological_process	GO:0009060 - aerobic respiration GO:0015990 - electron transport coupled proton transport GO:0019646 - aerobic electron transport chain GO:0055114 - oxidation-reduction process

Note(s):

Note(s): ...[more].

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PDB:

PFAM:

PRIDE:

PRODB:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

cyoABCDE

Operon arrangement:

Transcription unit	Promoter
cyoABCDE	cyoAp

Transcriptional Regulation
	Display Regulation
Activated by:	CRP, GadE, CusR, Fis
Repressed by:	FNR, Fur, HprR, Cra, ArcA, PdhR

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_546	447668	reverse	nd	[RS-EPT-CBR]	[1]
promoter	cyoEp3	447770	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.84. P-value: 7.948e-5 Read more >	[ICWHO]	[2]
promoter	TSS_547	448138	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_548 (cluster)	448146	reverse	For this promoter, there is a cluster of 4 transcription start sites,in the interval 448143 to 448146, where the highest frequency is at position 447369. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_549	448244	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_550 (cluster)	448247	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 448246 to 448247, where the highest frequency is at position 447471. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_551	448549	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_552	448681	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_553	449899	reverse	nd	[RS-EPT-CBR]	[1]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.
[2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

Reference(s)

[1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

[2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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