RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

cybB gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	cybB
Synonym(s):	ECK1410, EG10172, b1418
Genome position(nucleotides):	1490902 --> 1491432 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	47.65
External database links:

ASAP:	ABE-0004733
CGSC:	17728
ECHOBASE:	EB0169
ECOLIHUB:	cybB
OU-MICROARRAY:	b1418
STRING:	511145.b1418
COLOMBOS:	cybB

Product

Name:

superoxide oxidase

Synonym(s):

CybB, superoxide:ubiquinone oxidoreductase

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

20.286

Isoelectric point:

10.35

Motif(s):

Type	Positions	Sequence
	9 -> 29	QISIHWLVFLLVIAAYCAMEF
	137 -> 137	H
	165 -> 176	NTLLRMMPRKRS
	41 -> 61	INMIHVSCGISILVLMVVRLL
	85 -> 105	LGHLVIYLLFIALPVIGLVMM

Classification:

Multifun Terms (GenProtEC)
		1 - metabolism --> 1.4 - energy production/transport --> 1.4.3 - electron carriers
		1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.15 - large molecule carriers --> 1.6.15.1 - cytochromes
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
	molecular_function	GO:0009055 - electron transfer activity GO:0046872 - metal ion binding GO:0020037 - heme binding
	biological_process	GO:0019430 - removal of superoxide radicals GO:0022904 - respiratory electron transport chain GO:0055114 - oxidation-reduction process

Note(s):

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

Reference(s):

[1] Nakamura H., et al., 1988

External database links:

ECOCYC:

CYTOCHROME-B561-MONOMER

ECOLIWIKI:

INTERPRO:

INTERPRO:

PDB:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

cybB

Operon arrangement:

Transcription unit	Promoter
cybB

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_1803 (cluster)	1490746	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1490745 to 1490746, where the highest frequency is at position 1488770. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_1804 (cluster)	1490754	reverse	For this promoter, there is a cluster of 3 transcription start sites,in the interval 1490752 to 1490754, where the highest frequency is at position 1488777. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	cybBp5	1490761	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.535. P-value: 6.507e-5 Read more >	[ICWHO]	[3]
promoter	cybBp7	1490766	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.156. P-value: 2.020e-5 Read more >	[ICWHO]	[3]
promoter	cybBp6	1490887	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.69. P-value: 9.142e-5 Read more >	[ICWHO]	[3]

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] Nakamura H., Murakami H., Yamato I., Anraku Y., 1988, Nucleotide sequence of the cybB gene encoding cytochrome b561 in Escherichia coli K12., Mol Gen Genet 212(1):1-5
[2] 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.
[3] 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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