RegulonDB

Gene
Name:	cyoB
Synonym(s):	ECK0425, EG10179, b0431
Genome position(nucleotides):	448650 <-- 450641 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.96
External database links:

ASAP:	ABE-0001493
CGSC:	30997
ECHOBASE:	EB0176
MIM:	535000
MIM:	550500
MIM:	220110
MIM:	114500
MIM:	500008
OU-MICROARRAY:	b0431
PortEco:	cyoB
STRING:	511145.b0431
COLOMBOS:	cyoB

Gene

Name:

cyoB

Synonym(s):

ECK0425, EG10179, b0431

Genome position(nucleotides):

448650 <-- 450641 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.96

External database links:

ASAP:

CGSC:

ECHOBASE:

MIM:

MIM:

MIM:

MIM:

MIM:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

54 -> 54

173 -> 173

256 -> 256

284 -> 284

286 -> 286

Type

Positions

Sequence

54 -> 54

173 -> 173

256 -> 256

284 -> 284

286 -> 286

411 -> 411

75 -> 75

312 -> 326

GYTSLVWATVCITVL

421 -> 421

588 -> 606

NSGAGIVIAAFSTIFGFAM

17 -> 35

VMVTIAGIILGGLALVGLI

53 -> 80

DHKRLGIMYIIVAIVMLLRGFADAIMMR

56 -> 504

RLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAVL

98 -> 98

271 -> 307

NMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSR

341 -> 369

GANVNAFFGITTMIIAIPTGVKIFNWLFT

413 -> 445

SLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFG

55 -> 55

71 -> 71

138 -> 161

FPFLNNLSFWFTVVGVILVNVSLG

449 -> 477

NETWGKRAFWFWIIGFFVAFMPLYALGFM

540 -> 540

102 -> 102

188 -> 188

257 -> 257

333 -> 333

185 -> 215

VGVDYWIWSLQLSGIGTTLTGINFFVTILKM

378 -> 409

HSAMLWTIGFIVTFSVGGMTGVLLAVPGADFV

419 -> 419

614 -> 632

AIVGFAGMIITWIVKSFDE

106 -> 106

135 -> 135

225 -> 260

MPVFTWASLCANVLIIASFPILTVTVALLTLDRYLG

334 -> 334

481 -> 481

490 -> 521

QFHTMLMIAASGAVLIALGILCLVIQMYVSIR

80 -> 80

96 -> 132

PHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIG

101 -> 101

288 -> 288

362 -> 362

407 -> 407

482 -> 482

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

4 - transport --> 4.3 - Primary Active Transporters --> 4.3.D - Oxidoreduction-driven Active Transporters

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:0070469 - respirasome
GO:0009319 - cytochrome o ubiquinol oxidase complex

molecular_function

GO:0005507 - copper ion binding
GO:0005515 - protein binding
GO:0009055 - electron transfer activity
GO:0015453 - oxidoreduction-driven active transmembrane transporter activity
GO:0046872 - metal ion binding
GO:0015078 - proton transmembrane transporter activity
GO:0004129 - cytochrome-c oxidase activity
GO:0009486 - cytochrome bo3 ubiquinol oxidase activity
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0020037 - heme binding
GO:0048039 - ubiquinone binding

biological_process

GO:0006811 - ion transport
GO:0009060 - aerobic respiration
GO:0015990 - electron transport coupled proton transport
GO:0019646 - aerobic electron transport chain
GO:0022904 - respiratory electron transport chain
GO:0055114 - oxidation-reduction process

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

Transcriptional Regulation

Display Regulation

Activated by:

CRP, CusR, GadE, Fis

Repressed by:

FNR, Fur, HprR, Cra, ArcA, PdhR

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
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]	[7]
promoter	TSS_547	448138	reverse	nd	[RS-EPT-CBR]	[8]
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]	[8]
promoter	TSS_549	448244	reverse	nd	[RS-EPT-CBR]	[8]
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]	[8]
promoter	TSS_551	448549	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_552	448681	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_553	449899	reverse	nd	[RS-EPT-CBR]	[8]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

cyoEp3

447770

reverse

Similarity to the consensus
Read more >

[ICWHO]

[7]

promoter

TSS_547

448138

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_548 (cluster)

448146

reverse

For this promoter, there
Read more >

[RS-EPT-CBR]

[8]

promoter

TSS_549

448244

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_550 (cluster)

448247

reverse

For this promoter, there
Read more >

[RS-EPT-CBR]

[8]

promoter

TSS_551

448549

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_552

448681

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_553

449899

reverse

[RS-EPT-CBR]

[8]

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

Evidence

[ICWHO] Inferred computationally without human oversight

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Barker PD., Freund SM., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 2. Characterization by NMR of heme-ligand interactions., Biochemistry 35(42):13627-35
[2] Barker PD., Nerou EP., Cheesman MR., Thomson AJ., de Oliveira P., Hill HA., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 1. Spectroscopic and electrochemical characterization of the electronic properties., Biochemistry 35(42):13618-26
[3] Kobayashi K., Tagawa S., Mogi T., 2009, Electron transfer processes in subunit I mutants of cytochrome bo quinol oxidase in Escherichia coli., Biosci Biotechnol Biochem 73(7):1599-603
[4] Lin MT., Samoilova RI., Gennis RB., Dikanov SA., 2008, Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli., J Am Chem Soc 130(47):15768-9
[5] Melin F., Sabuncu S., Choi SK., Leprince A., Gennis RB., Hellwig P., 2018, Role of the tightly bound quinone for the oxygen reaction of cytochrome bo₃ oxidase from Escherichia coli., FEBS Lett 592(20):3380-3387
[6] Thomas JW., Lemieux LJ., Alben JO., Gennis RB., 1993, Site-directed mutagenesis of highly conserved residues in helix VIII of subunit I of the cytochrome bo ubiquinol oxidase from Escherichia coli: an amphipathic transmembrane helix that may be important in conveying protons to the binuclear center., Biochemistry 32(41):11173-80
[7] 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
[8] 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.

Reference(s)

[1] Barker PD., Freund SM., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 2. Characterization by NMR of heme-ligand interactions., Biochemistry 35(42):13627-35

[2] Barker PD., Nerou EP., Cheesman MR., Thomson AJ., de Oliveira P., Hill HA., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 1. Spectroscopic and electrochemical characterization of the electronic properties., Biochemistry 35(42):13618-26

[3] Kobayashi K., Tagawa S., Mogi T., 2009, Electron transfer processes in subunit I mutants of cytochrome bo quinol oxidase in Escherichia coli., Biosci Biotechnol Biochem 73(7):1599-603

[4] Lin MT., Samoilova RI., Gennis RB., Dikanov SA., 2008, Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli., J Am Chem Soc 130(47):15768-9

[5] Melin F., Sabuncu S., Choi SK., Leprince A., Gennis RB., Hellwig P., 2018, Role of the tightly bound quinone for the oxygen reaction of cytochrome bo₃ oxidase from Escherichia coli., FEBS Lett 592(20):3380-3387

[6] Thomas JW., Lemieux LJ., Alben JO., Gennis RB., 1993, Site-directed mutagenesis of highly conserved residues in helix VIII of subunit I of the cytochrome bo ubiquinol oxidase from Escherichia coli: an amphipathic transmembrane helix that may be important in conveying protons to the binuclear center., Biochemistry 32(41):11173-80

[7] 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

[8] 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.