RegulonDB

Gene
Name:	phoQ
Synonym(s):	ECK1115, EG10732, b1129
Genome position(nucleotides):	1188316 <-- 1189776
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.33
External database links:

ASAP:	ABE-0003805
CGSC:	31922
ECHOBASE:	EB0725
ECOLIHUB:	phoQ
OU-MICROARRAY:	b1129
STRING:	511145.b1129
COLOMBOS:	phoQ

Gene

Name:

phoQ

Synonym(s):

ECK1115, EG10732, b1129

Genome position(nucleotides):

1188316 <-- 1189776

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

51.33

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

10 -> 188

PLSLRVRFLLATAAVVLVLSLAYGMVALIGYSVSFDKTTFRLLRGESNLFYTLAKWENNKLHVELPENIDKQSPTMTLIYDENGQLLWAQRDVPWLMKMIQPDWLKSNGFHEIEADVNDTSLLLSGDHSIQQQLQEVREDDDDAEMTHSVAVNVYPATSRMPKLTIVVVDTIPVELKSS

17 -> 37

FLLATAAVVLVLSLAYGMVAL

UniProt: Helical.

27 -> 27

UniProt: Shows Mg(2+)-dependent signaling and partial gene activation activity; when associated with A-202..

30 -> 30

UniProt: Shows Mg(2+)-dependent signaling and displays higher gene activation activity than wild-type; when associated with A-202..

47 -> 47

UniProt: No significant effect (with or without MgCl(2) or CaCl(2))..

Type

Positions

Sequence

Comment

10 -> 188

PLSLRVRFLLATAAVVLVLSLAYGMVALIGYSVSFDKTTFRLLRGESNLFYTLAKWENNKLHVELPENIDKQSPTMTLIYDENGQLLWAQRDVPWLMKMIQPDWLKSNGFHEIEADVNDTSLLLSGDHSIQQQLQEVREDDDDAEMTHSVAVNVYPATSRMPKLTIVVVDTIPVELKSS

17 -> 37

FLLATAAVVLVLSLAYGMVAL

UniProt: Helical.

27 -> 27

UniProt: Shows Mg(2+)-dependent signaling and partial gene activation activity; when associated with A-202..

30 -> 30

UniProt: Shows Mg(2+)-dependent signaling and displays higher gene activation activity than wild-type; when associated with A-202..

47 -> 47

UniProt: No significant effect (with or without MgCl(2) or CaCl(2))..

48 -> 48

UniProt: Confers less than 30% of the wild-type levels of PhoP/PhoQ-signaling cascade in absence of CaCl(2) or MgCl(2)..

50 -> 50

UniProt: Large decrease in the transcriptional activation of PhoQ-dependent genes..

54 -> 54

UniProt: Very large decrease in the transcriptional activation of PhoQ-dependent genes..

68 -> 68

UniProt: No significant effect (with or without MgCl(2) or CaCl(2))..

90 -> 90

UniProt: No significant effect (with or without MgCl(2) or CaCl(2))..

148 -> 154

EDDDDAE

UniProt: Unable to bind divalent cations in vitro and impaired in the ability to respond to Mg(2+) deprivation in vivo..

149 -> 149

UniProt: Wild-type effect concerning mgrB transcription..

150 -> 150

UniProt: Wild-type effect concerning mgrB transcription..

151 -> 151

UniProt: Wild-type effect concerning mgrB transcription..

152 -> 152

UniProt: Wild-type effect concerning mgrB transcription..

179 -> 179

UniProt: Locked-on mutant defective in Mg(2+)-sensing and unable to control its phosphorylation state and phosphotransfer to phoP..

195 -> 215

FIYVLSANLLLVIPLLWVAAW

UniProt: Helical.

199 -> 199

UniProt: Shows Mg(2+)-dependent signaling and partial gene activation activity; when associated with A-202..

202 -> 202

UniProt: Is blind to signal, fails to activate transcription of PhoQ-dependent genes, and abrogates transcription when coexpressed with wild-type PhoQ..

203 -> 203

UniProt: Shows Mg(2+)-dependent signaling and partial gene activation activity; when associated with A-202..

205 -> 205

UniProt: Shows Mg(2+)-dependent signaling and partial gene activation activity; when associated with A-202..

215 -> 266

WWSLRPIEALAKEVRELEEHNRELLNPATTRELTSLVRNLNRLLKSERERYD

UniProt: HAMP.

274 -> 480

DLTHSLKTPLAVLQSTLRSLRSEKMSVSDAEPVMLEQISRISQQIGYYLHRASMRGGTLLSRELHPVAPLLDNLTSALNKVYQRKGVNISLDISPEISFVGEQNDFVEVMGNVLDNACKYCLEFVEISARQTDEHLYIVVEDDGPGIPLSKREVIFDRGQRVDTLRPGQGVGLAVAREITEQYEGKIVAGESMLGGARMEVIFGRQH

UniProt: Histidine kinase.

281 -> 281

T → R: loss of phosphatase activity and decreased kinase activity in vitro; does not lead to saturation in transcription of a PhoP regulated gene in vivo

376 -> 469

QNDFVEVMGNVLDNACKYCLEFVEISARQTDEHLYIVVEDDGPGIPLSKREVIFDRGQRVDTLRPGQGVGLAVAREITEQYEGKIVAGESMLGG

385 -> 393

NVLDNACKY

UniProt: ATP.

392 -> 392

UniProt: 44-fold decrease in ATP affinity and 6-fold decrease in activity..

415 -> 420

DDGPGI

UniProt: ATP.

434 -> 446

RVDTLRPGQGVGL

UniProt: ATP.

439 -> 439

UniProt: 3-fold decrease in ATP affinity and 2-fold increase in activity..

Multifun Terms (GenProtEC)

2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification

3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.4 - complex regulation --> 3.1.2.4.3 - two component regulatory systems (external signal)

3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.2 - covalent modification, demodification, maturation

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

molecular_function

GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0016740 - transferase activity
GO:0016772 - transferase activity, transferring phosphorus-containing groups
GO:0046872 - metal ion binding
GO:0016301 - kinase activity
GO:0004721 - phosphoprotein phosphatase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0000155 - phosphorelay sensor kinase activity
GO:0004673 - protein histidine kinase activity
GO:0042802 - identical protein binding

biological_process

GO:0006470 - protein dephosphorylation
GO:0016310 - phosphorylation
GO:0000160 - phosphorelay signal transduction system
GO:0007165 - signal transduction
GO:0007234 - osmosensory signaling via phosphorelay pathway
GO:0046777 - protein autophosphorylation
GO:0018106 - peptidyl-histidine phosphorylation
GO:0010350 - cellular response to magnesium starvation

Transcriptional Regulation
	Display Regulation
Activated by:	PhoP, PhoB
Repressed by:	PhoP

Transcriptional Regulation

Display Regulation

Activated by:

PhoP, PhoB

Repressed by:

PhoP

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_1466 (cluster)	1188265	reverse	nd	[RS-EPT-CBR]	[1]
promoter	ycfDp4	1188267	reverse	nd	[COMP-AINF], [RS-EPT-CBR]	[1], [2]
promoter	ycfDp5	1188270	reverse	nd	[COMP-AINF]	[2]
promoter	TSS_1468	1189078	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1469	1189096	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1470	1189968	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1471	1190330	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1472	1190342	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1473	1190470	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1474 (cluster)	1190474	reverse	nd	[RS-EPT-CBR]	[1]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_1466 (cluster)

1188265

reverse

[RS-EPT-CBR]

[1]

promoter

ycfDp4

1188267

reverse

[COMP-AINF], [RS-EPT-CBR]

[1], [2]

promoter

ycfDp5

1188270

reverse

[COMP-AINF]

[2]

promoter

TSS_1468

1189078

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_1469

1189096

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_1470

1189968

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_1471

1190330

forward

[RS-EPT-CBR]

[1]

promoter

TSS_1472

1190342

forward

[RS-EPT-CBR]

[1]

promoter

TSS_1473

1190470

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_1474 (cluster)

1190474

reverse

[RS-EPT-CBR]

[1]

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

Evidence

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

[COMP-AINF] 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