RegulonDB

Gene
Name:	nhaB
Synonym(s):	ECK1174, EG11392, b1186
Genome position(nucleotides):	1233176 <-- 1234717 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.85
External database links:

ASAP:	ABE-0003984
CGSC:	30269
ECHOBASE:	EB1365
ECOLIHUB:	nhaB
OU-MICROARRAY:	b1186
STRING:	511145.b1186
COLOMBOS:	nhaB

Gene

Name:

nhaB

Synonym(s):

ECK1174, EG11392, b1186

Genome position(nucleotides):

1233176 <-- 1234717 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.85

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

52 -> 72

IFTLAMALKCYPLLPGGLLAI

120 -> 140

LLLSIRSKMLLSLSFCVAAAF

144 -> 164

FLDALTVVAVVISVAVGFYGI

238 -> 258

FFLRMSPVTVPVLICGLLTCL

303 -> 323

AIIGVWLVTALALHLAEVGLI

Type

Positions

Sequence

52 -> 72

IFTLAMALKCYPLLPGGLLAI

120 -> 140

LLLSIRSKMLLSLSFCVAAAF

144 -> 164

FLDALTVVAVVISVAVGFYGI

238 -> 258

FFLRMSPVTVPVLICGLLTCL

303 -> 323

AIIGVWLVTALALHLAEVGLI

23 -> 43

LALIIFLIVNPLIFLISPFVA

202 -> 222

LMMHAGVGTALGGVMTMVGEP

1 -> 11

MEISWGRALWR

475 -> 495

VWMALPYTLVLTLVGLLCVEF

97 -> 117

LLLMFMVAGIYFMKQLLLFIF

348 -> 368

TESLPFTALLTVFFSVVAVII

391 -> 411

LFYIFNGLLSSISDNVFVGTI

447 -> 467

ATPNGQAAFLFLLTSALAPLI

Multifun Terms (GenProtEC)

4 - transport --> 4.2 - Electrochemical potential driven transporters --> 4.2.A - Porters (Uni-, Sym- and Antiporters)

5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH

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:0015297 - antiporter activity
GO:0015081 - sodium ion transmembrane transporter activity
GO:0015385 - sodium:proton antiporter activity

biological_process

GO:0006811 - ion transport
GO:0006814 - sodium ion transport
GO:0010226 - response to lithium ion
GO:0035725 - sodium ion transmembrane transport

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	dsbBp6	1233147		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.79. P-value: 1.721e-5 Read more >	[ICWHO]	[17]
	promoter	nhaBp7	1234767		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.436. P-value: 2.517e-5 Read more >	[ICWHO], [RS-EPT-CBR]	[17], [18]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

dsbBp6

1233147

reverse

Similarity to the consensus
Read more >

[ICWHO]

[17]

promoter

nhaBp7

1234767

reverse

Similarity to the consensus
Read more >

[ICWHO], [RS-EPT-CBR]

[17], [18]

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] Gerchman Y., Olami Y., Rimon A., Taglicht D., Schuldiner S., Padan E., 1993, Histidine-226 is part of the pH sensor of NhaA, a Na+/H+ antiporter in Escherichia coli., Proc Natl Acad Sci U S A 90(4):1212-6
[2] Inoue H., Noumi T., Tsuchiya T., Kanazawa H., 1995, Essential aspartic acid residues, Asp-133, Asp-163 and Asp-164, in the transmembrane helices of a Na+/H+ antiporter (NhaA) from Escherichia coli., FEBS Lett 363(3):264-8
[3] Ishikawa T., Hama H., Tsuda M., Tsuchiya T., 1987, Isolation and properties of a mutant of Escherichia coli possessing defective Na+/H+ antiporter., J Biol Chem 262(16):7443-6
[4] Kayahara T., Thelen P., Ogawa W., Inaba K., Tsuda M., Goldberg EB., Tsuchiya T., 1992, Properties of recombinant cells capable of growing on serine without NhaB Na+/H+ antiporter in Escherichia coli., J Bacteriol 174(22):7482-5
[5] Lewinson O., Padan E., Bibi E., 2004, Alkalitolerance: a biological function for a multidrug transporter in pH homeostasis., Proc Natl Acad Sci U S A 101(39):14073-8
[6] Maurer LM., Yohannes E., Bondurant SS., Radmacher M., Slonczewski JL., 2005, pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12., J Bacteriol 187(1):304-19
[7] Ohyama T., Imaizumi R., Igarashi K., Kobayashi H., 1992, Escherichia coli is able to grow with negligible sodium ion extrusion activity at alkaline pH., J Bacteriol 174(23):7743-9
[8] Padan E., Gerchman Y., Rimon A., Rothman A., Dover N., Carmel-Harel O., 1999, The molecular mechanism of regulation of the NhaA Na+/H+ antiporter of Escherichia coli, a key transporter in the adaptation to Na+ and H+., Novartis Found Symp 221:183-96: discussion 196-9
[9] Padan E., Maisler N., Taglicht D., Karpel R., Schuldiner S., 1989, Deletion of ant in Escherichia coli reveals its function in adaptation to high salinity and an alternative Na+/H+ antiporter system(s)., J Biol Chem 264(34):20297-302
[10] Rimon A., Gerchman Y., Olami Y., Schuldiner S., Padan E., 1995, Replacements of histidine 226 of NhaA-Na+/H+ antiporter of Escherichia coli. Cysteine (H226C) or serine (H226S) retain both normal activity and pH sensitivity, aspartate (H226D) shifts the pH profile toward basic pH, and alanine (H226A) inactivates the carrier at all pH values., J Biol Chem 270(45):26813-7
[11] Rimon A., Tzubery T., Padan E., 2007, Monomers of the NhaA Na+/H+ antiporter of Escherichia coli are fully functional yet dimers are beneficial under extreme stress conditions at alkaline pH in the presence of Na+ or Li+., J Biol Chem 282(37):26810-21
[12] Rowbury RJ., Goodson M., Humphrey TJ., 1994, Sodium chloride induces an NhaA/NhaR-independent acid sensitivity at neutral external pH in Escherichia coli., Appl Environ Microbiol 60(5):1630-4
[13] Rowbury RJ., Hussain NH., 1996, Exposure of Escherichia coli to acid habituation conditions sensitizes it to alkaline stress., Lett Appl Microbiol 22(1):57-61
[14] Shijuku T., Saito H., Kakegawa T., Kobayashi H., 2001, Expression of sodium/proton antiporter NhaA at various pH values in Escherichia coli., Biochim Biophys Acta 1506(3):212-7
[15] Shimamoto T., Inaba K., Thelen P., Ishikawa T., Goldberg EB., Tsuda M., Tsuchiya T., 1994, The NhaB Na+/H+ antiporter is essential for intracellular pH regulation under alkaline conditions in Escherichia coli., J Biochem 116(2):285-90
[16] Verkhovskaya ML., Verkhovsky MI., Wikstrom M., 1996, K+-dependent Na+ transport driven by respiration in Escherichia coli cells and membrane vesicles., Biochim Biophys Acta 1273(3):207-16
[17] 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
[18] 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] Gerchman Y., Olami Y., Rimon A., Taglicht D., Schuldiner S., Padan E., 1993, Histidine-226 is part of the pH sensor of NhaA, a Na+/H+ antiporter in Escherichia coli., Proc Natl Acad Sci U S A 90(4):1212-6

[2] Inoue H., Noumi T., Tsuchiya T., Kanazawa H., 1995, Essential aspartic acid residues, Asp-133, Asp-163 and Asp-164, in the transmembrane helices of a Na+/H+ antiporter (NhaA) from Escherichia coli., FEBS Lett 363(3):264-8

[3] Ishikawa T., Hama H., Tsuda M., Tsuchiya T., 1987, Isolation and properties of a mutant of Escherichia coli possessing defective Na+/H+ antiporter., J Biol Chem 262(16):7443-6

[4] Kayahara T., Thelen P., Ogawa W., Inaba K., Tsuda M., Goldberg EB., Tsuchiya T., 1992, Properties of recombinant cells capable of growing on serine without NhaB Na+/H+ antiporter in Escherichia coli., J Bacteriol 174(22):7482-5

[5] Lewinson O., Padan E., Bibi E., 2004, Alkalitolerance: a biological function for a multidrug transporter in pH homeostasis., Proc Natl Acad Sci U S A 101(39):14073-8

[6] Maurer LM., Yohannes E., Bondurant SS., Radmacher M., Slonczewski JL., 2005, pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12., J Bacteriol 187(1):304-19

[7] Ohyama T., Imaizumi R., Igarashi K., Kobayashi H., 1992, Escherichia coli is able to grow with negligible sodium ion extrusion activity at alkaline pH., J Bacteriol 174(23):7743-9

[8] Padan E., Gerchman Y., Rimon A., Rothman A., Dover N., Carmel-Harel O., 1999, The molecular mechanism of regulation of the NhaA Na+/H+ antiporter of Escherichia coli, a key transporter in the adaptation to Na+ and H+., Novartis Found Symp 221:183-96: discussion 196-9

[9] Padan E., Maisler N., Taglicht D., Karpel R., Schuldiner S., 1989, Deletion of ant in Escherichia coli reveals its function in adaptation to high salinity and an alternative Na+/H+ antiporter system(s)., J Biol Chem 264(34):20297-302

[10] Rimon A., Gerchman Y., Olami Y., Schuldiner S., Padan E., 1995, Replacements of histidine 226 of NhaA-Na+/H+ antiporter of Escherichia coli. Cysteine (H226C) or serine (H226S) retain both normal activity and pH sensitivity, aspartate (H226D) shifts the pH profile toward basic pH, and alanine (H226A) inactivates the carrier at all pH values., J Biol Chem 270(45):26813-7

[11] Rimon A., Tzubery T., Padan E., 2007, Monomers of the NhaA Na+/H+ antiporter of Escherichia coli are fully functional yet dimers are beneficial under extreme stress conditions at alkaline pH in the presence of Na+ or Li+., J Biol Chem 282(37):26810-21

[12] Rowbury RJ., Goodson M., Humphrey TJ., 1994, Sodium chloride induces an NhaA/NhaR-independent acid sensitivity at neutral external pH in Escherichia coli., Appl Environ Microbiol 60(5):1630-4

[13] Rowbury RJ., Hussain NH., 1996, Exposure of Escherichia coli to acid habituation conditions sensitizes it to alkaline stress., Lett Appl Microbiol 22(1):57-61

[14] Shijuku T., Saito H., Kakegawa T., Kobayashi H., 2001, Expression of sodium/proton antiporter NhaA at various pH values in Escherichia coli., Biochim Biophys Acta 1506(3):212-7

[15] Shimamoto T., Inaba K., Thelen P., Ishikawa T., Goldberg EB., Tsuda M., Tsuchiya T., 1994, The NhaB Na+/H+ antiporter is essential for intracellular pH regulation under alkaline conditions in Escherichia coli., J Biochem 116(2):285-90

[16] Verkhovskaya ML., Verkhovsky MI., Wikstrom M., 1996, K+-dependent Na+ transport driven by respiration in Escherichia coli cells and membrane vesicles., Biochim Biophys Acta 1273(3):207-16

[17] 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

[18] 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.