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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	clcA
Gene Synonym(s)	ECK0154, b0155, JW5012, eriC, yadQ^[1], yadQ
Product Desc.	EriC chloride ion ClC channel^[2]^[3] Voltage-gated ClC-type chloride channel; involved in the extreme acid response^[4]
Product Synonyms(s)	chloride channel, voltage-gated^[1], B0155^[2]^[1], EriC^[2]^[1], ClcA^[2]^[1], YadQ^[2]^[1] , ECK0154, eriC, JW5012, yadQ, b0155
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): clcA^[2]
Regulation/Activity
Quick Links
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Notes

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ClcA and ClcB encode redundant chloride channels. Single mutants have no phenotype.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	clcA
Mnemonic	Chloride channel
Synonyms	ECK0154, b0155, JW5012, eriC, yadQ^[1], yadQ
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	3.77 minutes	MG1655: 175107..176528 <gbrowseImage> name=NC_000913:175107..176528 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 177949..179370 <gbrowseImage> name=NC_012967:177949..179370 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 175106..176527 <gbrowseImage> name=NC_012759:175106..176527 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 175107..176528 <gbrowseImage> name=NC_007779:175107..176528 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 149211..150632 <gbrowseImage> name=NC_010473:149211..150632 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
clcAY445F,W		Y445F,W	No effect			seeded from UniProt:P37019
clcAY445L		Y445L	Alters stoichiometry of proton/chloride exchange			seeded from UniProt:P37019
clcAY445A		Y445A	Abolishes gating, permitting continuous rapid transit of chloride ions; when associated with A-148			seeded from UniProt:P37019
clcAE203C,I,L,V		E203C,I,L,V	Abolishes proton and chloride transport			seeded from UniProt:P37019
clcAE203D,H		E203D,H	No effect on proton and chloride transport			seeded from UniProt:P37019
clcAE203K,R		E203K,R	Decreased proton and chloride transport			seeded from UniProt:P37019
clcAE148A,Q		E148A,Q	Abolishes proton transport, but permits the transit of chloride ions. Abolishes gating, permitting continuous rapid transit of chloride ions; when associated with A-445			seeded from UniProt:P37019
clcAE203A,G,Q,S,T		E203A,G,Q,S,T	Abolishes proton transport, and reduces chloride transport			seeded from UniProt:P37019
clcAS107A		S107A	Uncouples chloride transport from proton transport			seeded from UniProt:P37019
clcA(del) (Keio:JW5012)	deletion	deletion		PMID:16738554	Shigen CGSC11127^[5]
yadQ::Tn5KAN-I-SceI (FB20025)	Insertion at nt 389 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20025	contains pKD46
clcA770(del)::kan				PMID:16738554	CGSC:100334
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW5012	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAACTGATACTCCCTCTTT Primer 2:CCAGTATTCTCGCTGGCTGATGC
15A7	Kohara Phage	Genobase	PMID:3038334
9H2	Kohara Phage	Genobase	PMID:3038334
4E4	Kohara Phage	Genobase	PMID:3038334
21C8	Kohara Phage	Genobase	PMID:3038334
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 36% ^[6]
yafC502::Tn10	Linked marker	CAG18436 = CGSC7328^[5]	est. P1 cotransduction: 6% ^[6] Synonyms:zae-502::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12331	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12331	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946715	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002206	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2235	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000533	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	ClcA
Synonyms	chloride channel, voltage-gated^[1], B0155^[2]^[1], EriC^[2]^[1], ClcA^[2]^[1], YadQ^[2]^[1] , ECK0154, eriC, JW5012, yadQ, b0155
Product description	EriC chloride ion ClC channel^[2]^[3] Voltage-gated ClC-type chloride channel; involved in the extreme acid response^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source
plasma membrane	C-terminus localized in the cytoplasm with 10 predicted transmembrane domains	Daley et al. (2005) ^[7]
plasma membrane			From EcoCyc^[3]
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MKTDTPSLET PQAARLRRRQ LIRQLLERDK TPLAILFMAA VVGTLVGLAA VAFDKGVAWL QNQRMGALVH TADNYPLLLT VAFLCSAVLA MFGYFLVRKY APEAGGSGIP EIEGALEDQR PVRWWRVLPV KFFGGLGTLG GGMVLGREGP TVQIGGNIGR MVLDIFRLKG DEARHTLLAT GAAAGLAAAF NAPLAGILFI IEEMRPQFRY TLISIKAVFI GVIMSTIMYR IFNHEVALID VGKLSDAPLN TLWLYLILGI IFGIFGPIFN KWVLGMQDLL HRVHGGNITK WVLMGGAIGG LCGLLGFVAP ATSGGGFNLI PIATAGNFSM GMLVFIFVAR VITTLLCFSS GAPGGIFAPM LALGTVLGTA FGMVAVELFP QYHLEAGTFA IAGMGALLAA SIRAPLTGII LVLEMTDNYQ LILPMIITGL GATLLAQFTG GKPLYSAILA RTLAKQEAEQ LARSKAASAS ENT
Length	473
Mol. Wt	50.351 kDa
pI	9.8 (calculated)
Extinction coefficient	46,410 - 46,785 (calc based on 9 Y, 6 W, and 3 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	88..438	PF00654 Voltage gated chloride channel		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=clcA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16128148	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946715	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000533	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37019	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12331	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12331	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946715	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002206	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2235	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	137	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	50	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	63	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
clcA
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:175087..175127 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0155 (EcoliWiki Page)	NCBI GEO profiles for clcA
microarray	GenExpDB:b0155 (EcoliWiki Page)	Summary of data for clcA from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to clcA Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12331	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2235	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0155
EcoGene	EcoGene:EG12331	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002206	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000533	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000018612 (score: 1.000; bootstrap: 100%) ENSANGP00000018663 (score: 0.067) ENSANGP00000019052 (score: 0.061)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000022004 (score: 1.000; bootstrap: 100%) ENSAPMP00000004269 (score: 0.097)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G26240 (score: 1.000; bootstrap: 71%) AT5G49890 (score: 0.334) AT5G33280 (score: 0.325) AT5G40890 (score: 0.312) AT3G27170 (score: 0.312)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000001973 (score: 1.000; bootstrap: 100%) ENSBTAP00000014770 (score: 0.797) ENSBTAP00000039858 (score: 0.772) ENSBTAP00000016291 (score: 0.116) ENSBTAP00000021122 (score: 0.110) ENSBTAP00000027587 (score: 0.099) ENSBTAP00000012099 (score: 0.098) ENSBTAP00000014531 (score: 0.062)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00041732 (score: 1.000; bootstrap: 100%) WBGene00026154 (score: 0.095) WBGene00033929 (score: 0.070) WBGene00026047 (score: 0.062) WBGene00034871 (score: 0.059) WBGene00025876 (score: 0.055)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00000530 (score: 1.000; bootstrap: 100%) WBGene00000531 (score: 0.283) WBGene00000529 (score: 0.236) WBGene00000528 (score: 0.228) WBGene00000532 (score: 0.070)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000024331 (score: 1.000; bootstrap: 100%) ENSCAFP00000028947 (score: 0.252) ENSCAFP00000011380 (score: 0.088) ENSCAFP00000023526 (score: 0.085) ENSCAFP00000016986 (score: 0.082)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000014414 (score: 1.000; bootstrap: 100%) ENSCINP00000008574 (score: 0.062)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1379 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-2313 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0217756 (score: 1.000; bootstrap: 100%) DDB0215359 (score: 0.403) DDB0215063 (score: 0.403) DDB0169026 (score: 0.364) DDB0218077 (score: 0.159)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0036566 (score: 1.000; bootstrap: 100%) FBgn0051116 (score: 0.072) FBgn0033755 (score: 0.062)	From Inparanoid:20070104
Drosophila pseudoobscura	GA18785-PA (score: 1.000; bootstrap: 100%) GA21190-PA (score: 0.087) GA16020-PA (score: 0.069)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000026752 (score: 1.000; bootstrap: 100%) ENSGALP00000031721 (score: 0.791) ENSGALP00000015730 (score: 0.779) ENSGALP00000009650 (score: 0.291) ENSGALP00000007290 (score: 0.091) ENSGALP00000023640 (score: 0.089) ENSGALP00000012212 (score: 0.078) ENSGALP00000024538 (score: 0.055)	From Inparanoid:20070104
Homo sapiens	ENSP00000343213 (score: 1.000; bootstrap: 100%) ENSP00000262649 (score: 0.798) ENSP00000353857 (score: 0.788) ENSP00000265593 (score: 0.112) ENSP00000262318 (score: 0.110) ENSP00000234487 (score: 0.106) ENSP00000339867 (score: 0.098) ENSP00000332771 (score: 0.060) ENSP00000349974 (score: 0.059)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000030357 (score: 1.000; bootstrap: 100%) ENSMMUP00000017923 (score: 0.585) ENSMMUP00000013392 (score: 0.420) ENSMMUP00000009864 (score: 0.114) ENSMMUP00000010286 (score: 0.109) ENSMMUP00000023981 (score: 0.060)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000004121 (score: 1.000; bootstrap: 100%) ENSMODP00000014144 (score: 1.000; bootstrap: 100%) ENSMODP00000021752 (score: 0.792) ENSMODP00000003669 (score: 0.751) ENSMODP00000003112 (score: 0.356) ENSMODP00000001665 (score: 0.329) ENSMODP00000020222 (score: 0.096) ENSMODP00000013721 (score: 0.088)	From Inparanoid:20070104
Mus musculus	MGI:99486 (score: 1.000; bootstrap: 100%) MGI:104571 (score: 0.784) MGI:103555 (score: 0.784) MGI:105061 (score: 0.113) MGI:1347048 (score: 0.112) MGI:1347049 (score: 0.110) MGI:88417 (score: 0.096) MGI:1329026 (score: 0.060) MGI:1930643 (score: 0.053)	From Inparanoid:20070104
Oryza gramene	Q6YVX5 (score: 1.000; bootstrap: 54%) Q8LPA1 (score: 0.924) Q8LPA0 (score: 0.883) Q8LPA2 (score: 0.859) Q84QC8 (score: 0.794) Q5N8W8 (score: 0.673) Q7XTM5 (score: 0.555) Q6ZDC2 (score: 0.547) Q851D8 (score: 0.357)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000041062 (score: 1.000; bootstrap: 100%) ENSPTRP00000028470 (score: 0.797) ENSPTRP00000037098 (score: 0.185) ENSPTRP00000026999 (score: 0.125) ENSPTRP00000012980 (score: 0.110) ENSPTRP00000000295 (score: 0.093) ENSPTRP00000000391 (score: 0.065)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000003895 (score: 1.000; bootstrap: 100%) ENSRNOP00000004778 (score: 0.719) ENSRNOP00000014845 (score: 0.719) ENSRNOP00000048776 (score: 0.103) ENSRNOP00000023615 (score: 0.100) ENSRNOP00000011287 (score: 0.094) ENSRNOP00000013103 (score: 0.052)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC19C71 (score: 1.000; bootstrap: 100%) SPBC8872 (score: 0.080)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000163159 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000169437 (score: 0.178)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00008386001 (score: 1.000; bootstrap: 68%) GSTENP00026719001 (score: 0.650) GSTENP00015349001 (score: 0.395) GSTENP00020608001 (score: 0.117) GSTENP00010593001 (score: 0.086) GSTENP00005643001 (score: 0.065) GSTENP00019420001 (score: 0.061)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000004481 (score: 1.000; bootstrap: 81%) ENSXETP00000034303 (score: 0.544) ENSXETP00000050058 (score: 0.531)	From Inparanoid:20070104
Shigella flexneri	YADQ	From SHIGELLACYC
E. coli O157	YADQ	From ECOO157CYC
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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00654 Voltage gated chloride channel
Panther (EcoliWiki Page)	PTHR11689:SF14
Superfamily (EcoliWiki Page)	SUPERFAMILY:81340
EcoCyc	EcoCyc:EG12331	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12331	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002206	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2235	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000533	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

clcA:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to clcA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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