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Expression|

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Standard Name	ybeX
Gene Synonym(s)	ECK0650, b0658, JW0655^[1], corC, JW0655
Product Desc.	predicted ion transport protein^[2]^[3] Salmonella ortholog involved in Co2+ and Mg2+ efflux; contains two CBS domains; integral membrane protein; possible hemolysin (by homology)^[4]
Product Synonyms(s)	predicteed ion transport^[1], B0658^[2]^[1], YbeX^[2]^[1] , corC, ECK0650, JW0655, b0658
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lnt^[2]
Regulation/Activity
Quick Links
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Notes

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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	ybeX
Mnemonic	Systematic nomenclature
Synonyms	ECK0650, b0658, JW0655^[1], corC, JW0655
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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	14.87 minutes	MG1655: 691007..690129 <gbrowseImage> name=NC_000913:690129..691007 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 673879..673001 <gbrowseImage> name=NC_012967:673001..673879 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 592889..593767 <gbrowseImage> name=NC_012759:592889..593767 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 692206..691328 <gbrowseImage> name=NC_007779:691328..692206 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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: Type	Phenotype: Description	Reference	Availability
ΔybeX (Keio:JW0655)	deletion	deletion			PMID:16738554	Shigen CGSC8746^[5]
ΔybeX::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔybeX789::kan					PMID:16738554	CGSC:103750
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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
JW0655	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGACGACAATTCACACAG Primer 2:CCTTCATCCAGCTTCGGCTGGGG
3A2	Kohara Phage	Genobase	PMID:3038334
16A8	Kohara Phage	Genobase	PMID:3038334
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 23% ^[6] Synonyms:zbe-280::Tn10
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[5]	est. P1 cotransduction: 70% ^[6] Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
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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:G6361	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13654	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002968	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946417	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3418	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002252	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	YbeX
Synonyms	predicteed ion transport^[1], B0658^[2]^[1], YbeX^[2]^[1] , corC, ECK0650, JW0655, b0658
Product description	predicted ion transport protein^[2]^[3] Salmonella ortholog involved in Co2+ and Mg2+ efflux; contains two CBS domains; integral membrane protein; possible hemolysin (by homology)^[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
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0050897	cobalt ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0170	F	Seeded from EcoCyc (v14.0)	complete
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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	References	Evidence
Protein	mcrB	PMID:19402753	LCMS(ID Probability):99.5
Protein	rfaE	PMID:19402753	MALDI(Z-score):26.920244
Protein	yrdA	PMID:19402753	MALDI(Z-score):19.281282
Protein	tolR	PMID:19402753	LCMS(ID Probability):97.7
Protein	ompN	PMID:19402753	LCMS(ID Probability):99.6
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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	Notes
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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 MSDDNSHSSD TISNKKGFFS LLLSQLFHGE PKNRDELLAL IRDSGQNDLI DEDTRDMLEG VMDIADQRVR DIMIPRSQMI TLKRNQTLDE CLDVIIESAH SRFPVISEDK DHIEGILMAK DLLPFMRSDA EAFSMDKVLR QAVVVPESKR VDRMLKEFRS QRYHMAIVID EFGGVSGLVT IEDILELIVG EIEDEYDEED DIDFRQLSRH TWTVRALASI EDFNEAFGTH FSDEEVDTIG GLVMQAFGHL PARGETIDID GYQFKVAMAD SRRIIQVHVK IPDDSPQPKL DE
Length	292
Mol. Wt	33.299 kDa
pI	4.4 (calculated)
Extinction coefficient	9,970 - 10,095 (calc based on 3 Y, 1 W, and 1 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	References
Domain	69..128	PF00571 CBS domain	PMID:19920124
Domain	135..190	PF00571 CBS domain	PMID:19920124
Domain	205..283	PF03471 Transporter associated domain	PMID:19920124
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<motif_map/>

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

Structures

<beststructure> gene=ybeX 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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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:16128641	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946417	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002252	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AE78	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6361	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13654	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946417	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002968	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3418	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	Notes	Reference(s)
Protein	E. coli K-12 MC4100	2.63E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	43.68+/-0.335	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.07336+/-0.00875	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.137813212	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	1280	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	665	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	1216	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)
lnt
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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_000913:690987..691027 source=MG1655 flip=1 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:b0658 (EcoliWiki Page)	NCBI GEO profiles for ybeX
microarray	GenExpDB:b0658 (EcoliWiki Page)	Summary of data for ybeX 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 ybeX Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6361	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3418	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0658
EcoGene	EcoGene:EG13654	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002968	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002252	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
Caenorhabditis briggsae	YP_026171 (score: 1.000; bootstrap: 100%) WBGene00035721 (score: 1.000; bootstrap: 100%) WBGene00023760 (score: 0.221) WBGene00034721 (score: 0.055)	From Inparanoid:20070104
Dictyostelium discoideum	YP_026171 (score: 0.060) DDB0206299 (score: 1.000; bootstrap: 80%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YP_026171 (score: 1.000; bootstrap: 100%) YOL060C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	YP_026171 (score: 1.000; bootstrap: 100%) SPCC4B33c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000128918 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000145364 (score: 0.294)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00003869001 (score: 1.000; bootstrap: 100%) GSTENP00010692001 (score: 0.424) GSTENP00025339001 (score: 0.291) GSTENP00025350001 (score: 0.276) GSTENP00025330001 (score: 0.211)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000009581 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	YBEX	From SHIGELLACYC
E. coli O157	YBEX	From ECOO157CYC
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Do-It-Yourself Web Tools

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)	PF03471 Transporter associated domain
Pfam (EcoliWiki Page)	PF00571 CBS domain
Pfam (EcoliWiki Page)	PF00571 CBS domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:54631
Superfamily (EcoliWiki Page)	SUPERFAMILY:54631
EcoCyc	EcoCyc:G6361	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13654	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002968	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3418	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002252	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).

ybeX: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 ybeX Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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