ybeZ:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

ybeZ

Gene Synonym(s)

ECK0652, b0660, JW0657, phoL[1], phoL

Product Desc.

predicted protein with nucleoside triphosphate hydrolase domain[2][3]

PhoH paralog, function unknown[4]

Product Synonyms(s)

predicted protein with nucleoside triphosphate hydrolase domain[1], B0660[2][1], YbeZ[2][1], PhoL[2][1] , ECK0652, JW0657, phoL, b0660

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ybeY[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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AFMB Structural Genomics target No. 14 (http://afmb.cnrs-mrs.fr/article171.html) ybeZ has been experimentally shown NOT to be part of the pho regulon: personal communication, March, 2003, B. Wanner, Purdue Univ., IN.[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

ybeZ

Mnemonic

Systematic nomenclature

Synonyms

ECK0652, b0660, JW0657, phoL[1], phoL

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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

14.91 minutes 

MG1655: 692640..691561
<gbrowseImage> name=NC_000913:691561..692640 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 675512..674433
<gbrowseImage> name=NC_012967:674433..675512 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 594321..595361
<gbrowseImage> name=NC_012759:594321..595361 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 693839..692760
<gbrowseImage> name=NC_007779:692760..693839 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 745193..744153
<gbrowseImage> name=NC_010473:744153..745193 source=DH10B preset=GeneLocation </gbrowseImage>

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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 Comments

ΔybeZ (Keio:JW0657)

deletion

deletion

PMID:16738554

Shigen
CGSC8748[5]

ΔybeZ720::kan

PMID:16738554

CGSC:103754


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Notes

Genetic Interactions

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<protect>

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

JW0657

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTCAGCTTCCGGCGGCATAC

Primer 2:CCTTTTTGTTCCTGTTCTTCGCG

16A8

Kohara Phage

Genobase

PMID:3038334

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[5]

est. P1 cotransduction: 21% [6]
Synonyms:zbe-280::Tn10

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[5]

est. P1 cotransduction: 74% [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:G6363

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13656

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002970

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948044

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3420

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002257

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

YbeZ

Synonyms

predicted protein with nucleoside triphosphate hydrolase domain[1], B0660[2][1], YbeZ[2][1], PhoL[2][1] , ECK0652, JW0657, phoL, b0660

Product description

predicted protein with nucleoside triphosphate hydrolase domain[2][3]

PhoH paralog, function unknown[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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003714

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

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 Notes References Evidence

Protein

ycfB

PMID:15690043

Experiment(s):EBI-887500

Protein

aceE

PMID:15690043

Experiment(s):EBI-887500

Protein

aceF

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

norV

PMID:15690043

Experiment(s):EBI-887500

Protein

deaD

PMID:15690043

Experiment(s):EBI-887500

Protein

fabZ

PMID:15690043

Experiment(s):EBI-887500

Protein

lpdA

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

pssA

PMID:15690043

Experiment(s):EBI-887500

Protein

rplA

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplB

PMID:15690043

Experiment(s):EBI-887500

Protein

rplC

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplD

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplE

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplF

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplI

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplJ

PMID:15690043

Experiment(s):EBI-887500

Protein

rplM

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplS

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplV

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rplX

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rpsA

PMID:15690043

Experiment(s):EBI-887500

Protein

rpsB

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rpsD

PMID:15690043

Experiment(s):EBI-887500

Protein

rpsE

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rpsG

PMID:15690043

Experiment(s):EBI-887500, EBI-893285

Protein

rpsM

PMID:15690043

Experiment(s):EBI-887500

Protein

secA

PMID:15690043

Experiment(s):EBI-887500

Protein

rnr

PMID:15690043

Experiment(s):EBI-887500

Protein

ycbY

PMID:15690043

Experiment(s):EBI-887500

Protein

rluB

PMID:15690043

Experiment(s):EBI-887500

Protein

yfcB

PMID:15690043

Experiment(s):EBI-887500

Protein

yfiF

PMID:15690043

Experiment(s):EBI-887500

Protein

fur

PMID:16606699

Experiment(s):EBI-1137631

Protein

cyaA

PMID:16606699

Experiment(s):EBI-1137631

Protein

malT

PMID:16606699

Experiment(s):EBI-1137631

Protein

cusB

PMID:16606699

Experiment(s):EBI-1137631

Protein

hupA

PMID:15690043

Experiment(s):EBI-893285

Protein

rplL

PMID:15690043

Experiment(s):EBI-893285

Protein

rplO

PMID:15690043

Experiment(s):EBI-893285

Protein

rplP

PMID:15690043

Experiment(s):EBI-893285

Protein

rplT

PMID:15690043

Experiment(s):EBI-893285

Protein

rplU

PMID:15690043

Experiment(s):EBI-893285

Protein

rplY

PMID:15690043

Experiment(s):EBI-893285

Protein

rpmB

PMID:15690043

Experiment(s):EBI-893285

Protein

rpmG

PMID:15690043

Experiment(s):EBI-893285

Protein

rpsC

PMID:15690043

Experiment(s):EBI-893285

Protein

rpsN

PMID:15690043

Experiment(s):EBI-893285

Protein

rpsP

PMID:15690043

Experiment(s):EBI-893285

Protein

rpsT

PMID:15690043

Experiment(s):EBI-893285

Protein

uvrD

PMID:15690043

Experiment(s):EBI-893285

Protein

ybcJ

PMID:15690043

Experiment(s):EBI-893285

Protein

yhbY

PMID:15690043

Experiment(s):EBI-893285

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

rfaD

PMID:19402753

MALDI(Z-score):24.352310

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):7.301335

Protein

rplY

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):37.441737

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):5.254930

Protein

rpsA

PMID:19402753

MALDI(Z-score):27.592595

Protein

rplS

PMID:19402753

LCMS(ID Probability):81.2 MALDI(Z-score):28.151356

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):33.498138

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

uvrD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753

LCMS(ID Probability):90.2 MALDI(Z-score):26.902453

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.830013

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.268957

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):20.747207

Protein

rplB

PMID:19402753

MALDI(Z-score):33.863813

Protein

prmB

PMID:19402753

MALDI(Z-score):25.226966

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.935310

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):33.866547

Protein

rpsD

PMID:19402753

MALDI(Z-score):39.178932

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):31.220102

Protein

yhbY

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):20.841996

Protein

pssA

PMID:19402753

MALDI(Z-score):25.353822

Protein

ybcJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rnr

PMID:19402753

MALDI(Z-score):27.338588

Protein

yfiF

PMID:19402753

MALDI(Z-score):34.396572

Protein

deaD

PMID:19402753

MALDI(Z-score):28.189812

Protein

rluB

PMID:19402753

MALDI(Z-score):34.419817

Protein

rplL

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 

MFSFRRHTDK RNGLNIDTRE ITLEPADNAR LLSLCGPFDD NIKQLERRLG IEINRRDNHF
KLTGRPICVT AAADILRSLY VDTAPMRGQI QDIEPEQIHL AIKEARVLEQ SAESVPEYGK
AVNIKTKRGV IKPRTPNQAQ YIANILDHDI TFGVGPAGTG KTYLAVAAAV DALERQEIRR
ILLTRPAVEA GEKLGFLPGD LSQKVDPYLR PLYDALFEML GFEKVEKLIE RNVIEVAPLA
YMRGRTLNDA FIILDESQNT TIEQMKMFLT RIGFNSKAVI TGDVTQIDLP RNTKSGLRHA
IEVLADVEEI SFNFFHSEDV VRHPVVARIV NAYEAWEEAE QKRKAALAAE RKREEQEQK
Length

359

Mol. Wt

40.655 kDa

pI

6.7 (calculated)

Extinction coefficient

17,420 - 17,670 (calc based on 8 Y, 1 W, and 2 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

117..321

PF02562 PhoH-like protein

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=ybeZ 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:145698230

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948044

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002257

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9K3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6363

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13656

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948044

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002970

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3420

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

1.13E+03

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

56.629+/-0.502

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.084337349

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

2115

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

885

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

1762

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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<protect>

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

Transcription unit(s)

ybeY

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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_000913:692620..692660 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

</protect>

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:b0660 (EcoliWiki Page)

NCBI GEO profiles for ybeZ

microarray

GenExpDB:b0660 (EcoliWiki Page)

Summary of data for ybeZ 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

GFP Fusion

Intergenic region (692572..692795) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:C5[7]

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Notes

Accessions Related to ybeZ Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6363

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3420

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0660

EcoGene

EcoGene:EG13656

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002970

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002257

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Xenopus tropicalis

  • ENSXETP00000023143 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YBEZ

From SHIGELLACYC

E. coli O157

YBEZ

From ECOO157CYC

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Do-It-Yourself Web Tools

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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

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF02562 PhoH-like protein

EcoCyc

EcoCyc:G6363

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13656

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002970

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3420

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002257

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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