ygeV: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

ygeV

Gene Synonym(s)

ECK2865, b2869, JW2837[1], JW2837

Product Desc.

putative transcriptional regulator[2][3]

Putative RpoN-dependent transcriptional activator, function unknown; induced by AI-2 pheromone[4]

Product Synonyms(s)

predicted DNA-binding transcriptional regulator[1], B2869[2][1], YgeV[2][1] , ECK2865, JW2837, b2869

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ygeV[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. 60 (http://afmb.cnrs-mrs.fr/article171.html).[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

ygeV

Mnemonic

Systematic nomenclature

Synonyms

ECK2865, b2869, JW2837[1], JW2837

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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

64.7 minutes 

MG1655: 3003808..3002030
<gbrowseImage> name=NC_000913:3002030..3003808 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2891541..2889763
<gbrowseImage> name=NC_012967:2889763..2891541 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2889178..2890956
<gbrowseImage> name=NC_012759:2889178..2890956 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3004442..3002664
<gbrowseImage> name=NC_007779:3002664..3004442 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3097678..3095900
<gbrowseImage> name=NC_010473:3095900..3097678 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

ΔygeV (Keio:JW2837)

deletion

deletion

PMID:16738554

Shigen
CGSC10206[5]

ΔygeV720::kan

PMID:16738554

CGSC:104956


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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

JW2837

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAGCTTGCTACTACGCAGTC

Primer 2:CCTGTGTTTAACAACTCATATTT

15G6

Kohara Phage

Genobase

PMID:3038334

10D8

Kohara Phage

Genobase

PMID:3038334

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[5]

est. P1 cotransduction: 9% [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[5]

est. P1 cotransduction: % [6]
Synonyms:zgd-210::Tn10, zgf-210::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:G7488

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13052

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004051

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947320

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2864

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009420

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

YgeV

Synonyms

predicted DNA-binding transcriptional regulator[1], B2869[2][1], YgeV[2][1] , ECK2865, JW2837, b2869

Product description

putative transcriptional regulator[2][3]

Putative RpoN-dependent transcriptional activator, function unknown; induced by AI-2 pheromone[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:0000160

two-component signal transduction system (phosphorelay)

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0902

P

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002197

F

Seeded from EcoCyc (v14.0)

complete

GO:0004871

signal transducer activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000014

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

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:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

PMID:15556475

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0AFB8
Swiss-Prot:P37344
Swiss-Prot:P19323

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002197

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000014

P

Seeded from EcoCyc (v14.0)

complete

GO:0008134

transcription factor binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:15556475

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0AFB8
Swiss-Prot:P37344
Swiss-Prot:P19323

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

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 Notes References Evidence

Protein

htpG

PMID:16606699

Experiment(s):EBI-1144158

Protein

rplB

PMID:16606699

Experiment(s):EBI-1144158

Protein

groL

PMID:16606699

Experiment(s):EBI-1144158

Protein

pyrG

PMID:16606699

Experiment(s):EBI-1144158

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1144158

Protein

ompL

PMID:16606699

Experiment(s):EBI-1144158

Protein

lon

PMID:15690043

Experiment(s):EBI-888778

Protein

lpdA

PMID:15690043

Experiment(s):EBI-888778

Protein

tufA

PMID:15690043

Experiment(s):EBI-888778

Protein

tufB

PMID:19402753

MALDI(Z-score):19.384884

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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 

MELATTQSVL MQIQPTIQRF ARMLASVLQL EVEIVDENLC RVAGTGAYGK FLGRQLSGNS
RLLRHVLETK TEKVVTQSRF DPLCEGCDSK ENCREKAFLG TPVILQDRCV GVISLIAVTH
EQQEHISDNL REFSDYVRHI STIFVSKLLE DQGPGDNISK IFATMIDNMD QGVLVVDDEN
RVQFVNQTAL KTLGVVQNNI IGKPIRFRPL TFESNFTHGH MQHIVSWDDK SELIIGQLHN
IQGRQLFLMA FHQSHTSFSV ANAPDEPHIE QLVGECRVMR QLKRLISRIA PSPSSVMVVG
ESGTGKEVVA RAIHKLSGRR NKPFIAINCA AIPEQLLESE LFGYVKGAFT GASANGKTGL
IQAANTGTLF LDEIGDMPLM LQAKLLRAIE AREILPIGAS SPIQVDIRII SATNQNLAQF
IAEGKFREDL FYRLNVIPIT LPPLRERQED IELLVHYFLH LHTRRLGSVY PGIAPDVVEI
LRKHRWPGNL RELSNLMEYL VNVVPSGEVI DSTLLPPNLL NNGTTEQSDV TEVSEAHLSL
DDAGGTALEE MEKQMIREAL SRHNSKKQVA DELGIGIATL YRKIKKYELL NT
Length

592

Mol. Wt

66.096 kDa

pI

6.5 (calculated)

Extinction coefficient

24,410 - 25,285 (calc based on 9 Y, 2 W, and 7 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

547..587

PF02954 Bacterial regulatory protein, Fis family

PMID:19920124

Domain

272..440

PF00158 Sigma-54 interaction 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=ygeV 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:16130771

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947320

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009420

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q46802

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7488

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13052

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947320

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004051

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2864

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

Ecoli K-12

1.041+/-0.044

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.005061867

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

11

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

7

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

0a

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

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)

ygeV

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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_000913:3003788..3003828 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:b2869 (EcoliWiki Page)

NCBI GEO profiles for ygeV

microarray

GenExpDB:b2869 (EcoliWiki Page)

Summary of data for ygeV 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 ygeV Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7488

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2864

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2869

EcoGene

EcoGene:EG13052

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004051

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009420

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Arabidopsis thaliana

  • AT1G19050 (score: 1.000; bootstrap: 100%)
  • AT1G74890 (score: 0.581)
  • AT5G24470 (score: 0.061)
  • AT5G02810 (score: 0.052)

From Inparanoid:20070104

Oryza gramene

  • Q4GZL0 (score: 1.000; bootstrap: 100%)
  • Q9FRY8 (score: 0.455)
  • Q6YVX7 (score: 0.448)
  • Q4GZK9 (score: 0.448)
  • Q7XRI1 (score: 0.361)
  • Q6H468 (score: 0.164)
  • Q9FRZ0 (score: 0.159)
  • Q9FXQ7 (score: 0.157)
  • Q7XKF6 (score: 0.157)
  • Q4GZK6 (score: 0.152)
  • Q942A1 (score: 0.152)
  • Q4GZK7 (score: 0.152)
  • Q9FRZ1 (score: 0.147)
  • Q6K9T0 (score: 0.144)
  • Q4GZK8 (score: 0.144)
  • Q4GZK2 (score: 0.137)
  • Q9FRY9 (score: 0.134)
  • Q9S7U8 (score: 0.134)
  • Q7XQA6 (score: 0.134)
  • Q4JF20 (score: 0.134)
  • Q4GZK5 (score: 0.134)
  • Q8H5N4 (score: 0.122)
  • Q4GZK4 (score: 0.122)
  • Q9ZQW0 (score: 0.117)
  • Q8GVV6 (score: 0.092)
  • Q4GZK3 (score: 0.092)
  • Q8GVV1 (score: 0.055)
  • Q6YZK8 (score: 0.055)

From Inparanoid:20070104

E. coli O157

YGEV

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

Pfam (EcoliWiki Page)

PF02954 Bacterial regulatory protein, Fis family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR10919:SF1

Superfamily (EcoliWiki Page)

SUPERFAMILY:55785

Pfam (EcoliWiki Page)

PF00158 Sigma-54 interaction domain

EcoCyc

EcoCyc:G7488

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13052

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004051

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2864

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009420

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 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. ↑ 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. ↑ 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).

Categories

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