yphG:On One Page

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

Quickview

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Standard Name

yphG

Gene Synonym(s)

ECK2546, b2549, JW5405[1], JW5405

Product Desc.

conserved protein[2][3]

Function unknown[4]

Product Synonyms(s)

conserved protein[1], B2549[2][1], YphG[2][1] , ECK2546, JW5405, b2549

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yphG[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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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

yphG

Mnemonic

Systematic nomenclature

Synonyms

ECK2546, b2549, JW5405[1], JW5405

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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

57.71 minutes, 57.71 minutes 

MG1655: 2680767..2677486
<gbrowseImage> name=NC_000913:2677486..2680767 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2603444..2600163
<gbrowseImage> name=NC_012967:2600163..2603444 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2563291..2566572
<gbrowseImage> name=NC_012759:2563291..2566572 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2681401..2678120
<gbrowseImage> name=NC_007779:2678120..2681401 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2772532..2769251
<gbrowseImage> name=NC_010473:2769251..2772532 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

ΔyphG (Keio:JW5405)

deletion

deletion

PMID:16738554

Shigen
CGSC11369[5]

ΔyphG::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔyphG723::kan

PMID:16738554

CGSC:105932


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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

JW5405

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTCCAGTAAAAGTGTGGCA

Primer 2:CCGTGAACGCGGTTAAAAATAAA

8E12

Kohara Phage

Genobase

PMID:3038334

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 60% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 28% [6]

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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:G7343

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13468

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003913

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947021

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3241

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008380

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

YphG

Synonyms

conserved protein[1], B2549[2][1], YphG[2][1] , ECK2546, JW5405, b2549

Product description

conserved protein[2][3]

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:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011990

F

Seeded from EcoCyc (v14.0)

complete

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 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

MRDYSAKTLP DCSIHCHKSF NSVCLVNIEG TMTPVKVWQE RVEIPTYETG PQDIHPMFLE
NRVYQGSSGA VYPYGVTDTL SEQKTLKSWQ AVWLENDYIK VMILPELGGR VHRAWDKVKQ
RDFVYHNEVI KPALVGLLGP WISGGIEFNW PQHHRPTTFM PVDFTLEAHE DGAQTVWVGE
TEPMHGLQVM TGFTLRPDRA ALEIASRVYN GNATPRHFLW WANPAVKGGE GHQSVFPPDV
TAVFDHGKRA VSAFPIATGT YYKVDYSAGV DISRYKNVPV PTSYMAEKSQ YDFVGAWCHD
EDGGLLHVAN HHIAPGKKQW SWGHSEFGQA WDKSLTDNNG PYIELMTGIF ADNQPDFTWL
DAYEEKRFEQ YFLPYHSLGM VQNASRDAVI KLQRSKRGIE WGLYAISPLN GYRLAIREIG
KCNALLDDAV ALMPATAIQG VLHGINPERL TIELSDADGN IVLSYQEHQP QALPLPDVAK
APLAAQDITS TDEAWFIGQH LEQYHHASRS PFDYYLRGVA LDPLDYRCNL ALAMLEYNRA
DFPQAVAYAT QALKRAHALN KNPQCGQASL IRASAYERQG QYQQAEEDFW RAVWSGNSKA
GGYYGLARLA ARNGNFDAGL DFCQQSLRAC PTNQEVLCLH NLLLVLSGRQ DNARVQREKL
LRDYPLNATL WWLNWFDGRS ESALAQWRGL CQGRDVNALM TAGQLINWGM PTLAAEMLNA
LDCQRTLPLY LQASLLPKAE RGELVAKAID VFPQFVRFPN TLEEVAALES IEECWFARHL
LACFYYNKRS YNKAIAFWQR CVEMSPEFAD GWRGLAIHAW NKQHDYELAA RYLDNAYQLA
PQDARLLFER DLLDKLSGAT PEKRLARLEN NLEIALKRDD MTAELLNLWH LTGQADKAAD
ILATRKFHPW EGGEGKVTSQ FILNQLLRAW QHLDARQPQQ ACELLHAALH YPENLSEGRL
PGQTDNDIWF WQAICANAQG DETEATRCLR LAATGDRTIN IHSYYNDQPV DYLFWQGMAL
RLLGEQQTAQ QLFSEMKQWA QEMAKTSIEA DFFAVSQPDL LSLYGDLQQQ HKEKCLMVAM
LASAGLGEVA QYESARAELT AINPAWPKAA LFTTVMPFIF NRVH
Length

1,124

Mol. Wt

127.285 kDa

pI

6.1 (calculated)

Extinction coefficient

259,550 - 261,925 (calc based on 45 Y, 35 W, and 19 C residues)


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

<motif_map/>

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

Structures

<beststructure> gene=yphG 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:162135907

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947021

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008380

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76585

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7343

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13468

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947021

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003913

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3241

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 MG1655

1a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

2

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

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)

yphG

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_000913:2680747..2680787 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


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2549 (EcoliWiki Page)

NCBI GEO profiles for yphG

microarray

GenExpDB:b2549 (EcoliWiki Page)

Summary of data for yphG from multiple microarray studies


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 (2680758..2680903) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ19; Well:C12[7]

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Notes

Accessions Related to yphG Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7343

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3241

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2549

EcoGene

EcoGene:EG13468

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003913

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008380

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

Organism Homologs (Statistics) Comments

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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:48452

Superfamily (EcoliWiki Page)

SUPERFAMILY:48452

Panther (EcoliWiki Page)

PTHR23083:SF42

EcoCyc

EcoCyc:G7343

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13468

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003913

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3241

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008380

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 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

Categories

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