fryA: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

fryA

Gene Synonym(s)

ypdD, ECK2379, b2383, JW2380[1][2][3], JW2380

Product Desc.

fused predicted PTS system enzymes: Hpr component, enzyme I component, enzyme IIA component[3][2]

Putative fructose-like PTS system Enzyme I; also contains Hpr and EIIA domains[4]

Product Synonyms(s)

fused predicted PTS enzymes: Hpr component[1], enzyme I component[1], enzyme IIA component[1], B2383[3][1], FryA[3][1], YpdD[3][1] , ECK2379, JW2380, ypdD, b2383

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ypdD[3]

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. 41 (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

fryA

Mnemonic

Fructose

Synonyms

ypdD, ECK2379, b2383, JW2380[1][2][3], JW2380

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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

53.88 minutes 

MG1655: 2502507..2500012
<gbrowseImage> name=NC_000913:2500012..2502507 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2436215..2438710
<gbrowseImage> name=NC_012967:2436215..2438710 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2385817..2388312
<gbrowseImage> name=NC_012759:2385817..2388312 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2509931..2507436
<gbrowseImage> name=NC_007779:2507436..2509931 source=W3110 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

ΔfryA721::kan

PMID:16738554

CGSC:106184


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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

10D3

Kohara Phage

Genobase

PMID:3038334

12H4

Kohara Phage

Genobase

PMID:3038334

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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:G7246

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14151

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003821

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946852

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3903

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007861

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

YpdD

Synonyms

fused predicted PTS enzymes: Hpr component[1], enzyme I component[1], enzyme IIA component[1], B2383[3][1], FryA[3][1], YpdD[3][1] , ECK2379, JW2380, ypdD, b2383

Product description

fused predicted PTS system enzymes: Hpr component, enzyme I component, enzyme IIA component[3][2]

Putative fructose-like PTS system Enzyme I; also contains Hpr and EIIA domains[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015813

F

Seeded from EcoCyc (v14.0)

complete

GO:0005215

transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016152

F

Seeded from EcoCyc (v14.0)

complete

GO:0005351

sugar:hydrogen symporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000032

F

Seeded from EcoCyc (v14.0)

complete

GO:0005351

sugar:hydrogen symporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002178

F

Seeded from EcoCyc (v14.0)

complete

GO:0005351

sugar:hydrogen symporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005698

F

Seeded from EcoCyc (v14.0)

complete

GO:0005351

sugar:hydrogen symporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008731

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008731

C

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

GO:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002178

P

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016152

P

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:0008643

carbohydrate transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0762

P

Seeded from EcoCyc (v14.0)

complete

GO:0008965

phosphoenolpyruvate-protein phosphotransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008731

F

Seeded from EcoCyc (v14.0)

complete

GO:0008965

phosphoenolpyruvate-protein phosphotransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.3.9

F

Seeded from EcoCyc (v14.0)

complete

GO:0008982

protein-N(PI)-phosphohistidine-sugar phosphotransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004715

F

Seeded from EcoCyc (v14.0)

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000032

P

Seeded from EcoCyc (v14.0)

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002178

P

Seeded from EcoCyc (v14.0)

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004715

P

Seeded from EcoCyc (v14.0)

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005698

P

Seeded from EcoCyc (v14.0)

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008731

P

Seeded from EcoCyc (v14.0)

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0598

P

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004715

C

Seeded from EcoCyc (v14.0)

complete

GO:0016301

kinase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0418

F

Seeded from EcoCyc (v14.0)

complete

GO:0016310

phosphorylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000121

P

Seeded from EcoCyc (v14.0)

complete

GO:0016310

phosphorylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008279

P

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016772

transferase activity, transferring phosphorus-containing groups

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000121

F

Seeded from EcoCyc (v14.0)

complete

GO:0016772

transferase activity, transferring phosphorus-containing groups

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006318

F

Seeded from EcoCyc (v14.0)

complete

GO:0016772

transferase activity, transferring phosphorus-containing groups

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008279

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

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

aceE

PMID:15690043

Experiment(s):EBI-888357

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

fadJ

PMID:19402753

MALDI(Z-score):28.982958

Protein

rpsC

PMID:19402753

MALDI(Z-score):22.617135

Protein

der

PMID:19402753

MALDI(Z-score):28.491835

Protein

fadI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.291873

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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 

MLTIQFLCPL PNGLHARPAW ELKEQCSQWQ SEITFINHRQ NAKADAKSSL ALIGTGTLFN
DSCSLNISGS DEEQARRVLE EYIQVRFIDS DSVQPTQAEL TAHPLPRSLS RLNPDLLYGN
VLASGVGVGT LTLLQSDSLD SYRAIPASAQ DSTRLEHSLA TLAEQLNQQL RERDGESKTI
LSAHLSLIQD DEFAGNIRRL MTEQHQGLGA AIISNMEQVC AKLSASASDY LRERVSDIRD
ISEQLLHITW PELKPRNKLV LEKPTILVAE DLTPSQFLSL DLKNLAGMIL EKTGRTSHTL
ILARASAIPV LSGLPLDAIA RYAGQPAVLD AQCGVLAINP NDAVSGYYQV AQTLADKRQK
QQAQAAAQLA YSRDNKRIDI AANIGTALEA PGAFANGAEG VGLFRTEMLY MDRDSAPDEQ
EQFEAYQQVL LAAGDKPIIF RTMDIGGDKS IPYLNIPQEE NPFLGYRAVR IYPEFAGLFR
TQLRAILRAA SFGNAQLMIP MVHSLDQILW VKGEIQKAIV ELKRDGLRHA ETITLGIMVE
VPSVCYIIDH FCDEVDFFSI GSNDMTQYLY AVDRNNPRVS PLYNPITPSF LRMLQQIVTT
AHQRGKWVGI CGELGGESRY LPLLLGLGLD ELSMSSPRIP AVKSQLRQLD SEACRELARQ
ACECRSAQEI EALLTAFTPE EDVRPLLALE NIFVDQDFSN KEQAIQFLCG NLGVNGRTEH
PFELEEDVWQ REEIVTTGVG FGVAIPHTKS QWIRHSSISI ARLAKPIGWQ SEMGEVELVI
MLTLGANEGM NHVKVFSQLA RKLVNKNFRQ SLFAAQDAQS ILTLLETELT F
Length

831

Mol. Wt

92.132 kDa

pI

5.1 (calculated)

Extinction coefficient

70,820 - 72,320 (calc based on 18 Y, 8 W, and 12 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

254..334

PF00391 PEP-utilising enzyme, mobile domain

PMID:19920124

Domain

359..651

PF02896 PEP-utilising enzyme, TIM barrel domain

PMID:19920124

Domain

1..86

PF00381 PTS HPr component phosphorylation site

PMID:19920124

Domain

685..828

PF00359 Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2

PMID:19920124

Domain

117..235

PF05524 PEP-utilising enzyme, N-terminal

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=fryA taxon=12017 </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:16130315

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946852

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007861

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77439

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7246

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14151

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946852

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003821

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3903

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

6

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

4

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)

ypdD

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File:.jpg

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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_000913:2502487..2502527 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:b2383 (EcoliWiki Page)

NCBI GEO profiles for fryA

microarray

GenExpDB:b2383 (EcoliWiki Page)

Summary of data for fryA 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 fryA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7246

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3903

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2383

EcoGene

EcoGene:EG14151

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003821

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007861

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

Arabidopsis thaliana

  • YP_026278 (score: 0.216)
  • AT4G15530 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • YP_026278 (score: 0.223)
  • Q7XJK0 (score: 1.000; bootstrap: 100%)
  • Q7XJK1 (score: 1.000; bootstrap: 100%)
  • O24612 (score: 1.000; bootstrap: 100%)
  • Q6AVA8 (score: 1.000; bootstrap: 100%)
  • Q84N32 (score: 0.981)
  • Q9SNY6 (score: 0.973)
  • Q7DMU6 (score: 0.926)
  • P11155 (score: 0.904)
  • Q5RZZ9 (score: 0.862)
  • Q75KR1 (score: 0.776)
  • O82032 (score: 0.774)
  • Q7XYB5 (score: 0.214)
  • Q4JIY1 (score: 0.171)
  • Q7XJJ9 (score: 0.140)
  • Q41847 (score: 0.084)

From Inparanoid:20070104

Shigella flexneri

S2588

From SHIGELLACYC

E. coli O157

Z3648

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)

PF00391 PEP-utilising enzyme, mobile domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:47831

Superfamily (EcoliWiki Page)

SUPERFAMILY:51621

Superfamily (EcoliWiki Page)

SUPERFAMILY:52009

Superfamily (EcoliWiki Page)

SUPERFAMILY:55594

Superfamily (EcoliWiki Page)

SUPERFAMILY:55804

Pfam (EcoliWiki Page)

PF02896 PEP-utilising enzyme, TIM barrel domain

Pfam (EcoliWiki Page)

PF00381 PTS HPr component phosphorylation site

Pfam (EcoliWiki Page)

PF00359 Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2

Pfam (EcoliWiki Page)

PF05524 PEP-utilising enzyme, N-terminal

EcoCyc

EcoCyc:G7246

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14151

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003821

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3903

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007861

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 EcoCyc (release 10.6; 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.

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