rfaD: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

rfaD

Gene Synonym(s)

ECK3609, b3619, JW3594, htrM, nbsB, waaD, hldD[1], gmhD, hldD

Product Desc.

ADP-L-glycero-D-mannoheptose-6-epimerase[2][3];

Component of ADP-L-glycero-D-mannoheptose-6-epimerase[3]

ADP-L-glycero-D-manno-heptose-6-epimerase; heat-inducible, LPS; allows high-temperature growth[4]

Product Synonyms(s)

ADP-L-glycero-D-mannoheptose-6-epimerase, NAD(P)-binding[1], B3619[2][1], HldD[2][1], WaaD[2][1], NbsB[2][1], HtrM[2][1], RfaD[2][1] , ECK3609, gmhD, hldD, htrM, JW3594, waaD, b3619

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rfaDFCL[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

rfaD

Mnemonic

Rough

Synonyms

ECK3609, b3619, JW3594, htrM, nbsB, waaD, hldD[1], gmhD, hldD

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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

81.73 minutes 

MG1655: 3792010..3792942
<gbrowseImage> name=NC_000913:3792010..3792942 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3733531..3734463
<gbrowseImage> name=NC_012967:3733531..3734463 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3680336..3681268
<gbrowseImage> name=NC_012759:3680336..3681268 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3846428..3845496
<gbrowseImage> name=NC_007779:3845496..3846428 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3889587..3890519
<gbrowseImage> name=NC_010473:3889587..3890519 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

Coding Start (SO:0000323)

MG1655

3792010

Edman degradation

PMID:2198271
PMID:9298646


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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

ΔrfaD (Keio:JW3594)

deletion

deletion

PMID:16738554

Shigen
CGSC10647[5]

hldDY140F

Y140F

Severely compromises epimerase activitie

seeded from UniProt:P67910

hldDK178M

K178M

Severely compromises epimerase activitie

seeded from UniProt:P67910

hldDK208M

K208M

Activity similar to that of the wild-type

seeded from UniProt:P67910

hldDD210N

D210N

Activity similar to that of the wild-type

seeded from UniProt:P67910

rfaD70

PMID:3882666

CGSC:19345

ΔrfaD731::kan

PMID:16738554

CGSC:102642


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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

JW3594

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATCATCGTTACCGGCGGCGC

Primer 2:CCTGCGTCGCGATTCAGCCAGGC

16B11

Kohara Phage

Genobase

PMID:3038334

5D2

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 23% [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:EG10838

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10838

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000829

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948134

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0831

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011843

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

RfaD

Synonyms

ADP-L-glycero-D-mannoheptose-6-epimerase, NAD(P)-binding[1], B3619[2][1], HldD[2][1], WaaD[2][1], NbsB[2][1], HtrM[2][1], RfaD[2][1] , ECK3609, gmhD, hldD, htrM, JW3594, waaD, b3619

Product description

ADP-L-glycero-D-mannoheptose-6-epimerase[2][3];

Component of ADP-L-glycero-D-mannoheptose-6-epimerase[3]

ADP-L-glycero-D-manno-heptose-6-epimerase; heat-inducible, LPS; allows high-temperature growth[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0009435

NAD biosynthetic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01601

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011912

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0119

P

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

P

Seeded from EcoCyc (v14.0)

complete

GO:0008712

ADP-glyceromanno-heptose 6-epimerase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01601

F

Seeded from EcoCyc (v14.0)

complete

GO:0008712

ADP-glyceromanno-heptose 6-epimerase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011912

F

Seeded from EcoCyc (v14.0)

complete

GO:0008712

ADP-glyceromanno-heptose 6-epimerase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.1.3.20

F

Seeded from EcoCyc (v14.0)

complete

GO:0009103

lipopolysaccharide biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0448

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

GO:0044237

cellular metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

P

Seeded from EcoCyc (v14.0)

complete

GO:0050661

NADP or NADPH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011912

F

Seeded from EcoCyc (v14.0)

complete

GO:0050662

coenzyme binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001509

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

Subunits of ADP-L-glycero-D-mannoheptose-6-epimerase

could be indirect

Protein

groL

PMID:16606699

Experiment(s):EBI-1146271

Protein

cysM

PMID:15690043

Experiment(s):EBI-884306

Protein

dnaK

PMID:15690043

Experiment(s):EBI-884306

Protein

entF

PMID:15690043

Experiment(s):EBI-884306

Protein

rplO

PMID:15690043

Experiment(s):EBI-884306

Protein

rpsG

PMID:15690043

Experiment(s):EBI-884306, EBI-891254

Protein

ybjX

PMID:15690043

Experiment(s):EBI-884306, EBI-879208

Protein

ddpD

PMID:15690043

Experiment(s):EBI-891254

Protein

rplC

PMID:15690043

Experiment(s):EBI-891254

Protein

rplS

PMID:15690043

Experiment(s):EBI-891254

Protein

secA

PMID:15690043

Experiment(s):EBI-891254

Protein

torA

PMID:15690043

Experiment(s):EBI-891254

Protein

ydaY

PMID:15690043

Experiment(s):EBI-891254

Protein

yhhN

PMID:15690043

Experiment(s):EBI-891254

Protein

yhjS

PMID:15690043

Experiment(s):EBI-891254

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):23.522411

Protein

torA

PMID:19402753

LCMS(ID Probability):99.0

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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

Cytoplasm

PMID:2198271

EchoLocation:rfaD


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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 

MIIVTGGAGF IGSNIVKALN DKGITDILVV DNLKDGTKFV NLVDLNIADY MDKEDFLIQI
MAGEEFGDVE AIFHEGACSS TTEWDGKYMM DNNYQYSKEL LHYCLEREIP FLYASSAATY
GGRTSDFIES REYEKPLNVY GYSKFLFDEY VRQILPEANS QIVGFRYFNV YGPREGHKGS
MASVAFHLNT QLNNGESPKL FEGSENFKRD FVYVGDVADV NLWFLENGVS GIFNLGTGRA
ESFQAVADAT LAYHKKGQIE YIPFPDKLKG RYQAFTQADL TNLRAAGYDK PFKTVAEGVT
EYMAWLNRDA
Length

310

Mol. Wt

34.893 kDa

pI

4.7 (calculated)

Extinction coefficient

44,810 - 45,060 (calc based on 19 Y, 3 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

2..236

PF01370 NAD dependent epimerase/dehydratase family

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=rfaD 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:16131490

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948134

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011843

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P67910

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10838

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10838

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948134

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000829

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0831

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

2.28E+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

147.463+/-0.687

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.24418+/-0.01439

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.174356223

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 EMG2

220

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: MISO

PMID: 9298646

Protein

E. coli K-12 MG1655

8651

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

2094

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

4625

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)

rfaDFCL

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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_000913:3791990..3792030 source=MG1655 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:b3619 (EcoliWiki Page)

NCBI GEO profiles for rfaD

microarray

GenExpDB:b3619 (EcoliWiki Page)

Summary of data for rfaD 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 (3791250..3791645) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ18; Well:E3[7]

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Notes

Accessions Related to rfaD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10838

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0831

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3619

EcoGene

EcoGene:EG10838

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000829

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011843

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

Apis mellifera

  • ENSAPMP00000017862 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RFAD

From SHIGELLACYC

E. coli O157

RFAD

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)

PF01370 NAD dependent epimerase/dehydratase family

Superfamily (EcoliWiki Page)

SUPERFAMILY:51735

Panther (EcoliWiki Page)

PTHR10366:SF29

EcoCyc

EcoCyc:EG10838

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10838

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000829

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0831

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011843

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 1.14 1.15 1.16 1.17 1.18 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 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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