deaD: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

deaD

Gene Synonym(s)

ECK3150, b3162, JW5531, mssB, rhlD[1], csdA, rhlD

Product Desc.

CsdA, DEAD-box RNA helicase[2][3]

Translation factor W2, putative RNA helix-destabilizer; facilitates translation of mRNAs with 5' secondary structures; multicopy suppressor of rpsB(Ts) mutations[4]

Product Synonyms(s)

ATP-dependent RNA helicase[1], B3162[2][1], RhlD[2][1], MssB[2][1], DeaD[2][1] , csdA, ECK3150, JW5531, mssB, rhlD, b3162

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): deaD[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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Mechanism of DeaD 50S biogenesis differs from that for SrmB 50S biogenesis. stabilizes exposed mRNA, possibly by protecting or destabilizing secondary structure of RNase E sites. Cold shock-inducible; acid-inducible.[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

deaD

Mnemonic

DEAD motif

Synonyms

ECK3150, b3162, JW5531, mssB, rhlD[1], csdA, rhlD

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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

71.21 minutes 

MG1655: 3305882..3303993
<gbrowseImage> name=NC_000913:3303993..3305882 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3243094..3241205
<gbrowseImage> name=NC_012967:3241205..3243094 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3191141..3193030
<gbrowseImage> name=NC_012759:3191141..3193030 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3307715..3305826
<gbrowseImage> name=NC_007779:3305826..3307715 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3403627..3401738
<gbrowseImage> name=NC_010473:3401738..3403627 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

3303996

Edman degradation

PMID:8552679
PMID:10216955


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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

deaDE157Q

E157Q

Abolishes ATPase activity, drastically reduces helicase activity. In vivo acts as a dominant negative mutation in the presence of the wild-type protein at low temperature

seeded from UniProt:P0A9P6

deaD(del) (Keio:JW5531)

deletion

deletion

PMID:16738554

Shigen
CGSC11447[5]

deaD::Tn5KAN-I-SceI (FB21048)

Insertion at nt 1255 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21048

does not contain pKD46

deaD::Tn5KAN-I-SceI (FB21049)

Insertion at nt 1255 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21049

contains pKD46

deaD774(del)::kan

PMID:16738554

CGSC:100566


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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

JW5531

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCTGAATTCGAAACCACTTT

Primer 2:CCtGCATCACCACCGAAACGACG

13A9

Kohara Phage

Genobase

PMID:3038334

E4G11S

Kohara Phage

Genobase

PMID:3038334

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: % [6]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 35% [6]
Synonyms:zgj-203::Tn10, zha-203::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:EG10215

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10215

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000209

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947674

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0211

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010392

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

DeaD

Synonyms

ATP-dependent RNA helicase[1], B3162[2][1], RhlD[2][1], MssB[2][1], DeaD[2][1] , csdA, ECK3150, JW5531, mssB, rhlD, b3162

Product description

CsdA, DEAD-box RNA helicase[2][3]

Translation factor W2, putative RNA helix-destabilizer; facilitates translation of mRNAs with 5' secondary structures; multicopy suppressor of rpsB(Ts) mutations[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:0000027

ribosomal large subunit assembly

PMID:15148362

IMP: Inferred from Mutant Phenotype

P

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:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000629

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0003724

RNA helicase activity

PMID:8552679

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0004004

ATP-dependent RNA helicase activity

PMID:15196029

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0004004

ATP-dependent RNA helicase activity

PMID:17259309

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:10361280

IPI: Inferred from Physical Interaction

UniProtKB:P0ABF1

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:15836769

IPI: Inferred from Physical Interaction

UniProtKB:P42641

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000629

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

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

GO:0006401

RNA catabolic process

PMID:15554978

IGI: Inferred from Genetic Interaction

UniProtKB:P21513

P

Seeded from EcoCyc (v14.0)

complete

GO:0070417

cellular response to cold

PMID:8552679

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc (v14.0)

complete

GO:0070417

cellular response to cold

PMID:8552679

IMP: Inferred from Mutant Phenotype

P

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

accA

PMID:15690043

Experiment(s):EBI-888958

Protein

aceE

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

hrpA

PMID:15690043

Experiment(s):EBI-888958

Protein

rplA

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rplI

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rplM

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rplV

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsA

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsB

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsC

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsD

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsE

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsG

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsM

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rpsU

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

srmB

PMID:15690043

Experiment(s):EBI-888958

Protein

ycbY

PMID:15690043

Experiment(s):EBI-888958

Protein

rluB

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

yfiF

PMID:15690043

Experiment(s):EBI-888958, EBI-879491, EBI-881486

Protein

ygiF

PMID:15690043

Experiment(s):EBI-888958

Protein

rplB

PMID:15690043

Experiment(s):EBI-888958, EBI-881486

Protein

rnr

PMID:15690043

Experiment(s):EBI-888958, EBI-883997, EBI-881486

Protein

acpP

PMID:15690043

Experiment(s):EBI-881486

Protein

sixA

PMID:15690043

Experiment(s):EBI-881486

Protein

bglA

PMID:15690043

Experiment(s):EBI-881486

Protein

dacA

PMID:15690043

Experiment(s):EBI-881486

Protein

dppC

PMID:15690043

Experiment(s):EBI-881486

Protein

evgA

PMID:15690043

Experiment(s):EBI-881486

Protein

gsk

PMID:15690043

Experiment(s):EBI-881486

Protein

hupA

PMID:15690043

Experiment(s):EBI-881486

Protein

hupB

PMID:15690043

Experiment(s):EBI-881486

Protein

rplC

PMID:15690043

Experiment(s):EBI-881486

Protein

rplF

PMID:15690043

Experiment(s):EBI-881486

Protein

rplK

PMID:15690043

Experiment(s):EBI-881486

Protein

rplP

PMID:15690043

Experiment(s):EBI-881486

Protein

rplQ

PMID:15690043

Experiment(s):EBI-881486

Protein

rplR

PMID:15690043

Experiment(s):EBI-881486

Protein

rplS

PMID:15690043

Experiment(s):EBI-881486

Protein

rplU

PMID:15690043

Experiment(s):EBI-881486

Protein

rplW

PMID:15690043

Experiment(s):EBI-881486

Protein

rplX

PMID:15690043

Experiment(s):EBI-881486

Protein

rpmA

PMID:15690043

Experiment(s):EBI-881486

Protein

rpmB

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsF

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsH

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsI

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsK

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsN

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsO

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsP

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsR

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsS

PMID:15690043

Experiment(s):EBI-881486

Protein

sucD

PMID:15690043

Experiment(s):EBI-881486

Protein

uraA

PMID:15690043

Experiment(s):EBI-881486

Protein

hcp

PMID:15690043

Experiment(s):EBI-881486

Protein

yhiR

PMID:15690043

Experiment(s):EBI-881486

Protein

yihQ

PMID:15690043

Experiment(s):EBI-881486

Protein

sufC

PMID:15690043

Experiment(s):EBI-881486

Protein

rpsT

PMID:15690043

Experiment(s):EBI-881486

Protein

rplK

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.499464

Protein

acpP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):18.261563

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.082768

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):7.700577

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):15.678591

Protein

rpsK

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.007437

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):26.788003

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.484300

Protein

rpsH

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):6.833274

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.589053

Protein

rpsS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsO

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):9.114247

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):35.503180

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmA

PMID:19402753

LCMS(ID Probability):99.4

Protein

rpsL

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):33.439795

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.065302

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):25.836351

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):49.766331

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.018295

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

dacA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):4.899346

Protein

rpsU

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

sufC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.709148

Protein

yphE

PMID:19402753

LCMS(ID Probability):99.6

Protein

cspC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.434341

Protein

rpsQ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):10.782348

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.5

Protein

srmB

PMID:19402753

MALDI(Z-score):28.361090

Protein

yfiF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.920449

Protein

rluB

PMID:19402753

LCMS(ID Probability):99.2 MALDI(Z-score):37.368522

Protein

ygiF

PMID:19402753

MALDI(Z-score):39.147611

Protein

pssA

PMID:19402753

MALDI(Z-score):26.949774

Protein

rnr

PMID:19402753

LCMS(ID Probability):99.2 MALDI(Z-score):28.380982

Protein

yibL

PMID:19402753

LCMS(ID Probability):99.6

Protein

hcp

PMID:19402753

LCMS(ID Probability):99.4

Protein

hrpA

PMID:19402753

MALDI(Z-score):18.737310

Protein

rluC

PMID:19402753

LCMS(ID Probability):95.6 MALDI(Z-score):36.951557

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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

From EcoCyc[3]


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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 

MMSYVDWPPL ILRHTYYMAE FETTFADLGL KAPILEALND LGYEKPSPIQ AECIPHLLNG
RDVLGMAQTG SGKTAAFSLP LLQNLDPELK APQILVLAPT RELAVQVAEA MTDFSKHMRG
VNVVALYGGQ RYDVQLRALR QGPQIVVGTP GRLLDHLKRG TLDLSKLSGL VLDEADEMLR
MGFIEDVETI MAQIPEGHQT ALFSATMPEA IRRITRRFMK EPQEVRIQSS VTTRPDISQS
YWTVWGMRKN EALVRFLEAE DFDAAIIFVR TKNATLEVAE ALERNGYNSA ALNGDMNQAL
REQTLERLKD GRLDILIATD VAARGLDVER ISLVVNYDIP MDSESYVHRI GRTGRAGRAG
RALLFVENRE RRLLRNIERT MKLTIPEVEL PNAELLGKRR LEKFAAKVQQ QLESSDLDQY
RALLSKIQPT AEGEELDLET LAAALLKMAQ GERTLIVPPD APMRPKREFR DRDDRGPRDR
NDRGPRGDRE DRPRRERRDV GDMQLYRIEV GRDDGVEVRH IVGAIANEGD ISSRYIGNIK
LFASHSTIEL PKGMPGEVLQ HFTRTRILNK PMNMQLLGDA QPHTGGERRG GGRGFGGERR
EGGRNFSGER REGGRGDGRR FSGERREGRA PRRDDSTGRR RFGGDA
Length

646

Mol. Wt

72.715 kDa

pI

9.0 (calculated)

Extinction coefficient

35,870 - 35,995 (calc based on 13 Y, 3 W, and 1 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

Initiator Methionine

1

Removed

UniProt:P0A9P6

Domain

30..197

PF00270 DEAD/DEAH box helicase

PMID:19920124

Domain

263..340

PF00271 Helicase conserved C-terminal domain

PMID:19920124

Domain

487..560

PF03880 DbpA RNA binding domain

PMID:19920124

Domain

568..629

PF12343 Cold shock protein DEAD box A

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=deaD taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

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</protect>

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:90111550

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947674

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010392

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9P6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10215

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10215

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947674

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000209

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0211

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

1.99E+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

72.605+/-0.581

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.05749+/-0.00589

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.235839068

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

9221

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

858

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

2801

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)

deaD

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Figure courtesy of RegulonDB

</protect>

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_000913:3305862..3305902 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b3162 (EcoliWiki Page)

NCBI GEO profiles for deaD

microarray

GenExpDB:b3162 (EcoliWiki Page)

Summary of data for deaD 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 (3305456..3305692) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:E2[7]

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Notes

Accessions Related to deaD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10215

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0211

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3162

EcoGene

EcoGene:EG10215

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000209

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010392

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

Anopheles gambiae

  • ENSANGP00000020417 (score: 1.000; bootstrap: 57%)
  • ENSANGP00000014802 (score: 0.518)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000021327 (score: 1.000; bootstrap: 59%)
  • ENSBTAP00000019596 (score: 0.516)
  • ENSBTAP00000000144 (score: 0.507)
  • ENSBTAP00000018962 (score: 0.416)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00031575 (score: 1.000; bootstrap: 50%)
  • WBGene00026478 (score: 0.097)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00002083 (score: 1.000; bootstrap: 52%)
  • WBGene00022029 (score: 0.462)
  • WBGene00018007 (score: 0.462)
  • WBGene00018997 (score: 0.358)
  • WBGene00000479 (score: 0.060)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000020343 (score: 1.000; bootstrap: 54%)
  • ENSCAFP00000020312 (score: 0.431)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000016005 (score: 1.000; bootstrap: 49%)
  • ENSCINP00000005836 (score: 0.379)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040426-915 (score: 1.000; bootstrap: 53%)
  • ZDB-CDNA-040425-1843 (score: 1.000; bootstrap: 51%)
  • ZDB-CDNA-040425-269 (score: 0.525)
  • ZDB-GENE-031030-2 (score: 0.525)
  • ZDB-CDNA-040425-270 (score: 0.514)
  • ZDB-GENE-040120-6 (score: 0.514)
  • ZDB-CDNA-040425-3749 (score: 0.265)
  • ZDB-GENE-040426-2802 (score: 0.265)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0191511 (score: 1.000; bootstrap: 57%)
  • DDB0191262 (score: 0.345)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0001942 (score: 1.000; bootstrap: 56%)
  • FBgn0037573 (score: 1.000; bootstrap: 59%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA20384-PA (score: 1.000; bootstrap: 69%)
  • GA21521-PA (score: 0.503)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000014119 (score: 1.000; bootstrap: 52%)
  • ENSGALP00000013887 (score: 0.385)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000277806 (score: 1.000; bootstrap: 53%)
  • ENSP00000277804 (score: 0.424)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000012539 (score: 1.000; bootstrap: 54%)
  • ENSMMUP00000009247 (score: 0.823)
  • ENSMMUP00000004942 (score: 0.511)
  • ENSMMUP00000017746 (score: 0.507)
  • ENSMMUP00000009900 (score: 0.301)
  • ENSMMUP00000026101 (score: 0.188)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000002662 (score: 1.000; bootstrap: 65%)
  • ENSMODP00000008799 (score: 0.509)
  • ENSMODP00000026607 (score: 0.507)

From Inparanoid:20070104

Mus musculus

  • MGI:1923731 (score: 1.000; bootstrap: 56%)
  • MGI:3644832 (score: 1.000; bootstrap: 55%)
  • MGI:3644226 (score: 0.952)
  • MGI:3646594 (score: 0.947)
  • MGI:106906 (score: 0.519)
  • MGI:95303 (score: 0.510)
  • MGI:3645437 (score: 0.457)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000004431 (score: 1.000; bootstrap: 59%)
  • ENSPTRP00000004429 (score: 0.423)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000002484 (score: 1.000; bootstrap: 62%)
  • ENSRNOP00000011096 (score: 1.000; bootstrap: 62%)
  • ENSRNOP00000043538 (score: 0.879)
  • ENSRNOP00000037170 (score: 0.565)
  • ENSRNOP00000004891 (score: 0.172)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YHR065C (score: 1.000; bootstrap: 53%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC8238c (score: 1.000; bootstrap: 56%)
  • SPBC5436c (score: 0.062)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00004149001 (score: 1.000; bootstrap: 57%)
  • GSTENP00013198001 (score: 0.398)
  • GSTENP00014223001 (score: 0.395)
  • GSTENP00014966001 (score: 0.321)
  • GSTENP00031682001 (score: 0.305)
  • GSTENP00007510001 (score: 0.135)

From Inparanoid:20070104

Shigella flexneri

DEAD

From SHIGELLACYC

E. coli O157

DEAD

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)

PF00271 Helicase conserved C-terminal domain

Pfam (EcoliWiki Page)

PF00270 DEAD/DEAH box helicase

Pfam (EcoliWiki Page)

PF03880 DbpA RNA binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR24031:SF163

Pfam (EcoliWiki Page)

PF12343 Cold shock protein DEAD box A

EcoCyc

EcoCyc:EG10215

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10215

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000209

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0211

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010392

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 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 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 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

Categories

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