pnp: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

pnp

Gene Synonym(s)

ECK3152, b3164, JW5851, bfl[1], bfl

Product Desc.

Pnp[2][3];

Component of polynucleotide phosphorylase[3]; degradosome[3]

Polynucleotide phosphorylase; exoribonuclease; PNPase component of RNA degradosome; cold shock protein required for growth at low temperatures[4]

Product Synonyms(s)

polynucleotide phosphorylase/polyadenylase[1], B3164[2][1], Bfl[2][1], Pnp[2][1], polynucleotide phosphorylase[2][1] , bfl, ECK3152, JW5851, b3164

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpsO-pnp[2], pnp[2], metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp[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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Implicated in degadation of sRNAs[5]

Cold induction occurs by reversal of post-translational autoregulation. The pnp mRNA leader is cleaved by RNase III, allowing PNPase to repress its own translation. Mutation of Gly454 impairs autogenous regulation without affecting catalytic activity. Mutants have elevated OM vesiculation (McBroom, 2006). Pnp can add long polynucleotide tails to mRNAs terminated by Rho factor (Mohanty, 2006). The overexpression of the Pnp S1 domain suppresses the cold growth defect of quadruple cspABEG mutant strain BX04 (Xia, 2001).[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

pnp

Mnemonic

Polynucleotide phosphorylase

Synonyms

ECK3152, b3164, JW5851, bfl[1], bfl

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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

71.28 minutes 

MG1655: 3309259..3307055
<gbrowseImage> name=NC_000913:3307055..3309259 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3246471..3244267
<gbrowseImage> name=NC_012967:3244267..3246471 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3194203..3196338
<gbrowseImage> name=NC_012759:3194203..3196338 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3311092..3308888
<gbrowseImage> name=NC_007779:3308888..3311092 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3407004..3404800
<gbrowseImage> name=NC_010473:3404800..3407004 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

3307055

Edman degradation

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

Δpnp (Keio:JW5851)

deletion

deletion

PMID:16738554

Shigen

pnp::Tn5KAN-I-SceI (FB21050)

Insertion at nt 556 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21050

does not contain pKD46

pnp::Tn5KAN-I-SceI (FB21051)

Insertion at nt 1758 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21051

contains pKD46

pnp-13

CGSC:8760

pnp-7

CGSC:8810

pnp-27

CGSC:11782


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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

JW5851

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGCAGAAGATCGGGTATTAA

Primer 2:CCtTCGCCCTGTTCAGCAGCCGG

13A9

Kohara Phage

Genobase

PMID:3038334

E4G11S

Kohara Phage

Genobase

PMID:3038334

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[6]

est. P1 cotransduction: % [7]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[6]

est. P1 cotransduction: 40% [7]
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:EG10743

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10743

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000734

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947672

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0736

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010397

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

Pnp

Synonyms

polynucleotide phosphorylase/polyadenylase[1], B3164[2][1], Bfl[2][1], Pnp[2][1], polynucleotide phosphorylase[2][1] , bfl, ECK3152, JW5851, b3164

Product description

Pnp[2][3];

Component of polynucleotide phosphorylase[3]; degradosome[3]

Polynucleotide phosphorylase; exoribonuclease; PNPase component of RNA degradosome; cold shock protein required for growth at low temperatures[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:0000175

3'-5'-exoribonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001247

F

Seeded from EcoCyc (v14.0)

complete

GO:0000175

3'-5'-exoribonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015847

F

Seeded from EcoCyc (v14.0)

complete

GO:0000175

3'-5'-exoribonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015848

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001247

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003029

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004087

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004088

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012162

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015847

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015848

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018111

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:0004654

polyribonucleotide nucleotidyltransferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01595

F

Seeded from EcoCyc (v14.0)

complete

GO:0004654

polyribonucleotide nucleotidyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012162

F

Seeded from EcoCyc (v14.0)

complete

GO:0004654

polyribonucleotide nucleotidyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.8

F

Seeded from EcoCyc (v14.0)

complete

GO:0005739

mitochondrion

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012162

C

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006396

RNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001247

P

Seeded from EcoCyc (v14.0)

complete

GO:0006396

RNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015847

P

Seeded from EcoCyc (v14.0)

complete

GO:0006396

RNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015848

P

Seeded from EcoCyc (v14.0)

complete

GO:0006402

mRNA catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01595

P

Seeded from EcoCyc (v14.0)

complete

GO:0006402

mRNA catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012162

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:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

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:0016779

nucleotidyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

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 polynucleotide phosphorylase

could be indirect

Protein

metK

PMID:15690043

Experiment(s):EBI-883913

Protein

recA

PMID:15690043

Experiment(s):EBI-883913

Protein

rplB

PMID:15690043

Experiment(s):EBI-883913

Protein

rplD

PMID:15690043

Experiment(s):EBI-883913, EBI-891089

Protein

rplF

PMID:15690043

Experiment(s):EBI-883913

Protein

rplI

PMID:15690043

Experiment(s):EBI-883913, EBI-891089

Protein

rplM

PMID:15690043

Experiment(s):EBI-883913, EBI-891089

Protein

rpoA

PMID:15690043

Experiment(s):EBI-883913

Protein

rpsC

PMID:15690043

Experiment(s):EBI-883913

Protein

rpsD

PMID:15690043

Experiment(s):EBI-883913

Protein

rpsE

PMID:15690043

Experiment(s):EBI-883913, EBI-891089

Protein

rpsG

PMID:15690043

Experiment(s):EBI-883913, EBI-891089

Protein

rpsM

PMID:15690043

Experiment(s):EBI-883913, EBI-891089

Protein

srmB

PMID:15690043

Experiment(s):EBI-883913

Protein

rplE

PMID:15690043

Experiment(s):EBI-883913

Protein

pgk

PMID:15690043

Experiment(s):EBI-891089, EBI-890008

Protein

rplA

PMID:15690043

Experiment(s):EBI-891089

Protein

rplO

PMID:15690043

Experiment(s):EBI-891089

Protein

rplQ

PMID:15690043

Experiment(s):EBI-891089

Protein

rplU

PMID:15690043

Experiment(s):EBI-891089

Protein

rplV

PMID:15690043

Experiment(s):EBI-891089

Protein

rplX

PMID:15690043

Experiment(s):EBI-891089

Protein

rpsO

PMID:15690043

Experiment(s):EBI-891089

Protein

rpsR

PMID:15690043

Experiment(s):EBI-891089

Protein

rpsS

PMID:15690043

Experiment(s):EBI-891089

Protein

rpsT

PMID:15690043

Experiment(s):EBI-891089

Protein

hupA

PMID:15690043

Experiment(s):EBI-891089

Protein

rpsS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

MALDI(Z-score):28.336587

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

eno

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):39.324472

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.209278

Protein

rpsO

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):20.758343

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.4

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):18.361833

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

MALDI(Z-score):35.080787

Protein

srmB

PMID:19402753

MALDI(Z-score):26.241773

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):8.655067

Protein

rpsD

PMID:19402753

LCMS(ID Probability):95.3 MALDI(Z-score):19.991630

Protein

rplB

PMID:19402753

LCMS(ID Probability):94.5 MALDI(Z-score):35.593951

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):16.114612

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):16.007735

Protein

rhlB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):37.285496

Protein

deaD

PMID:19402753

MALDI(Z-score):18.761801

Protein

rluB

PMID:19402753

MALDI(Z-score):33.707783

Protein

Subunits of degradosome

could be indirect


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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 

MRRRSGINTS AVRYCLRKRK DITLLNPIVR KFQYGQHTVT LETGMMARQA TAAVMVSMDD
TAVFVTVVGQ KKAKPGQDFF PLTVNYQERT YAAGRIPGSF FRREGRPSEG ETLIARLIDR
PIRPLFPEGF VNEVQVIATV VSVNPQVNPD IVAMIGASAA LSLSGIPFNG PIGAARVGYI
NDQYVLNPTQ DELKESKLDL VVAGTEAAVL MVESEAQLLS EDQMLGAVVF GHEQQQVVIQ
NINELVKEAG KPRWDWQPEP VNEALNARVA ALAEARLSDA YRITDKQERY AQVDVIKSET
IATLLAEDET LDENELGEIL HAIEKNVVRS RVLAGEPRID GREKDMIRGL DVRTGVLPRT
HGSALFTRGE TQALVTATLG TARDAQVLDE LMGERTDTFL FHYNFPPYSV GETGMVGSPK
RREIGHGRLA KRGVLAVMPD MDKFPYTVRV VSEITESNGS SSMASVCGAS LALMDAGVPI
KAAVAGIAMG LVKEGDNYVV LSDILGDEDH LGDMDFKVAG SRDGISALQM DIKIEGITKE
IMQVALNQAK GARLHILGVM EQAINAPRGD ISEFAPRIHT IKINPDKIKD VIGKGGSVIR
ALTEETGTTI EIEDDGTVKI AATDGEKAKH AIRRIEEITA EIEVGRVYTG KVTRIVDFGA
FVAIGGGKEG LVHISQIADK RVEKVTDYLQ MGQEVPVKVL EVDRQGRIRL SIKEATEQSQ
PAAAPEAPAA EQGE
Length

734

Mol. Wt

79.845 kDa

pI

5.3 (calculated)

Extinction coefficient

31,860 - 32,110 (calc based on 14 Y, 2 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

Modification Site

675

phosphorylation site at S675

probability greater than 75%

PMID:17938405

Domain

555..612

PF00013 KH domain

PMID:19920124

Domain

241..320

PF03726 Polyribonucleotide nucleotidyltransferase, RNA binding domain

PMID:19920124

Domain

13..144

PF01138 3' exoribonuclease family, domain 1

PMID:19920124

Domain

323..456

PF01138 3' exoribonuclease family, domain 1

PMID:19920124

Domain

147..211

PF03725 3' exoribonuclease family, domain 2

PMID:19920124

Domain

459..529

PF03725 3' exoribonuclease family, domain 2

PMID:19920124

Domain

618..690

PF00575 S1 RNA binding domain

PMID:19920124

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<motif_map/>

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

Structures

<beststructure> gene=pnp 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:145698316

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947672

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010397

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P05055

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10743

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10743

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947672

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000734

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0736

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

5.70E+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

938.13+/-5.62

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.3027+/-0.0129

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.423548094

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

200

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: M59

PMID: 9298646

Protein

E. coli K-12 MG1655

11905

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

3545

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

7930

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)

rpsO-pnp

pnp

metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp

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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_000913:3309239..3309279 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:b3164 (EcoliWiki Page)

NCBI GEO profiles for pnp

microarray

GenExpDB:b3164 (EcoliWiki Page)

Summary of data for pnp 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 (3308790..3309137) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:E3[8]

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Notes

Accessions Related to pnp Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10743

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0736

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3164

EcoGene

EcoGene:EG10743

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000734

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010397

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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

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

  • ENSANGP00000021260 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000026805 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G14580 (score: 1.000; bootstrap: 63%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000011729 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00035470 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00015266 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000004294 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0039846 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA10930-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000012877 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000260604 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000009189 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000002420 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1918951 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6KAI0 (score: 1.000; bootstrap: 52%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000020501 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000004919 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC3G90c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000129340 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00014316001 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000013381 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

PNP

From SHIGELLACYC

E. coli O157

PNP

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)

PF03726 Polyribonucleotide nucleotidyltransferase, RNA binding domain

Pfam (EcoliWiki Page)

PF00013 KH domain

Pfam (EcoliWiki Page)

PF03725 3' exoribonuclease family, domain 2

Pfam (EcoliWiki Page)

PF03725 3' exoribonuclease family, domain 2

Pfam (EcoliWiki Page)

PF01138 3' exoribonuclease family, domain 1

Pfam (EcoliWiki Page)

PF01138 3' exoribonuclease family, domain 1

Superfamily (EcoliWiki Page)

SUPERFAMILY:46915

Superfamily (EcoliWiki Page)

SUPERFAMILY:50249

Panther (EcoliWiki Page)

PTHR11252:SF0

Superfamily (EcoliWiki Page)

SUPERFAMILY:54211

Superfamily (EcoliWiki Page)

SUPERFAMILY:54211

Superfamily (EcoliWiki Page)

SUPERFAMILY:54791

Superfamily (EcoliWiki Page)

SUPERFAMILY:55666

Superfamily (EcoliWiki Page)

SUPERFAMILY:55666

Pfam (EcoliWiki Page)

PF00575 S1 RNA binding domain

PFAM (EcoliWiki Page)

PFAM:PF01138

EcoCyc

EcoCyc:EG10743

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10743

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000734

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0736

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010397

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 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 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 3.4 3.5 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. ↑ Andrade, JM & Arraiano, CM (2008) PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins. RNA 14 543-51 PubMed
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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).
  8. ↑ 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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