acpS:On One Page

From EcoliWiki
Jump to: navigation, search

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

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

Quickview

[back to top]


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

<protect>

Standard Name

acpS

Gene Synonym(s)

ECK2561, b2563, JW2547, dpj, G220[1][2]

Product Desc.

AcpS[2][3];

Component of [[:Category:Complex:holo-[acyl-carrier-protein] synthase|holo-[acyl-carrier-protein] synthase]][2][3]

ACP-CoA phosphopantetheinyltransferase; Holo-ACP synthase[4]

Product Synonyms(s)

holo-[acyl-carrier-protein] synthase 1[1], B2563[2][1], Dpj[2][1], AcpS[2][1] , dpj, ECK2561, JW2547, b2563

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): pdxJ-acpS[2], rnc-era-recO-pdxJ-acpS[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


acpS(dpj) was demonstrated to be an essential gene (Takiff, 1992), consistent with the results of Baba (2006).[4]



Gene

[back to top]


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

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

acpS

Mnemonic

Acyl carrier protein

Synonyms

ECK2561, b2563, JW2547, dpj, G220[1][2]

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

58.16 minutes, 58.16 minutes 

MG1655: 2699020..2698640
<gbrowseImage> name=NC_000913:2698640..2699020 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2622490..2622110
<gbrowseImage> name=NC_012967:2622110..2622490 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2584445..2584825
<gbrowseImage> name=NC_012759:2584445..2584825 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2699654..2699274
<gbrowseImage> name=NC_007779:2699274..2699654 source=W3110 preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


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

2698643

Edman degradation

PMID:7559576


<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

acpSG5D

G5D

5-fold reduction in catalytic activity

seeded from UniProt:P24224

acpS1

G4D substitution: G to A transition in the fifth codon (underlined), GCAATATTTAGATXx

G4D

Auxotrophies

G4D mutation causes a 5 fold reduction in catalytic efficiency, Fig. 7,8,9.

PMID:10625633

Mutant K-12 strain used was e. coli MP4.

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2547

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAATATTAGGTTTAGGCAC

Primer 2:CCACTTTCAATAATTACCGTGGC

7G4

Kohara Phage

Genobase

PMID:3038334

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 24% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 69% [6]

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10247

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10247

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000241

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947037

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0243

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008433

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


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

Nomenclature

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

Standard name

AcpS

Synonyms

holo-[acyl-carrier-protein] synthase 1[1], B2563[2][1], Dpj[2][1], AcpS[2][1] , dpj, ECK2561, JW2547, b2563

Product description

AcpS[2][3];

Component of [[:Category:Complex:holo-[acyl-carrier-protein] synthase|holo-[acyl-carrier-protein] synthase]][2][3]

ACP-CoA phosphopantetheinyltransferase; Holo-ACP synthase[4]

EC number (for enzymes)

<protect></protect>

Notes

Function

[back to top]


<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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002582

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004568

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008278

F

Seeded from EcoCyc (v14.0)

complete

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:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00101

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:0006633

fatty acid biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00101

P

Seeded from EcoCyc (v14.0)

complete

GO:0006633

fatty acid biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002582

P

Seeded from EcoCyc (v14.0)

complete

GO:0006633

fatty acid biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004568

P

Seeded from EcoCyc (v14.0)

complete

GO:0006633

fatty acid biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0275

P

Seeded from EcoCyc (v14.0)

complete

GO:0008610

lipid biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0444

P

Seeded from EcoCyc (v14.0)

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00101

F

Seeded from EcoCyc (v14.0)

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002582

F

Seeded from EcoCyc (v14.0)

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004568

F

Seeded from EcoCyc (v14.0)

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008278

F

Seeded from EcoCyc (v14.0)

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.8.7

F

Seeded from EcoCyc (v14.0)

complete

GO:0009059

macromolecule biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008278

P

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

GO:0016740

transferase activity

PMID:7559576

TAS: Traceable Author Statement

F

complete

GO:0006633

fatty acid biosynthetic process

PMID:7559576

NAS: Non-traceable Author Statement

P

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

PMID:7559576

IDA: Inferred from Direct Assay

F

complete

GO:0005625

soluble fraction

PMID:7559576

IDA: Inferred from Direct Assay

C

complete

GO:0042803

protein homodimerization activity

PMID:7559576

IDA: Inferred from Direct Assay

F

complete

GO:0018070

peptidyl-serine phosphopantetheinylation

PMID:14294075

IDA: Inferred from Direct Assay

P

complete

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of [[:Category:Complex:holo-[acyl-carrier-protein] synthase|holo-[acyl-carrier-protein] synthase]]

could be indirect

Protein

ybiB

PMID:16606699

Experiment(s):EBI-1143271

Protein

rplD

PMID:16606699

Experiment(s):EBI-1143271

Protein

groL

PMID:16606699

Experiment(s):EBI-1143271

Protein

rplF

PMID:16606699

Experiment(s):EBI-1143271

Protein

rplB

PMID:16606699

Experiment(s):EBI-1143271

Protein

oxyR

PMID:16606699

Experiment(s):EBI-1143271

Protein

rpsG

PMID:16606699

Experiment(s):EBI-1143271

Protein

yfeK

PMID:16606699

Experiment(s):EBI-1143271

Protein

yphE

PMID:16606699

Experiment(s):EBI-1143271

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1143271

Protein

tufB

PMID:19402753

MALDI(Z-score):18.215873

Protein

murC

PMID:19402753

MALDI(Z-score):24.922879

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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

MAILGLGTDI VEIARIEAVI ARSGDRLARR VLSDNEWAIW KTHHQPVRFL AKRFAVKEAA
AKAFGTGIRN GLAFNQFEVF NDELGKPRLR LWGEALKLAE KLGVANMHVT LADERHYACA
TVIIES
Length

126

Mol. Wt

14.052 kDa

pI

9.6 (calculated)

Extinction coefficient

17,990 - 18,115 (calc based on 1 Y, 3 W, and 1 C residues)


Domains/Motifs/Modification Sites

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

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P24224

Domain

6..73

PF01648 4'-phosphopantetheinyl transferase superfamily

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=acpS taxon=562,83333 </beststructure>

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130488

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947037

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008433

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P24224

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10247

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10247

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947037

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000241

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0243

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

Ecoli K-12

11.815+/-0.083

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.064473684

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

372

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

142

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

99a

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

pdxJ-acpS

rnc-era-recO-pdxJ-acpS

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

[back to top]


<protect><gbrowseImage> name=NC_000913:2699000..2699040 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

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


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

Type Reference Notes

microarray

GEO Profiles:b2563 (EcoliWiki Page)

NCBI GEO profiles for acpS

microarray

GenExpDB:b2563 (EcoliWiki Page)

Summary of data for acpS from multiple microarray studies


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

Resource Name Resource Type Description Source Notes

<protect></protect>

Notes

Accessions Related to acpS Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10247

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0243

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2563

EcoGene

EcoGene:EG10247

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000241

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008433

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


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

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Dictyostelium discoideum

  • DDB0217726 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

ACPS

From SHIGELLACYC

E. coli O157

ACPS

From ECOO157CYC


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF01648 4'-phosphopantetheinyl transferase superfamily

Superfamily (EcoliWiki Page)

SUPERFAMILY:56214

EcoCyc

EcoCyc:EG10247

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10247

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000241

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0243

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008433

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 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 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 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 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).

Categories

[back to top]