acpT: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

acpT

Gene Synonym(s)

ECK3459, b3475, JW3440, yhhU[1], yhhU

Product Desc.

holo-[acyl carrier protein] synthase 2[2][3]

CoA-phosphopantetheinyltransferase; native apo-protein substrate unknown, possibly a back-up gene for acpS; multicopy suppressor of acpS1, can modify ACP when overexpressed[4]

Product Synonyms(s)

holo-(acyl carrier protein) synthase 2[1], B3475[2][1], YhhU[2][1], AcpT[2][1] , ECK3459, JW3440, yhhU, b3475

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): acpT[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]


A nonsense mutation making a truncated YejM causes increased outer membrane permeability,TS growth, and reduced of lipid A synthesis; these phenotypes, and the lethality of a null mutation, are suppressible by a multicopy acpT clone (Hirvas, 1997; De Lay, 2008).[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

acpT

Mnemonic

Acyl carrier protein

Synonyms

ECK3459, b3475, JW3440, yhhU[1], yhhU

</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

77.83 minutes 

MG1655: 3610992..3611579
<gbrowseImage> name=NC_000913:3610992..3611579 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3543657..3544244
<gbrowseImage> name=NC_012967:3543657..3544244 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3499486..3500073
<gbrowseImage> name=NC_012759:3499486..3500073 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4027446..4026859
<gbrowseImage> name=NC_007779:4026859..4027446 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3708737..3709324
<gbrowseImage> name=NC_010473:3708737..3709324 source=DH10B 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

<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

ΔacpT (Keio:JW3440)

deletion

deletion

PMID:16738554

Shigen

acpT over-expression

Auxotrophies

acpT can functionally replace acpS only if over-expressed. Fig. 8, plate 2. Fig. 9, lane 3.

PMID:10625633


<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

JW3440

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTATCGGATAGTTCTGGGGAA

Primer 2:CCGTTAACTGAATCGATCCATTG

5F2

Kohara Phage

Genobase

PMID:3038334

7H7

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: 49% [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: % [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:EG12221

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12221

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002107

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947979

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2135

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011351

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

AcpT

Synonyms

holo-(acyl carrier protein) synthase 2[1], B3475[2][1], YhhU[2][1], AcpT[2][1] , ECK3459, JW3440, yhhU, b3475

Product description

holo-[acyl carrier protein] synthase 2[2][3]

CoA-phosphopantetheinyltransferase; native apo-protein substrate unknown, possibly a back-up gene for acpS; multicopy suppressor of acpS1, can modify ACP when overexpressed[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

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: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:0009059

macromolecule biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008278

P

Seeded from EcoCyc (v14.0)

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

PMID:16824108

IDA: Inferred from Direct Assay

F

complete

GO:0005625

soluble fraction

PMID:16824108

IDA: Inferred from Direct Assay

C

complete

GO:0018070

peptidyl-serine phosphopantetheinylation

PMID:8939709

NAS: Non-traceable Author Statement

P

complete

GO:0008897

holo-(acyl-carrier-protein) synthase activity

PMID:16824108

IMP: Inferred from Mutant Phenotype

F

Substrate is Z4853 from e. coli 0157:H7, Figure 3.

complete

GO:0006633

fatty acid biosynthetic process

PMID:10625633

IGI: Inferred from Genetic Interaction

EcoliWiki:acpS


P

Fig. 1

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

</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

MYRIVLGKVS TLSAAPLPPG LREQAPQGPR RERWLAGRAL LSHTLSPLPE IIYGEQGKPA
FAPEMPLWFN LSHSGDDIAL LLSDEGEVGC DIEVIRPRAN WRWLANAVFS LGEHAEMDAV
HPDQQLEMFW RIWTRKEAIV KQRGGSAWQI VSVDSTYHSS LSVSHCQLEN LSLAICTPTP
FTLTADSVQW IDSVN
Length

195

Mol. Wt

21.767 kDa

pI

5.7 (calculated)

Extinction coefficient

48,470 - 48,845 (calc based on 3 Y, 8 W, and 3 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

Domain

88..151

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=acpT 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:16131347

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947979

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011351

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P37623

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12221

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12221

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947979

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002107

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2135

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

E. coli K-12 MG1655

474

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

125

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

199

molecules/cell/generation

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

Ribosome Profiling

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)

acpT

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_000913:3610972..3611012 source=MG1655 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:b3475 (EcoliWiki Page)

NCBI GEO profiles for acpT

microarray

GenExpDB:b3475 (EcoliWiki Page)

Summary of data for acpT 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 acpT Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG12221

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2135

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3475

EcoGene

EcoGene:EG12221

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002107

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011351

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

Shigella flexneri

YHHU

From SHIGELLACYC

E. coli O157

Z4867

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

Panther (EcoliWiki Page)

PTHR12215:SF2

Superfamily (EcoliWiki Page)

SUPERFAMILY:56214

Superfamily (EcoliWiki Page)

SUPERFAMILY:56214

EcoCyc

EcoCyc:EG12221

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12221

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002107

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2135

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011351

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 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 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]