astC:On One Page

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

Quickview

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Standard Name

astC

Gene Synonym(s)

ECK1746, b1748, JW1737, argM, cstC, ydjW[1], ydjW

Product Desc.

AstC[2][3];

Component of SUCCORNTRANSAM-CPLX[2]

Succinylornithine transaminase, mutant cannot catabolize arginine, overproduction complements argD mutants; carbon starvation protein[4]

Product Synonyms(s)

succinylornithine transaminase, PLP-dependent[1], B1748[2][1], YdjW[2][1], CstC[2][1], ArgM[2][1], AstC[2][1] , argM, cstC, ECK1746, JW1737, ydjW, b1748

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): astCADBE[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

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Gene

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Nomenclature

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

Standard name

astC

Mnemonic

Arginine

Synonyms

ECK1746, b1748, JW1737, argM, cstC, ydjW[1], ydjW

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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

39.42 minutes 

MG1655: 1830006..1828786
<gbrowseImage> name=NC_000913:1828786..1830006 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1809247..1808027
<gbrowseImage> name=NC_012967:1808027..1809247 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1720845..1722065
<gbrowseImage> name=NC_012759:1720845..1722065 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1833696..1832476
<gbrowseImage> name=NC_007779:1832476..1833696 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1920577..1919357
<gbrowseImage> name=NC_010473:1919357..1920577 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

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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

ΔastC (Keio:JW1737)

deletion

deletion

PMID:16738554

Shigen


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Notes

Genetic Interactions

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<protect>

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

JW1737

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTCAGCCAATTACGCGTGA

Primer 2:CCTGATGAACCTCGGCTAACAAA

5E12

Kohara Phage

Genobase

PMID:3038334

4B8

Kohara Phage

Genobase

PMID:3038334

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: 9% [6]
Synonyms:zdh-925::Tn10

zdj-276::Tn10

Linked marker

CAG18464 = CGSC7387[5]

est. P1 cotransduction: 88% [6]
Synonyms:zdi-276::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:G6944

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13999

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003532

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946255

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3755

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005824

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

AstC

Synonyms

succinylornithine transaminase, PLP-dependent[1], B1748[2][1], YdjW[2][1], CstC[2][1], ArgM[2][1], AstC[2][1] , argM, cstC, ECK1746, JW1737, ydjW, b1748

Product description

AstC[2][3];

Component of SUCCORNTRANSAM-CPLX[2]

Succinylornithine transaminase, mutant cannot catabolize arginine, overproduction complements argD mutants; carbon starvation protein[4]

EC number (for enzymes)

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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015421

F

Seeded from EcoCyc (v14.0)

complete

GO:0006520

cellular amino acid metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017652

P

Seeded from EcoCyc (v14.0)

complete

GO:0006525

arginine metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004636

P

Seeded from EcoCyc (v14.0)

complete

GO:0006525

arginine metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0056

P

Seeded from EcoCyc (v14.0)

complete

GO:0008483

transaminase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01173

F

Seeded from EcoCyc (v14.0)

complete

GO:0008483

transaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004636

F

Seeded from EcoCyc (v14.0)

complete

GO:0008483

transaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005814

F

Seeded from EcoCyc (v14.0)

complete

GO:0008483

transaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017652

F

Seeded from EcoCyc (v14.0)

complete

GO:0043825

succinylornithine transaminase activity

PMID:9696779

IDA: Inferred from Direct Assay

F

complete

GO:0008483

transaminase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0032

F

Seeded from EcoCyc (v14.0)

complete

GO:0006593

ornithine catabolic process

PMID:9696779

IMP: Inferred from Mutant Phenotype

P

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:0006527

arginine catabolic process

PMID:9696779

IMP: Inferred from Mutant Phenotype

P

complete

GO:0019544

arginine catabolic process to glutamate

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01173

P

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01173

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005814

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015421

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017652

F

Seeded from EcoCyc (v14.0)

complete

GO:0043825

succinylornithine transaminase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.6.1.81

F

Seeded from EcoCyc (v14.0)

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 SUCCORNTRANSAM-CPLX

could be indirect

Protein

groL

PMID:16606699

Experiment(s):EBI-1140689

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

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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

MSQPITRENF DEWMIPVYAP APFIPVRGEG SRLWDQQGKE YIDFAGGIAV NALGHAHPEL
REALNEQASK FWHTGNGYTN EPVLRLAKKL IDATFADRVF FCNSGAEANE AALKLARKFA
HDRYGSHKSG IVAFKNAFHG RTLFTVSAGG QPAYSQDFAP LPADIRHAAY NDINSASALI
DDSTCAVIVE PIQGEGGVVP ASNAFLQGLR ELCNRHNALL IFDEVQTGVG RTGELYAYMH
YGVTPDLLTT AKALGGGFPV GALLATEECA RVMTVGTHGT TYGGNPLASA VAGKVLELIN
TPEMLNGVKQ RHDWFVERLN TINHRYGLFS EVRGLGLLIG CVLNADYAGQ AKQISQEAAK
AGVMVLIAGG NVVRFAPALN VSEEEVTTGL DRFAAACEHF VSRGSS
Length

406

Mol. Wt

43.665 kDa

pI

6.3 (calculated)

Extinction coefficient

39,880 - 40,630 (calc based on 12 Y, 4 W, and 6 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

24..345

PF00202 Aminotransferase class-III

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=astC 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:16129702

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946255

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005824

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77581

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6944

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13999

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946255

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003532

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3755

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

Ecoli K-12

19.916+/-0.406

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.016803279

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

6a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

94

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

0a

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

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<protect>

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

Transcription unit(s)

astCADBE

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_000913:1829986..1830026 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


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

Type Reference Notes

microarray

GEO Profiles:b1748 (EcoliWiki Page)

NCBI GEO profiles for astC

microarray

GenExpDB:b1748 (EcoliWiki Page)

Summary of data for astC 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

GFP Fusion

Intergenic region (1829915..1830498) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ13; Well:B2[7]

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Notes

Accessions Related to astC Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6944

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3755

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1748

EcoGene

EcoGene:EG13999

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003532

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005824

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

  • ENSANGP00000010754 (score: 1.000; bootstrap: 99%)
  • ENSANGP00000014450 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000010852 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G80600 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000009097 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00030775 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00015814 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000016293 (score: 1.000; bootstrap: 76%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0231481 (score: 1.000; bootstrap: 94%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0022774 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA21318-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000000068 (score: 1.000; bootstrap: 98%)
  • ENSGALP00000000529 (score: 0.424)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000224242 (score: 1.000; bootstrap: 95%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000008293 (score: 1.000; bootstrap: 46%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000020699 (score: 1.000; bootstrap: 92%)

From Inparanoid:20070104

Mus musculus

  • MGI:97394 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Oryza gramene

  • Q688Q8 (score: 1.000; bootstrap: 99%)
  • Q6Z3A4 (score: 0.299)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000005344 (score: 1.000; bootstrap: 94%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000022628 (score: 1.000; bootstrap: 92%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YOL140W (score: 1.000; bootstrap: 94%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPCC7779c (score: 1.000; bootstrap: 98%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000160825 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00035924001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000050564 (score: 1.000; bootstrap: 96%)
  • ENSXETP00000051809 (score: 0.176)

From Inparanoid:20070104

E. coli O157

CSTC

From ECOO157CYC


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)

PF00202 Aminotransferase class-III

Superfamily (EcoliWiki Page)

SUPERFAMILY:53383

Panther (EcoliWiki Page)

PTHR11986:SF19

EcoCyc

EcoCyc:G6944

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13999

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003532

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3755

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005824

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. 5.0 5.1 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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