gapC: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

gapC

Gene Synonym(s)

Note that this is a pseudogene in K12 strains., ECK1409, JW1413, JW5906, b4493

Product Desc.

Note that this is a pseudogene in K12 strains.

glyceraldehyde 3-phosphate dehydrogenase C, interrupted[1][2]; split glyceraldehyde 3-phosphate dehydrogenase C[1][2]

Product Synonyms(s)

GapC[1], GapC_2[1], B1416[1], GapC_1[1], B1417[1],, ECK1409, JW1413, JW5906, b4493

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): gapCC_2[1]

Regulation/Activity
Quick Links

porteco.png regulondb.jpg

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

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Notes

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This is a pseudogene in K12 strains.


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

gapC

Mnemonic
Synonyms

Note that this is a pseudogene in K12 strains., ECK1409, JW1413, JW5906, b4493

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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

32.07 minutes 

MG1655: 1487988..1487737
<gbrowseImage> name=NC_000913:1487737..1487988 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1491678..1491427
<gbrowseImage> name=NC_007779:1491427..1491678 source=W3110 preset=GeneLocation </gbrowseImage>

MG1655

32.07 minutes 

MG1655: 1488737..1487985
<gbrowseImage> name=NC_000913:1487985..1488737 source=ecoli preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1492427..1491675
<gbrowseImage> name=NC_007779:1491675..1492427 source=W3110 preset=GeneLocation </gbrowseImage>

MG1655

 

MG1655: 1488737..1487737
<gbrowseImage> name=NC_000913:1487737..1488737 source=ecoli preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1492427..1491427
<gbrowseImage> name=NC_007779:1491427..1492427 source=W3110 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

gapC_2::Tn5KAN-2 (FB20315)

Insertion at nt 128 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20314

contains pKD46

gapC_2::Tn5KAN-2 (FB20315)

Insertion at nt 128 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20315

does not contain pKD46

ΔgapC777::kan

PMID:16738554

CGSC:101092


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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

3C9

Kohara Phage

Genobase

PMID:3038334

24D6

Kohara Phage

Genobase

PMID:3038334

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[3]

est. P1 cotransduction: 7% [4]

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[3]

est. P1 cotransduction: 82% [4]

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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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1417

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:GAPC

NCBI (EcoliWiki Page)

GeneID:2847738

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004456

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

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

GapC

Synonyms

GapC[1], GapC_2[1], B1416[1], GapC_1[1], B1417[1],, ECK1409, JW1413, JW5906, b4493

Product description

Note that this is a pseudogene in K12 strains.

glyceraldehyde 3-phosphate dehydrogenase C, interrupted[1][2]; split glyceraldehyde 3-phosphate dehydrogenase C[1][2]

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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0004365

glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000173

F

Seeded from EcoCyc (v14.0)

complete

GO:0004365

glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.2.1.12

F

Seeded from EcoCyc (v14.0)

complete

GO:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

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:0006006

glucose metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000173

P

Seeded from EcoCyc (v14.0)

complete

GO:0006006

glucose metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006424

P

Seeded from EcoCyc (v14.0)

complete

GO:0006096

glycolysis

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0324

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

P

Seeded from EcoCyc (v14.0)

complete

GO:0008943

glyceraldehyde-3-phosphate dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006424

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0051287

NAD or NADH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000173

F

Seeded from EcoCyc (v14.0)

complete

GO:0051287

NAD or NADH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006424

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000173

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006424

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

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

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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

E. coli B strain REL606 GapC GenBank record #ACT39045.1

Sequence
MSKVGINGFGRIGRLVLRRLLEVKSNIDVVAINDLTSPKILAYLLKHDSNYGPFPWSVDFTEDSLIVDGK
SIAVYAEKEAKNIPWKAKGAEIIVECTGFYTSAEKSQAHLDAGAKKVLISAPAGEMKTIVYNVNDDTLDG
NDTIVSVASCTTNCLAPMAKALHDSFGIEVGTMTTIHAYTGTQSLVDGPRGKDLRASRAAAENIIPHTTG
AAKAIGLVIPELSGKLKGHAQRVPVKTGSVTELVSILGKKVTAEEVNNALKQATTNNESFGYTDEEIVSS
DIIGSHFGSVFDATQTEITAVGDLQLVKTVAWYDNEYGFVTQLIRTLEKFAKL
Length

333

Mol. Wt

35.748 kDa

pI

6.2 (calculated)

Extinction coefficient

29,910 - 30,285 (calc based on 9 Y, 3 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

2..150

PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain

PMID:19920124

Domain

155..313

PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=gapC_1 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)

GeneID:2847738

Escherichia coli str. K-12 substr. MG1655

ASAP (EcoliWiki Page)

ASAP:ABE-0004729

Escherichia coli str. K-12 substr. MG1655

ASAP (EcoliWiki Page)

ASAP:ABE-0285094

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P33898

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:2847738

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004456

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

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)

Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

gapC_1C_2

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_000913:1487968..1488008 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:b1417 (EcoliWiki Page)

NCBI GEO profiles for gapC_1

microarray

GenExpDB:b1417 (EcoliWiki Page)

Summary of data for gapC_1 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

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Notes

Accessions Related to gapC Expression

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

Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1417

RegulonDB

RegulonDB:ECK120004456

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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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Do-It-Yourself Web Tools

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Notes

Families

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

Organism Homologs (Statistics) Comments

E. coli O157

GAPC

From ECOO157CYC

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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

Pfam (EcoliWiki Page)

PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain

Pfam (EcoliWiki Page)

PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain


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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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  2. 2.0 2.1 2.2 2.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. 4.0 4.1 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

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