mcbR: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

mcbR

Gene Synonym(s)

ECK1444, b1450, JW1445, yncC[1], JW1445, yncC

Product Desc.

predicted DNA-binding transcriptional regulator[2][3]

Product Synonyms(s)

predicted DNA-binding transcriptional regulator[1], B1450[2][1], YncC[2][1] , ECK1444, JW1445, yncC, b1450

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression
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

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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

mcbR

Mnemonic

MqsR-controlled Colanic acid and Biofilm

Synonyms

ECK1444, b1450, JW1445, yncC[1], JW1445, yncC

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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

32.72 minutes 

MG1655: 1518286..1518951
<gbrowseImage> name=NC_000913:1518286..1518951 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1490372..1491037
<gbrowseImage> name=NC_012967:1490372..1491037 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1521976..1522641
<gbrowseImage> name=NC_007779:1521976..1522641 source=W3110 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1410345..1411010
<gbrowseImage> name=NC_012759:1410345..1411010 source=BW2952 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

ΔyncC (Keio:JW1445)

deletion

deletion

PMID:16738554

Shigen


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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

JW1445

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCCTGGAACGGGAAAAATGAA

Primer 2:CCACGATTGTATTGCTGGTATAA

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[4]

est. P1 cotransduction: 40% [5]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[4]

est. P1 cotransduction: 54% [5]
Synonyms:zdc-235::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:G6761

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13773

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003350

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946014

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3535

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004837

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

YncC

Synonyms

predicted DNA-binding transcriptional regulator[1], B1450[2][1], YncC[2][1] , ECK1444, JW1445, yncC, b1450

Product description

predicted DNA-binding transcriptional regulator[2][3]

EC number (for enzymes)

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

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. 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:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000524

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:18309357

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:15690043

IPI: Inferred from Physical Interaction

UniProtKB:P60438

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000524

C

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:18309357

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:18309357

IDA: Inferred from Direct Assay

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

Protein

rplC

PMID:15690043

Experiment(s):EBI-880850

Protein

ydbH

PMID:16606699

Experiment(s):EBI-1139864

Protein

lacZ

PMID:16606699

Experiment(s):EBI-1139864

Protein

stfR

PMID:16606699

Experiment(s):EBI-1139864

Protein

rrmA

PMID:16606699

Experiment(s):EBI-1139864

Protein

hchA

PMID:16606699

Experiment(s):EBI-1139864

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

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

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

MNSFCHAGRV GQKTREGIKM PGTGKMKHVS LTLQVENDLK HQLSIGALKP GARLITKNLA
EQLGMSITPV REALLRLVSV NALSVAPAQA FTVPEVGKRQ LDEINRIRYE LELMAVALAV
ENLTPQDLAE LQELLEKLQQ AQEKGDMEQI INVNRLFRLA IYHRSNMPIL CEMIEQLWVR
MGPGLHYLYE AINPAELREH IENYHLLLAA LKAKDKEGCR HCLAEIMQQN IAILYQQYNR
Length

240

Mol. Wt

27.253 kDa

pI

7.9 (calculated)

Extinction coefficient

15,930 - 16,430 (calc based on 7 Y, 1 W, and 4 C residues)

See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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

12..74

PF00392 Bacterial regulatory proteins, gntR family

PMID:19920124

Domain

84..210

PF07729 FCD domain

PMID:19920124

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

<motif_map/>

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

Structures

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

Models

View models at:

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

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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

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

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:90111276

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946014

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004837

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76114

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6761

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13773

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946014

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003350

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3535

Escherichia coli str. K-12 substr. MG1655

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

Notes

Links

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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.



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 MG1655

7a

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

56

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

Transcription unit(s)

yncC

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_000913:1518266..1518306 source=MG1655 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:b1450 (EcoliWiki Page)

NCBI GEO profiles for yncC

microarray

GenExpDB:b1450 (EcoliWiki Page)

Summary of data for yncC 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 (1518020..1518258) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ06; Well:E11[6]

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Notes

Accessions Related to mcbR Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6761

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3535

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1450

EcoGene

EcoGene:EG13773

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003350

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004837

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

Shigella flexneri

S1897

From SHIGELLACYC

E. coli O157

Z2269

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)

PF00392 Bacterial regulatory proteins, gntR family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46785

Pfam (EcoliWiki Page)

PF07729 FCD domain

EcoCyc

EcoCyc:G6761

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13773

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003350

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3535

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004837

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. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 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 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 CGSC: The Coli Genetics Stock Center
  5. 5.0 5.1 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).
  6. 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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