ygbI: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

ygbI

Gene Synonym(s)

ECK2730, b2735, JW2705[1], JW2705

Product Desc.

predicted DNA-binding transcriptional regulator, DEOR-type[2][3]

Function unknown[4]

Product Synonyms(s)

predicted DNA-binding transcriptional regulator[1], B2735[2][1], YgbI[2][1] , ECK2730, JW2705, b2735

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ygbI[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

ygbI

Mnemonic

Systematic nomenclature

Synonyms

ECK2730, b2735, JW2705[1], JW2705

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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

61.61 minutes 

MG1655: 2859286..2858489
<gbrowseImage> name=NC_000913:2858489..2859286 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2756124..2755327
<gbrowseImage> name=NC_012967:2755327..2756124 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2744301..2745098
<gbrowseImage> name=NC_012759:2744301..2745098 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2859920..2859123
<gbrowseImage> name=NC_007779:2859123..2859920 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2951828..2951031
<gbrowseImage> name=NC_010473:2951031..2951828 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

ΔygbI (Keio:JW2705)

deletion

deletion

PMID:16738554

Shigen
CGSC10128[5]

ΔygbI::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938

ΔygbI::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔygbI740::kan

PMID:16738554

CGSC:104884


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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

JW2705

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCAGCAGGACAAAGGAAGGA

Primer 2:CCTTCATTTTTCGCTACCAGCAA

25D2

Kohara Phage

Genobase

PMID:3038334

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 27% [6]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

cysI95::Tn10

Linked marker

CAG12173 = CGSC7425[5]

est. P1 cotransduction: 35% [6]
Synonyms:cysC95::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:G7416

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13103

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003981

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947204

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2906

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008982

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

YgbI

Synonyms

predicted DNA-binding transcriptional regulator[1], B2735[2][1], YgbI[2][1] , ECK2730, JW2705, b2735

Product description

predicted DNA-binding transcriptional regulator, DEOR-type[2][3]

Function unknown[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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001034

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001034

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

PMID:15556475

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACK5

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001034

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

P

Seeded from EcoCyc (v14.0)

complete

GO:0016564

transcription repressor activity

PMID:15556475

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACK5

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

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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

MSAGQRKEQK LIPVERRQII LEMVAEKGIV SIAELTDRMN VSHMTIRRDL QKLEQQGAVV
LVSGGVQSPG RVAHEPSHQV KTALAMTQKA AIGKLAASLV QPGSCIYLDA GTTTLAIAQH
LIHMESLTVV TNDFVIADYL LDNSNCTIIH TGGAVCRENR SCVGEAAATM LRSLMIDQAF
ISASSWSVRG ISTPAEDKVT VKRAIASASR QRVLVCDATK YGQVATWLAL PLSEFDQIIT
DDGLPESASR ALVKQDLSLL VAKNE
Length

265

Mol. Wt

28.56 kDa

pI

7.5 (calculated)

Extinction coefficient

15,470 - 16,095 (calc based on 3 Y, 2 W, and 5 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

86..241

PF00455 Bacterial regulatory proteins, deoR family

PMID:19920124

Domain

16..72

PF08220 DeoR-like helix-turn-helix domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=ygbI 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:226524741

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947204

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008982

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P52598

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7416

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13103

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003981

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2906

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

E. coli K-12 MG1655

207

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

87

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

167

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

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<protect>

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

Transcription unit(s)

ygbI

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_000913:2859266..2859306 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:b2735 (EcoliWiki Page)

NCBI GEO profiles for ygbI

microarray

GenExpDB:b2735 (EcoliWiki Page)

Summary of data for ygbI 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 (2859197..2859499) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:A10[7]

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Notes

Accessions Related to ygbI Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7416

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2906

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2735

EcoGene

EcoGene:EG13103

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003981

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008982

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

YGBI

From SHIGELLACYC


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)

PF00455 Bacterial regulatory proteins, deoR family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46785

Superfamily (EcoliWiki Page)

SUPERFAMILY:100950

Pfam (EcoliWiki Page)

PF08220 DeoR-like helix-turn-helix domain

PFAM (EcoliWiki Page)

PFAM:PF00455

EcoCyc

EcoCyc:G7416

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13103

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003981

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2906

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008982

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 2.6 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 5.2 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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