ybiB:On One Page

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

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Standard Name

ybiB

Gene Synonym(s)

ECK0789, b0800, JW0785[1], ybiB

Product Desc.

predicted transferase/phosphorylase[2][3]

Function unknown[4]

Product Synonyms(s)

predicted transferase/phosphorylase[1], B0800[2][1], YbiB[2][1]

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s):

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

ybiB

Mnemonic

Systematic nomenclature

Synonyms

ECK0789, b0800, JW0785[1], ybiB

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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

17.99 minutes 

MG1655: 834471..835433
<gbrowseImage> name=NC_000913:834471..835433 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 827873..828835
<gbrowseImage> name=NC_012967:827873..828835 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 737439..738401
<gbrowseImage> name=NC_012759:737439..738401 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 835670..836632
<gbrowseImage> name=NC_007779:835670..836632 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 888399..889361
<gbrowseImage> name=NC_010473:888399..889361 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

ΔybiB (Keio:JW0785)

deletion

deletion

PMID:16738554

Shigen
CGSC8836[5]

ΔybiB772::kan

PMID:16738554

CGSC:103834


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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

JW0785

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGACTATCGCAAAATCATTAA

Primer 2:CCAAATGCCTGATTAACGCGCGC

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: 63% [6]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: % [6]
Synonyms:zbj-1230::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:EG10338

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10338

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000332

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0334

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000299

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

Cra

Synonyms

DNA-binding transcriptional dual regulator, B0080, Shl, FruC, FruR, Cra , cra, ECK0081, fruC, fruS?, JW0078, serR?, shl, b0080, Cra

Product description

FruR transcriptional dual regulator;

Component of FruR transcriptional dual regulator; FruR-fructose-1,6-bisphosphate; FruR-fructose-1-phosphate

Regulatory gene for fru operon, other catabolite-regulated genes

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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010982

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012781

F

Seeded from EcoCyc (v14.0)

complete

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:IPR000843

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000843

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:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000843

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:IPR012781

P

Seeded from EcoCyc (v14.0)

complete

GO:0009750

response to fructose stimulus

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012781

P

Seeded from EcoCyc (v14.0)

complete

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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 FruR transcriptional dual regulator

could be indirect

Protein

matC

PMID:16606699

Experiment(s):EBI-1135523

Protein

groL

PMID:16606699

Experiment(s):EBI-1135523

Protein

nadE

PMID:16606699

Experiment(s):EBI-1135523

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1135523

Protein

hldD

PMID:15690043

Experiment(s):EBI-889721

Protein

rpsC

PMID:15690043

Experiment(s):EBI-889721

Protein

tufA

PMID:15690043

Experiment(s):EBI-889721

Protein

ssb

PMID:19402753

MALDI(Z-score):26.363338

Protein

fadB

PMID:19402753

MALDI(Z-score):21.861324

Protein

Subunits of FruR-fructose-1,6-bisphosphate

could be indirect

Protein

Subunits of FruR-fructose-1-phosphate

could be indirect


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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 

MKLDEIARLA GVSRTTASYV INGKAKQYRV SDKTVEKVMA VVREHNYHPN AVAAGLRAGR
TRSIGLVIPD LENTSYTRIA NYLERQARQR GYQLLIACSE DQPDNEMRCI EHLLQRQVDA
IIVSTSLPPE HPFYQRWAND PFPIVALDRA LDREHFTSVV GADQDDAEML AEELRKFPAE
TVLYLGALPE LSVSFLREQG FRTAWKDDPR EVHFLYANSY EREAAAQLFE KWLETHPMPQ
ALFTTSFALL QGVMDVTLRR DGKLPSDLAI ATFGDNELLD FLQCPVLAVA QRHRDVAERV
LEIVLASLDE PRKPKPGLTR IKRNLYRRGV LSRS
Length

334

Mol. Wt

37.999 kDa

pI

7.0 (calculated)

Extinction coefficient

32,890 - 33,265 (calc based on 11 Y, 3 W, and 3 C residues)

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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..50

PF00356 Bacterial regulatory proteins, lacI family

PMID:19920124

Domain

61..327

PF00532 family

PMID:19920124

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

Structures

<beststructure> gene=fruR taxon=12017 </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:16128073

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944804

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACP1

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944804

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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)

Protein

E. coli K-12 MC4100

3.78E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

51.812+/-0.598

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.048856549

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

817

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

875

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

722

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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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)
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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_000913:834451..834491 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
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0800 (EcoliWiki Page)

NCBI GEO profiles for ybiB

microarray

GenExpDB:b0800 (EcoliWiki Page)

Summary of data for ybiB from multiple microarray studies

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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 ybiB Expression

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Database Accession Notes

EcoCyc

EcoCyc:EG10338

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0334

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0800

EcoGene

EcoGene:EG10338

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000332

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000299

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

YBIB

From SHIGELLACYC

E. coli O157

YBIB

From ECOO157CYC

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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)

PF02885 Glycosyl transferase family, helical bundle domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:47648

Superfamily (EcoliWiki Page)

SUPERFAMILY:52418

Panther (EcoliWiki Page)

PTHR11922:SF15

EcoCyc

EcoCyc:EG10338

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10338

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000332

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0334

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000299

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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).

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