cpsB:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

cpsB

Gene Synonym(s)

ECK2043, b2049, JW2034, manC, mni, rfbM, rfb[1][2]

Product Desc.

Colanic acid (CPS) biosynthesis; mannose 1-P guanyltransferase synthesis[3]

Product Synonyms(s)

mannose-1-phosphate guanyltransferase[1], B2049[2][1], RfbM[2][1], Rfb[2][1], Mni[2][1], ManC[2][1], CpsB[2][1] , ECK2043, JW2034, manC, mni, rfbM, b2049

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): wzxC[2]

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

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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

Standard name

cpsB

Mnemonic

Capsular polysaccharide

Synonyms

ECK2043, b2049, JW2034, manC, mni, rfbM, rfb[1][2]

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

45.72 minutes 

MG1655: 2122544..2121108
<gbrowseImage> name=NC_000913:2121108..2122544 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2057725..2056289
<gbrowseImage> name=NC_012967:2056289..2057725 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2013591..2015027
<gbrowseImage> name=NC_012759:2013591..2015027 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2126657..2125221
<gbrowseImage> name=NC_007779:2125221..2126657 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2213552..2212116
<gbrowseImage> name=NC_010473:2212116..2213552 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔcpsB (Keio:JW2034)

deletion

deletion

PMID:16738554

Shigen
CGSC9671[4]

cpsB::Tn5KAN-2 (FB20597)

Insertion at nt 965 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20597

contains pKD46

rfb-2

CGSC:10897

ΔcpsB747::kan

PMID:16738554

CGSC:100382


<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2034

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGCAGTCGAAACTCTATCC

Primer 2:CCaACCCGTCCGTAGCGATCCGC

10A9

Kohara Phage

Genobase

PMID:3038334

7A3

Kohara Phage

Genobase

PMID:3038334

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[4]

est. P1 cotransduction: 21% [5]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[4]

est. P1 cotransduction: 7% [5]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10161

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10161

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000157

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946580

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0159

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006791

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

CpsB

Synonyms

mannose-1-phosphate guanyltransferase[1], B2049[2][1], RfbM[2][1], Rfb[2][1], Mni[2][1], ManC[2][1], CpsB[2][1] , ECK2043, JW2034, manC, mni, rfbM, b2049

Product description

Colanic acid (CPS) biosynthesis; mannose 1-P guanyltransferase synthesis[3]

EC number (for enzymes)

<protect></protect>

Notes

Function

[back to top]


<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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0004475

mannose-1-phosphate guanylyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.13

F

Seeded from EcoCyc (v14.0)

complete

GO:0005525

GTP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0342

F

Seeded from EcoCyc (v14.0)

complete

GO:0009103

lipopolysaccharide biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006375

P

Seeded from EcoCyc (v14.0)

complete

GO:0009103

lipopolysaccharide biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0448

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

rplB

PMID:16606699

Experiment(s):EBI-1141773

Protein

galF

PMID:16606699

Experiment(s):EBI-1141773

Protein

carB

PMID:16606699

Experiment(s):EBI-1141773

</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

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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

MAQSKLYPVV MAGGSGSRLW PLSRVLYPKQ FLCLKGDLTM LQTTICRLNG VECESPVVIC
NEQHRFIVAE QLRQLNKLTE NIILEPAGRN TAPAIALAAL AAKRHSPESD PLMLVLAADH
VIADEDAFRA AVRNAMPYAE AGKLVTFGIV PDLPETGYGY IRRGEVSAGE QDMVAFEVAQ
FVEKPNLETA QAYVASGEYY WNSGMFLFRA GRYLEELKKY RPDILDACEK AMSAVDPDLN
FIRVDEEAFL ACPEESVDYA VMERTADAVV VPMDAGWSDV GSWSSLWEIS AHTAEGNVCH
GDVINHKTEN SYVYAESGLV TTVGVKDLVV VQTKDAVLIA DRNAVQDVKK VVEQIKADGR
HEHRVHREVY RPWGKYDSID AGDRYQVKRI TVKPGEGLSV QMHHHRAEHW VVVAGTAKVT
IDGDIKLLGE NESIYIPLGA THCLENPGKI PLDLIEVRSG SYLEEDDVVR FADRYGRV
Length

478

Mol. Wt

53.015 kDa

pI

5.2 (calculated)

Extinction coefficient

66,810 - 67,810 (calc based on 19 Y, 7 W, and 8 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

323..473

PF01050 Mannose-6-phosphate isomerase

PMID:19920124

Domain

7..296

PF00483 Nucleotidyl transferase

PMID:19920124

<motif_map/>

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

Structures

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

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129989

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946580

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006791

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P24174

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10161

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10161

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946580

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000157

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0159

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

3a

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

4

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

[back to top]


<protect>

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

Transcription unit(s)

wzxC

Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:2122524..2122564 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]


<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:b2049 (EcoliWiki Page)

NCBI GEO profiles for cpsB

microarray

GenExpDB:b2049 (EcoliWiki Page)

Summary of data for cpsB 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

<protect></protect>

Notes

Accessions Related to cpsB Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10161

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0159

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2049

EcoGene

EcoGene:EG10161

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000157

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006791

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Xenopus tropicalis

  • ENSXETP00000018513 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

CPSB

From SHIGELLACYC

E. coli O157

CPSB

From ECOO157CYC


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF01050 Mannose-6-phosphate isomerase

Pfam (EcoliWiki Page)

PF00483 Nucleotidyl transferase

Superfamily (EcoliWiki Page)

SUPERFAMILY:51182

Panther (EcoliWiki Page)

PTHR12526:SF1

Superfamily (EcoliWiki Page)

SUPERFAMILY:53448

EcoCyc

EcoCyc:EG10161

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10161

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000157

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0159

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006791

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 1.17 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. 4.0 4.1 4.2 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).

Categories

[back to top]