lpxD:Gene Product(s): Difference between revisions

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PMID:19402753
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MALDI(Z-score):39.513239  
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MALDI(Z-score):34.741324  
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PMID:19402753
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MALDI(Z-score):27.424997  
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MALDI(Z-score):31.976205  
MALDI(Z-score):31.976205  
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Protein
Protein
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[[ydgI:Gene_Product(s)|ydgI]]
ydgI
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!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P21645 Protein Model Portal]
* [http://www.proteinmodelportal.org/query/uniprot/P21645 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P21645 PSI-PRED (P21645)]
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P21645 Genomes TO Protein (P21645)] (GTOP)


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!|Database!!Accession!!Notes
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWiki Page]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000610&formSubmitReturn=1 ASAP:ABE-0000610]
ASAP:ABE-0000610
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10316 ECOCYC:EG10316]
EcoCyc:EG10316
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10316 EcoGene:EG10316]
EcoGene:EG10316
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120000310
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB0312
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:22, 17 February 2015

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

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

LpxD

Synonyms

UDP-3-O-(3-hydroxymyristoyl)-glucosamine N-acyltransferase[1], B0179[2][1], OmsA[2][1], Ssc[2][1], OsmA[2][1], FirA[2][1], LpxD[2][1] , ECK0178, firA, JW0174, omsA, ssc, b0179

Product description

UDP-3-O-(3-hydroxymyristoyl)-glucosamine N-acyltransferase

Lipid A biosynthesis, UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase[3]

EC number (for enzymes) 
2.3.1.-[1]
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Notes

Function

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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:0009245

lipid A biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00523

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007691

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020573

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0441

P

Seeded from EcoCyc (v14.0)

complete

GO:0046677

response to antibiotic

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

P

Seeded from EcoCyc (v14.0)

complete

GO:0016410

N-acyltransferase activity

PMID:3288280[4]

IDA: Inferred from Direct Assay

F

complete

GO:0009245

lipid A biosynthetic process

PMID:8366125[5]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0016410

N-acyltransferase activity

PMID:8366125[5]

IDA: Inferred from Direct Assay

F

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

uniparc:UPI00000D382C

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

ydfR

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

cbpA

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

glnS

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

pssA

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

hldD

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

rho

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

rplB

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

rplD

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rplI

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rplO

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rplU

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rpsB

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rpsC

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rpsD

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rpsE

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

rpsG

PMID:15690043[6]

Experiment(s):EBI-886059, EBI-892599

Protein

tyrA

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

rluB

PMID:15690043[6]

Experiment(s):EBI-886059

Protein

lpxA

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rpsD

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rpsG

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rplR

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rplB

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rpsR

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rpsI

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

sdhA

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

ycbY

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rpsM

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rplA

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rpsC

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

phnA

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rplD

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

rpoC

PMID:16606699[7]

Experiment(s):EBI-1135798

Protein

aspA

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

csdA

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

ccmB

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

dnaJ

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rnk

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplC

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplK

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplL

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplM

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplP

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplS

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplT

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplV

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplX

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rpmG

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rpsH

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rpsJ

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rpsP

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rpsR

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rpsT

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

yfiF

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

yhbY

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

yjfI

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

ydgI

PMID:15690043[6]

Experiment(s):EBI-892599

Protein

rplP

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):5.589311

Protein

rfaD

PMID:19402753[8]

MALDI(Z-score):39.513239

Protein

ccmB

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

rplO

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

rplU

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

rplI

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

rho

PMID:19402753[8]

MALDI(Z-score):21.565908

Protein

rplA

PMID:19402753[8]

MALDI(Z-score):24.027450

Protein

rplB

PMID:19402753[8]

MALDI(Z-score):34.741324

Protein

aspA

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

rpsC

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):25.212997

Protein

rpsD

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):36.130305

Protein

pssA

PMID:19402753[8]

MALDI(Z-score):27.424997

Protein

cbpA

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):19.850514

Protein

rplD

PMID:19402753[8]

LCMS(ID Probability):99.0 MALDI(Z-score):20.126458

Protein

csdA

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

yfiF

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

rluB

PMID:19402753[8]

MALDI(Z-score):31.976205

Protein

yjfI

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

rnk

PMID:19402753[8]

LCMS(ID Probability):99.0

Protein

ydgI

PMID:19402753[8]

LCMS(ID Probability):99.0

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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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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 

MPSIRLADLA QQLDAELHGD GDIVITGVAS MQSAQTGHIT FMVNPKYREH LGLCQASAVV
MTQDDLPFAK SAALVVKNPY LTYARMAQIL DTTPQPAQNI APSAVIDATA KLGNNVSIGA
NAVIESGVEL GDNVIIGAGC FVGKNSKIGA GSRLWANVTI YHEIQIGQNC LIQSGTVVGA
DGFGYANDRG NWVKIPQIGR VIIGDRVEIG ACTTIDRGAL DDTIIGNGVI IDNQCQIAHN
VVIGDNTAVA GGVIMAGSLK IGRYCMIGGA SVINGHMEIC DKVTVTGMGM VMRPITEPGV
YSSGIPLQPN KVWRKTAALV MNIDDMSKRL KSLERKVNQQ D
Length

341

Mol. Wt

36.037 kDa

pI

6.5 (calculated)

Extinction coefficient

26,930 - 27,805 (calc based on 7 Y, 3 W, and 7 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

Initiator Methionine

1

Removed

UniProt:P21645

Domain

127..144

PF00132 Bacterial transferase hexapeptide (three repeats)

PMID:19920124[9]

Domain

21..90

PF04613 UDP-3-O-[3-hydroxymyristoyl glucosamine N-acyltransferase, LpxD ]

PMID:19920124[9]

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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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
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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:16128172

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944882

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000610

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P21645

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10316

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944882

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000310

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0312

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

[back to top]


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 1.8 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. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ Anderson, MS et al. (1988) Biosynthesis of lipid A in Escherichia coli: identification of UDP-3-O-[(R)-3-hydroxymyristoyl]-alpha-D-glucosamine as a precursor of UDP-N2,O3-bis[(R)-3-hydroxymyristoyl]-alpha-D-glucosamine. Biochemistry 27 1908-17 PubMed
  5. ↑ 5.0 5.1 Kelly, TM et al. (1993) The firA gene of Escherichia coli encodes UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase. The third step of endotoxin biosynthesis. J. Biol. Chem. 268 19866-74 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 6.14 6.15 6.16 6.17 6.18 6.19 6.20 6.21 6.22 6.23 6.24 6.25 6.26 6.27 6.28 6.29 6.30 6.31 6.32 6.33 6.34 6.35 6.36 6.37 6.38 6.39 6.40 6.41 6.42 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ 9.0 9.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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