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Revision as of 19:15, 10 February 2009

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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

amiD

Gene Synonym(s)

ECK0858, b0867, JW0851, ybjR[1], JW0851, ybjR

Product Desc.

predicted amidase and lipoprotein[2][3]

Product Synonyms(s)

predicted amidase and lipoprotein[1], YbjR[2][1], B0867[2][1] , ECK0858, JW0851, ybjR, b0867

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ybjQ

Regulation/Activity
Quick Links



        

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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

amiD

Mnemonic

Systematic nomenclature

Synonyms

ECK0858, b0867, JW0851, ybjR[1], JW0851, ybjR

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Notes

Location(s) and DNA Sequence

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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

BW2952

NC_012759: 807104..807934
<gbrowseImage> name=NC_012759:807104..807934 source=BW2952 preset=GeneLocation </gbrowseImage>

MG1655

19.49 minutes 

MG1655: 904136..904966
<gbrowseImage> name=NC_000913:904136..904966 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 921620..922450
<gbrowseImage> name=NC_012967:921620..922450 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 905335..906165
<gbrowseImage> name=NC_007779:905335..906165 source=W3110 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

ΔybjR (Keio:JW0851)

deletion

deletion

PMID:16738554

Shigen
CGSC8887[4]


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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

JW0851

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGAAGATTCTTCTGGCTGGT

Primer 2:CCATCCTGCCCGTATTTCTCCAG

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[4]

est. P1 cotransduction: % [5]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[4]

est. P1 cotransduction: 16% [5]
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:G6452

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13687

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003052

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945494

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3451

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002947

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

AmiD

Synonyms

predicted amidase and lipoprotein[1], YbjR[2][1], B0867[2][1] , ECK0858, JW0851, ybjR, b0867

Product description

predicted amidase and lipoprotein[2][3]

EC number (for enzymes)
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See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Notes

Function

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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:0008745

N-acetylmuramoyl-L-alanine amidase activity

PMID:17526703[6]

IDA: Inferred from Direct Assay

F

complete

GO:0019867

outer membrane

PMID:17526703[6]

IDA: Inferred from Direct Assay

C

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:17526703[6]

IDA: Inferred from Direct Assay

F

complete

GO:0007047

cellular cell wall organization

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0008745

N-acetylmuramoyl-L-alanine amidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002502

F

Seeded from EcoCyc (v14.0)

complete

GO:0008745

N-acetylmuramoyl-L-alanine amidase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.1.28

F

Seeded from EcoCyc (v14.0)

complete

GO:0009253

peptidoglycan catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002502

P

Seeded from EcoCyc (v14.0)

complete

GO:0009279

cell outer membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0998

C

Seeded from EcoCyc (v14.0)

complete

GO:0031225

anchored to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9901

C

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

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


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 

MRRFFWLVAA ALLLAGCAGE KGIVEKEGYQ LDTRRQAQAA YPRIKVLVIH YTADDFDSSL
ATLTDKQVSS HYLVPAVPPR YNGKPRIWQL VPEQELAWHA GISAWRGATR LNDTSIGIEL
ENRGWQKSAG VKYFAPFEPA QIQALIPLAK DIIARYHIKP ENVVAHADIA PQRKDDPGPL
FPWQQLAQQG IGAWPDAQRV NFYLAGRAPH TPVDTASLLE LLARYGYDVK PDMTPREQRR
VIMAFQMHFR PTLYNGEADA ETQAIAEALL EKYGQD
Length

276

Mol. Wt

31.072 kDa

pI

7.8 (calculated)

Extinction coefficient

56,380 - 56,505 (calc based on 12 Y, 7 W, and 1 C residues)

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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

35..180

PF01510 N-acetylmuramoyl-L-alanine amidase

PMID:19920124[7]

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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=amiD taxon=562,83333 </beststructure>

Models

View models at:

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

Structure figures

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

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:16128835

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945494

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002947

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75820

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6452

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13687

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945494

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003052

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3451

Escherichia coli str. K-12 substr. MG1655

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

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

141

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

82

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

54a

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

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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)

ybjQ

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Figure courtesy of RegulonDB


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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<gbrowseImage> name=NC_000913:904116..904156 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


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

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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:b0867 (EcoliWiki Page)

NCBI GEO profiles for ybjR

microarray

GenExpDB:b0867 (EcoliWiki Page)

Summary of data for ybjR 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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<protect>

Notes

Accessions Related to amiD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6452

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3451

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0867

EcoGene

EcoGene:EG13687

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003052

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002947

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

Apis mellifera

  • ENSAPMP00000027049 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

S0863

From SHIGELLACYC

E. coli O157

Z1100

From ECOO157CYC

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Do-It-Yourself Web Tools


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)

PF01510 N-acetylmuramoyl-L-alanine amidase

Superfamily (EcoliWiki Page)

SUPERFAMILY:47090

Superfamily (EcoliWiki Page)

SUPERFAMILY:55846

EcoCyc

EcoCyc:G6452

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13687

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003052

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3451

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002947

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 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).
  6. ↑ 6.0 6.1 6.2 Uehara, T & Park, JT (2007) An anhydro-N-acetylmuramyl-L-alanine amidase with broad specificity tethered to the outer membrane of Escherichia coli. J. Bacteriol. 189 5634-41 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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