yebA: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

yebA

Gene Synonym(s)

ECK1857, b1856, JW5304, yebA'[1][2]

Product Desc.

conserved protein[2][3]

Putative metalloprotease, function unknown; M37 family[4]

Product Synonyms(s)

predicted peptidase[1], YebA[2][1], B1856[2][1] , ECK1857, JW5304, b1856

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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NlpD, YgeR, YebA and EnvC are paralogs. SwissProt predicts a 34 aa type I signal peptide that cannot be confirmed using SignalP.[4]



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

yebA

Mnemonic

Systematic nomenclature

Synonyms

ECK1857, b1856, JW5304, yebA'[1][2]

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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

41.78 minutes 

MG1655: 1939659..1938337
<gbrowseImage> name=NC_000913:1938337..1939659 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1920148..1918889
<gbrowseImage> name=NC_012967:1918889..1920148 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1830396..1831718
<gbrowseImage> name=NC_012759:1830396..1831718 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1943349..1942027
<gbrowseImage> name=NC_007779:1942027..1943349 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2030230..2028908
<gbrowseImage> name=NC_010473:2028908..2030230 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

ΔyebA (Keio:JW5304)

deletion

deletion

PMID:16738554

Shigen

yebA::Tn5KAN-I-SceI (FB20476)

Insertion at nt 506 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20476

contains pKD46

ΔyebA::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔyebA::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938

ΔyebA::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938

ΔyebA::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938

ΔyebA::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938

ΔyebA::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938

ΔyebA

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔyebA ΔenvC

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔyebA ΔnlpD

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔyebA ΔygeR

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔyebA ΔenvC ΔnlpD

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔyebA ΔenvC ΔygeR

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔyebA ΔnlpD ΔygeR

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345

ΔyebA ΔnlpD ΔygeR ΔenvC

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345


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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

JW5304

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAACAGATAGCCCGCTCTGT

Primer 2:CCATCAAACCGTAGCTGCGGCAC

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[5]

est. P1 cotransduction: 76% [6]

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[5]

est. P1 cotransduction: 8% [6]

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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:EG10013

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000011

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946376

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0013

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006189

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

YebA

Synonyms

predicted peptidase[1], YebA[2][1], B1856[2][1] , ECK1857, JW5304, b1856

Product description

conserved protein[2][3]

Putative metalloprotease, function unknown; M37 family[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:0000920

cytokinetic cell separation

PMID:19525345

IGI: Inferred from Genetic Interaction

UniProtKB:P0ADA3 UniProtKB:P37690 UniProtKB:Q46798


P

Seeded from EcoCyc (v14.0)

complete

GO:0004222

metalloendopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002886

F

Seeded from EcoCyc (v14.0)

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:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002886

P

Seeded from EcoCyc (v14.0)

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:0008233

peptidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0645

F

Seeded from EcoCyc (v14.0)

complete

GO:0008237

metallopeptidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0482

F

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:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9904

C

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016998

cell wall macromolecule catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002482

P

Seeded from EcoCyc (v14.0)

complete

GO:0016998

cell wall macromolecule catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018392

P

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0000920

cytokinetic cell separation

PMID:19525345

IGI: Inferred from Genetic Interaction

UniProtKB:P37690


P

complete

GO:0000920

cytokinetic cell separation

PMID:19525345

IGI: Inferred from Genetic Interaction

UniProtKB:P0ADA3 UniProtKB:P37690 UniProtKB:Q46798


P

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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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 

MLGSLTVLTL AVAVWRPYVY HRDATPIVKT IELEQNEIRS LLPEASEPID QAAQEDEAIP
QDELDDKIAG EAGVHEYVVS TGDTLSSILN QYGIDMGDIT QLAAADKELR NLKIGQQLSW
TLTADGELQR LTWEVSRRET RTYDRTAANG FKMTSEMQQG EWVNNLLKGT VGGSFVASAR
NAGLTSAEVS AVIKAMQWQM DFRKLKKGDE FAVLMSREML DGKREQSQLL GVRLRSEGKD
YYAIRAEDGK FYDRNGTGLA KGFLRFPTAK QFRISSNFNP RRTNPVTGRV APHRGVDFAM
PQGTPVLSVG DGEVVVAKRS GAAGYYVAIR HGRSYTTRYM HLRKILVKPG QKVKRGDRIA
LSGNTGRSTG PHLHYEVWIN QQAVNPLTAK LPRTEGLTGS DRREFLAQAK EIVPQLRFD
Length

419

Mol. Wt

46.657 kDa

pI

9.7 (calculated)

Extinction coefficient

52,370 (calc based on 13 Y, 6 W, and 0 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

312..407

PF01551 Peptidase family M23

PMID:19920124

Domain

94..176

PF04225 Opacity-associated protein A LysM-like domain

PMID:19920124

Domain

10..40

PF08525 Opacity-associated protein A N-terminal motif

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=yebA 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:90111345

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006189

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AFS9

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10013

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10013

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946376

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000011

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946376

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0013

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

341

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

379

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

569

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_000913:1939639..1939679 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
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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:b1856 (EcoliWiki Page)

NCBI GEO profiles for yebA

microarray

GenExpDB:b1856 (EcoliWiki Page)

Summary of data for yebA 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 yebA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10013

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0013

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1856

EcoGene

EcoGene:EG10013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000011

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006189

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

Anopheles gambiae

  • ENSANGP00000001481 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YEBA

From SHIGELLACYC

E. coli O157

YEBA

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)

PF01551 Peptidase family M23

Pfam (EcoliWiki Page)

PF04225 Opacity-associated protein A LysM-like domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:51261

Panther (EcoliWiki Page)

PTHR21666:SF7

Pfam (EcoliWiki Page)

PF08525 Opacity-associated protein A N-terminal motif

EcoCyc

EcoCyc:EG10013

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000011

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0013

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006189

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 2.7 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 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 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).

Categories

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