pepT: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

pepT

Gene Synonym(s)

ECK1113, b1127, JW1113[1], JW1113

Product Desc.

PepT[2][3];

Component of peptidase T[3]

Peptidase T, aminotripeptidase; anaerobically induced, biofilm-induced, cell-density induced[4]

Product Synonyms(s)

peptidase T[1], B1127[2][1] , ECK1113, JW1113, b1127

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): pepT[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


HT_Cmplx34_Cyt: ArgD+CbpA+PepT.[4]



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

pepT

Mnemonic

Peptidase

Synonyms

ECK1113, b1127, JW1113[1], JW1113

edit table

</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

25.54 minutes 

MG1655: 1185067..1186293
<gbrowseImage> name=NC_000913:1185067..1186293 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1201214..1202440
<gbrowseImage> name=NC_012967:1201214..1202440 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1088992..1090218
<gbrowseImage> name=NC_012759:1088992..1090218 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1187421..1188647
<gbrowseImage> name=NC_007779:1187421..1188647 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1240512..1241738
<gbrowseImage> name=NC_010473:1240512..1241738 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</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
edit table

<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

ΔpepT (Keio:JW1113)

deletion

deletion

PMID:16738554

Shigen
CGSC9044[5]

pepT::Tn5KAN-2 (FB20259)

Insertion at nt 828 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20259

does not contain pKD46

ΔpepT777::kan

PMID:16738554

CGSC:102292


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

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

</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

JW1113

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATAAACTACTTGAGCGATT

Primer 2:CCtTTCCGTTGCGCCGTTAACTC

7F9

Kohara Phage

Genobase

PMID:3038334

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[5]

est. P1 cotransduction: 31% [6]

zcf-117::Tn10

Linked marker

CAG18463 = CGSC7363[5]

est. P1 cotransduction: 37% [6]

edit table

<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:EG11549

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11549

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001503

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946333

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1511

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003800

Escherichia coli str. K-12 substr. MG1655

edit table

<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

PepT

Synonyms

peptidase T[1], B1127[2][1] , ECK1113, JW1113, b1127

Product description

PepT[2][3];

Component of peptidase T[3]

Peptidase T, aminotripeptidase; anaerobically induced, biofilm-induced, cell-density induced[4]

EC number (for enzymes)


edit table

<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:0004177

aminopeptidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0031

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00550

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010161

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00550

P

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001261

P

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002933

P

Seeded from EcoCyc (v14.0)

complete

GO:0006518

peptide metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010161

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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001261

F

Seeded from EcoCyc (v14.0)

complete

GO:0008237

metallopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002933

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:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00550

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010161

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:0016787

hydrolase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011650

F

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:0045148

tripeptide aminopeptidase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00550

F

Seeded from EcoCyc (v14.0)

complete

GO:0045148

tripeptide aminopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010161

F

Seeded from EcoCyc (v14.0)

complete

GO:0045148

tripeptide aminopeptidase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.4.11.4

F

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:0046983

protein dimerization activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011650

F

Seeded from EcoCyc (v14.0)

complete

edit table

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 peptidase T

could be indirect

Protein

dps

PMID:15690043

Experiment(s):EBI-887434

Protein

fusA

PMID:15690043

Experiment(s):EBI-887434

Protein

pflB

PMID:15690043

Experiment(s):EBI-887434, EBI-893272

Protein

tpiA

PMID:15690043

Experiment(s):EBI-887434, EBI-879853, EBI-884726

Protein

tufA

PMID:15690043

Experiment(s):EBI-887434

Protein

wcaL

PMID:15690043

Experiment(s):EBI-887434

Protein

pepE

PMID:15690043

Experiment(s):EBI-893272

Protein

proA

PMID:15690043

Experiment(s):EBI-893272

Protein

yihI

PMID:15690043

Experiment(s):EBI-893272

Protein

hns

PMID:16606699

Experiment(s):EBI-1138943

Protein

rhsD

PMID:16606699

Experiment(s):EBI-1138943

Protein

rplO

PMID:16606699

Experiment(s):EBI-1138943

Protein

ygaC

PMID:16606699

Experiment(s):EBI-1138943

Protein

nadE

PMID:16606699

Experiment(s):EBI-1138943

Protein

glnB

PMID:16606699

Experiment(s):EBI-1138943

Protein

pflB

PMID:16606699

Experiment(s):EBI-1138943

Protein

fusA

PMID:19402753

MALDI(Z-score):19.589566

Protein

proA

PMID:19402753

LCMS(ID Probability):99.6

Protein

yihI

PMID:19402753

LCMS(ID Probability):99.6

Protein

dps

PMID:19402753

MALDI(Z-score):37.725610

Protein

pepE

PMID:19402753

LCMS(ID Probability):99.6

Protein

pflB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.176524

edit table

</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
edit table

<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 

MDKLLERFLN YVSLDTQSKA GVRQVPSTEG QWKLLHLLKE QLEEMGLINV TLSEKGTLMA
TLPANVPGDI PAIGFISHVD TSPDCSGKNV NPQIVENYRG GDIALGIGDE VLSPVMFPVL
HQLLGQTLIT TDGKTLLGAD DKAGIAEIMT ALAVLQQKKI PHGDIRVAFT PDEEVGKGAK
HFDVDAFDAR WAYTVDGGGV GELEFENFNA ASVNIKIVGN NVHPGTAKGV MVNALSLAAR
IHAEVPADES PEMTEGYEGF YHLASMKGTV ERADMHYIIR DFDRKQFEAR KRKMMEIAKK
VGKGLHPDCY IELVIEDSYY NMREKVVEHP HILDIAQQAM RDCDIEPELK PIRGGTDGAQ
LSFMGLPCPN LFTGGYNYHG KHEFVTLEGM EKAVQVIVRI AELTAQRK
Length

408

Mol. Wt

44.923 kDa

pI

5.4 (calculated)

Extinction coefficient

27,390 - 27,890 (calc based on 11 Y, 2 W, and 4 C residues)

edit table


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

74..403

PF01546 Peptidase family M20/M25/M40

PMID:19920124

Domain

205..308

PF07687 Peptidase dimerisation domain

PMID:19920124

edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table
</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
edit table

<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:16129090

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946333

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003800

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P29745

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11549

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11549

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946333

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001503

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1511

Escherichia coli str. K-12 substr. MG1655

edit table

<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 MC4100

1.94E+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

14.968+/-0.137

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.13132137

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

244

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

341

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

222

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

edit table

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)

pepT

edit table
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_000913:1185047..1185087 source=MG1655 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
edit table


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

Type Reference Notes

microarray

GEO Profiles:b1127 (EcoliWiki Page)

NCBI GEO profiles for pepT

microarray

GenExpDB:b1127 (EcoliWiki Page)

Summary of data for pepT from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (1184732..1185133) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:B8[7]

edit table

<protect></protect>

Notes

Accessions Related to pepT Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11549

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1511

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1127

EcoGene

EcoGene:EG11549

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001503

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003800

Escherichia coli str. K-12 substr. MG1655

edit table

<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

Shigella flexneri

PEPT

From SHIGELLACYC

E. coli O157

PEPT

From ECOO157CYC

edit table


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)

PF01546 Peptidase family M20/M25/M40

Panther (EcoliWiki Page)

PTHR11014:SF3

Superfamily (EcoliWiki Page)

SUPERFAMILY:53187

Superfamily (EcoliWiki Page)

SUPERFAMILY:55031

Pfam (EcoliWiki Page)

PF07687 Peptidase dimerisation domain

EcoCyc

EcoCyc:EG11549

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11549

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001503

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1511

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003800

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 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 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=pepT:On_One_Page&oldid=219513"