ydcP: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

ydcP

Gene Synonym(s)

ECK1429, b1435, JW1431[1], JW1431

Product Desc.

putative collagenase[2][3]

Function unknown, U32 peptidase family[4]

Product Synonyms(s)

predicted peptidase[1], YdcP[2][1], B1435[2][1] , ECK1429, JW1431, b1435

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ydcP[2]

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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ydcP, yegQ, yhbU, and yhbV are paralogs.[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

ydcP

Mnemonic

Systematic nomenclature

Synonyms

ECK1429, b1435, JW1431[1], JW1431

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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

32.43 minutes 

MG1655: 1504805..1506766
<gbrowseImage> name=NC_000913:1504805..1506766 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1476891..1478852
<gbrowseImage> name=NC_012967:1476891..1478852 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1396864..1398825
<gbrowseImage> name=NC_012759:1396864..1398825 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1508495..1510456
<gbrowseImage> name=NC_007779:1508495..1510456 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1595400..1597361
<gbrowseImage> name=NC_010473:1595400..1597361 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

ΔydcP (Keio:JW1431)

deletion

deletion

PMID:16738554

Shigen
CGSC9251[5]

ΔydcP726::kan

PMID:16738554

CGSC:104176


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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

JW1431

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACCGTATCTTCTCATCGACT

Primer 2:CCgCCTTTTCGCTTCGGCAATGT

1A6

Kohara Phage

Genobase

PMID:3038334

10D6

Kohara Phage

Genobase

PMID:3038334

5F11

Kohara Phage

Genobase

PMID:3038334

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[5]

est. P1 cotransduction: 69% [6]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: 30% [6]
Synonyms:zdc-235::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:G6746

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13759

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003335

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945993

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3522

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004786

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

YdcP

Synonyms

predicted peptidase[1], YdcP[2][1], B1435[2][1] , ECK1429, JW1431, b1435

Product description

putative collagenase[2][3]

Function unknown, U32 peptidase 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:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001539

P

Seeded from EcoCyc (v14.0)

complete

GO:0008233

peptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001539

F

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: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

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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

rplA

PMID:15690043

Experiment(s):EBI-880468, EBI-886031

Protein

tufA

PMID:15690043

Experiment(s):EBI-880468

Protein

rplB

PMID:16606699

Experiment(s):EBI-1139836

Protein

mrdA

PMID:16606699

Experiment(s):EBI-1139836

Protein

fumA

PMID:16606699

Experiment(s):EBI-1139836

Protein

yhgF

PMID:16606699

Experiment(s):EBI-1139836

Protein

dnaE

PMID:16606699

Experiment(s):EBI-1139836

Protein

groL

PMID:16606699

Experiment(s):EBI-1139836

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1139836

Protein

arpA

PMID:16606699

Experiment(s):EBI-1139836

Protein

ycgE

PMID:16606699

Experiment(s):EBI-1139836

Protein

cysI

PMID:16606699

Experiment(s):EBI-1139836

Protein

cirA

PMID:16606699

Experiment(s):EBI-1139836

Protein

kbl

PMID:15690043

Experiment(s):EBI-886031

Protein

rho

PMID:15690043

Experiment(s):EBI-886031

Protein

rplC

PMID:15690043

Experiment(s):EBI-886031

Protein

rplI

PMID:15690043

Experiment(s):EBI-886031

Protein

rplL

PMID:15690043

Experiment(s):EBI-886031

Protein

rplS

PMID:15690043

Experiment(s):EBI-886031

Protein

rplT

PMID:15690043

Experiment(s):EBI-886031

Protein

rplV

PMID:15690043

Experiment(s):EBI-886031

Protein

rplX

PMID:15690043

Experiment(s):EBI-886031

Protein

rpmG

PMID:15690043

Experiment(s):EBI-886031

Protein

rpsA

PMID:15690043

Experiment(s):EBI-886031

Protein

rpsC

PMID:15690043

Experiment(s):EBI-886031

Protein

rpsE

PMID:15690043

Experiment(s):EBI-886031

Protein

rpsG

PMID:15690043

Experiment(s):EBI-886031

Protein

rpsN

PMID:15690043

Experiment(s):EBI-886031

Protein

selB

PMID:15690043

Experiment(s):EBI-886031

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rho

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.190084

Protein

rplD

PMID:19402753

LCMS(ID Probability):98.7 MALDI(Z-score):5.780482

Protein

kbl

PMID:19402753

LCMS(ID Probability):99.6

Protein

selB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

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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 

MAKIAAIFQL LDKNVTVSSH RLELLSPARD AAIAREAILH GADAVYIGGP GFGARHNASN
SLKDIAELVP FAHRYGAKIF VTLNTILHDD ELEPAQRLIT DLYQTGVDAL IVQDMGILEL
DIPPIELHAS TQCDIRTVEK AKFLSDVGFT QIVLARELNL DQIRAIHQAT DATIEFFIHG
ALCVAYSGQC YISHAQTGRS ANRGDCSQAC RLPYTLKDDQ GRVVSYEKHL LSMKDNDQTA
NLGALIDAGV RSFKIEGRYK DMSYVKNITA HYRQMLDAII EERGDLARAS SGRTEHFFVP
STEKTFHRGS TDYFVNARKG DIGAFDSPKF IGLPVGEVVK VAKDHLDVAV TEPLANGDGL
NVLIKREVVG FRANTVEKTG ENQYRVWPNE MPADLHKIRP HHPLNRNLDH NWQQALTKTS
SERRVAVDIE LGGWQEQLIL TLTSEEGVSI THTLDGQFDE ANNAEKAMNN LKDGLAKLGQ
TLYYARDVQI NLPGALFVPN SLLNQFRREA ADMLDAARLA SYQRGSRKPV ADPAPVYPQT
HLSFLANVYN QKAREFYHRY GVQLIDAAYE AHEEKGEVPV MITKHCLRFA FNLCPKQAKG
NIKSWKATPM QLVNGDEVLT LKFDCRPCEM HVIGKIKNHI LKMPLPGSVV ASVSPDELLK
TLPKRKG
Length

667

Mol. Wt

74.228 kDa

pI

7.3 (calculated)

Extinction coefficient

51,800 - 52,925 (calc based on 20 Y, 4 W, and 9 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

motif

1-20

UniProt Manual:Signal Peptides

UniProt:P76104

Domain

78..307

PF01136 Peptidase family U32

PMID:19920124

Domain

390..508

PF12392 Collagenase

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=ydcP 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:90111273

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945993

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004786

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76104

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6746

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13759

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945993

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003335

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3522

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

Ecoli K-12

11+/-0.115

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.024222336

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

810

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

203

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

324

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)

ydcP

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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_000913:1504785..1504825 source=MG1655 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:b1435 (EcoliWiki Page)

NCBI GEO profiles for ydcP

microarray

GenExpDB:b1435 (EcoliWiki Page)

Summary of data for ydcP 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 ydcP Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6746

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3522

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1435

EcoGene

EcoGene:EG13759

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003335

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004786

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

Xenopus tropicalis

  • ENSXETP00000041806 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

YDCP

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)

PF01136 Peptidase family U32

Pfam (EcoliWiki Page)

PF12392 Collagenase

EcoCyc

EcoCyc:G6746

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13759

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003335

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3522

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004786

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 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 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).

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