ydgD: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

ydgD

Gene Synonym(s)

ECK1593, b1598, JW1590[1], JW1590

Product Desc.

predicted peptidase[2][3]

Putative periplasmic serine protease; function unknown[4]

Product Synonyms(s)

predicted peptidase[1], B1598[2][1], YdgD[2][1] , ECK1593, JW1590, b1598

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ydgD[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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Family S01. First 21 aa are predicted to be a type I signal peptide.[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

ydgD

Mnemonic

Systematic nomenclature

Synonyms

ECK1593, b1598, JW1590[1], JW1590

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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

35.99 minutes 

MG1655: 1669984..1670805
<gbrowseImage> name=NC_000913:1669984..1670805 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1649155..1649976
<gbrowseImage> name=NC_012967:1649155..1649976 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1562043..1562864
<gbrowseImage> name=NC_012759:1562043..1562864 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1673674..1674495
<gbrowseImage> name=NC_007779:1673674..1674495 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1760945..1761766
<gbrowseImage> name=NC_010473:1760945..1761766 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

ΔydgD (Keio:JW1590)

deletion

deletion

PMID:16738554

Shigen
CGSC9352[5]

ΔydgD746::kan

PMID:16738554

CGSC:104268


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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

E3F2

Kohara Phage

Genobase

PMID:3038334

11H12

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: % [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: % [6]
Synonyms:zdh-925::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:G6856

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13925

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003445

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946436

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3684

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005340

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

YdgD

Synonyms

predicted peptidase[1], B1598[2][1], YdgD[2][1] , ECK1593, JW1590, b1598

Product description

predicted peptidase[2][3]

Putative periplasmic serine protease; function unknown[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009003

F

Seeded from EcoCyc (v14.0)

complete

GO:0004252

serine-type endopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001254

F

Seeded from EcoCyc (v14.0)

complete

GO:0004252

serine-type endopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018114

F

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001254

P

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008256

P

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018114

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:0008236

serine-type peptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008256

F

Seeded from EcoCyc (v14.0)

complete

GO:0008236

serine-type peptidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0720

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
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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 

MRTTIAVVLG AISLTSAFVF ADKPDVARSA NDEVSTLFFG HDDRVPVNDT TQSPWDAVGQ
LETASGNLCT ATLIAPNLAL TAGHCLLTPP KGKADKAVAL RFVSNKGLWR YEIHDIEGRV
DPTLGKRLKA DGDGWIVPPA AAPWDFGLIV LRNPPSGITP LPLFEGDKAA LTAALKAAGR
KVTQAGYPED HLDTLYSHQN CEVTGWAQTS VMSHQCDTLP GDSGSPLMLH TDDGWQLIGV
QSSAPAAKDR WRADNRAISV TGFRDKLDQL SQK
Length

273

Mol. Wt

29.277 kDa

pI

6.2 (calculated)

Extinction coefficient

42,970 - 43,470 (calc based on 3 Y, 7 W, and 4 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

1-21

UniProt Manual:Signal Peptides

UniProt:P76176

Domain

44..266

PF00089 Trypsin

PMID:19920124

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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=ydgD 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:16129556

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946436

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005340

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76176

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6856

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13925

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946436

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003445

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3684

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

103

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

92

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

79

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)

ydgD

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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_000913:1669964..1670004 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:b1598 (EcoliWiki Page)

NCBI GEO profiles for ydgD

microarray

GenExpDB:b1598 (EcoliWiki Page)

Summary of data for ydgD 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

GFP Fusion

Intergenic region (1669623..1670067) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ15; Well:F4[7]

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Notes

Accessions Related to ydgD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6856

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3684

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1598

EcoGene

EcoGene:EG13925

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003445

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005340

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

Mus musculus

  • MGI:2682935 (score: 1.000; bootstrap: 60%)
  • MGI:1354381 (score: 0.213)
  • MGI:2155445 (score: 0.210)
  • MGI:2384877 (score: 0.192)
  • MGI:1933407 (score: 0.180)
  • MGI:1196620 (score: 0.163)
  • MGI:1919003 (score: 0.149)
  • MGI:2686594 (score: 0.146)
  • MGI:3513175 (score: 0.140)
  • MGI:1349451 (score: 0.138)
  • MGI:3521861 (score: 0.131)
  • MGI:1338881 (score: 0.131)
  • MGI:1197523 (score: 0.130)
  • MGI:96942 (score: 0.127)
  • MGI:1917064 (score: 0.125)
  • MGI:1916698 (score: 0.124)
  • MGI:1349391 (score: 0.122)
  • MGI:1923810 (score: 0.122)
  • MGI:1100881 (score: 0.122)
  • MGI:2661234 (score: 0.121)
  • MGI:2684853 (score: 0.121)
  • MGI:2450123 (score: 0.121)
  • MGI:2442348 (score: 0.118)
  • MGI:96943 (score: 0.118)
  • MGI:2444058 (score: 0.115)
  • MGI:1920586 (score: 0.111)
  • MGI:1918253 (score: 0.111)
  • MGI:87884 (score: 0.110)
  • MGI:2685120 (score: 0.110)
  • MGI:1353645 (score: 0.107)
  • MGI:2385221 (score: 0.104)
  • MGI:2685865 (score: 0.103)
  • MGI:2442893 (score: 0.103)
  • MGI:2665280 (score: 0.103)
  • MGI:1270856 (score: 0.101)
  • MGI:1918287 (score: 0.099)
  • MGI:2681414 (score: 0.098)
  • MGI:1922252 (score: 0.098)
  • MGI:2149952 (score: 0.097)
  • MGI:1920632 (score: 0.094)
  • MGI:2149951 (score: 0.094)
  • MGI:88559 (score: 0.092)
  • MGI:1918085 (score: 0.091)
  • MGI:88558 (score: 0.090)
  • MGI:95316 (score: 0.089)
  • MGI:3605764 (score: 0.088)
  • MGI:105937 (score: 0.087)
  • MGI:3687012 (score: 0.087)
  • MGI:97611 (score: 0.087)
  • MGI:2684822 (score: 0.086)
  • MGI:97771 (score: 0.086)
  • MGI:102759 (score: 0.085)
  • MGI:95293 (score: 0.084)
  • MGI:1920876 (score: 0.084)
  • MGI:109325 (score: 0.084)
  • MGI:102758 (score: 0.083)
  • MGI:892019 (score: 0.083)
  • MGI:102757 (score: 0.082)
  • MGI:3646222 (score: 0.082)
  • MGI:3045752 (score: 0.082)
  • MGI:1914623 (score: 0.082)
  • MGI:98839 (score: 0.081)
  • MGI:892023 (score: 0.081)
  • MGI:1270857 (score: 0.081)
  • MGI:97322 (score: 0.080)
  • MGI:1343166 (score: 0.078)
  • MGI:95314 (score: 0.077)
  • MGI:102850 (score: 0.077)
  • MGI:892020 (score: 0.074)
  • MGI:88384 (score: 0.074)
  • MGI:3615275 (score: 0.073)
  • MGI:1346336 (score: 0.070)
  • MGI:95291 (score: 0.070)
  • MGI:109266 (score: 0.070)
  • MGI:891981 (score: 0.069)
  • MGI:892021 (score: 0.068)
  • MGI:88380 (score: 0.067)
  • MGI:97320 (score: 0.067)
  • MGI:1916761 (score: 0.067)
  • MGI:1929977 (score: 0.067)
  • MGI:892022 (score: 0.067)
  • MGI:891980 (score: 0.066)
  • MGI:1298232 (score: 0.066)
  • MGI:1916790 (score: 0.066)
  • MGI:1343327 (score: 0.066)
  • MGI:2447533 (score: 0.066)
  • MGI:2447303 (score: 0.066)
  • MGI:95292 (score: 0.066)
  • MGI:892018 (score: 0.065)
  • MGI:88492 (score: 0.062)
  • MGI:87931 (score: 0.062)
  • MGI:1921556 (score: 0.059)
  • MGI:2447564 (score: 0.059)
  • MGI:1915118 (score: 0.058)
  • MGI:1921082 (score: 0.057)
  • MGI:1915918 (score: 0.055)
  • MGI:1923951 (score: 0.054)
  • MGI:109254 (score: 0.053)

From Inparanoid:20070104

Shigella flexneri

S1751

From SHIGELLACYC

E. coli O157

Z2592

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)

PF00089 Trypsin

Superfamily (EcoliWiki Page)

SUPERFAMILY:50494

EcoCyc

EcoCyc:G6856

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13925

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003445

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3684

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005340

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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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