degS:On One Page
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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 |
degS |
|---|---|
| Gene Synonym(s) |
ECK3224, b3235, JW3204, hhoB, htrH[1], htrH |
| Product Desc. |
inner membrane serine protease required for the extracytoplasmic stress response mediated by sigmaE[2]; serine endoprotease, periplasmic[3] Serine protease, degrades periplasmic RseA, activating RpoE; multicopy suppressor of prc; periplasmic stress sensor for unfolded or misfolded OMPs[4] |
| Product Synonyms(s) |
serine endoprotease, periplasmic[1], B3235[2][1], HtrH[2][1], HhoB[2][1], DegS[2][1] , ECK3224, hhoB, htrH, JW3204, b3235 |
| Function from GO |
<GO_nr /> |
| Knock-Out Phenotype | |
| Regulation/Expression | |
| Regulation/Activity | |
| Quick Links | |
| edit table |
See Help:Quickview for help with entering information in the Quickview table.
Notes
degS is an essential gene. DegS may be anchored to the inner membrane. Mutants have elevated OM vesiculation (McBroom, 2006).[4]
Gene
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
degS |
|---|---|
| Mnemonic |
Degradative protease |
| Synonyms |
ECK3224, b3235, JW3204, hhoB, htrH[1], htrH |
| edit table |
Notes
Location(s) and DNA Sequence
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 |
72.85 minutes |
MG1655: 3380222..3381289 |
||
|
NC_012967: 3310098..3311165 |
||||
|
NC_012759: 3267370..3268437 |
||||
|
W3110 |
|
W3110: 3382055..3383122 |
||
|
DH10B: 3477967..3479034 |
||||
| edit table |
Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
| edit table |
Notes
Alleles and Phenotypes
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 |
|---|---|---|---|---|---|---|---|
|
degS::Tn5KAN-I-SceI (FB21079) |
Insertion at nt 931 in Plus orientation |
PMID:15262929 |
contains pKD46 | ||||
| edit table |
Notes
Genetic Interactions
| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW3204 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCTTTGTGAAGCTCTTACGTTC Primer 2:CCATTGGTTGCCGGATATTCCTG | |
|
Kohara Phage |
PMID:3038334 | ||
|
Kohara Phage |
PMID:3038334 | ||
|
Linked marker |
est. P1 cotransduction: 56% [6] | ||
|
Linked marker |
est. P1 cotransduction: 25% [6] | ||
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001596 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EchoBASE:EB1605 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010611 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
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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 |
DegS |
|---|---|
| Synonyms |
serine endoprotease, periplasmic[1], B3235[2][1], HtrH[2][1], HhoB[2][1], DegS[2][1] , ECK3224, hhoB, htrH, JW3204, b3235 |
| Product description |
inner membrane serine protease required for the extracytoplasmic stress response mediated by sigmaE[2]; serine endoprotease, periplasmic[3] Serine protease, degrades periplasmic RseA, activating RpoE; multicopy suppressor of prc; periplasmic stress sensor for unfolded or misfolded OMPs[4] |
| EC number (for enzymes) | |
| edit table |
Notes
Function
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:0031225 |
anchored to membrane |
C |
Seeded from Riley et al 2006 [1]. |
Missing: evidence, reference | ||||
| GO:0003824 |
catalytic activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004252 |
serine-type endopeptidase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004252 |
serine-type endopeptidase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004252 |
serine-type endopeptidase activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0005515 |
protein binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006508 |
proteolysis |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006508 |
proteolysis |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0006508 |
proteolysis |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0008233 |
peptidase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0008236 |
serine-type peptidase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0016787 |
hydrolase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0042597 |
periplasmic space |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
C |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0042597 |
periplasmic space |
IEA: Inferred from Electronic Annotation |
SP_SL:SL-0200 |
C |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0071575 |
integral to external side of plasma membrane |
IMP: Inferred from Mutant Phenotype |
C |
complete | ||||
| GO:0006508 |
proteolysis |
IDA: Inferred from Direct Assay |
P |
complete | ||||
| GO:0006508 |
proteolysis |
IMP: Inferred from Mutant Phenotype |
P |
complete | ||||
| GO:0008233 |
peptidase activity |
IMP: Inferred from Mutant Phenotype |
F |
complete | ||||
| GO:0008236 |
serine-type peptidase activity |
IMP: Inferred from Mutant Phenotype |
F |
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 |
nfnB |
Experiment(s):EBI-1145244 | ||
|
Protein |
rpsD |
Experiment(s):EBI-1145244 | ||
|
Protein |
gltI |
LCMS(ID Probability):99.6 | ||
| edit table |
Notes
Localization
See Help:Product_localization for how to add or edit information in this section of EcoliWiki.
| Compartment | Description | Evidence | Reference/Source | Notes |
|---|---|---|---|---|
|
plasma membrane |
From EcoCyc[3] |
| ||
| edit table |
Notes
Structure and Physical Properties
Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MFVKLLRSVA IGLIVGAILL VAMPSLRSLN PLSTPQFDST DETPASYNLA VRRAAPAVVN VYNRGLNTNS HNQLEIRTLG SGVIMDQRGY IITNKHVIND ADQIIVALQD GRVFEALLVG SDSLTDLAVL KINATGGLPT IPINARRVPH IGDVVLAIGN PYNLGQTITQ GIISATGRIG LNPTGRQNFL QTDASINHGN SGGALVNSLG ELMGINTLSF DKSNDGETPE GIGFAIPFQL ATKIMDKLIR DGRVIRGYIG IGGREIAPLH AQGGGIDQLQ GIVVNEVSPD GPAANAGIQV NDLIISVDNK PAISALETMD QVAEIRPGSV IPVVVMRDDK QLTLQVTIQE YPATN |
| Length |
355 |
| Mol. Wt |
37.581 kDa |
| pI |
5.4 (calculated) |
| Extinction coefficient |
8,940 (calc based on 6 Y, 0 W, and 0 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
|
Structure figures
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
| Resource type | Source | Notes/Reference |
|---|---|---|
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
ASAP:ABE-0010611 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EcoCyc:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120001596 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1605 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
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
| Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
|---|---|---|---|---|---|---|---|
|
Protein |
E. coli K-12 MG1655 |
406 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
133 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
144 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
| edit table |
Notes
Transcription and Transcriptional Regulation
|
See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
|
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
<gbrowseImage> name=NC_000913:3380202..3380242 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
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 |
NCBI GEO profiles for degS | |
|
microarray |
Summary of data for degS 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 |
|---|---|---|---|---|
| edit table |
<protect>
Notes
Accessions Related to degS Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1605 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001596 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010611 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Evolution
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Homologs in Other Organisms
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.
| Organism | Homologs (Statistics) | Comments |
|---|---|---|
|
Anopheles gambiae |
|
From Inparanoid:20070104 |
|
Apis mellifera |
|
From Inparanoid:20070104 |
|
Bos taurus |
|
From Inparanoid:20070104 |
|
Canis familiaris |
|
From Inparanoid:20070104 |
|
Danio rerio |
|
From Inparanoid:20070104 |
|
Dictyostelium discoideum |
|
From Inparanoid:20070104 |
|
Drosophila melanogaster |
|
From Inparanoid:20070104 |
|
Drosophila pseudoobscura |
|
From Inparanoid:20070104 |
|
Gallus gallus |
|
From Inparanoid:20070104 |
|
Homo sapiens |
|
From Inparanoid:20070104 |
|
Macaca mulatta |
|
From Inparanoid:20070104 |
|
Monodelphis domestica |
|
From Inparanoid:20070104 |
|
Mus musculus |
|
From Inparanoid:20070104 |
|
Oryza gramene |
|
From Inparanoid:20070104 |
|
Pan troglodytes |
|
From Inparanoid:20070104 |
|
Rattus norvegicus |
|
From Inparanoid:20070104 |
|
Saccharomyces cerevisiae |
|
From Inparanoid:20070104 |
|
Schizosaccharomyces pombe |
|
From Inparanoid:20070104 |
|
Takifugu rubripes |
|
From Inparanoid:20070104 |
|
Tetraodon nigroviridis |
|
From Inparanoid:20070104 |
|
Xenopus tropicalis |
|
From Inparanoid:20070104 |
|
Shigella flexneri |
DEGS |
From SHIGELLACYC |
|
E. coli O157 |
DEGS |
From ECOO157CYC |
| edit table |
Do-It-Yourself Web Tools
Notes
Families
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG11652 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120001596 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB1605 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0010611 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 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.
- ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
- ↑ 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).
- ↑ Alba, BM et al. (2001) degS (hhoB) is an essential Escherichia coli gene whose indispensable function is to provide sigma (E) activity. Mol. Microbiol. 40 1323-33 PubMed
- ↑ Li, X et al. (2009) Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage. Proc. Natl. Acad. Sci. U.S.A. 106 14837-42 PubMed
- ↑ 9.0 9.1 Sohn, J et al. (2009) OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism. Structure 17 1411-21 PubMed
- ↑ Sohn, J et al. (2007) Allosteric activation of DegS, a stress sensor PDZ protease. Cell 131 572-83 PubMed
- ↑ 11.0 11.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
- ↑ Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
- ↑ 13.0 13.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
Categories
- GO:0031225 ! anchored component of membrane
- GO:0003824 ! catalytic activity
- GO:0004252 ! serine-type endopeptidase activity
- GO:0005515 ! protein binding
- GO:0006508 ! proteolysis
- GO:0008233 ! peptidase activity
- GO:0008236 ! serine-type peptidase activity
- GO:0016787 ! hydrolase activity
- GO:0042597 ! periplasmic space
- GO:0071575 ! integral component of external side of plasma membrane
- Genes with homologs in Anopheles gambiae
- Genes with homologs in Apis mellifera
- Genes with homologs in Bos taurus
- Genes with homologs in Canis familiaris
- Genes with homologs in Danio rerio
- Genes with homologs in Dictyostelium discoideum
- Genes with homologs in Drosophila melanogaster
- Genes with homologs in Drosophila pseudoobscura
- Genes with homologs in Gallus gallus
- Genes with homologs in Homo sapiens
- Genes with homologs in Macaca mulatta
- Genes with homologs in Monodelphis domestica
- Genes with homologs in Mus musculus
- Genes with homologs in Oryza gramene
- Genes with homologs in Pan troglodytes
- Genes with homologs in Rattus norvegicus
- Genes with homologs in Saccharomyces cerevisiae
- Genes with homologs in Schizosaccharomyces pombe
- Genes with homologs in Takifugu rubripes
- Genes with homologs in Tetraodon nigroviridis
- Genes with homologs in Xenopus tropicalis
- Genes with homologs in Shigella flexneri
- Genes with homologs in E. coli O157



