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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	transcription unit(s): degQ^[2]
Regulation/Activity
Quick Links
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Notes

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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

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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
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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	72.85 minutes	MG1655: 3380222..3381289 <gbrowseImage> name=NC_000913:3380222..3381289 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3310098..3311165 <gbrowseImage> name=NC_012967:3310098..3311165 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3267370..3268437 <gbrowseImage> name=NC_012759:3267370..3268437 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3382055..3383122 <gbrowseImage> name=NC_007779:3382055..3383122 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3477967..3479034 <gbrowseImage> name=NC_010473:3477967..3479034 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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
degS::Tn5KAN-I-SceI (FB21079)	Insertion at nt 931 in Plus orientation				PMID:15262929	E. coli Genome Project:FB21079	contains pKD46
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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
JW3204	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTTGTGAAGCTCTTACGTTC Primer 2:CCATTGGTTGCCGGATATTCCTG
1E3	Kohara Phage	Genobase	PMID:3038334
3G9	Kohara Phage	Genobase	PMID:3038334
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 56% ^[6] Synonyms:zha-6::Tn10
acrF3083::Tn10	Linked marker	CAG12075 = CGSC7447^[5]	est. P1 cotransduction: 25% ^[6] Synonyms:zhd-3083::Tn10, zhe-3083::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:EG11652	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11652	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001596	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947865	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1605	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010611	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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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)	3.4.21.-^[1]
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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:0031225	anchored to membrane				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	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:IPR001940	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004252	serine-type endopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011783	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001478	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:IPR001940	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011783	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: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
	GO:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	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	PMID:11442831	IMP: Inferred from Mutant Phenotype		C		complete
	GO:0006508	proteolysis	PMID:19706448	IDA: Inferred from Direct Assay		P		complete
	GO:0006508	proteolysis	PMID:19836340	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0008233	peptidase activity	PMID:19836340	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0008236	serine-type peptidase activity	PMID:17981123	IMP: Inferred from Mutant Phenotype		F		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	References	Evidence
Protein	nfnB	PMID:16606699	Experiment(s):EBI-1145244
Protein	rpsD	PMID:16606699	Experiment(s):EBI-1145244
Protein	gltI	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
plasma membrane			From EcoCyc^[3]
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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 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)
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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	1-28	UniProt Manual:Signal Peptides	UniProt:P0AEE3
Domain	50..245	PF00089 Trypsin		PMID:19920124
Domain	248..336	PF00595 PDZ domain (Also known as DHR or GLGF)		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=degS 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:16131125	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947865	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010611	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AEE3	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11652	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11652	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947865	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001596	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1605	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	Reference(s)
Protein	E. coli K-12 MG1655	406	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	133	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	144	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
degQ
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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_000913:3380202..3380242 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

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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:b3235 (EcoliWiki Page)	NCBI GEO profiles for degS
microarray	GenExpDB:b3235 (EcoliWiki Page)	Summary of data for degS 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 degS Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11652	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1605	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3235
EcoGene	EcoGene:EG11652	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001596	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010611	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	ENSANGP00000012547 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000014738 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000026026 (score: 1.000; bootstrap: 100%) ENSBTAP00000011042 (score: 1.000; bootstrap: 100%) ENSBTAP00000004564 (score: 0.425) ENSBTAP00000026804 (score: 0.313)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000018471 (score: 1.000; bootstrap: 100%) ENSCAFP00000021445 (score: 1.000; bootstrap: 100%) ENSCAFP00000008772 (score: 0.562) ENSCAFP00000012325 (score: 0.385)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040704-64 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040704-64 (score: 1.000; bootstrap: 100%) ZDB-GENE-040801-245 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040801-260 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0204001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0038233 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21097-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000025070 (score: 1.000; bootstrap: 100%) ENSGALP00000025068 (score: 0.468) ENSGALP00000021805 (score: 0.218) ENSGALP00000021600 (score: 0.070)	From Inparanoid:20070104
Homo sapiens	ENSP00000303766 (score: 1.000; bootstrap: 100%) ENSP00000299020 (score: 0.469) ENSP00000305919 (score: 0.354) ENSP00000258080 (score: 0.242)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000011963 (score: 1.000; bootstrap: 100%) ENSMMUP00000029846 (score: 1.000; bootstrap: 100%) ENSMMUP00000007924 (score: 0.437) ENSMMUP00000002846 (score: 0.365)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000003793 (score: 1.000; bootstrap: 100%) ENSMODP00000010233 (score: 0.456) ENSMODP00000013256 (score: 0.338) ENSMODP00000005932 (score: 0.220)	From Inparanoid:20070104
Mus musculus	MGI:3036260 (score: 1.000; bootstrap: 100%) MGI:1929076 (score: 0.433) MGI:1925808 (score: 0.355) MGI:1928676 (score: 0.210)	From Inparanoid:20070104
Oryza gramene	Q6AUN5 (score: 1.000; bootstrap: 99%) Q7XUW0 (score: 0.180)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000005327 (score: 1.000; bootstrap: 100%) ENSPTRP00000020762 (score: 1.000; bootstrap: 100%) ENSPTRP00000034549 (score: 0.395)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000022166 (score: 1.000; bootstrap: 100%) ENSRNOP00000027860 (score: 0.437) ENSRNOP00000010852 (score: 0.341) ENSRNOP00000030076 (score: 0.215)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL123W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC23G32c (score: 1.000; bootstrap: 100%) SPBC16855 (score: 0.229)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000136976 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000160494 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000180577 (score: 0.579) NEWSINFRUP00000170339 (score: 0.153)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00022346001 (score: 1.000; bootstrap: 100%) GSTENP00031557001 (score: 1.000; bootstrap: 100%) GSTENP00006681001 (score: 0.425) GSTENP00032214001 (score: 0.198)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000033992 (score: 1.000; bootstrap: 100%) ENSXETP00000033189 (score: 1.000; bootstrap: 100%) ENSXETP00000043887 (score: 0.435)	From Inparanoid:20070104
Shigella flexneri	DEGS	From SHIGELLACYC
E. coli O157	DEGS	From ECOO157CYC
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Do-It-Yourself Web Tools

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:50156
Superfamily (EcoliWiki Page)	SUPERFAMILY:50494
Pfam (EcoliWiki Page)	PF00595 PDZ domain (Also known as DHR or GLGF)
EcoCyc	EcoCyc:EG11652	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11652	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001596	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1605	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010611	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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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).

degS:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to degS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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