sohB: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

sohB

Gene Synonym(s)

ECK1266, b1272, JW1264[1], JW1264

Product Desc.

predicted inner membrane peptidase[2][3]

Multicopy suppressor of htrA(degP); probable protease[4]

Product Synonyms(s)

predicted inner membrane peptidase[1], B1272[2][1], SohB[2][1] , ECK1266, JW1264, b1272

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): sohB[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]


SohB is homologous to inner membrane protease IV, which digests cleaved signal peptides.[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

sohB

Mnemonic

Suppressor of htr

Synonyms

ECK1266, b1272, JW1264[1], JW1264

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

28.61 minutes 

MG1655: 1327356..1328405
<gbrowseImage> name=NC_000913:1327356..1328405 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1327704..1328753
<gbrowseImage> name=NC_012967:1327704..1328753 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1218205..1219254
<gbrowseImage> name=NC_012759:1218205..1219254 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1331046..1332095
<gbrowseImage> name=NC_007779:1331046..1332095 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1416752..1417801
<gbrowseImage> name=NC_010473:1416752..1417801 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

ΔsohB (Keio:JW1264)

deletion

deletion

PMID:16738554

Shigen
CGSC9139[5]

sohB::Tn5KAN-2 (FB20279)

Insertion at nt 450 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20279

does not contain pKD46

ΔsohB780::kan

PMID:16738554

CGSC:102986


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

JW1264

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAATTGTTGTCTGAATATGG

Primer 2:CCCATCAATGGCTTTTGACCCCG

4F1

Kohara Phage

Genobase

PMID:3038334

13F9

Kohara Phage

Genobase

PMID:3038334

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[5]

est. P1 cotransduction: 72% [6]
Synonyms:trpB83::Tn10

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[5]

est. P1 cotransduction: 17% [6]
Synonyms:zci-233::Tn10

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:EG10956

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10956

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000945

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945858

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0949

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004267

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

SohB

Synonyms

predicted inner membrane peptidase[1], B1272[2][1], SohB[2][1] , ECK1266, JW1264, b1272

Product description

predicted inner membrane peptidase[2][3]

Multicopy suppressor of htrA(degP); probable protease[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:0004252

serine-type endopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013703

F

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013703

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002142

P

Seeded from EcoCyc (v14.0)

complete

GO:0008233

peptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002142

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:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9904

C

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

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

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsK

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):5.143992

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.2 MALDI(Z-score):12.665046

Protein

tehB

PMID:19402753

MALDI(Z-score):19.092511

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):16.993641

Protein

rnr

PMID:19402753

LCMS(ID Probability):99.6

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

plasma membrane

C-terminus localized in the cytoplasm with 1 predicted transmembrane domains

Daley et al. (2005) [7]

periplasm

From EcoCyc[3]


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 

MELLSEYGLF LAKIVTVVLA IAAIAAIIVN VAQRNKRQRG ELRVNNLSEQ YKEMKEELAA
ALMDSHQQKQ WHKAQKKKHK QEAKAAKAKA KLGEVATDSK PRVWVLDFKG SMDAHEVNSL
REEITAVLAA FKPQDQVVLR LESPGGMVHG YGLAASQLQR LRDKNIPLTV TVDKVAASGG
YMMACVADKI VSAPFAIVGS IGVVAQMPNF NRFLKSKDID IELHTAGQYK RTLTLLGENT
EEGREKFREE LNETHQLFKD FVKRMRPSLD IEQVATGEHW YGQQAVEKGL VDEINTSDEV
ILSLMEGREV VNVRYMQRKR LIDRFTGSAA ESADRLLLRW WQRGQKPLM
Length

349

Mol. Wt

39.366 kDa

pI

9.6 (calculated)

Extinction coefficient

37,930 - 38,055 (calc based on 7 Y, 5 W, and 1 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

160..311

PF01343 Peptidase family S49

PMID:19920124

Domain

1..158

PF08496 Peptidase family S49 N-terminal

PMID:19920124

edit table

<motif_map/>

tmhmm.php?gene=sohB&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=sohB 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:16129233

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945858

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004267

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AG14

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10956

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10956

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945858

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000945

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0949

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

1.41E+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

42.35+/-0.34

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.09914204

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

1334

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

538

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

613

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)

sohB

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_000913:1327336..1327376 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:b1272 (EcoliWiki Page)

NCBI GEO profiles for sohB

microarray

GenExpDB:b1272 (EcoliWiki Page)

Summary of data for sohB 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 (1327041..1327426) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ03; Well:E5[8]

edit table

<protect></protect>

Notes

Accessions Related to sohB Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10956

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0949

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1272

EcoGene

EcoGene:EG10956

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000945

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004267

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

Xenopus tropicalis

  • ENSXETP00000033248 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

SOHB

From SHIGELLACYC

E. coli O157

SOHB

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:52096

Pfam (EcoliWiki Page)

PF01343 Peptidase family S49

Pfam (EcoliWiki Page)

PF08496 Peptidase family S49 N-terminal

EcoCyc

EcoCyc:EG10956

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10956

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000945

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0949

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004267

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 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 3.2 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. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  8. ↑ 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=sohB:On_One_Page&oldid=219666"