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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Gene Name

alx (synonyms: ECK3079, b3088, JW5515, ygjT)[1]

Product(s)

Alx product[1]: predicted inner membrane protein, part of terminus product, B3088 product, YgjT product

Description

putative membrane-bound redox modulator that is induced by high pH[2][3]

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): sraF[2]

Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name

alx

Mnemonic
Synonyms

ECK3079, b3088, JW5515, ygjT[1]

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Notes

Location(s) and DNA Sequence

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StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

69.76 minutes 

MG1655: 3236602..3237567
gbrowse_img.php?coord=3235602..3238567&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3237236..3238201
gbrowse_img.php?coord=3236236..3239201&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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Notes

Sequence Features

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Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

Δalx (Keio:JW5515)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC11438[5]

Δalx-778::kan

PMID:16738554[4]

CGSC:99988


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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW5515

Plasmid clone

Shigen

PMID:16769691[6]

Status:cloned as old JW

Primer 1:GCCAATACTGTCGGCACGCCGTT

Primer 2:CCTCCACCCCGCTGCTTATCATG

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: 46% [7]

Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: % [7]

Synonyms:zgj-203::Tn10, zha-203::Tn10

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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7607

EchoBASE (EcoliWiki Page)

EchoBASE:EB2589

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3088

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3846

EcoGene (EcoliWiki Page)

EcoGene:EG12731

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YGJT

ASAP (EcoliWikiPage)

ASAP:ABE-0010151


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Notes

Links

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NameURLComments
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Categories

Product(s)

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Nomenclature

Standard name

Alx

Synonyms

predicted inner membrane protein, part of terminus[1], B3088[2][1], Alx[2][1], YgjT[2][1]

Product description

putative membrane-bound redox modulator that is induced by high pH[2][3]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus
GO:0016020

membrane

GO_REF:0000004
GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0397
SP_KW:KW-0472

C

Seeded from EcoCyc 12.5 [8]

complete

GO:0016021

integral to membrane

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR005496
SP_KW:KW-0812

C

Seeded from EcoCyc 12.5 [8]

complete

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Interactions

Partner TypePartnerNotesReferences
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Notes

Localization

CompartmentDescriptionEvidenceNotes

plasma membrane

C-terminus localized in the cytoplasm with 9 predicted transmembrane domains

Daley et al. (2005) [9]/>

membrane

From EcoCyc[3]

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Notes

Structure and Physical Properties

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Physical Properties

Sequence

at EcoCyc 

MNTVGTPLLW GGFAVVVAIM LAIDLLLQGR RGAHAMTMKQ AAAWSLVWVT LSLLFNAAFW
WYLVQTEGRA VADPQALAFL TGYLIEKSLA VDNVFVWLML FSYFSVPAAL QRRVLVYGVL
GAIVLRTIMI FTGSWLISQF DWILYIFGAF LLFTGVKMAL AHEDESGIGD KPLVRWLRGH
LRMTDTIDNE HFFVRKNGLL YATPLMLVLI LVELSDVIFA VDSIPAIFAV TTDPFIVLTS
NLFAILGLRA MYFLLAGVAE RFSMLKYGLA VILVFIGIKM LIVDFYHIPI AVSLGVVFGI
LVMTFIINAW VNYRHDKQRG G
Mol. Wt

35.91 kDa (calc) [2]

pI
Extinction coefficient

69900 (calc based on 10 Y, 10 W, and 0 C residues)

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Domains/Motifs/Modification Sites

TypeResiduesDescriptionNotes

Domain

264 - 286

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

290 - 312

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

10 - 29

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

42 - 64

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

88 - 110

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

115 - 137

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

142 - 161

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

198 - 220

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

235 - 257

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

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

Structure

Structures
  • No results found.
Models

View models at:

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Notes

Gene Product Resources

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Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7607-MONOMER

UniProt (EcoliWiki Page)

UniProt:P42601

PFAM (EcoliWiki Page)

PFAM:PF03741

RefSeq (EcoliWiki Page)

RefSeq:YP_026201


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Notes

Links

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NameURLComments
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Categories

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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.

Transcription and Transcriptional Regulation

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Transcription unit(s)

sraF

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Figure courtesy of RegulonDB
Figure courtesy of RegulonDB

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

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gbrowse_img.php?coord=3236582..3236622&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled&width=400&.png
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

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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Mutations Affecting Expression

Allele NameMutationPhenotypeReference
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Expression Studies

TypeReferenceNotes

microarray

GenExpDB:b3088 (EcoliWiki Page)

Summary of data for alx from multiple microarray studies

microarray

GEO Profiles:b3088 (EcoliWiki Page)

NCBI GEO profiles for alx

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Expression Resources

Resource NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to alx Expression

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7607

EchoBASE (EcoliWiki Page)

EchoBASE:EB2589

EcoliGenExpDB (EcoliWiki Page)

GenExpDB:b3088

EcoGene (EcoliWiki Page)

EcoGene:EG12731

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Notes

Links

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NameURLComments
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Categories

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Evolution

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Homologs in Other Organisms

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OrganismHomologs (Statistics)Comments

Shigella flexneri

YGJT

From SHIGELLACYC

E. coli O157

YGJT

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF03741

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Notes

Links

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NameURLComments
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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 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 Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
  7. ↑ 7.0 7.1 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).
  8. ↑ 8.0 8.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page
  10. ↑ 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 10.8 Krogh A et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-80 PubMed EcoliWiki page

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