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

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Standard Name

damX

Gene Synonym(s)

ECK3375, b3388, JW3351, yhfB[1]

Product Desc.

predicted membrane-anchored protein[2]; predicted membrane-anchored protein, interferes with cell division[3]

Interferes with cell division, upstream of dam gene[4]

Product Synonyms(s)

predicted protein[1], B3388[2][1], YhfB[2][1], DamX[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): damX-dam-rpe-gph-trpS[2], aroKB-damX-dam-rpe-gph-trpS[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(damX)    Textpresso(damX)

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Notes

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Overexpression causes filamentous biofilm formation. HT_Cmplx49_Mem: DamX+BamA.[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

damX

Mnemonic

DNA adenine methylase

Synonyms

ECK3375, b3388, JW3351, yhfB[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

75.74 minutes 

MG1655: 3515328..3514042
gbrowse_img.php?coord=3514042..3515328&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3445988..3444702
gbrowse_img.php?coord=3444702..3445988&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4123110..4124396
gbrowse_img.php?coord=4123110..4124396&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3613073..3611787
gbrowse_img.php?coord=3611787..3613073&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

DH10B

DH10B: 3613073..3611787
gbrowse_img.php?coord=3611787..3613073&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3401199..3402485
gbrowse_img.php?coord=3401199..3402485&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

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

ΔdamX (Keio:JW3351)

deletion

deletion

PMID:16738554

Shigen
CGSC10500[5]

damX::Tn5KAN

PMID:12519969

ASAP

At position 461 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB21149

damX::Tn5KAN

PMID:12519969

ASAP

At position 461 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB21150

ΔdamX723::kan

PMID:16738554

CGSC:100528


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW3351

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATGAATTCAAACCAGAAGA

Primer 2:CCtTTCAGATCGGCCTGTACCTG

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 68% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[5]

est. P1 cotransduction: 10% [6]
Synonyms:zhg-3086::Tn10, zhh-21::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11183

EchoBASE (EcoliWiki Page)

EchoBASE:EB1170

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3388

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4158

EcoGene (EcoliWiki Page)

EcoGene:EG11183

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DAMX

ASAP (EcoliWikiPage)

ASAP:ABE-0011065


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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

DamX

Synonyms

predicted protein[1], B3388[2][1], YhfB[2][1], DamX[2][1]

Product description

predicted membrane-anchored protein[2]; predicted membrane-anchored protein, interferes with cell division[3]

Interferes with cell division, upstream of dam gene[4]

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:0016021

integral to membrane

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc [7]

complete

GO:0051301

cell division

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0132

P

Seeded from EcoCyc [7]

complete

GO:0016020

membrane

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc [7]

complete

GO:0007049

cell cycle

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0131

P

Seeded from EcoCyc [7]

complete

GO:0000910

cytokinesis

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005886

plasma membrane

GO_REF:0000004
GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003
SP_SL:SL-0039

C

Seeded from EcoCyc [7]

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 TypePartnerNotesReferencesEvidence

Protein

glpD

PMID:16606699

Experiment(s):EBI-1145762

Protein

nfnB

PMID:16606699

Experiment(s):EBI-1145762

Protein

dsbC

PMID:16606699

Experiment(s):EBI-1145762

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1145762

Protein

cusA

PMID:16606699

Experiment(s):EBI-1145762

Protein

rpsE

PMID:16606699

Experiment(s):EBI-1145762

Protein

ycgL

PMID:16606699

Experiment(s):EBI-1145762

Protein

ybaB

PMID:16606699

Experiment(s):EBI-1145762

Protein

nuoI

PMID:16606699

Experiment(s):EBI-1145762

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1145762

Protein

yciG

PMID:16606699

Experiment(s):EBI-1145762

Protein

yraN

PMID:16606699

Experiment(s):EBI-1145762

Protein

rplO

PMID:16606699

Experiment(s):EBI-1145762

Protein

rplD

PMID:16606699

Experiment(s):EBI-1145762

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MDEFKPEDEL KPDPSDRRTG RSRQSSERSE RTERGEPQIN FDDIELDDTD DRRPTRAQKE
RNEEPEIEEE IDESEDETVD EERVERRPRK RKKAASKPAS RQYMMMGVGI LVLLLLIIGI
GSALKAPSTT SSDQTASGEK SIDLAGNATD QANGVQPAPG TTSAENTQQD VSLPPISSTP
TQGQTPVATD GQQRVEVQGD LNNALTQPQN QQQLNNVAVN STLPTEPATV APVRNGNASR
DTAKTQTAER PSTTRPARQQ AVIEPKKPQA TVKTEPKPVA QTPKRTEPAA PVASTKAPAA
TSTPAPKETA TTAPVQTASP AQTTATPAAG AKTAGNVGSL KSAPSSHYTL QLSSSSNYDN
LNGWAKKENL KNYVVYETTR NGQPWYVLVS GVYASKEEAK KAVSTLPADV QAKNPWAKPL
RQVQADLK
Length

428

Mol. Wt

46.16 kDa

pI

5.6 (calculated)

Extinction coefficient

26,930 (calc based on 7 Y, 3 W, and 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.

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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11183-MONOMER

UniProt (EcoliWiki Page)

UniProt:P11557

RefSeq (EcoliWiki Page)

RefSeq:NP_417847


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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)

damX-dam-rpe-gph-trpS

aroKB-damX-dam-rpe-gph-trpS

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Figure courtesy of RegulonDB

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=3515308..3515348&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.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 See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b3388 (EcoliWiki Page)

NCBI GEO profiles for damX

microarray

GenExpDB:b3388 (EcoliWiki Page)

Summary of data for damX 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to damX Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11183

EchoBASE (EcoliWiki Page)

EchoBASE:EB1170

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3388

EcoGene (EcoliWiki Page)

EcoGene:EG11183


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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.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000012452 (score: 1.000; bootstrap: 54%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000001859 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000019668 (score: 1.000; bootstrap: 54%)
  • ENSBTAP00000029508 (score: 0.290)
  • ENSBTAP00000003517 (score: 0.207)
  • ENSBTAP00000029264 (score: 0.204)
  • ENSBTAP00000024572 (score: 0.165)
  • ENSBTAP00000007041 (score: 0.149)
  • ENSBTAP00000017997 (score: 0.148)
  • ENSBTAP00000023744 (score: 0.111)
  • ENSBTAP00000008948 (score: 0.084)
  • ENSBTAP00000038262 (score: 0.083)
  • ENSBTAP00000038280 (score: 0.083)
  • ENSBTAP00000021516 (score: 0.083)
  • ENSBTAP00000017139 (score: 0.083)
  • ENSBTAP00000021456 (score: 0.082)
  • ENSBTAP00000001108 (score: 0.082)
  • ENSBTAP00000024881 (score: 0.082)
  • ENSBTAP00000009976 (score: 0.080)
  • ENSBTAP00000016832 (score: 0.080)
  • ENSBTAP00000020622 (score: 0.078)
  • ENSBTAP00000018291 (score: 0.078)
  • ENSBTAP00000006440 (score: 0.078)
  • ENSBTAP00000038253 (score: 0.078)
  • ENSBTAP00000008857 (score: 0.077)
  • ENSBTAP00000009402 (score: 0.077)
  • ENSBTAP00000027749 (score: 0.074)
  • ENSBTAP00000006450 (score: 0.074)
  • ENSBTAP00000000515 (score: 0.074)
  • ENSBTAP00000009403 (score: 0.072)
  • ENSBTAP00000001988 (score: 0.072)
  • ENSBTAP00000016839 (score: 0.072)
  • ENSBTAP00000018255 (score: 0.070)
  • ENSBTAP00000021066 (score: 0.070)
  • ENSBTAP00000018185 (score: 0.068)
  • ENSBTAP00000000818 (score: 0.067)
  • ENSBTAP00000023927 (score: 0.066)
  • ENSBTAP00000015960 (score: 0.065)
  • ENSBTAP00000023926 (score: 0.065)
  • ENSBTAP00000018077 (score: 0.063)
  • ENSBTAP00000000746 (score: 0.062)
  • ENSBTAP00000010255 (score: 0.061)
  • ENSBTAP00000009540 (score: 0.060)
  • ENSBTAP00000023156 (score: 0.060)
  • ENSBTAP00000021519 (score: 0.058)
  • ENSBTAP00000026752 (score: 0.058)
  • ENSBTAP00000009541 (score: 0.056)
  • ENSBTAP00000028819 (score: 0.056)
  • ENSBTAP00000023373 (score: 0.054)
  • ENSBTAP00000018110 (score: 0.053)
  • ENSBTAP00000009975 (score: 0.052)
  • ENSBTAP00000015606 (score: 0.051)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000014597 (score: 1.000; bootstrap: 53%)
  • ENSCAFP00000022453 (score: 0.092)
  • ENSCAFP00000014295 (score: 0.083)
  • ENSCAFP00000013315 (score: 0.079)
  • ENSCAFP00000014576 (score: 0.066)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0039257 (score: 1.000; bootstrap: 54%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000046856 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000040074 (score: 0.223)
  • ENSRNOP00000024730 (score: 0.088)
  • ENSRNOP00000041465 (score: 0.075)
  • ENSRNOP00000026707 (score: 0.053)
  • ENSRNOP00000031747 (score: 0.051)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000021861 (score: 1.000; bootstrap: 56%)
  • ENSXETP00000022466 (score: 0.081)
  • ENSXETP00000050560 (score: 0.078)
  • ENSXETP00000043332 (score: 0.053)

From Inparanoid:20070104

Shigella flexneri

DAMX

From SHIGELLACYC

E. coli O157

DAMX

From ECOO157CYC

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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 1.8 1.9 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 2.7 2.8 2.9 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. ↑ 7.0 7.1 7.2 7.3 7.4 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

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