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Expression|

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Standard Name	yhdJ
Gene Synonym(s)	ECK3249, b3262, JW5543, ccrM^[1], ccrM
Product Desc.	predicted methyltransferase^[2]; DNA adenine methyltransferase^[3] DNA adenine methyltransferase, SAM-dependent^[4]
Product Synonyms(s)	predicted methyltransferase^[1], B3262^[2]^[1], YhdJ^[2]^[1], CcrM^[2]^[1] , ccrM, ECK3249, JW5543, b3262
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yhdJ^[2]
Regulation/Activity
Quick Links
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Notes

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In vitro DNA adenine methyltransferase activity has been demonstrated for YhdJ; overexpression of YhdJ leads to protection of chromosomal DNA from NsiI digestion, but DNA from wild type cells is not protected (Broadbent (2007). DNA from a DNA methyltransferase deficient strain (dam-, dcm-, EcoK-) does not react with anti-N6-methylA or anti-N4-methylC antibodies when YhdJ is expressed from the pBR322 Tet promoter; the yhdJ-containing pBR322 derivative was not resistant to a variety of restriction (personal communication: R. Vaisvila, S. Stickel and R.J. Roberts, unpublished results, April, 2006). The Kossykh (2004) report describing yhdJ as ccrM, an adenine methyltransferase, has been retracted.^[4]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	yhdJ
Mnemonic	Systematic nomenclature
Synonyms	ECK3249, b3262, JW5543, ccrM^[1], ccrM
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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	73.49 minutes	MG1655: 3409675..3410559 <gbrowseImage> name=NC_000913:3409675..3410559 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3339544..3340428 <gbrowseImage> name=NC_012967:3339544..3340428 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3296823..3297707 <gbrowseImage> name=NC_012759:3296823..3297707 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3411508..3412392 <gbrowseImage> name=NC_007779:3411508..3412392 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3507420..3508304 <gbrowseImage> name=NC_010473:3507420..3508304 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)	Reference	Availability
ΔyhdJ (Keio:JW5543)	deletion	deletion	PMID:16738554	Shigen CGSC11454^[5]
ΔyhdJ780::kan			PMID:16738554	CGSC:105148
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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
JW5543	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGAACAGGATGTGAACCGAC Primer 2:CCtTTTGTAATGAGATCGGGGTC
6G3	Kohara Phage	Genobase	PMID:3038334
6G9	Kohara Phage	Genobase	PMID:3038334
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 13% ^[6] Synonyms:zha-6::Tn10
acrF3083::Tn10	Linked marker	CAG12075 = CGSC7447^[5]	est. P1 cotransduction: 84% ^[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:EG11498	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11498	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001454	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947695	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1461	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010706	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	YhdJ
Synonyms	predicted methyltransferase^[1], B3262^[2]^[1], YhdJ^[2]^[1], CcrM^[2]^[1] , ccrM, ECK3249, JW5543, b3262
Product description	predicted methyltransferase^[2]; DNA adenine methyltransferase^[3] DNA adenine methyltransferase, SAM-dependent^[4]
EC number (for enzymes)
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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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002052	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001091	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002941	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006306	DNA methylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001091	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006306	DNA methylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002941	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008170	N-methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001091	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008170	N-methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002941	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009007	site-specific DNA-methyltransferase (adenine-specific) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.1.1.72	F	Seeded from EcoCyc (v14.0)	complete
	GO:0032259	methylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002052	P	Seeded from EcoCyc (v14.0)	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	Notes	References	Evidence
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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
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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 MTMRTGCEPT RFGNEAKTII HGDALAELKK IPAESVDLIF ADPPYNIGKN FDGLIEAWKE DLFIDWLFEV IAECHRVLKK QGSMYIMNST ENMPFIDLQC RKLFTIKSRI VWSYDSSGVQ AKKHYGSMYE PILMMVKDAK NYTFNGDAIL VEAKTGSQRA LIDYRKNPPQ PYNHQKVPGN VWDFPRVRYL MDEYENHPTQ KPEALLKRII LASSNPGDIV LDPFAGSFTT GAVAIASGRK FIGIEINSEY IKMGLRRLDV ASHYSAEELA KVKKRKTGNL SKRSRLSEVD PDLITK
Length	296
Mol. Wt	33.63 kDa
pI	9.1 (calculated)
Extinction coefficient	39,880 - 40,255 (calc based on 12 Y, 4 W, and 3 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
Domain	34..254	PF01555 DNA methylase		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=yhdJ 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:90111566	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947695	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010706	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P28638	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11498	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11498	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947695	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001454	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1461	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	Notes	Reference(s)
Protein	E. coli K-12 MG1655	6^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	2^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
yhdJ
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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_000913:3409655..3409695 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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:b3262 (EcoliWiki Page)	NCBI GEO profiles for yhdJ
microarray	GenExpDB:b3262 (EcoliWiki Page)	Summary of data for yhdJ 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
	GFP Fusion	Intergenic region (3409120..3409297) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:A1^[7]
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Notes

Accessions Related to yhdJ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11498	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1461	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3262
EcoGene	EcoGene:EG11498	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001454	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010706	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
Xenopus tropicalis	ENSXETP00000012955 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YHDJ	From SHIGELLACYC
E. coli O157	YHDJ	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)	PF01555 DNA methylase
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
EcoCyc	EcoCyc:EG11498	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11498	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001454	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1461	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010706	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.

↑ ^1.0 ^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)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 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 ^5.2 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yhdJ: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 yhdJ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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