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Gene |

Product(s) |

Expression|

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Standard Name	dacD
Gene Synonym(s)	ECK2004, b2010, JW5329, pbp, phsE, yeeC^[1], phsF, yeeC
Product Desc.	DD-carboxypeptidase, penicillin-binding protein 6b^[2]^[3] D-alanine D-alanine carboxypeptidase PBP6b; penicillin-binding protein 6b^[4]
Product Synonyms(s)	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6b)^[1], B2010^[2]^[1], YeeC^[2]^[1], PhsE^[2]^[1], DacD^[2]^[1] , ECK2004, JW5329, phsE, phsF, yeeC, b2010
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dacD^[2]
Regulation/Activity
Quick Links
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Notes

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First 21 aa predicted to be a type I signal peptide.^[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	dacD
Mnemonic	D-Alanine carboxypeptidase
Synonyms	ECK2004, b2010, JW5329, pbp, phsE, yeeC^[1], phsF, yeeC
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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	44.82 minutes	MG1655: 2080571..2079405 <gbrowseImage> name=NC_000913:2079405..2080571 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2012990..2011824 <gbrowseImage> name=NC_012967:2011824..2012990 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1971888..1973054 <gbrowseImage> name=NC_012759:1971888..1973054 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2084684..2083518 <gbrowseImage> name=NC_007779:2083518..2084684 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2171579..2170413 <gbrowseImage> name=NC_010473:2170413..2171579 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
ΔdacD (Keio:JW5329)	deletion	deletion	PMID:16738554	Shigen CGSC11322^[5]
ΔdacD779::kan			PMID:16738554	CGSC:100522
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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
JW5329	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACGCCGTCTTATTATTGC Primer 2:CCGGCCTTATGGTGGAAATAATC
3B12	Kohara Phage	Genobase	PMID:3038334
2G4	Kohara Phage	Genobase	PMID:3038334
6D9	Kohara Phage	Genobase	PMID:3038334
zed-3069::Tn10	Linked marker	CAG18451 = CGSC7395^[5]	est. P1 cotransduction: 16% ^[6]
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 88% ^[6] Synonyms:zee-3129::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:EG11893	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11893	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001823	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946518	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1839	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006680	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	DacD
Synonyms	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 6b)^[1], B2010^[2]^[1], YeeC^[2]^[1], PhsE^[2]^[1], DacD^[2]^[1] , ECK2004, JW5329, phsE, phsF, yeeC, b2010
Product description	DD-carboxypeptidase, penicillin-binding protein 6b^[2]^[3] D-alanine D-alanine carboxypeptidase PBP6b; penicillin-binding protein 6b^[4]
EC number (for enzymes)	3.4.16.4^[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:0030288	outer membrane-bounded periplasmic space				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0004180	carboxypeptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0121	F	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:IPR001967	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012907	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015956	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018044	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008360	regulation of cell shape	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0133	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001967	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012907	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018044	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.4.16.4	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009252	peptidoglycan biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0573	P	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:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	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
plasma membrane
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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 MLLKRRLIIA ASLFVFNLSS GFAAENIPFS PQPPEIHAGS WVLMDYTTGQ ILTAGNEHQQ RNPASLTKLM TGYVVDRAID SHRITPDDIV TVGRDAWAKD NPVFVGSSLM FLKEGDRVSV RDLSRGLIVD SGNDACVALA DYIAGGQRQF VEMMNNYAEK LHLKDTHFET VHGLDAPGQH SSAYDLAVLS RAIIHGEPEF YHMYSEKSLT WNGITQQNRN GLLWDKTMNV DGLKTGHTSG AGFNLIASAV DGQRRLIAVV MGADSAKGRE EEARKLLRWG QQNFTTVQIL HRGKKVGTER IWYGDKENID LGTEQEFWMV LPKAEIPHIK AKYTLDGKEL TAPISAHQRV GEIELYDRDK QVAHWPLVTL ESVGEGSMFS RLSDYFHHKA
Length	390
Mol. Wt	43.572 kDa
pI	6.8 (calculated)
Extinction coefficient	60,390 - 60,515 (calc based on 11 Y, 8 W, and 1 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	1-21	UniProt Manual:Signal Peptides	UniProt:P33013
Domain	25..263	PF00768 D-alanyl-D-alanine carboxypeptidase		PMID:19920124
Domain	282..373	PF07943 Penicillin-binding protein 5, C-terminal domain		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=dacD 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:162135904	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946518	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006680	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P33013	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11893	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11893	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946518	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001823	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1839	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	29	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	6	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	17^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)
dacD
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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_000913:2080551..2080591 source=MG1655 flip=1 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:b2010 (EcoliWiki Page)	NCBI GEO profiles for dacD
microarray	GenExpDB:b2010 (EcoliWiki Page)	Summary of data for dacD 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 dacD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11893	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1839	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2010
EcoGene	EcoGene:EG11893	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001823	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006680	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	ENSXETP00000051393 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	DACD	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:56601
Superfamily (EcoliWiki Page)	SUPERFAMILY:69189
Pfam (EcoliWiki Page)	PF00768 D-alanyl-D-alanine carboxypeptidase
Pfam (EcoliWiki Page)	PF07943 Penicillin-binding protein 5, C-terminal domain
EcoCyc	EcoCyc:EG11893	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11893	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001823	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1839	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006680	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 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).

dacD: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 dacD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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