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Standard Name	opgD
Gene Synonym(s)	ECK1418, b1424, JW1420, ydcG, opgD, yzzZ, mdoD^[1], mdoD, yzzZ
Product Desc.	glucan biosynthesis protein D^[2]^[3]
Product Synonyms(s)	glucan biosynthesis protein, periplasmic^[1], B1424^[2]^[1], YzzZ^[2]^[1], YdcG^[2]^[1], MdoD^[2]^[1], OpgD^[2]^[1] , ECK1418, JW1420, mdoD, ydcG, yzzZ, b1424
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): opgD^[2]
Regulation/Activity
Quick Links
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Notes

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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	opgD
Mnemonic	Osmoregulated periplasmic glucans
Synonyms	ECK1418, b1424, JW1420, ydcG, opgD, yzzZ, mdoD^[1], mdoD, yzzZ
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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	32.22 minutes	MG1655: 1494910..1496535 <gbrowseImage> name=NC_000913:1494910..1496535 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 1386939..1388594 <gbrowseImage> name=NC_012759:1386939..1388594 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1498600..1500225 <gbrowseImage> name=NC_007779:1498600..1500225 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1585475..1587130 <gbrowseImage> name=NC_010473:1585475..1587130 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
Coding Start (SO:0000323)	MG1655	1494976	Edman degradation	PMID:9298646
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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
ΔmdoD (Keio:JW1420)	deletion	deletion	PMID:16738554	Shigen CGSC9244^[4]
ΔmdoD785::kan			PMID:16738554	CGSC:101780
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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
JW1420	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTATGGCgGCCGTGTGCGGTACCAGCGGC Primer 2:CCACTCATCACGCGGTCGTCAAC
24D6	Kohara Phage	Genobase	PMID:3038334
1A6	Kohara Phage	Genobase	PMID:3038334
trg-2::Tn10	Linked marker	CAG12026 = CGSC7376^[4]	est. P1 cotransduction: 97% ^[5]
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[4]	est. P1 cotransduction: 18% ^[5] Synonyms:zdc-235::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:EG12859	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2701	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1424
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C1849
EcoGene	EcoGene:EG12859	Escherichia coli str. K-12 substr. MG1655
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YDCG
ASAP	ASAP:ABE-0004754	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	ECOCYC:EG12859	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945994	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002405	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	OpgD
Synonyms	glucan biosynthesis protein, periplasmic^[1], B1424^[2]^[1], YzzZ^[2]^[1], YdcG^[2]^[1], MdoD^[2]^[1], OpgD^[2]^[1] , ECK1418, JW1420, mdoD, ydcG, yzzZ, b1424
Product description	glucan biosynthesis protein D^[2]^[3]
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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011013	F	Seeded from EcoCyc (v14.0)	complete
	GO:0032951	regulation of beta-glucan biosynthetic process	PMID:15175282	IDA: Inferred from Direct Assay		P		complete
	GO:0009250	glucan biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01068	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016051	carbohydrate biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007444	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030246	carbohydrate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011013	F	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	References	Evidence
Protein	yijP	PMID:16606699	Experiment(s):EBI-1139815
Protein	ptrA	PMID:16606699	Experiment(s):EBI-1139815
Protein	ygcB	PMID:16606699	Experiment(s):EBI-1139815
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Notes

Localization

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

Compartment	Evidence	Reference/Source
periplasm
Periplasm	PMID:9298646	EchoLocation:mdoD
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Notes

Translocated via the Tat pathway ^[6]

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 MDRRRFIKGS MAMAAVCGTS GIASLFSQAA FAADSDIADG QTQRFDFSIL QSMAHDLAQT AWRGAPRPLP DTLATMTPQA YNSIQYDAEK SLWHNVENRQ LDAQFFHMGM GFRRRVRMFS VDPATHLARE IHFRPELFKY NDAGVDTKQL EGQSDLGFAG FRVFKAPELA RRDVVSFLGA SYFRAVDDTY QYGLSARGLA IDTYTDSKEE FPDFTAFWFD TVKPGATTFT VYALLDSASI TGAYKFTIHC EKSQVIMDVE NHLYARKDIK QLGIAPMTSM FSCGTNERRM CDTIHPQIHD SDRLSMWRGN GEWICRPLNN PQKLQFNAYT DNNPKGFGLL QLDRDFSHYQ DIMGWYNKRP SLWVEPRNKW GKGTIGLMEI PTTGETLDNI VCFWQPEKAV KAGDEFAFQY RLYWSAQPPV HCPLARVMAT RTGMGGFSEG WAPGEHYPEK WARRFAVDFV GGDLKAAAPK GIEPVITLSS GEAKQIEILY IEPIDGYRIQ FDWYPTSDST DPVDMRMYLR CQGDAISETW LYQYFPPAPD KRQYVDDRVM S
Length	551
Mol. Wt	62.759 kDa
pI	6.3 (calculated)
Extinction coefficient	111,270 - 112,270 (calc based on 23 Y, 14 W, and 8 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	1-32	UniProt Manual:Signal Peptides	UniProt:P40120
Domain	45..536	PF04349 Periplasmic glucan biosynthesis protein, MdoG		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=mdoD 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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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:145698256	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945994	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004754	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P40120	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12859	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12859	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945994	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002405	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2701	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	Reference(s)
Protein	E. coli K-12 MC4100	2.29E+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	E. coli K-12 MG1655	596	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	259	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	428	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	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)
mdoD
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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_000913:1494890..1494930 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:b1424 (EcoliWiki Page)	NCBI GEO profiles for mdoD
microarray	GenExpDB:b1424 (EcoliWiki Page)	Summary of data for mdoD 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 (1494575..1494905) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ17; Well:H10^[7]
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Notes

Accessions Related to opgD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12859	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2701	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1424
EcoGene	EcoGene:EG12859	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002405	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004754	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
Shigella flexneri	YDCG	From SHIGELLACYC
E. coli O157	YDCG	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)	PF04349 Periplasmic glucan biosynthesis protein, MdoG
Superfamily (EcoliWiki Page)	SUPERFAMILY:74650
Superfamily (EcoliWiki Page)	SUPERFAMILY:81296
EcoCyc	EcoCyc:EG12859	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12859	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002405	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2701	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004754	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 ^2.11 ^2.12 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 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).
↑ Norinder, U & Högberg, T (1992) PLS-based quantitative structure-activity relationship for substituted benzamides of clebopride type. Application of experimental design in drug design. Acta Chem. Scand. 46 363-6 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

opgD: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 opgD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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