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Gene |

Product(s) |

Expression|

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Standard Name	ispD
Gene Synonym(s)	ECK2742, b2747, JW2717, ygbP^[1], ygbP
Product Desc.	4-diphosphocytidyl-2C-methyl-D-erythritol synthetase^[2]^[3]; Component of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase^[3] 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; alternative nonmevalonate (DXP) pathway for terpenoid biosynthesis; essential gene^[4]
Product Synonyms(s)	4-diphosphocytidyl-2C-methyl-D-erythritol synthase^[1], YgbP^[2]^[1], IspD^[2]^[1], B2747^[2]^[1] , ECK2742, JW2717, ygbP, b2747
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ispDF^[3]
Regulation/Activity
Quick Links
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Notes

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IspD is also called 4-diphosphocytidyl-2-C-methylerythritol synthase.^[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	ispD
Mnemonic	Isoprenoid
Synonyms	ECK2742, b2747, JW2717, ygbP^[1], ygbP
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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	61.85 minutes	MG1655: 2870512..2869802 <gbrowseImage> name=NC_000913:2869802..2870512 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2767351..2766641 <gbrowseImage> name=NC_012967:2766641..2767351 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2755614..2756324 <gbrowseImage> name=NC_012759:2755614..2756324 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2871146..2870436 <gbrowseImage> name=NC_007779:2870436..2871146 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2963054..2962344 <gbrowseImage> name=NC_010473:2962344..2963054 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	2869805	Edman degradation	PMID:10518523
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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	AA change(s)	Phenotype: Description	Comments
ispDK27A,S	K27A,S	Strong decrease in activity	seeded from UniProt:Q46893
ispDE191K	E191K	Loss of activity	seeded from UniProt:Q46893
ispDT140I	T140I	Loss of activity	seeded from UniProt:Q46893
ispDK213S	K213S	Decrease in activity	seeded from UniProt:Q46893
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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
JW2717	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCAACCACTCATTTGGATGT Primer 2:CCTGTATTCTCCTGATGGATGGT
25D2	Kohara Phage	Genobase	PMID:3038334
1B5	Kohara Phage	Genobase	PMID:3038334
6C8	Kohara Phage	Genobase	PMID:3038334
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 14% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
cysI95::Tn10	Linked marker	CAG12173 = CGSC7425^[5]	est. P1 cotransduction: 57% ^[6] Synonyms:cysC95::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:G7423	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13110	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003988	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948269	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2913	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009017	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	IspD
Synonyms	4-diphosphocytidyl-2C-methyl-D-erythritol synthase^[1], YgbP^[2]^[1], IspD^[2]^[1], B2747^[2]^[1] , ECK2742, JW2717, ygbP, b2747
Product description	4-diphosphocytidyl-2C-methyl-D-erythritol synthetase^[2]^[3]; Component of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase^[3] 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; alternative nonmevalonate (DXP) pathway for terpenoid biosynthesis; essential gene^[4]
EC number (for enzymes)	2.7.7.60^[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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008299	isoprenoid biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001228	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008299	isoprenoid biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018294	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008299	isoprenoid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0414	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016114	terpenoid biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00108	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00108	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.60	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050897	cobalt ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0170	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	Notes	References	Evidence
Protein	Subunits of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase	could be indirect
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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 MATTHLDVCA VVPAAGFGRR MQTECPKQYL SIGNQTILEH SVHALLAHPR VKRVVIAISP GDSRFAQLPL ANHPQITVVD GGDERADSVL AGLKAAGDAQ WVLVHDAARP CLHQDDLARL LALSETSRTG GILAAPVRDT MKRAEPGKNA IAHTVDRNGL WHALTPQFFP RELLHDCLTR ALNEGATITD EASALEYCGF HPQLVEGRAD NIKVTRPEDL ALAEFYLTRT IHQENT
Length	236
Mol. Wt	25.736 kDa
pI	6.6 (calculated)
Extinction coefficient	15,470 - 16,095 (calc based on 3 Y, 2 W, and 5 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
Initiator Methionine	1	Removed	UniProt:Q46893
Domain	8..229	PF01128 Uncharacterized protein family UPF0007		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=ispD 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:16130654	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948269	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009017	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q46893	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7423	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13110	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948269	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003988	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2913	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	1.67E+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	485	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	123	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	314	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)
ispDF
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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_000913:2870492..2870532 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:b2747 (EcoliWiki Page)	NCBI GEO profiles for ispD
microarray	GenExpDB:b2747 (EcoliWiki Page)	Summary of data for ispD 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 ispD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7423	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2913	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2747
EcoGene	EcoGene:EG13110	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003988	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009017	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
Arabidopsis thaliana	AT2G02500 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000020061 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000003520 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000017536 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000335555 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000030602 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000002015 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1923097 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5N8G1 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000008312 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000165278 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00021930001 (score: 1.000; bootstrap: 100%) GSTENP00036315001 (score: 0.253)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000049329 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGBP	From SHIGELLACYC
E. coli O157	YGBP	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)	PF01128 Uncharacterized protein family UPF0007
Superfamily (EcoliWiki Page)	SUPERFAMILY:53448
EcoCyc	EcoCyc:G7423	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13110	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003988	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2913	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009017	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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 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 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).

ispD:On One Page

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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 ispD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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