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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	ispA
Gene Synonym(s)	ECK0415, b0421, JW0411^[1], JW0411
Product Desc.	Farnesyl diphosphate synthase, isoprenoid biosynthesis^[2]
Product Synonyms(s)	geranyltranstransferase^[1], B0421^[3]^[1], IspA^[3]^[1] , ECK0415, JW0411, b0421
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): xseB-ispA-dxs-yajO^[3]
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	ispA
Mnemonic	Isoprenoid
Synonyms	ECK0415, b0421, JW0411^[1], JW0411
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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	9.47 minutes	MG1655: 440325..439426 <gbrowseImage> name=NC_000913:439426..440325 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 409523..408624 <gbrowseImage> name=NC_012967:408624..409523 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 342185..343084 <gbrowseImage> name=NC_012759:342185..343084 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 440325..439426 <gbrowseImage> name=NC_007779:439426..440325 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 379656..378757 <gbrowseImage> name=NC_010473:378757..379656 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	439426	Edman degradation	PMID:9740056
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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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
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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
JW0411	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGACTTTCCGCAGCAACTCGA Primer 2:CCTTTATTACGCTGGATGATGTA
19F6	Kohara Phage	Genobase	PMID:3038334
2H5	Kohara Phage	Genobase	PMID:3038334
tsx-247::Tn10	Linked marker	CAG12148 = CGSC7337^[4]	est. P1 cotransduction: 76% ^[5]
zaj-3054::Tn10	Linked marker	CAG12017 = CGSC7339^[4]	est. P1 cotransduction: 48% ^[5] Synonyms:zba-3054::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:EG10508	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10508	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000501	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945064	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0503	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001463	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	IspA
Synonyms	geranyltranstransferase^[1], B0421^[3]^[1], IspA^[3]^[1] , ECK0415, JW0411, b0421
Product description	Farnesyl diphosphate synthase, isoprenoid biosynthesis^[2]
EC number (for enzymes)	2.5.1.10^[1] 2.5.1.1^[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:0004337	geranyltranstransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.5.1.10	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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	eutQ	PMID:15690043	Experiment(s):EBI-889772
Protein	dnaK	PMID:15690043	Experiment(s):EBI-889772
Protein	flxA	PMID:15690043	Experiment(s):EBI-889772
Protein	purT	PMID:15690043	Experiment(s):EBI-889772
Protein	rplC	PMID:15690043	Experiment(s):EBI-889772
Protein	rplK	PMID:15690043	Experiment(s):EBI-889772
Protein	rplL	PMID:15690043	Experiment(s):EBI-889772
Protein	rplM	PMID:15690043	Experiment(s):EBI-889772
Protein	rpsB	PMID:15690043	Experiment(s):EBI-889772
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-889772
Protein	rpmG	PMID:15690043	Experiment(s):EBI-889772
Protein	ydjX	PMID:16606699	Experiment(s):EBI-1136547
Protein	rplB	PMID:16606699	Experiment(s):EBI-1136547
Protein	yfiC	PMID:16606699	Experiment(s):EBI-1136547
Protein	fliY	PMID:16606699	Experiment(s):EBI-1136547
Protein	yafT	PMID:16606699	Experiment(s):EBI-1136547
Protein	rplA	PMID:19402753	MALDI(Z-score):30.479858
Protein	rpsD	PMID:19402753	MALDI(Z-score):19.775499
Protein	rpsC	PMID:19402753	MALDI(Z-score):33.397333
Protein	tufB	PMID:19402753	MALDI(Z-score):22.733187
Protein	rho	PMID:19402753	MALDI(Z-score):27.198092
Protein	flxA	PMID:19402753	LCMS(ID Probability):99.0
Protein	purT	PMID:19402753	LCMS(ID Probability):99.0
Protein	eutQ	PMID:19402753	LCMS(ID Probability):99.0
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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 MDFPQQLEAC VKQANQALSR FIAPLPFQNT PVVETMQYGA LLGGKRLRPF LVYATGHMFG VSTNTLDAPA AAVECIHAYS LIHDDLPAMD DDDLRRGLPT CHVKFGEANA ILAGDALQTL AFSILSDADM PEVSDRDRIS MISELASASG IAGMCGGQAL DLDAEGKHVP LDALERIHRH KTGALIRAAV RLGALSAGDK GRRALPVLDK YAESIGLAFQ VQDDILDVVG DTATLGKRQG ADQQLGKSTY PALLGLEQAR KKARDLIDDA RQSLKQLAEQ SLDTSALEAL ADYIIQRNK
Length	299
Mol. Wt	32.16 kDa
pI	5.3 (calculated)
Extinction coefficient	8,940 - 9,440 (calc based on 6 Y, 0 W, and 4 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	32..295	PF00348 Polyprenyl synthetase		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=ispA 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:16128406	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945064	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001463	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P22939	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10508	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10508	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945064	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000501	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0503	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	Ecoli K-12	22.682+/-0.166	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.045606229	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	950	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	294	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	641	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)
xseB-ispA-dxs-yajO
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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_000913:440305..440345 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:b0421 (EcoliWiki Page)	NCBI GEO profiles for ispA
microarray	GenExpDB:b0421 (EcoliWiki Page)	Summary of data for ispA 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 ispA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10508	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0503	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0421
EcoGene	EcoGene:EG10508	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000501	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001463	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	AT3G29430 (score: 1.000; bootstrap: 100%) AT3G32040 (score: 0.871) AT3G14550 (score: 0.808) AT3G14530 (score: 0.796) AT3G14510 (score: 0.596) AT4G36810 (score: 0.514) AT2G18620 (score: 0.439) AT2G18640 (score: 0.424) AT2G23800 (score: 0.392) AT3G20160 (score: 0.380) AT1G49530 (score: 0.306)	From Inparanoid:20070104
Oryza gramene	Q7XI92 (score: 1.000; bootstrap: 99%) Q9XHX1 (score: 0.242)	From Inparanoid:20070104
Shigella flexneri	ISPA	From SHIGELLACYC
E. coli O157	ISPA	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:48576
Panther (EcoliWiki Page)	PTHR12001:SF23
Pfam (EcoliWiki Page)	PF00348 Polyprenyl synthetase
EcoCyc	EcoCyc:EG10508	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10508	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000501	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0503	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001463	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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).

ispA: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 ispA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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