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Gene |

Product(s) |

Expression|

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Standard Name	speF
Gene Synonym(s)	ECK0681, b0693, JW0680^[1], JW0680
Product Desc.	SpeF^[2]^[3]; Component of ornithine decarboxylase, degradative^[2]^[3] Ornthine decarboxylase, inducible^[4]
Product Synonyms(s)	ornithine decarboxylase isozyme, inducible^[1], B0693^[2]^[1], SpeF^[2]^[1] , ECK0681, JW0680, b0693
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): speF-potE^[2]
Regulation/Activity
Quick Links
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Notes

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Lack of cadBA opereon induction results in an increase in speF-potE operon expression.^[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	speF
Mnemonic	Spermidine
Synonyms	ECK0681, b0693, JW0680^[1], JW0680
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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	15.46 minutes	MG1655: 719683..717485 <gbrowseImage> name=NC_000913:717485..719683 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 702555..700357 <gbrowseImage> name=NC_012967:700357..702555 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 620245..622443 <gbrowseImage> name=NC_012759:620245..622443 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 720882..718684 <gbrowseImage> name=NC_007779:718684..720882 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 772275..770077 <gbrowseImage> name=NC_010473:770077..772275 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
ΔspeF (Keio:JW0680)	deletion	deletion	PMID:16738554	Shigen CGSC8764^[5]
ΔspeF741::kan			PMID:16738554	CGSC:103002
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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
JW0680	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCAAAATTAAAAATTGCGGT Primer 2:CCTAATTTTTCCCCTTTCAACAG
11A10	Kohara Phage	Genobase	PMID:3038334
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[5]	est. P1 cotransduction: 55% ^[6] Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
nadA57::Tn10	Linked marker	CAG12147 = CGSC7351^[5]	est. P1 cotransduction: 4% ^[6]
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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:EG10964	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10964	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000953	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945297	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0957	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002362	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	SpeF
Synonyms	ornithine decarboxylase isozyme, inducible^[1], B0693^[2]^[1], SpeF^[2]^[1] , ECK0681, JW0680, b0693
Product description	SpeF^[2]^[3]; Component of ornithine decarboxylase, degradative^[2]^[3] Ornthine decarboxylase, inducible^[4]
EC number (for enzymes)	4.1.1.17^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000310	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008286	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015422	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004586	ornithine decarboxylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.1.17	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011193	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006520	cellular amino acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011193	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008295	spermidine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0745	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016831	carboxy-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005308	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016831	carboxy-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011193	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016831	carboxy-lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0210	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030170	pyridoxal phosphate binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015422	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 ornithine decarboxylase, degradative	could be indirect
Protein	glnS		PMID:16606699	Experiment(s):EBI-1137711
Protein	selB		PMID:16606699	Experiment(s):EBI-1137711
Protein	nadE		PMID:16606699	Experiment(s):EBI-1137711
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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 MSKLKIAVSD SCPDCFTTQR ECIYINESRN IDVAAIVLSL NDVTCGKLDE IDATGYGIPV FIATENQERV PAEYLPRISG VFENCESRRE FYGRQLETAA SHYETQLRPP FFRALVDYVN QGNSAFDCPG HQGGEFFRRH PAGNQFVEYF GEALFRADLC NADVAMGDLL IHEGAPCIAQ QHAAKVFNAD KTYFVLNGTS SSNKVVLNAL LTPGDLVLFD RNNHKSNHHG ALLQAGATPV YLETARNPYG FIGGIDAHCF EESYLRELIA EVAPQRAKEA RPFRLAVIQL GTYDGTIYNA RQVVDKIGHL CDYILFDSAW VGYEQFIPMM ADCSPLLLDL NENDPGILVT QSVHKQQAGF SQTSQIHKKD SHIKGQQRYV PHKRMNNAFM MHASTSPFYP LFAALNINAK MHEGVSGRNM WMDCVVNGIN ARKLILDNCQ HIRPFVPELV DGKPWQSYET AQIAVDLRFF QFVPGEHWHS FEGYAENQYF VDPCKLLLTT PGIDARNGEY EAFGVPATIL ANFLRENGVV PEKCDLNSIL FLLTPAEDMA KLQQLVALLV RFEKLLESDA PLAEVLPSIY KQHEERYAGY TLRQLCQEMH DLYARHNVKQ LQKEMFRKEH FPRVSMNPQE ANYAYLRGEV ELVRLPDAEG RIAAEGALPY PPGVLCVVPG EIWGGAVLRY FSALEEGINL LPGFAPELQG VYIEEHDGRK QVWCYVIKPR DAQSTLLKGE KL
Length	732
Mol. Wt	82.416 kDa
pI	5.8 (calculated)
Extinction coefficient	79,190 - 81,440 (calc based on 31 Y, 6 W, and 18 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	References
Domain	109..551	PF01276 Orn/Lys/Arg decarboxylase, major domain	PMID:19920124
Domain	576..709	PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain	PMID:19920124
Domain	4..103	PF03709 Orn/Lys/Arg decarboxylase, N-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=speF 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:16128669	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945297	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002362	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P24169	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10964	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10964	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945297	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000953	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0957	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	0^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	0^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)
speF-potE
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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_000913:719663..719703 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:b0693 (EcoliWiki Page)	NCBI GEO profiles for speF
microarray	GenExpDB:b0693 (EcoliWiki Page)	Summary of data for speF 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 (719388..720088) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:E7^[7]
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Notes

Accessions Related to speF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10964	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0957	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0693
EcoGene	EcoGene:EG10964	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000953	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002362	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF01276 Orn/Lys/Arg decarboxylase, major domain
Pfam (EcoliWiki Page)	PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain
Pfam (EcoliWiki Page)	PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:52172
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
Superfamily (EcoliWiki Page)	SUPERFAMILY:55904
EcoCyc	EcoCyc:EG10964	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10964	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000953	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0957	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002362	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 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 ^3.2 ^3.3 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

speF: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 speF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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