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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	speC
Gene Synonym(s)	ECK2960, b2965, JW5482^[1], JW5482
Product Desc.	SpeC^[2]^[3]; Component of ornithine decarboxylase, biosynthetic^[2]^[3] Ornithine decarboxylase^[4]
Product Synonyms(s)	ornithine decarboxylase, constitutive^[1], B2965^[2]^[1], SpeC^[2]^[1] , ECK2960, JW5482, b2965
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): speC^[2], OP00166
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	speC
Mnemonic	Spermidine
Synonyms	ECK2960, b2965, JW5482^[1], JW5482
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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	66.92 minutes	MG1655: 3107177..3105042 <gbrowseImage> name=NC_000913:3105042..3107177 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2994815..2992680 <gbrowseImage> name=NC_012967:2992680..2994815 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2992190..2994325 <gbrowseImage> name=NC_012759:2992190..2994325 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3107811..3105676 <gbrowseImage> name=NC_007779:3105676..3107811 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3209142..3211277 <gbrowseImage> name=NC_010473:3209142..3211277 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
speC(del) (Keio:JW5482)	deletion	deletion			PMID:16738554	Shigen CGSC11419^[5]
speC::Tn5KAN-I-SceI (FB20996)	Insertion at nt 1009 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20996	does not contain pKD46
speC::Tn5KAN-I-SceI (FB20997)	Insertion at nt 1009 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20997	contains pKD46
speC3						CGSC:11866
speC740(del)::kan					PMID:16738554	CGSC:102996
yeeF(del) speA(del) speB(del) speC(del) potA(del) potB(del) potC(del) potD(del)	deletion	deletion	Motility	Deletion of yeeF in a speA(del) speB(del) speC(del) potA(del) potB(del) potC(del) potD(del) genetic background resulted in severe inhibition of surface motility under the same conditions, fig 2.	PMID:21266585
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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
JW5482	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAATCAATGAATATTGCCGC Primer 2:CCtTTCAACACATAACCGTACAA
3A9	Kohara Phage	Genobase	PMID:3038334
3D11	Kohara Phage	Genobase	PMID:3038334
nupG511::Tn10	Linked marker	CAG18472 = CGSC7433^[5]	est. P1 cotransduction: 96% ^[6]
metC162::Tn10	Linked marker	CAG18475 = CGSC7435^[5]	est. P1 cotransduction: 13% ^[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:EG10961	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10961	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000950	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947457	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0954	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009730	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	SpeC
Synonyms	ornithine decarboxylase, constitutive^[1], B2965^[2]^[1], SpeC^[2]^[1] , ECK2960, JW5482, b2965
Product description	SpeC^[2]^[3]; Component of ornithine decarboxylase, biosynthetic^[2]^[3] Ornithine decarboxylase^[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, biosynthetic	could be indirect
Protein	dapD		PMID:19402753	LCMS(ID Probability):99.6
Protein	hpt		PMID:19402753	LCMS(ID Probability):99.6
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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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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 MGQGFPPCPV FLLPRNGFAL MKSMNIAASS ELVSRLSSHR RVVALGDTDF TDVAAVVITA ADSRSGILAL LKRTGFHLPV FLYSEHAVEL PAGVTAVING NEQQWLELES AACQYEENLL PPFYDTLTQY VEMGNSTFAC PGHQHGAFFK KHPAGRHFYD FFGENVFRAD MCNADVKLGD LLIHEGSAKD AQKFAAKVFH ADKTYFVLNG TSAANKVVTN ALLTRGDLVL FDRNNHKSNH HGALIQAGAT PVYLEASRNP FGFIGGIDAH CFNEEYLRQQ IRDVAPEKAD LPRPYRLAII QLGTYDGTVY NARQVIDTVG HLCDYILFDS AWVGYEQFIP MMADSSPLLL ELNENDPGIF VTQSVHKQQA GFSQTSQIHK KDNHIRGQAR FCPHKRLNNA FMLHASTSPF YPLFAALDVN AKIHEGESGR RLWAECVEIG IEARKAILAR CKLFRPFIPP VVDGKLWQDY PTSVLASDRR FFSFEPGAKW HGFEGYAADQ YFVDPCKLLL TTPGIDAETG EYSDFGVPAT ILAHYLRENG IVPEKCDLNS ILFLLTPAES HEKLAQLVAM LAQFEQHIED DSPLVEVLPS VYNKYPVRYR DYTLRQLCQE MHDLYVSFDV KDLQKAMFRQ QSFPSVVMNP QDAHSAYIRG DVELVRIRDA EGRIAAEGAL PYPPGVLCVV PGEVWGGAVQ RYFLALEEGV NLLPGFSPEL QGVYSETDAD GVKRLYGYVL K
Length	731
Mol. Wt	81.56 kDa
pI	6.1 (calculated)
Extinction coefficient	77,700 - 79,325 (calc based on 30 Y, 6 W, and 13 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	101..543	PF01276 Orn/Lys/Arg decarboxylase, major domain	PMID:19920124
Domain	568..701	PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain	PMID:19920124
Domain	4..95	PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain	PMID:19920124
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<motif_map/>

Structure
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Structures

<beststructure> gene=speC taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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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:90111522	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947457	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009730	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P21169	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10961	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10961	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947457	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000950	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0954	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 MC4100	1.14E+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	Ecoli K-12	3.562+/-0.052	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.016393443	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	684	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	249	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	267	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)
speC
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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_000913:3107157..3107197 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:b2965 (EcoliWiki Page)	NCBI GEO profiles for speC
microarray	GenExpDB:b2965 (EcoliWiki Page)	Summary of data for speC 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 (3107139..3107571) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:H11^[7]
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Notes

Accessions Related to speC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10961	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0954	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2965
EcoGene	EcoGene:EG10961	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000950	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009730	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	SPEC	From SHIGELLACYC
E. coli O157	SPEC	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)	PF01276 Orn/Lys/Arg decarboxylase, major domain
Pfam (EcoliWiki Page)	PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain
Pfam (EcoliWiki Page)	PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:52172
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
Superfamily (EcoliWiki Page)	SUPERFAMILY:55904
EcoCyc	EcoCyc:EG10961	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10961	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000950	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0954	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009730	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 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

speC: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 speC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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