speA:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

speA

Gene Synonym(s)

ECK2933, b2938, JW2905[1], JW2905

Product Desc.

SpeA[2][3];

Component of arginine decarboxylase, biosynthetic[2][3]

Biosynthetic decarboxylase[4]

Product Synonyms(s)

biosynthetic arginine decarboxylase, PLP-binding[1], B2938[2][1], SpeA[2][1] , ECK2933, JW2905, b2938

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): speAB[2], OP00287

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

speA

Mnemonic

Spermidine

Synonyms

ECK2933, b2938, JW2905[1], JW2905

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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

66.43 minutes 

MG1655: 3083933..3081957
<gbrowseImage> name=NC_000913:3081957..3083933 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2971662..2969686
<gbrowseImage> name=NC_012967:2969686..2971662 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2969105..2971081
<gbrowseImage> name=NC_012759:2969105..2971081 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3084567..3082591
<gbrowseImage> name=NC_007779:3082591..3084567 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3179002..3177026
<gbrowseImage> name=NC_010473:3177026..3179002 source=DH10B preset=GeneLocation </gbrowseImage>

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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

speA(del) (Keio:JW2905)

deletion

deletion

PMID:16738554

Shigen

CGSC10249[5]

speA::Tn5KAN-I-SceI (FB20985)

Insertion at nt 526 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20985

contains pKD46

speA::Tn5KAN-I-SceI (FB20986)

Insertion at nt 526 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20986

does not contain pKD46

speA210::Tn10

Insertion at 3,082,776 bp in MG1655 (NC_000913)

adapted from Nichols et al.[6]

CAG12168 = CGSC7431[5]

Synonyms: zgd-210::Tn10, zgf-210::Tn10

speA210::Tn10

PMID:2540407 PMID:9829956 PMID:368027

CGSC:9661

speA1

CGSC:14423

speA0

CGSC:33659

speA3156::Tn10kan

PMID:2540407 PMID:9829956

CGSC:40111

speA786(del)::kan

PMID:16738554

CGSC:102994

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

JW2905

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGACGACATGTCTATGGG

Primer 2:CCtTCATCTTCAAGATAAGTATA

1H10

Kohara Phage

Genobase

PMID:3038334

23G4S

Kohara Phage

Genobase

PMID:3038334

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[5]

est. P1 cotransduction: % [6]

nupG511::Tn10

Linked marker

CAG18472 = CGSC7433[5]

est. P1 cotransduction: 44% [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:EG10959

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10959

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000948

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947432

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0952

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009634

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

SpeA

Synonyms

biosynthetic arginine decarboxylase, PLP-binding[1], B2938[2][1], SpeA[2][1] , ECK2933, JW2905, b2938

Product description

SpeA[2][3];

Component of arginine decarboxylase, biosynthetic[2][3]

Biosynthetic decarboxylase[4]

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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

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:0006527

arginine catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002985

P

Seeded from EcoCyc (v14.0)

complete

GO:0008295

spermidine biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01417

P

Seeded from EcoCyc (v14.0)

complete

GO:0008295

spermidine biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002985

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:0008792

arginine decarboxylase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01417

F

Seeded from EcoCyc (v14.0)

complete

GO:0008792

arginine decarboxylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002985

F

Seeded from EcoCyc (v14.0)

complete

GO:0008792

arginine decarboxylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.1.19

F

Seeded from EcoCyc (v14.0)

complete

GO:0009446

putrescine biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0661

P

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0574

C

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0200

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 Notes References Evidence

Protein

Subunits of arginine decarboxylase, biosynthetic

could be indirect

Protein

ydeP

PMID:16606699

Experiment(s):EBI-1144358

Protein

yaiV

PMID:16606699

Experiment(s):EBI-1144358

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1144358

Protein

rpsG

PMID:16606699

Experiment(s):EBI-1144358

Protein

nadE

PMID:16606699

Experiment(s):EBI-1144358

Protein

rplQ

PMID:16606699

Experiment(s):EBI-1144358

Protein

rpsB

PMID:16606699

Experiment(s):EBI-1144358

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1144358

Protein

rhaS

PMID:16606699

Experiment(s):EBI-1144358

Protein

rplB

PMID:16606699

Experiment(s):EBI-1144358

Protein

rpoC

PMID:16606699

Experiment(s):EBI-1144358

Protein

priC

PMID:16606699

Experiment(s):EBI-1144358
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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

periplasm

From EcoCyc[3]


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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 

MSDDMSMGLP SSAGEHGVLR SMQEVAMSSQ EASKMLRTYN IAWWGNNYYD VNELGHISVC
PDPDVPEARV DLAQLVKTRE AQGQRLPALF CFPQILQHRL RSINAAFKRA RESYGYNGDY
FLVYPIKVNQ HRRVIESLIH SGEPLGLEAG SKAELMAVLA HAGMTRSVIV CNGYKDREYI
RLALIGEKMG HKVYLVIEKM SEIAIVLDEA ERLNVVPRLG VRARLASQGS GKWQSSGGEK
SKFGLAATQV LQLVETLREA GRLDSLQLLH FHLGSQMANI RDIATGVRES ARFYVELHKL
GVNIQCFDVG GGLGVDYEGT RSQSDCSVNY GLNEYANNII WAIGDACEEN GLPHPTVITE
SGRAVTAHHT VLVSNIIGVE RNEYTVPTAP AEDAPRALQS MWETWQEMHE PGTRRSLREW
LHDSQMDLHD IHIGYSSGIF SLQERAWAEQ LYLSMCHEVQ KQLDPQNRAH RPIIDELQER
MADKMYVNFS LFQSMPDAWG IDQLFPVLPL EGLDQVPERR AVLLDITCDS DGAIDHYIDG
DGIATTMPMP EYDPENPPML GFFMVGAYQE ILGNMHNLFG DTEAVDVFVF PDGSVEVELS
DEGDTVADML QYVQLDPKTL LTQFRDQVKK TDLDAELQQQ FLEEFEAGLY GYTYLEDE
Length

658

Mol. Wt

73.898 kDa

pI

4.7 (calculated)

Extinction coefficient

86,750 - 87,750 (calc based on 25 Y, 9 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

Domain

98..368

PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain

PMID:19920124

Domain

371..587

PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet 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=speA 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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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:16130839

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947432

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009634

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P21170

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10959

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10959

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947432

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000948

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0952

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

1.11E+03

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

9452

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

1823

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

4279

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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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

speAB

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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_000913:3083913..3083953 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:b2938 (EcoliWiki Page)

NCBI GEO profiles for speA

microarray

GenExpDB:b2938 (EcoliWiki Page)

Summary of data for speA 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 speA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10959

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0952

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2938

EcoGene

EcoGene:EG10959

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000948

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009634

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

  • AT4G34710 (score: 1.000; bootstrap: 100%)
  • AT2G16500 (score: 0.711)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000016163 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q9SNN0 (score: 1.000; bootstrap: 100%)
  • Q6J285 (score: 1.000; bootstrap: 100%)
  • Q7XRA1 (score: 0.159)
  • P22220 (score: 0.136)

From Inparanoid:20070104

Shigella flexneri

SPEA

From SHIGELLACYC

E. coli O157

SPEA

From ECOO157CYC

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Do-It-Yourself Web Tools

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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)

PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain

Pfam (EcoliWiki Page)

PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:50621

Superfamily (EcoliWiki Page)

SUPERFAMILY:51419

Panther (EcoliWiki Page)

PTHR11482:SF3

EcoCyc

EcoCyc:EG10959

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10959

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000948

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0952

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009634

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 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. ↑ 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. ↑ 5.0 5.1 5.2 5.3 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 6.2 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).

Categories

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