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Expression|

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Standard Name	adiA
Gene Synonym(s)	ECK4110, b4117, JW5731, adi^[1], adi
Product Desc.	Adi^[2]^[3]; Component of arginine decarboxylase, degradative^[2]^[3] Arginine decarboxylase, acid-inducible; arginine-dependent acid resistance^[4]
Product Synonyms(s)	biodegradative arginine decarboxylase^[1], B4117^[2]^[1], AdiA^[2]^[1], Adi^[2]^[1] , adi, ECK4110, JW5731, b4117
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): adiA^[2]
Regulation/Activity
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Notes

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AdiA is homologous to CadA, SpeC, and SpeF. AdiA is regulated by CysB and AdiY.^[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	adiA
Mnemonic	Arginine decarboxylase, induced
Synonyms	ECK4110, b4117, JW5731, adi^[1], adi
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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
BW2952		NC_012759: 4275012..4277282 <gbrowseImage> name=NC_012759:4275012..4277282 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
MG1655	93.46 minutes	MG1655: 4338547..4336277 <gbrowseImage> name=NC_000913:4336277..4338547 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4319238..4316968 <gbrowseImage> name=NC_012967:4316968..4319238 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 4345202..4342932 <gbrowseImage> name=NC_007779:4342932..4345202 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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	4336277	Edman degradation	PMID:4204273
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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: Description	Reference	Availability	Comments
Strain DH10B		V537I	Nonsynonomous mutation	PMID:18245285	ASAP	This is a SNP in E. coli K-12 Strain DH10B
ΔadiA (Keio:JW5731)	deletion	deletion		PMID:16738554	Shigen CGSC11542^[5]
ΔadiA743::kan				PMID:16738554	CGSC:99918
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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
JW5731	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATGAAAGTATTAATTGTTGA Primer 2:CCtGCTTTCACGCACATAACGTG
2C12	Kohara Phage	Genobase	PMID:3038334
8H1	Kohara Phage	Genobase	PMID:3038334
5H2	Kohara Phage	Genobase	PMID:3038334
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 30% ^[6]
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 48% ^[6] Synonyms:zjd-2231::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:EG11501	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11501	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001457	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948638	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1464	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013483	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	AdiA
Synonyms	biodegradative arginine decarboxylase^[1], B4117^[2]^[1], AdiA^[2]^[1], Adi^[2]^[1] , adi, ECK4110, JW5731, b4117
Product description	Adi^[2]^[3]; Component of arginine decarboxylase, degradative^[2]^[3] Arginine decarboxylase, acid-inducible; arginine-dependent acid resistance^[4]
EC number (for enzymes)	4.1.1.19^[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	Aspect	Status
	GO:0008792	arginine decarboxylase activity	PMID:4870599	IDA: Inferred from Direct Assay	F	complete
	GO:0005625	soluble fraction	PMID:4870599	IDA: Inferred from Direct Assay	C	complete
	GO:0006527	arginine catabolic process	PMID:4870599	IDA: Inferred from Direct Assay	P	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, degradative	could be indirect
Protein	rplB		PMID:15690043	Experiment(s):EBI-880730
Protein	rplO		PMID:15690043	Experiment(s):EBI-880730
Protein	rrmJ		PMID:15690043	Experiment(s):EBI-886815
Protein	sucA		PMID:15690043	Experiment(s):EBI-886815
Protein	yahF		PMID:15690043	Experiment(s):EBI-886815
Protein	ybgI		PMID:15690043	Experiment(s):EBI-886815
Protein	ybgI		PMID:19402753	LCMS(ID Probability):99.6
Protein	sucA		PMID:19402753	LCMS(ID Probability):99.6
Protein	rlmE		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplB		PMID:19402753	MALDI(Z-score):39.306923
Protein	yahF		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
cytoplasm			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 MMKVLIVESE FLHQDTWVGN AVERLADALS QQNVTVIKST SFDDGFAILS SNEAIDCLMF SYQMEHPDEH QNVRQLIGKL HERQQNVPVF LLGDREKALA AMDRDLLELV DEFAWILEDT ADFIAGRAVA AMTRYRQQLL PPLFSALMKY SDIHEYSWAA PGHQGGVGFT KTPAGRFYHD YYGENLFRTD MGIERTSLGS LLDHTGAFGE SEKYAARVFG ADRSWSVVVG TSGSNRTIMQ ACMTDNDVVV VDRNCHKSIE QGLMLTGAKP VYMVPSRNRY GIIGPIYPQE MQPETLQKKI SESPLTKDKA GQKPSYCVVT NCTYDGVCYN AKEAQDLLEK TSDRLHFDEA WYGYARFNPI YADHYAMRGE PGDHNGPTVF ATHSTHKLLN ALSQASYIHV REGRGAINFS RFNQAYMMHA TTSPLYAICA SNDVAVSMMD GNSGLSLTQE VIDEAVDFRQ AMARLYKEFT ADGSWFFKPW NKEVVTDPQT GKTYDFADAP TKLLTTVQDC WVMHPGESWH GFKDIPDNWS MLDPIKVSIL APGMGEDGEL EETGVPAALV TAWLGRHGIV PTRTTDFQIM FLFSMGVTRG KWGTLVNTLC SFKRHYDANT PLAQVMPELV EQYPDTYANM GIHDLGDTMF AWLKENNPGA RLNEAYSGLP VAEVTPREAY NAIVDNNVEL VSIENLPGRI AANSVIPYPP GIPMLLSGEN FGDKNSPQVS YLRSLQSWDH HFPGFEHETE GTEIIDGIYH VMCVKA
Length	756
Mol. Wt	84.556 kDa
pI	5.1 (calculated)
Extinction coefficient	123,190 - 124,440 (calc based on 31 Y, 14 W, and 10 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	140..590	PF01276 Orn/Lys/Arg decarboxylase, major domain	PMID:19920124
Domain	615..747	PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain	PMID:19920124
Domain	16..134	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=adiA 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:221800782	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948638	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013483	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P28629	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11501	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11501	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948638	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001457	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1464	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	2.804+/-0.066	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.001762115	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	5^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	8	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	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)
adiA
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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_000913:4338527..4338567 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:b4117 (EcoliWiki Page)	NCBI GEO profiles for adiA
microarray	GenExpDB:b4117 (EcoliWiki Page)	Summary of data for adiA 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 (4338021..4338367) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ02; Well:D6^[7]
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Notes

Accessions Related to adiA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11501	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1464	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4117
EcoGene	EcoGene:EG11501	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001457	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013483	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	ADIA	From SHIGELLACYC
E. coli O157	ADIA	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)	PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain
Pfam (EcoliWiki Page)	PF01276 Orn/Lys/Arg decarboxylase, major domain
Pfam (EcoliWiki Page)	PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:53383
Superfamily (EcoliWiki Page)	SUPERFAMILY:55904
EcoCyc	EcoCyc:EG11501	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11501	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001457	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1464	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013483	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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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 ^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

adiA: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 adiA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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