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amiA:On One Page

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Gene Name	amiA (synonyms: ECK2430, b2435, JW2428, yfeE)^[1]
Product(s)	AmiA product^[1]: N-acetylmuramoyl-l-alanine amidase I product, B2435 product, YfeE product
Description	N-acetylmuramoyl-L-alanine amidase 1^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): amiA-hemF^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	amiA
Mnemonic
Synonyms	ECK2430, b2435, JW2428, yfeE^[1]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	54.97 minutes	MG1655: 2550374..2551243	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 2557798..2558667	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

54.97 minutes

MG1655: 2550374..2551243
gbrowse_img.php?coord=2549374..2552243&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 2557798..2558667
gbrowse_img.php?coord=2556798..2559667&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

GBrowse(W3110)

FASTA Dump

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Notes

Sequence Features

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Feature type	Location	Description
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Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔamiA (Keio:JW2428)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC9934^[5]
ΔamiA764::kan			PMID:16738554^[4]	CGSC:99990
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW2428	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCAGCACTTTTAAACCACTAAA Primer 2:CCTCGCTTTTTCGAATGTGCTTT
nupC510::Tn10	Linked marker	CAG18468 = CGSC7410^[5]	est. P1 cotransduction: 18% ^[7]
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 15% ^[7]
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11823
EchoBASE (EcoliWiki Page)	EchoBASE:EB1770
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2435
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C2969
EcoGene (EcoliWiki Page)	EcoGene:EG11823
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:AMIA
CGSC (EcoliWiki Page)	CGSC:18541
ASAP (EcoliWikiPage)	ASAP:ABE-0008032
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

Standard name	AmiA
Synonyms	N-acetylmuramoyl-l-alanine amidase I^[1], B2435^[2]^[1], YfeE^[2]^[1], AmiA^[2]^[1]
Product description	N-acetylmuramoyl-L-alanine amidase 1^[2]^[3]
EC number (for enzymes)	3.5.1.28^[1]
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Notes

Function

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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(s)	Evidence Code	with/from	Aspect	Notes	Status
	GO:0016787	hydrolase activity	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0007047	cell wall organization	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0961	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0008745	N-acetylmuramoyl-L-alanine amidase activity	GO_REF:0000002 GO_REF:0000003	IEA: Inferred from Electronic Annotation	InterPro:IPR002508 EC:3.5.1.28	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0009253	peptidoglycan catabolic process	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002508	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0030288	outer membrane-bounded periplasmic space				C	Seeded from Riley et al 2006 ^[1].	required fields missing
	GO:0009252	peptidoglycan biosynthetic process	PMID:11454209^[9]	IGI: Inferred from Genetic Interaction	EcoliWiki:amiB\|EcoliWiki:amiC	P	Seeded from EcoCyc 11.1^[3].	complete
	GO:0042597	periplasmic space	PMID:12787347^[10]	IDA: Inferred from Direct Assay		C		complete
	GO:0008745	N-acetylmuramoyl-L-alanine amidase activity	PMID:11454209^[9]	IDA: Inferred from Direct Assay		F		complete
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Interactions

Partner Type	Partner	Notes	References
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Notes

Localization

Compartment	Description	Evidence	Notes
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Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MSTFKPLKTL TSRRQVLKAG LAALTLSGMS QAIAKDELLK TSNGHSKPKA KKSGGKRVVV LDPGHGGIDT GAIGRNGSKE KHVVLAIAKN VRSILRNHGI DARLTRSGDT FIPLYDRVEI AHKHGADLFM SIHADGFTNP KAAGASVFAL SNRGASSAMA KYLSERENRA DEVAGKKATD KDHLLQQVLF DLVQTDTIKN SLTLGSHILK KIKPVHKLHS RNTEQAAFVV LKSPSVPSVL VETSFITNPE EERLLGTAAF RQKIATAIAE GVISYFHWFD NQKAHSKKR
Mol. Wt	31.41 kDa (calc) ^[2]
pI
Extinction coefficient	9970 (calc based on 3 Y, 1 W, and 0 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
motif	1-34	UniProt Manual:Signal Peptides	UniProt:P36548
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Structure

Structures	Representative homolog: 1JWQ\|A (Paenibacillus polymyxa) 2-108 of 289 residues (E-value: 1.0e-22) (Percent Identity: 40.37) View all other structures.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

Representative homolog:
1JWQ|A (Paenibacillus polymyxa)
2-108 of 289 residues (E-value: 1.0e-22) (Percent Identity: 40.37)
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Models

View models at:

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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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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:NACMURLALAAMI1-MONOMER
SwissModel (EcoliWiki Page)	SwissModel:P36548
UniProt (EcoliWiki Page)	UniProt:P36548
PFAM (EcoliWiki Page)	PFAM:PF01520
RefSeq (EcoliWiki Page)	RefSeq:NP_416930
ModBase (EcoliWiki Page)	ModBase:P36548
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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.

Transcription and Transcriptional Regulation

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Transcription unit(s)
amiA-hemF
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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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gbrowse_img.php?coord=2550354..2550394&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled&width=400&.png
This picture shows the sequence around the N-terminus.

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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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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Mutations Affecting Expression

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b2435 (EcoliWiki Page)	Summary of data for amiA from multiple microarray studies
microarray	GEO Profiles:b2435 (EcoliWiki Page)	NCBI GEO profiles for amiA
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (2550175..2550394) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:E1^[11]
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Notes

Accessions Related to amiA Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11823
EchoBASE (EcoliWiki Page)	EchoBASE:EB1770
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b2435
EcoGene (EcoliWiki Page)	EcoGene:EG11823
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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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Organism	Homologs (Statistics)	Comments
Shigella flexneri	AMIA	From SHIGELLACYC
E. coli O157	AMIA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF01520
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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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
↑ ^7.0 ^7.1 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).
↑ ^8.0 ^8.1 ^8.2 ^8.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^9.0 ^9.1 Heidrich C et al. (2001) Involvement of N-acetylmuramyl-L-alanine amidases in cell separation and antibiotic-induced autolysis of Escherichia coli. Mol Microbiol 41: 167-78 PubMed EcoliWiki page
↑ Bernhardt TG & de Boer PA (2003) The Escherichia coli amidase AmiC is a periplasmic septal ring component exported via the twin-arginine transport pathway. Mol Microbiol 48: 1171-82 PubMed EcoliWiki page
↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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Retrieved from "http://ecoliwiki.net/colipedia/index.php/amiA:On_One_Page"

amiA:On One Page

From EcoliWiki

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Expression

Overview

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to amiA Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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