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amiB:On One Page

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Gene Name	amiB (synonyms: ECK4165, b4169, JW4127, yjeD)^[1]
Product(s)	AmiB product^[1]: N-acetylmuramoyl-l-alanine amidase II product, B4169 product, YjeD product
Description	N-acetylmuramoyl-L-alanine amidase 2^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yjeFE-amiB-mutL-miaA-hfq-hflXKC^[2], ORF55-ORF17-amiB-mutL-miaA-hfq-hflXKC
Regulation/Activity
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Gene

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Nomenclature

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Standard name	amiB
Mnemonic
Synonyms	ECK4165, b4169, JW4127, yjeD^[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	94.71 minutes	MG1655: 4394088..4395425	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 4400745..4402082	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

94.71 minutes

MG1655: 4394088..4395425
gbrowse_img.php?coord=4393088..4396425&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 4400745..4402082
gbrowse_img.php?coord=4399745..4403082&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
ΔamiB (Keio:JW4127)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC10970^[5]
ΔamiB790::kan			PMID:16738554^[4]	CGSC:99992
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW4127	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCATGTATCGCATCAGAAATTG Primer 2:CCGTTTGGCAGCGTGCGATCTGG
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 21% ^[7] Synonyms:zjd-2231::Tn10
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[5]	est. P1 cotransduction: 28% ^[7]
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11363
EchoBASE (EcoliWiki Page)	EchoBASE:EB1338
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4169
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C5253
EcoGene (EcoliWiki Page)	EcoGene:EG11363
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:AMIB
CGSC (EcoliWiki Page)	CGSC:34432
ASAP (EcoliWikiPage)	ASAP:ABE-0013653
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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	AmiB product
Synonyms	N-acetylmuramoyl-l-alanine amidase II product^[1], B4169 product^[2]^[1], YjeD product^[2]^[1], AmiB product^[2]^[1]
Product description	N-acetylmuramoyl-L-alanine amidase 2^[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:0009253	peptidoglycan catabolic process	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002508	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: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: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:amiA:EcoliWiki:amiC	P	Seeded from EcoCyc 11.1^[3].	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 MMYRIRNWLV ATLLLLCTPV GAATLSDIQV SNGNQQARIT LSFIGDPDYA FSHQSKRTVA LDIKQTGVIQ GLPLLFSGNN LVKAIRSGTP KDAQTLRLVV DLTENGKTEA VKRQNGSNYT VVFTINADVP PPPPPPPVVA KRVETPAVVA PRVSEPARNP FKTESNRTTG VISSNTVTRP AARATANTGD KIIIAIDAGH GGQDPGAIGP GGTREKNVTI AIARKLRTLL NDDPMFKGVL TRDGDYFISV MGRSDVARKQ NANFLVSIHA DAAPNRSATG ASVWVLSNRR ANSEMASWLE QHEKQSELLG GAGDVLANSQ SDPYLSQAVL DLQFGHSQRV GYDVATSMIS QLQRIGEIHK RRPEHASLGV LRSPDIPSVL VETGFISNNS EERLLASDDY QQQLAEAIYK GLRNYFLAHP MQSAPQGATA QTASTVTTPD RTLPN
Mol. Wt	47.99 kDa (calc) ^[2]
pI	9.43^[2]
Extinction coefficient	29910 - 30035 (calc based on 9 Y, 3 W, and 1 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
motif	1-22	UniProt Manual:Signal Peptides	UniProt:P26365
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Structure

Structures	Representative homolog: 1JWQ\|A (Paenibacillus polymyxa) 3-111 of 445 residues (E-value: 3.2e-21) (Percent Identity: 33.33) 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)
3-111 of 445 residues (E-value: 3.2e-21) (Percent Identity: 33.33)
View all other structures.

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:NACMURLALAAMI2-MONOMER
SwissModel (EcoliWiki Page)	SwissModel:P26365
UniProt (EcoliWiki Page)	UniProt:P26365
PFAM (EcoliWiki Page)	PFAM:PF01520
RefSeq (EcoliWiki Page)	RefSeq:NP_418590
ModBase (EcoliWiki Page)	ModBase:P26365
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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)
yjeFE-amiB-mutL-miaA-hfq-hflXKC
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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=4394068..4394108&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

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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Mutations Affecting Expression

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b4169 (EcoliWiki Page)	Summary of data for amiB from multiple microarray studies
microarray	GEO Profiles:b4169 (EcoliWiki Page)	NCBI GEO profiles for amiB
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to amiB Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11363
EchoBASE (EcoliWiki Page)	EchoBASE:EB1338
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b4169
EcoGene (EcoliWiki Page)	EcoGene:EG11363
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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	AMIB	From SHIGELLACYC
E. coli O157	AMIB	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 ^2.7 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

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

amiB: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 amiB Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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