E. coli is indeed the coolest thing on the planet - Carl Zimmer

amiC:On One Page

From EcoliWiki

Jump to: navigation, search

Quickview

Gene

Gene Product(s)

Expression

Evolution

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

Gene Name	amiC (synonyms: ECK2813, b2817, JW5449, ygdN)^[1]
Product(s)	AmiC^[1]: N-acetylmuramoyl-L-alanine amidase, B2817, YgdN
Description	N-acetylmuramyl-L-alanine amidase^[2]^[3]
Knock-Out Phenotype	Septation defect^[4]. Increases the number of cells in chains
Regulation/Expression	transcription unit(s): amiC^[2]
Regulation/Activity
edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]

Gene

[back to top]

Nomenclature

[back to top]

Standard name	amiC
Mnemonic
Synonyms	ECK2813, b2817, JW5449, ygdN^[1]
edit table

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Notes

Location(s) and DNA Sequence

[back to top]

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	63.49 minutes	MG1655: 2947032..2945779	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 2947666..2946413	GBrowse(W3110)	FASTA Dump
edit table

Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

63.49 minutes

MG1655: 2947032..2945779
gbrowse_img.php?coord=2944779..2948032&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 2947666..2946413
gbrowse_img.php?coord=2945413..2948666&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

GBrowse(W3110)

FASTA Dump

edit table

See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

[back to top]

Feature type	Location	Description
edit table

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

[back to top]

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability
ΔamiC (Keio:JW5449)	deletion	deletion			PMID:16738554^[5]	Shigen CGSC11395^[6]
ΔamiC742::kan					PMID:16738554^[5]	CGSC:99994
∆amiC::Kan			Colony Morphology	20-30% of the population exists as chains of 3 to 6 unseparated cells.	PMID:11454209^[7]
edit table

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

[back to top]

Resource	Resource Type	Source	Notes/Reference
JW5449	Plasmid clone	Shigen	PMID:16769691^[8] Status:Clone OK Primer 1:GCCTCAGGATCCAACACTGCAAT Primer 2:CCTCCCCTTCTCGCCAGCGTCGC
fucP3072::Tn10	Linked marker	CAG12079 = CGSC7427^[6]	est. P1 cotransduction: 62% ^[9] Synonyms:fuc-3072::Tn10
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[6]	est. P1 cotransduction: 85% ^[9]
edit table

See Help:Gene_resources for help entering information into the Genetic Resources table.

Notes

Accessions in Other Databases

[back to top]

Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7458
EchoBASE (EcoliWiki Page)	EchoBASE:EB2895
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2817
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3411
EcoGene (EcoliWiki Page)	EcoGene:EG13086
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:Z4134
ASAP (EcoliWikiPage)	ASAP:ABE-0009238
edit table

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

Notes

Links

[back to top]

Name	URL	Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

Categories

Product(s)

[back to top]

Nomenclature

Standard name	AmiC
Synonyms	N-acetylmuramoyl-L-alanine amidase^[1], B2817^[2]^[1], YgdN^[2]^[1], AmiC^[2]^[1]
Product description	N-acetylmuramyl-L-alanine amidase^[2]^[3]
EC number (for enzymes)	3.5.1.28^[1]
edit table

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

Notes

Function

[back to top]

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 ^[10]	complete
	GO:0009253	peptidoglycan catabolic process	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002508	P	Seeded from EcoCyc 12.5 ^[10]	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 ^[10]	complete
	GO:0007047	cell wall organization	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0961	P	Seeded from EcoCyc 12.5 ^[10]	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^[7]	IGI: Inferred from Genetic Interaction	EcoliWiki:amiA\|EcoliWiki:amiB	P	Seeded from EcoCyc 11.1^[3].	complete
	GO:0042493	response to drug				P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0000910	cytokinesis				P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0042597	periplasmic space	PMID:12787347^[11]	IDA: Inferred from Direct Assay		C		complete
	GO:0008745	N-acetylmuramoyl-L-alanine amidase activity	PMID:11454209^[7]	IDA: Inferred from Direct Assay		F		complete
edit table

Interactions

Partner Type	Partner	Notes	References
edit table

See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Notes

Localization

Compartment	Description	Evidence	Notes
periplasm
edit table

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Notes

Structure and Physical Properties

[back to top]

Physical Properties

Sequence	at EcoCyc MTDYASFAKV SGQISRLLVT QLRFLLLGRG MSGSNTAISR RRLLQGAGAM WLLSVSQVSL AAVSQVVAVR VWPASSYTRV TVESNRQLKY KQFALSNPER VVVDIEDVNL NSVLKGMAAQ IRADDPFIKS ARVGQFDPQT VRMVFELKQN VKPQLFALAP VAGFKERLVM DLYPANAQDM QDPLLALLED YNKGDLEKQV PPAQSGPQPG KAGRDRPIVI MLDPGHGGED SGAVGKYKTR EKDVVLQIAR RLRSLIEKEG NMKVYMTRNE DIFIPLQVRV AKAQKQRADL FVSIHADAFT SRQPSGSSVF ALSTKGATST AAKYLAQTQN ASDLIGGVSK SGDRYVDHTM FDMVQSLTIA DSLKFGKAVL NKLGKINKLH KNQVEQAGFA VLKAPDIPSI LVETAFISNV EEERKLKTAT FQQEVAESIL AGIKAYFADG ATLARRG
Mol. Wt	45.63 kDa (calc) ^[2]
pI
Extinction coefficient	25900 (calc based on 10 Y, 2 W, and 0 C residues)
edit table

See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
motif	1-31	UniProt Manual:Signal Peptides	UniProt:P63883
edit table

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

Structure

Structures	Representative homolog: 1JWQ\|A (Paenibacillus polymyxa) 3-120 of 447 residues (E-value: 6.3e-22) (Percent Identity: 33.90) View all other structures.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
edit table

Structures

Representative homolog:
1JWQ|A (Paenibacillus polymyxa)
3-120 of 447 residues (E-value: 6.3e-22) (Percent Identity: 33.90)
View all other structures.

Models

View models at:

edit table

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

Notes

Gene Product Resources

[back to top]

Resource type	Source	Notes/Reference
edit table

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

Notes

Accessions in Other Databases

[back to top]

Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7458-MONOMER
SwissModel (EcoliWiki Page)	SwissModel:P63883
UniProt (EcoliWiki Page)	UniProt:P63883
PFAM (EcoliWiki Page)	PFAM:PF01520
RefSeq (EcoliWiki Page)	RefSeq:NP_417294
ModBase (EcoliWiki Page)	ModBase:P63883
edit table

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

Notes

Links

[back to top]

Name	URL	Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

Categories

[back to top]

Expression

[back to top]

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

[back to top]

Transcription unit(s)
amiC
edit table

Figure courtesy of RegulonDB

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

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

[back to top]

gbrowse_img.php?coord=2947012..2947052&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled+flip&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

[back to top]

Mutations Affecting Expression

Allele Name	Mutation	Phenotype	Reference
edit table

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

Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b2817 (EcoliWiki Page)	Summary of data for amiC from multiple microarray studies
microarray	GEO Profiles:b2817 (EcoliWiki Page)	NCBI GEO profiles for amiC
edit table

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

Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (2947024..2947324) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:D1^[12]
edit table

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

Notes

Accessions Related to amiC Expression

[back to top]

Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7458
EchoBASE (EcoliWiki Page)	EchoBASE:EB2895
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b2817
EcoGene (EcoliWiki Page)	EcoGene:EG13086
edit table

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

Notes

Links

[back to top]

Name	URL	Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

Categories

[back to top]

Evolution

[back to top]

Homologs in Other Organisms

[back to top]

Organism	Homologs (Statistics)	Comments
Xenopus tropicalis	ENSXETP00000026055 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	S3025	From SHIGELLACYC
E. coli O157	Z4134	From ECOO157CYC
edit table

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

Do-It-Yourself Web Tools

Notes

Families

[back to top]

Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF01520
edit table

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

Notes

Links

[back to top]

Name	URL	Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

References

[back to top]

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 ^3.3 ^3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Priyadarshini R et al. (2006) Daughter cell separation by penicillin-binding proteins and peptidoglycan amidases in Escherichia coli. J Bacteriol 188: 5345-55 PubMed EcoliWiki page
↑ ^5.0 ^5.1 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
↑ ^6.0 ^6.1 ^6.2 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 ^7.2 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
↑ 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
↑ ^9.0 ^9.1 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).
↑ ^10.0 ^10.1 ^10.2 ^10.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ 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

Categories

[back to top]

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

amiC: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 amiC Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Views

Personal tools

Navigation

Search

Toolbox