chiA:On One Page

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

Quickview

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Standard Name

chiA

Gene Synonym(s)

ECK3325, b3338, JW3300, yheB, yheB'[1][2]

Product Desc.

endochitinase[2][3]

Periplasmic endochitinase/lysozyme, Hns-repressible[4]

Product Synonyms(s)

periplasmic endochitinase[1], B3338[2][1], ChiA[2][1], YheB[2][1] , ECK3325, JW3300, yheB, b3338

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): chiA[2]

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

chiA

Mnemonic

Chitin

Synonyms

ECK3325, b3338, JW3300, yheB, yheB'[1][2]

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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

74.69 minutes, 74.69 minutes 

MG1655: 3467875..3465182
<gbrowseImage> name=NC_000913:3465182..3467875 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3397758..3395065
<gbrowseImage> name=NC_012967:3395065..3397758 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3352339..3355032
<gbrowseImage> name=NC_012759:3352339..3355032 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4170563..4173256
<gbrowseImage> name=NC_007779:4170563..4173256 source=W3110 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

Strain DH10B

W362STOP

Nonsense mutation

PMID:18245285

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔchiA (Keio:JW3300)

deletion

deletion

PMID:16738554

Shigen
CGSC10468[5]

ΔchiA748::kan

PMID:16738554

CGSC:100308


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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

JW3300

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAATTAAATATATTTACTAA

Primer 2:CCTTGCTTAGTAAACGGCGCGAA

3F8

Kohara Phage

Genobase

PMID:3038334

9H3

Kohara Phage

Genobase

PMID:3038334

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 22% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 21% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

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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:EG11237

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11237

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001215

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947837

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1219

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010909

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

ChiA

Synonyms

periplasmic endochitinase[1], B3338[2][1], ChiA[2][1], YheB[2][1] , ECK3325, JW3300, yheB, b3338

Product description

endochitinase[2][3]

Periplasmic endochitinase/lysozyme, Hns-repressible[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:0030288

outer membrane-bounded periplasmic space

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000272

polysaccharide catabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0624

P

Seeded from EcoCyc (v14.0)

complete

GO:0003796

lysozyme activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.2.1.17

F

Seeded from EcoCyc (v14.0)

complete

GO:0005576

extracellular region

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003610

C

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003610

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0119

P

Seeded from EcoCyc (v14.0)

complete

GO:0006032

chitin catabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0146

P

Seeded from EcoCyc (v14.0)

complete

GO:0008061

chitin binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0147

F

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc (v14.0)

complete

GO:0030246

carbohydrate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003610

F

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

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

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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

Periplasm

PMID:10760150

EchoLocation:chiA


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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

MKLNIFTKSM IGMGLVCSAL PALAMEAWNN QQGGNKYQVI FDGKIYENAW WVSSTNCPGK
AKANDATNPW RLKRTATAAE ISQFGNTLSC EKSGSSSSSN SNTPASNTPA NGGSATPAQG
TVPSNSSVVA WNKQQGGQTW YVVFNGAVYK NAWWVASSNC PGDAKSNDAS NPWRYVRAAT
ATEISETSNP QSCTSAPQPS PDVKPAPDVK PAPDVQPAPA DKSNDNYAVV AWKGQEGSST
WYVIYNGGIY KNAWWVGAAN CPGDAKENDA SNPWRYVRAA TATEISQYGN PGSCSVKPDN
NGGAVTPVDP TPETPVTPTP DNSEPSTPAD SVNDYSLQAW SGQEGSEIYH VIFNGNVYKN
AWWVGSKDCP RGTSAENSNN PWRLERTATA AELSQYGNPT TCEIDNGGVI VADGFQASKA
YSADSIVDYN DAHYKTSVDQ DAWGFVPGGD NPWKKYEPAK AWSASTVYVK GDRVVVDGQA
YEALFWTQSD NPALVANQNA TGSNSRPWKP LGKAQSYSNE ELNNAPQFNP ETLYASDTLI
RFNGVNYISQ SKVQKVSPSD SNPWRVFVDW TGTKERVGTP KKAWPKHVYA PYVDFTLNTI
PDLAALAKNH NVNHFTLAFV VSKDANTCLP TWGTAYGMQN YAQYSKIKAL REAGGDVMLS
IGGANNAPLA ASCKNVDDLM QHYYDIVDNL NLKVLDFDIE GTWVADQASI ERRNLAVKKV
QDKWKSEGKD IAIWYTLPIL PTGLTPEGMN VLSDAKAKGV ELAGVNVMTM DYGNAICQSA
NTEGQNIHGK CATSAIANLH SQLKGLHPNK SDAEIDAMMG TTPMVGVNDV QGEVFYLSDA
RLVMQDAQKR NLGMVGIWSI ARDLPGGTNL SPEFHGLTKE QAPKYAFSEI FAPFTKQ
Length

897

Mol. Wt

97.056 kDa

pI

5.5 (calculated)

Extinction coefficient

222,650 - 224,275 (calc based on 35 Y, 31 W, and 13 C residues)


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

motif

1-24

UniProt Manual:Signal Peptides

UniProt:P13656

Domain

459..508

PF02839 Carbohydrate binding domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=chiA 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:16131217

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947837

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010909

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P13656

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11237

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11237

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947837

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001215

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1219

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 MG1655

97

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

30

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

60

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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)

chiA

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_000913:3467855..3467895 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


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

Type Reference Notes

microarray

GEO Profiles:b3338 (EcoliWiki Page)

NCBI GEO profiles for chiA

microarray

GenExpDB:b3338 (EcoliWiki Page)

Summary of data for chiA from multiple microarray studies


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 (3467405..3467835) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:D3[7]

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Notes

Accessions Related to chiA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11237

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1219

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3338

EcoGene

EcoGene:EG11237

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001215

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010909

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Dictyostelium discoideum

  • DDB0189769 (score: 1.000; bootstrap: 100%)
  • DDB0204402 (score: 0.241)

From Inparanoid:20070104


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)

PF02839 Carbohydrate binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:51055

Superfamily (EcoliWiki Page)

SUPERFAMILY:51445

EcoCyc

EcoCyc:EG11237

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11237

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001215

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1219

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010909

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. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 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. 3.0 3.1 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 CGSC: The Coli Genetics Stock Center
  6. 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).
  7. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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