proC:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0381, b0386, JW0377, pro2, pro3, pro(3)''<ref name='LIB:Riley_2006'/>
''ECK0381, b0386, JW0377, pro2, pro3, pro(3)''<ref name='LIB:Riley_2006'/>, pro, Pro2''


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{|   id="R46a9aeced71da"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9aeced71da"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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W3110: 404868..404059<br /><gbrowseImage>
W3110: 404868..404059<br /><gbrowseImage>
name=AC_000091:404059..404868
name=NC_007779:404059..404868
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|403059|405868|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|403059|405868|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|404059|404868|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|404059|404868|FASTA Dump}}  
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{|   id="T46a9aecfc5a25"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9aecfc5a25"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="C46a9aed0427d8"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="C46a9aed0427d8"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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{|   id="L4e04c181c19dd"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L4e04c181c19dd"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=142 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=142 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:6A12|6A12]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=143 Genobase]
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PMID:3038334  
PMID:3038334  
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est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  
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[[:Category:Kohara_Phage:6A12|6A12]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=143 Genobase]
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PMID:3038334


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{|   id="U46a9aed232fbb"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9aed232fbb"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10769 EcoCyc:EG10769]
EcoCyc:EG10769
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0762 EchoBASE:EB0762]
EcoGene:EG10769
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0386 EcoliGenExpDB:b0386]
RegulonDB:ECK120000760
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C0493 ECOL199310CYC:C0493]
[http://www.ncbi.nlm.nih.gov/gene?term=945034 GeneID:945034]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10769 EcoGene:EG10769]
EchoBASE:EB0762
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=PROC ECOO157CYC:PROC]
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ASAP:ABE-0001338
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/362 CGSC:362]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001338&formSubmitReturn=1 ASAP:ABE-0001338]
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!|Name!!URL!!Comments
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Latest revision as of 20:28, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

proC

Mnemonic

Proline

Synonyms

ECK0381, b0386, JW0377, pro2, pro3, pro(3)[1], pro, Pro2

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Notes

Location(s) and DNA Sequence

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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

8.71 minutes 

MG1655: 404868..404059
<gbrowseImage> name=NC_000913:404059..404868 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 373290..372481
<gbrowseImage> name=NC_012967:372481..373290 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 306818..307627
<gbrowseImage> name=NC_012759:306818..307627 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 404868..404059
<gbrowseImage> name=NC_007779:404059..404868 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 344199..343390
<gbrowseImage> name=NC_010473:343390..344199 source=DH10B 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

Coding Start (SO:0000323)

MG1655

404059

Edman degradation

PMID:6089111[2]


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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

ΔproC (Keio:JW0377)

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

Shigen

CGSC8554[4]

proC14

Auxotrophies

Requires proline for growth

CGSC:4929

proC32

Auxotrophies

Requires proline for growth

CGSC:5085

proC47

Auxotrophies

Requires proline for growth

CGSC:5514

proC34

Auxotrophies

Requires proline for growth

CGSC:5702

proC24

Auxotrophies

Requires proline for growth

CGSC:5825

proC55

Auxotrophies

Requires proline for growth

CGSC:6485

proC83

Auxotrophies

Requires proline for growth

CGSC:10340

proC43

Auxotrophies

Requires proline for growth

CGSC:11027

proC29

Auxotrophies

Requires proline for growth

CGSC:11502

proC9999

Auxotrophies

Requires proline for growth

CGSC:39363

proC677(tetR)::Tn5-132

Auxotrophies

Requires proline for growth

CGSC:75247

proC471::Tn5

Auxotrophies

Requires proline for growth

CGSC:90706

ΔproC751::kan

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

CGSC:102470


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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

JW0377

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGAAAAGAAAATCGGTTTTAT

Primer 2:CCGGATTTGCTGAGTTTTTCTGA

1A10

Kohara Phage

Genobase

PMID:3038334[6]

6A12

Kohara Phage

Genobase

PMID:3038334[6]

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[4]

est. P1 cotransduction: 72% [7]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[4]

est. P1 cotransduction: 35% [7]

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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:EG10769

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10769

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000760

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945034

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0762

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001338

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Deutch, AH et al. (1984) Analysis of the Escherichia coli proBA locus by DNA and protein sequencing. Nucleic Acids Res. 12 6337-55 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 6.0 6.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  7. ↑ 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).

Categories

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