malF:Gene: Difference between revisions
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<noinclude>{{TabsTop}} | <noinclude>{{TabsTop}} | ||
{{Tab|Quickview|malF}}{{Tab On|Gene|malF}}{{Tab|Gene Product(s)|malF}}{{Tab|Expression|malF}}{{Tab|Evolution|malF}}{{Tab|On One Page|malF}}{{TabsBottom}} | {{Tab|Quickview|malF}}{{Tab On|Gene|malF}}{{Tab|Gene Product(s)|malF}}{{Tab|Expression|malF}}{{Tab|Evolution|malF}}{{Tab|On One Page|malF}}{{TabsBottom}} | ||
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|{{Sub}}[[#Nomenclature |Nomenclature]] | |{{Sub}}[[#Nomenclature |Nomenclature]] | ||
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]] | |{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]] | ||
|{{Sub}}[[#Sequence Features|Sequence Features]] | |||
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]] | |{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]] | ||
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]] | |||
|{{Sub}}[[#Genetic Resources |Genetic Resources]] | |{{Sub}}[[#Genetic Resources |Genetic Resources]] | ||
|{{Sub}}[[#Accessions in Other Databases |Accessions]] | |{{Sub}}[[#Accessions in Other Databases |Accessions]] | ||
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</noinclude><protect> | </noinclude><protect> | ||
==Nomenclature== | ==Nomenclature== | ||
<!--box uid=421aa90e079fa326b6494f812ad13e79.. | {{BacktoTop}} | ||
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{| id="Y46aa0543b0c08" class=" tableEdit Gene_nomenclature_table" | |||
|- | |- | ||
!{{table_heading_style}} |Standard name | !align=left {{table_heading_style}} |Standard name | ||
| | || | ||
''malF'' | ''malF'' | ||
|- | |||
!align=left {{table_heading_style}} |Mnemonic | |||
|| | |||
Maltose | |||
|- | |- | ||
!{{table_heading_style}} | | !align=left {{table_heading_style}} |Synonyms | ||
| | || | ||
''ECK4025, b4033, JW3993''<ref name='LIB:Riley_2006'/>, JW3993, malJ'' | |||
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|} | |} | ||
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===Notes=== | ===Notes=== | ||
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==Location(s) and DNA Sequence== | ==Location(s) and DNA Sequence== | ||
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<protect> | <protect> | ||
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="R46aa05443f453" class=" tableEdit Gene_location_table" | |||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links | !|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links | ||
|- | |- | ||
| | | | ||
MG1655 | MG1655 | ||
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91.42 minutes, 91.42 minutes | 91.42 minutes, 91.42 minutes | ||
| | | | ||
MG1655: 4243098..4241554<br /> | MG1655: 4243098..4241554<br /><gbrowseImage> | ||
name=NC_000913:4241554..4243098 | |||
source=MG1655 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | | | ||
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10555 EcoCyc] | *[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10555 EcoCyc] | ||
{{GBrowseLink|MG1655|NC_000913|4240554|4244098|GBrowse(MG1655)}} | |||
| | | | ||
{{GBrowseFastaLink|MG1655|NC_000913|4241554|4243098|FASTA Dump}} | |||
*[http://biocyc.org/ECOLI/sequence?object=EG10555 EcoCyc Sequence Dump] | *[http://biocyc.org/ECOLI/sequence?object=EG10555 EcoCyc Sequence Dump] | ||
|- | |- | ||
| | |||
[[REL606]] | |||
| | |||
| | |||
NC_012967: 4224007..4222463<br /><gbrowseImage> | |||
name=NC_012967:4222463..4224007 | |||
source=REL606 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | |||
{{GBrowseLink|REL606|NC_012967|4222463|4224007|GBrowse (REL606)}} | |||
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{{GBrowseFastaLink|REL606|NC_012967|4222463|4224007|FASTA Dump}} | |||
|- | |||
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[[BW2952]] | |||
| | |||
| | |||
NC_012759: 4180399..4181943<br /><gbrowseImage> | |||
name=NC_012759:4180399..4181943 | |||
source=BW2952 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | |||
{{GBrowseLink|BW2952|NC_012759|4180399|4181943|GBrowse (BW2952)}} | |||
| | |||
{{GBrowseFastaLink|BW2952|NC_012759|4180399|4181943|FASTA Dump}} | |||
|- | |||
| | | | ||
W3110 | W3110 | ||
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| | ||
| | | | ||
W3110: 4248665..4247121<br /> | W3110: 4248665..4247121<br /><gbrowseImage> | ||
name=NC_007779:4247121..4248665 | |||
source=W3110 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | | | ||
{{GBrowseLink|W3110|NC_007779|4246121|4249665|GBrowse(W3110)}} | |||
| | | | ||
{{GBrowseFastaLink|W3110|NC_007779|4247121|4248665|FASTA Dump}} | |||
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|[{{SERVER}} | | | ||
[[DH10B]] | |||
| | |||
| | |||
DH10B: 4342794..4341250<br /><gbrowseImage> | |||
name=NC_010473:4341250..4342794 | |||
source=DH10B | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | |||
{{GBrowseLink|DH10B|NC_010473|4338162|4345882|GBrowse(DH10B)}} | |||
| | |||
{{GBrowseFastaLink|DH10B|NC_010473|4338162|4345882|FASTA Dump}} | |||
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<!--Location_notes--></protect> | <!--Location_notes--></protect> | ||
===Notes=== | ===Notes=== | ||
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==Sequence Features== | ==Sequence Features== | ||
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|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!Feature | !|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes | ||
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<protect><!--Sequence_notes--></protect> | <protect><!--Sequence_notes--></protect> | ||
====Notes==== | ====Notes==== | ||
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==Alleles and Phenotypes== | ==Alleles and Phenotypes== | ||
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="D46aa0545516e9" class=" tableEdit Gene_allele_table dataTable" | |||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!! | !|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments | ||
|- | |- | ||
|[{{SERVER}} | | | ||
''malF(del)'' (Keio:JW3993) | |||
| | |||
deletion | |||
| | |||
deletion | |||
| | |||
| | |||
| | |||
PMID:16738554 | |||
| | |||
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] | |||
[http://cgsc2.biology.yale.edu/Strain.php?ID=109155 CGSC10874]<ref name='LIB:cgsc'/> | |||
| | |||
|- | |||
| | |||
malFP420A | |||
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P420A | |||
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No effect | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malFG380C,S | |||
| | |||
| | |||
G380C,S | |||
| | |||
| | |||
No growth on maltose | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malFE401A,C,K,L | |||
| | |||
| | |||
E401A,C,K,L | |||
| | |||
| | |||
Reduction of transport rate | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malFS403C,D,K,L | |||
| | |||
| | |||
S403C,D,K,L | |||
| | |||
| | |||
Reduction of transport rate | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malFG407A,P | |||
| | |||
| | |||
G407A,P | |||
| | |||
| | |||
No effect | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malFL334W | |||
| | |||
| | |||
L334W | |||
| | |||
| | |||
Ability to transport lactose in a saturable manner | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malFL372W | |||
| | |||
| | |||
L372W | |||
| | |||
| | |||
Growth on maltose but not on media containing either maltoheptaose or maltoheptaose plus maltose | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malFN376K,H | |||
| | |||
| | |||
N376K,H | |||
| | |||
| | |||
No growth on maltose | |||
| | |||
| | |||
| | |||
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916] | |||
|- | |||
| | |||
malF3089::Tn10 | |||
| | |||
Insertion at 4,242,342 bp in [[MG1655]] (NC_000913) | |||
| | |||
| | |||
| | |||
| | |||
adapted from Nichols ''et al.''<ref name ='LIB:Nichols_linked_Tn'/> | |||
| | |||
CAG12164 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40371 CGSC7476]<ref name='LIB:cgsc'/> | |||
| | |||
Synonyms: | |||
|- | |||
| | |||
''malF64''(Oc) | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
[[cgscmutation:7076|CGSC:7076]] | |||
| | |||
ochre (UAA) mutation | |||
|- | |||
| | |||
''malF55::Tn10'' | |||
| | |||
| | |||
| | |||
| | |||
| | |||
| | |||
[[cgscmutation:9952|CGSC:9952]] | |||
| | |||
|- | |||
| | |||
''malF59::Tn5'' | |||
| | |||
| | |||
| | |||
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| | |||
| | |||
[[cgscmutation:9960|CGSC:9960]] | |||
| | |||
|- | |||
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''malF3089::Tn10'' | |||
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| | |||
| | |||
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| | |||
PMID:2540407 | |||
| | |||
[[cgscmutation:40369|CGSC:40369]] | |||
| | |||
|- | |||
| | |||
''malF3180::Tn10kan'' | |||
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| | |||
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PMID:2540407 | |||
| | |||
[[cgscmutation:40372|CGSC:40372]] | |||
| | |||
|- | |||
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''malF729(del)::kan'' | |||
| | |||
| | |||
| | |||
| | |||
| | |||
PMID:16738554 | |||
| | |||
[[cgscmutation:101732|CGSC:101732]] | |||
| | |||
|- | |||
| | |||
''malF(del)'' | |||
| | |||
deletion | |||
| | |||
deletion | |||
| | |||
Resistant to | |||
| | |||
Thio(5)maltose increase resistance. | |||
| | |||
PMID:6998971 | |||
| | |||
| | |||
Selection for mutant maltose transport system | |||
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<protect><!--Alleles_notes--></protect> | <protect><!--Alleles_notes--></protect> | ||
===Notes=== | ===Notes=== | ||
==Genetic Interactions== | |||
{{BacktoTop}} | |||
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18625.C4e04bec5804ad--> | |||
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="C4e04bec5804ad" class=" tableEdit Genetic_interaction_table dataTable" | |||
|- {{table_heading_style}} | |||
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes | |||
|- class="tableEdit_footer" | |||
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<!-- Genetic Interacdtions Notes --> | |||
===Notes=== | |||
==Genetic Resources== | ==Genetic Resources== | ||
<!--box uid=421aa90e079fa326b6494f812ad13e79.. | {{BacktoTop}} | ||
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J46aa0546185ab" class=" tableEdit Gene_resource_table" | |||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!Resource!!Resource Type!!Source!!Notes/Reference | !|Resource!!Resource Type!!Source!!Notes/Reference | ||
|- | |- | ||
|[{{SERVER}} | | | ||
JW3993 | |||
| | |||
Plasmid clone | |||
| | |||
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen] | |||
| | |||
PMID:16769691 | |||
Status:Clone OK | |||
Primer 1:GCCGATGTCATTAAAAAGAAACA | |||
Primer 2:CCATCAAACTTCATTCGCGTGGC | |||
|- | |||
| | |||
[[:Category:Kohara_Phage:7A4|7A4]] | |||
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Kohara Phage | |||
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=633 Genobase] | |||
| | |||
PMID:3038334 | |||
|- | |||
| | |||
[[:Category:Kohara_Phage:1F8|1F8]] | |||
| | |||
Kohara Phage | |||
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=634 Genobase] | |||
| | |||
PMID:3038334 | |||
|- | |||
| | |||
[[thiC:Gene|thiC39::Tn10]] | |||
| | |||
Linked marker | |||
| | |||
CAG18500 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40361 CGSC7472]<ref name='LIB:cgsc'/> | |||
| | |||
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/> <br /> | |||
Synonyms:thi-39::Tn10 | |||
|- | |||
| | |||
[[yjcS:Gene|zje-2241::Tn10]] | |||
| | |||
Linked marker | |||
| | |||
CAG18427 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40603 CGSC7481]<ref name='LIB:cgsc'/> | |||
| | |||
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/> | |||
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===Notes=== | ===Notes=== | ||
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==Accessions in Other Databases== | ==Accessions in Other Databases== | ||
<!--box uid=421aa90e079fa326b6494f812ad13e79.. | {{BacktoTop}} | ||
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|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!Database!!Accession!!Notes | !|Database!!Accession!!Notes | ||
|- | |- | ||
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[[EcoCyc]] | |||
| | | | ||
EcoCyc:EG10555 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[EcoGene]] | |||
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EcoGene:EG10555 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[RegulonDB]] | |||
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RegulonDB:ECK120000548 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[http:// | [http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]]) | ||
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[http:// | [http://www.ncbi.nlm.nih.gov/gene?term=948532 GeneID:948532] | ||
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Escherichia coli str. K-12 substr. MG1655 | |||
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[[EchoBASE]] | |||
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EchoBASE:EB0550 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[ASAP]] | |||
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ASAP:ABE-0013195 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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==References== | ==References== | ||
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__NOTOC__ | __NOTOC__ | ||
===Categories=== | |||
[[Category:Gene List:MG1655]] | |||
[[Category:Gene List:W3110]] | |||
[[Category:Genes in the Keio knockout collection]] | |||
[[Category:Genes in the ASKA clone collection]] | |||
[[Category:mal genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]] | |||
[[Category:Gene_List:BW2952]] | |||
Latest revision as of 20:51, 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
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
malF |
|---|---|
| Mnemonic |
Maltose |
| Synonyms |
ECK4025, b4033, JW3993[1], JW3993, malJ |
| edit table |
Notes
Location(s) and DNA Sequence
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 |
91.42 minutes, 91.42 minutes |
MG1655: 4243098..4241554 |
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NC_012967: 4224007..4222463 |
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NC_012759: 4180399..4181943 |
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W3110 |
|
W3110: 4248665..4247121 |
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|
DH10B: 4342794..4341250 |
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| edit table |
Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
| edit table |
Notes
Alleles and Phenotypes
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 |
|---|---|---|---|---|---|---|---|
|
malF(del) (Keio:JW3993) |
deletion |
deletion |
|||||
|
malFP420A |
P420A |
No effect |
seeded from UniProt:P02916 | ||||
|
malFG380C,S |
G380C,S |
No growth on maltose |
seeded from UniProt:P02916 | ||||
|
malFE401A,C,K,L |
E401A,C,K,L |
Reduction of transport rate |
seeded from UniProt:P02916 | ||||
|
malFS403C,D,K,L |
S403C,D,K,L |
Reduction of transport rate |
seeded from UniProt:P02916 | ||||
|
malFG407A,P |
G407A,P |
No effect |
seeded from UniProt:P02916 | ||||
|
malFL334W |
L334W |
Ability to transport lactose in a saturable manner |
seeded from UniProt:P02916 | ||||
|
malFL372W |
L372W |
Growth on maltose but not on media containing either maltoheptaose or maltoheptaose plus maltose |
seeded from UniProt:P02916 | ||||
|
malFN376K,H |
N376K,H |
No growth on maltose |
seeded from UniProt:P02916 | ||||
|
malF3089::Tn10 |
Insertion at 4,242,342 bp in MG1655 (NC_000913) |
adapted from Nichols et al.[4] |
Synonyms: | ||||
|
malF64(Oc) |
ochre (UAA) mutation | ||||||
|
malF55::Tn10 |
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malF59::Tn5 |
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malF3089::Tn10 |
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malF3180::Tn10kan |
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malF729(del)::kan |
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|
malF(del) |
deletion |
deletion |
Resistant to |
Thio(5)maltose increase resistance. |
Selection for mutant maltose transport system | ||
| edit table |
Notes
Genetic Interactions
| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW3993 |
Plasmid clone |
Status:Clone OK Primer 1:GCCGATGTCATTAAAAAGAAACA Primer 2:CCATCAAACTTCATTCGCGTGGC | |
|
Kohara Phage |
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|
Kohara Phage |
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|
Linked marker |
est. P1 cotransduction: 12% [4] | ||
|
Linked marker |
est. P1 cotransduction: 3% [4] | ||
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
<protect>
References
See Help:References for how to manage references in EcoliWiki.
- ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 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
- ↑ 3.0 3.1 3.2 3.3 CGSC: The Coli Genetics Stock Center
- ↑ 4.0 4.1 4.2 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).
- ↑ 5.0 5.1 Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 PubMed
- ↑ Ferenci, T (1980) Methyl-alpha-maltoside and 5-thiomaltose: analogs transported by the Escherichia coli maltose transport system. J. Bacteriol. 144 7-11 PubMed
- ↑ 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
- ↑ 8.0 8.1 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