ybjX:Gene Product(s): Difference between revisions
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!align=left {{table heading style}} |Synonyms | !align=left {{table heading style}} |Synonyms | ||
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conserved protein<ref name='LIB:Riley_2006'/>, B0877<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbjX<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> | ''conserved protein<ref name='LIB:Riley_2006'/>, B0877<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbjX<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0868, JW0861, b0877'' | ||
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!align=left {{table heading style}} |Product description | !align=left {{table heading style}} |Product description | ||
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****************************************************************************************** -->{{Product_GO_help}} | ****************************************************************************************** -->{{Product_GO_help}} | ||
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!|Qualifier!!GO ID!!GO term name!!Reference | !|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status | ||
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****************************************************************************************** -->{{Product_interactions_help}} | ****************************************************************************************** -->{{Product_interactions_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="S46aa48a9e9da0" class=" tableEdit Product_interactions_table dataTable" | ||
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!|Partner Type!!Partner!!Notes!!References!!Evidence | !|Partner Type!!Partner!!Notes!!References!!Evidence | ||
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Protein | Protein | ||
| | | | ||
rpmC | |||
| | | | ||
| Line 646: | Line 646: | ||
Protein | Protein | ||
| | | | ||
rpmG | |||
| | | | ||
| Line 657: | Line 657: | ||
Protein | Protein | ||
| | | | ||
rpmB | |||
| | | | ||
| Line 668: | Line 668: | ||
Protein | Protein | ||
| | | | ||
rpsA | |||
| | | | ||
| Line 679: | Line 679: | ||
Protein | Protein | ||
| | | | ||
rplJ | |||
| | | | ||
| Line 690: | Line 690: | ||
Protein | Protein | ||
| | | | ||
rplT | |||
| | | | ||
| Line 701: | Line 701: | ||
Protein | Protein | ||
| | | | ||
rplO | |||
| | | | ||
| Line 712: | Line 712: | ||
Protein | Protein | ||
| | | | ||
rplE | |||
| | | | ||
| Line 723: | Line 723: | ||
Protein | Protein | ||
| | | | ||
rfaD | |||
| | | | ||
| Line 729: | Line 729: | ||
PMID:19402753 | PMID:19402753 | ||
| | | | ||
MALDI(Z-score):38.502110 | |||
|- | |- | ||
| | | | ||
Protein | Protein | ||
| | | | ||
rplU | |||
| | | | ||
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Protein | Protein | ||
| | | | ||
tufB | |||
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PMID:19402753 | PMID:19402753 | ||
| | | | ||
MALDI(Z-score):20.676555 | |||
|- | |- | ||
| | | | ||
Protein | Protein | ||
| | | | ||
rplI | |||
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Protein | Protein | ||
| | | | ||
rplF | |||
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Protein | Protein | ||
| | | | ||
rplQ | |||
| | | | ||
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Protein | Protein | ||
| | | | ||
rpsF | |||
| | | | ||
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Protein | Protein | ||
| | | | ||
hupB | |||
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Protein | Protein | ||
| | | | ||
rplS | |||
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Protein | Protein | ||
| | | | ||
rplM | |||
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Protein | Protein | ||
| | | | ||
hupA | |||
| | | | ||
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Protein | Protein | ||
| | | | ||
rpsD | |||
| | | | ||
| Line 855: | Line 855: | ||
Protein | Protein | ||
| | | | ||
rpsM | |||
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Protein | Protein | ||
| | | | ||
rplX | |||
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| Line 877: | Line 877: | ||
Protein | Protein | ||
| | | | ||
rpsC | |||
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Protein | Protein | ||
| | | | ||
rplA | |||
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Protein | Protein | ||
| | | | ||
rplB | |||
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Protein | Protein | ||
| | | | ||
srmB | |||
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PMID:19402753 | PMID:19402753 | ||
| | | | ||
MALDI(Z-score):24.880466 | |||
|- | |||
| | |||
Protein | |||
| | |||
dnaJ | |||
| | |||
| | |||
PMID:19402753 | |||
| | |||
LCMS(ID Probability):99.6 | |||
|- | |||
| | |||
Protein | |||
| | |||
rplD | |||
| | |||
| | |||
PMID:19402753 | |||
| | |||
LCMS(ID Probability):99.6 MALDI(Z-score):18.911757 | |||
|- | |||
| | |||
Protein | |||
| | |||
yfiF | |||
| | |||
| | |||
PMID:19402753 | |||
| | |||
LCMS(ID Probability):97.8 MALDI(Z-score):7.664643 | |||
|- | |||
| | |||
Protein | |||
| | |||
rnr | |||
| | |||
| | |||
PMID:19402753 | |||
| | |||
MALDI(Z-score):26.041938 | |||
|- | |||
| | |||
Protein | |||
| | |||
rplL | |||
| | |||
| | |||
PMID:19402753 | |||
| | |||
LCMS(ID Probability):99.6 | |||
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{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="O46a7da6eee7ac" class=" tableEdit Product_localization_table" | ||
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!|Compartment!!Description!!Evidence!!Source!!Notes | !|Compartment!!Description!!Evidence!!Reference/Source!!Notes | ||
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!align=left {{table heading style}} |Name | |||
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****************************************************************************************** -->{{Product_domains_motifs_help}} | ****************************************************************************************** -->{{Product_domains_motifs_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="W46aa48ac15a38" class=" tableEdit Product_motif_table dataTable" | ||
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!|Type!!Residues!!Description!!Notes!!References | !|Type!!Residues!!Description!!Notes!!References | ||
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View models at: | View models at: | ||
* [http:// | * [http://www.proteinmodelportal.org/query/uniprot/P75829 Protein Model Portal] | ||
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P75829 PSI-PRED (P75829)] | |||
* [http://bioinf.cs.ucl.ac.uk/ | * [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P75829 Genomes TO Protein (P75829)] (GTOP) | ||
* [http://spock.genes.nig.ac.jp/~genome/ | |||
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!|Resource type!!Source!!Notes/Reference | !|Resource type!!Source!!Notes/Reference | ||
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{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Z46aa48ad0712c" class=" tableEdit Gene_accessions_table" | ||
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!|Database!!Accession!!Notes | !|Database!!Accession!!Notes | ||
|- | |- | ||
| | | | ||
[http:// | [http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]]) | ||
| | | | ||
[http:// | [http://www.ncbi.nlm.nih.gov/protein/16128845 GI:16128845] | ||
| | | | ||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |||
| | |||
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]]) | |||
| | |||
[http://www.ncbi.nlm.nih.gov/protein/NP_415398.1 GeneID:946025] | |||
| | |||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |||
| | |||
[[ASAP]] | |||
| | |||
ASAP:ABE-0002982 | |||
| | |||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |||
| | |||
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]]) | |||
| | |||
[http://www.uniprot.org/uniprot/P75829 UniProtKB/Swiss-Prot:P75829] | |||
| | |||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |||
| | |||
[[EcoCyc]] | |||
| | |||
EcoCyc:G6460 | |||
| | |||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |||
| | |||
[[EcoGene]] | |||
| | |||
EcoGene:EG13693 | |||
| | |||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |- | ||
| | | | ||
[http:// | [http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]]) | ||
| | | | ||
[http://www. | [http://www.ncbi.nlm.nih.gov/gene?term=946025 GeneID:946025] | ||
| | | | ||
Escherichia coli str. K-12 substr. MG1655 | |||
|- | |- | ||
| | | | ||
[[RegulonDB]] | |||
| | | | ||
RegulonDB:ECK120003060 | |||
| | | | ||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
|- | |- | ||
| | | | ||
[[EchoBASE]] | |||
| | | | ||
EchoBASE:EB3457 | |||
| | | | ||
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="G46a7da738b608" class=" tableEdit Links_table" | ||
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!|Name!!URL!!Comments | !|Name!!URL!!Comments | ||
Latest revision as of 20:31, 17 February 2015
{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>
| Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
| Nomenclature | Function | Interactions | Localization | Sequence | Domains | Structure | Resources | Accessions | Links | References | Suggestions |
Nomenclature
See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.
| Standard name |
YbjX |
|---|---|
| Synonyms |
conserved protein[1], B0877[2][1], YbjX[2][1] , ECK0868, JW0861, b0877 |
| Product description |
Function unknown, homologous to somA (S.t.) and virK (S.f.)[4] |
| EC number (for enzymes) |
|
| edit table |
Notes
Function
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:0006974 |
response to DNA damage stimulus |
IEP: Inferred from Expression Pattern |
P |
complete | ||||
| edit table |
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 |
|---|---|---|---|---|
|
Protein |
lpdA |
Experiment(s):EBI-879208 | ||
|
Protein |
pssA |
Experiment(s):EBI-879208 | ||
|
Protein |
rplA |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rplB |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rplC |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rplD |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rplE |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rplF |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rplM |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rplV |
Experiment(s):EBI-879208 | ||
|
Protein |
rpoC |
Experiment(s):EBI-879208 | ||
|
Protein |
rpsA |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rpsB |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rpsC |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rpsD |
Experiment(s):EBI-879208 | ||
|
Protein |
rpsG |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
srmB |
Experiment(s):EBI-879208 | ||
|
Protein |
tufA |
Experiment(s):EBI-879208, EBI-882921 | ||
|
Protein |
rnr |
Experiment(s):EBI-879208 | ||
|
Protein |
rluB |
Experiment(s):EBI-879208 | ||
|
Protein |
rplX |
Experiment(s):EBI-882921 | ||
|
Protein |
rpmB |
Experiment(s):EBI-882921 | ||
|
Protein |
rpmC |
Experiment(s):EBI-882921 | ||
|
Protein |
rpmG |
Experiment(s):EBI-882921 | ||
|
Protein |
rpsE |
Experiment(s):EBI-882921 | ||
|
Protein |
rpsF |
Experiment(s):EBI-882921 | ||
|
Protein |
rpsM |
Experiment(s):EBI-882921 | ||
|
Protein |
rpsS |
Experiment(s):EBI-882921 | ||
|
Protein |
rpsT |
Experiment(s):EBI-882921 | ||
|
Protein |
aceF |
Experiment(s):EBI-882921 | ||
|
Protein |
dnaJ |
Experiment(s):EBI-882921 | ||
|
Protein |
hupA |
Experiment(s):EBI-882921 | ||
|
Protein |
hupB |
Experiment(s):EBI-882921 | ||
|
Protein |
rplI |
Experiment(s):EBI-882921 | ||
|
Protein |
rplJ |
Experiment(s):EBI-882921 | ||
|
Protein |
rplL |
Experiment(s):EBI-882921 | ||
|
Protein |
rplO |
Experiment(s):EBI-882921 | ||
|
Protein |
rplQ |
Experiment(s):EBI-882921 | ||
|
Protein |
rplS |
Experiment(s):EBI-882921 | ||
|
Protein |
rplT |
Experiment(s):EBI-882921 | ||
|
Protein |
rplU |
Experiment(s):EBI-882921 | ||
|
Protein |
perM |
Experiment(s):EBI-1138231 | ||
|
Protein |
yciH |
Experiment(s):EBI-1138231 | ||
|
Protein |
rplB |
Experiment(s):EBI-1138231 | ||
|
Protein |
appY |
Experiment(s):EBI-1138231 | ||
|
Protein |
groL |
Experiment(s):EBI-1138231 | ||
|
Protein |
mutH |
Experiment(s):EBI-1138231 | ||
|
Protein |
rpmC |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpmG |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpmB |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsA |
LCMS(ID Probability):99.6 MALDI(Z-score):21.224236 | ||
|
Protein |
rplJ |
LCMS(ID Probability):99.4 MALDI(Z-score):3.385515 | ||
|
Protein |
rplT |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplO |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplE |
LCMS(ID Probability):99.6 MALDI(Z-score):27.323521 | ||
|
Protein |
rfaD |
MALDI(Z-score):38.502110 | ||
|
Protein |
rplU |
LCMS(ID Probability):99.6 | ||
|
Protein |
tufB |
MALDI(Z-score):20.676555 | ||
|
Protein |
rplI |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplF |
LCMS(ID Probability):99.6 MALDI(Z-score):29.180248 | ||
|
Protein |
rplQ |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsF |
LCMS(ID Probability):99.6 | ||
|
Protein |
hupB |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplS |
LCMS(ID Probability):99.6 MALDI(Z-score):2.654204 | ||
|
Protein |
rplM |
LCMS(ID Probability):99.6 MALDI(Z-score):32.496120 | ||
|
Protein |
hupA |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsD |
LCMS(ID Probability):97.9 MALDI(Z-score):34.058088 | ||
|
Protein |
rpsM |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplX |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsC |
LCMS(ID Probability):99.6 MALDI(Z-score):26.378458 | ||
|
Protein |
rplA |
LCMS(ID Probability):99.6 MALDI(Z-score):23.679102 | ||
|
Protein |
rplB |
LCMS(ID Probability):99.6 MALDI(Z-score):37.287562 | ||
|
Protein |
srmB |
MALDI(Z-score):24.880466 | ||
|
Protein |
dnaJ |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplD |
LCMS(ID Probability):99.6 MALDI(Z-score):18.911757 | ||
|
Protein |
yfiF |
LCMS(ID Probability):97.8 MALDI(Z-score):7.664643 | ||
|
Protein |
rnr |
MALDI(Z-score):26.041938 | ||
|
Protein |
rplL |
LCMS(ID Probability):99.6 | ||
| edit table |
Notes
Localization
See Help:Product_localization for how to add or edit information in this section of EcoliWiki.
| Compartment | Description | Evidence | Reference/Source | Notes |
|---|---|---|---|---|
| edit table |
Notes
Structure and Physical Properties
Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MVKSTPCITI DFMNMSQLTE RTFTPSESLS SLSLFLSLAR GQCRPGKFWH RRSFRQKFLL RSLIMPRLSV EWMNELSHWP NLNVLLTRQP RLPVRLHRPY LAANLSRKQL LEALRYHYAL LRECMSAEEF SLYLNTPGLQ LAKLEGKNGE QFTLELTMMI SMDKEGDSTI LFRNSEGIPL AEITFTLCEY QGKRTMFIGG LQGAKWEIPH QEIQNATKAC HGLFPKRLVM EAACLFAQRL QVEQIIAVSN ETHIYRSLRY RDKEGKIHAD YNAFWESVGG VCDAERHYRL PAQIARKEIA EIASKKRAEY RRRYEMLDAI QPQMATMFRG |
| Length |
330 |
| Mol. Wt |
38.358 kDa |
| pI |
9.7 (calculated) |
| Extinction coefficient |
43,890 - 44,765 (calc based on 11 Y, 5 W, and 7 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
|
Structure figures
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
| Resource type | Source | Notes/Reference |
|---|---|---|
| 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 | ||
|
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 |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 1.2 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
- ↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
- ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 6.14 6.15 6.16 6.17 6.18 6.19 6.20 6.21 6.22 6.23 6.24 6.25 6.26 6.27 6.28 6.29 6.30 6.31 6.32 6.33 6.34 6.35 6.36 6.37 6.38 6.39 6.40 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
- ↑ 7.0 7.1 7.2 7.3 7.4 7.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
- ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 8.29 8.30 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
- ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
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