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m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "") |
m (Text replacement - "gene Genbank" to "gene RefSeq") |
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__TOC__ | |||
<protect> | <protect> | ||
<aureodatabase> | <aureodatabase>annotation</aureodatabase> | ||
=Summary= | =Summary= | ||
* <aureodatabase>organism</aureodatabase> | *<aureodatabase>organism</aureodatabase> | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>pan locus</aureodatabase> | *<aureodatabase>pan locus</aureodatabase> | ||
* <aureodatabase>gene symbol</aureodatabase> | *<aureodatabase>gene symbol</aureodatabase> | ||
* <aureodatabase>pan gene symbol</aureodatabase> | *<aureodatabase>pan gene symbol</aureodatabase> | ||
* <aureodatabase>gene synonyms</aureodatabase> | *<aureodatabase>gene synonyms</aureodatabase> | ||
* <aureodatabase>product</aureodatabase> | *<aureodatabase>product</aureodatabase> | ||
</protect> | </protect> | ||
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==General== | ==General== | ||
* <aureodatabase>gene type</aureodatabase> | *<aureodatabase>gene type</aureodatabase> | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>gene symbol</aureodatabase> | *<aureodatabase>gene symbol</aureodatabase> | ||
* <aureodatabase>product</aureodatabase> | *<aureodatabase>product</aureodatabase> | ||
* <aureodatabase>gene replicon</aureodatabase> | *<aureodatabase>gene replicon</aureodatabase> | ||
* <aureodatabase>strand</aureodatabase> | *<aureodatabase>strand</aureodatabase> | ||
* <aureodatabase>gene coordinates</aureodatabase> | *<aureodatabase>gene coordinates</aureodatabase> | ||
* <aureodatabase>gene length</aureodatabase> | *<aureodatabase>gene length</aureodatabase> | ||
* <aureodatabase>essential</aureodatabase> | *<aureodatabase>essential</aureodatabase> | ||
*<aureodatabase>gene comment</aureodatabase> | |||
</protect> | </protect> | ||
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==Accession numbers== | ==Accession numbers== | ||
* <aureodatabase>gene GI</aureodatabase> | *<aureodatabase>gene GI</aureodatabase> | ||
* <aureodatabase>gene | *<aureodatabase>gene RefSeq</aureodatabase> | ||
*<aureodatabase>gene BioCyc</aureodatabase> | |||
*<aureodatabase>gene MicrobesOnline</aureodatabase> | |||
</protect> | </protect> | ||
<protect> | <protect> | ||
==Phenotype== | ==Phenotype== | ||
</protect> | </protect> | ||
Share your knowledge and add information here. [<span class="plainlinks">[//aureowiki.med.uni-greifswald.de/index.php?title={{PAGENAMEE}}&veaction=edit§ion=6 edit]</span>] | |||
<protect> | <protect> | ||
==DNA sequence== | ==DNA sequence== | ||
* <aureodatabase>gene sequence</aureodatabase> | *<aureodatabase>gene sequence</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
<aureodatabase>RNA regulated operons</aureodatabase> | |||
</protect> | |||
<protect> | |||
=Protein= | =Protein= | ||
<aureodatabase>protein 3D view</aureodatabase> | <aureodatabase>protein 3D view</aureodatabase> | ||
==General== | ==General== | ||
* <aureodatabase>locus</aureodatabase> | *<aureodatabase>locus</aureodatabase> | ||
* <aureodatabase>protein symbol</aureodatabase> | *<aureodatabase>protein symbol</aureodatabase> | ||
* <aureodatabase>protein description</aureodatabase> | *<aureodatabase>protein description</aureodatabase> | ||
* <aureodatabase>protein length</aureodatabase> | *<aureodatabase>protein length</aureodatabase> | ||
* <aureodatabase>theoretical pI</aureodatabase> | *<aureodatabase>theoretical pI</aureodatabase> | ||
* <aureodatabase>theoretical MW</aureodatabase> | *<aureodatabase>theoretical MW</aureodatabase> | ||
* <aureodatabase>GRAVY</aureodatabase> | *<aureodatabase>GRAVY</aureodatabase> | ||
</protect> | </protect> | ||
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==Function== | ==Function== | ||
* <aureodatabase>protein reaction</aureodatabase> | *<aureodatabase>protein reaction</aureodatabase> | ||
* <aureodatabase>protein TIGRFAM</aureodatabase> | *<aureodatabase>protein TIGRFAM</aureodatabase> | ||
* <aureodatabase>protein TheSeed</aureodatabase> | *<aureodatabase>protein TheSeed</aureodatabase> | ||
* <aureodatabase>protein PFAM</aureodatabase> | *<aureodatabase>protein PFAM</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
==Structure, modifications & | ==Structure, modifications & cofactors== | ||
* <aureodatabase>protein domains</aureodatabase> | *<aureodatabase>protein domains</aureodatabase> | ||
* <aureodatabase>protein modifications</aureodatabase> | *<aureodatabase>protein modifications</aureodatabase> | ||
* <aureodatabase>protein cofactors</aureodatabase> | *<aureodatabase>protein cofactors</aureodatabase> | ||
* <aureodatabase>protein effectors</aureodatabase> | *<aureodatabase>protein effectors</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein regulated operons</aureodatabase> | ||
</protect> | </protect> | ||
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==Localization== | ==Localization== | ||
* <aureodatabase>protein Psortb</aureodatabase> | *<aureodatabase>protein Psortb</aureodatabase> | ||
* <aureodatabase>protein LocateP</aureodatabase> | *<aureodatabase>protein LocateP</aureodatabase> | ||
* <aureodatabase>protein SignalP</aureodatabase> | *<aureodatabase>protein SignalP</aureodatabase> | ||
* <aureodatabase>protein TMHMM</aureodatabase> | *<aureodatabase>protein TMHMM</aureodatabase> | ||
</protect> | </protect> | ||
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==Accession numbers== | ==Accession numbers== | ||
* <aureodatabase>protein GI</aureodatabase> | *<aureodatabase>protein GI</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein RefSeq</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein UniProt</aureodatabase> | ||
</protect> | </protect> | ||
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==Protein sequence== | ==Protein sequence== | ||
* <aureodatabase>protein sequence</aureodatabase> | *<aureodatabase>protein sequence</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
== | ==Experimental data== | ||
* <aureodatabase>protein validated peptides</aureodatabase> | *<aureodatabase>protein validated peptides</aureodatabase> | ||
*<aureodatabase>protein validated localization</aureodatabase> | |||
*<aureodatabase>protein validated quantitative data</aureodatabase> | |||
*<aureodatabase>protein partners</aureodatabase> | |||
</protect> | </protect> | ||
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==Operon== | ==Operon== | ||
* <aureodatabase>operons</aureodatabase> | *<aureodatabase>operons</aureodatabase> | ||
</protect> | </protect> | ||
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==Regulation== | ==Regulation== | ||
*<aureodatabase>regulators</aureodatabase> | |||
* <aureodatabase>regulators</aureodatabase> | |||
</protect> | </protect> | ||
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==Transcription pattern== | ==Transcription pattern== | ||
* <aureodatabase>expression browser</aureodatabase> | *<aureodatabase>expression browser</aureodatabase> | ||
</protect> | </protect> | ||
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==Protein synthesis (provided by Aureolib)== | ==Protein synthesis (provided by Aureolib)== | ||
* <aureodatabase>protein synthesis Aureolib</aureodatabase> | *<aureodatabase>protein synthesis Aureolib</aureodatabase> | ||
</protect> | </protect> | ||
<protect> | <protect> | ||
== | ==Protein stability== | ||
* <aureodatabase>protein half-life</aureodatabase> | *<aureodatabase>protein half-life</aureodatabase> | ||
</protect> | </protect> | ||
Latest revision as of 08:16, 11 March 2016
NCBI: 10-JUN-2013
⊟Summary[edit | edit source]
- organism: Staphylococcus aureus COL
- locus tag: SACOL1227 [new locus tag: SACOL_RS06285 ]
- pan locus tag?: SAUPAN003498000
- symbol: def2
- pan gene symbol?: def2
- synonym:
- product: peptide deformylase
⊟Genome View[edit | edit source]
⊟Gene[edit | edit source]
⊟General[edit | edit source]
- type: CDS
- locus tag: SACOL1227 [new locus tag: SACOL_RS06285 ]
- symbol: def2
- product: peptide deformylase
- replicon: chromosome
- strand: +
- coordinates: 1237405..1237893
- length: 489
- essential: unknown other strains
⊟Accession numbers[edit | edit source]
- Gene ID: 3237852 NCBI
- RefSeq: YP_186090 NCBI
- BioCyc: see SACOL_RS06285
- MicrobesOnline: 912695 MicrobesOnline
⊟Phenotype[edit | edit source]
Share your knowledge and add information here. [edit]
⊟DNA sequence[edit | edit source]
- 1
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481ATGGCGATTAAAAAGTTAGTACCAGCATCGCATCCTATTTTAACGAAAAAAGCGCAAGCA
GTTAAAACATTTGATGATTCGTTAAAAAGATTATTACAAGATTTAGAAGATACAATGTAT
GCACAAGAAGCTGCTGGCTTATGTGCACCTCAAATTAATCAGTCATTGCAAGTGGCAATT
ATTGATATGGAAATGGAAGGATTATTACAACTTGTTAATCCGAAAATTATTAGTCAATCA
AATGAAACAATAACAGACTTAGAAGGTTCAATTACATTGCCAGATGTTTACGGCGAAGTG
ACAAGAAGTAAAATGATAGTTGTCGAAAGTTATGACGTCAATGGGAACAAAGTTGAACTA
ACTGCACATGAAGATGTAGCAAGAATGATTTTGCATATTATAGATCAAATGAACGGTATC
CCTTTTACAGAACGTGCGGACCGTATTTTAACAGATAAAGAAGTGGAGGCATATTTTATA
AATGACTAA60
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⊟Protein[edit | edit source]
⊟General[edit | edit source]
- locus tag: SACOL1227 [new locus tag: SACOL_RS06285 ]
- symbol: Def2
- description: peptide deformylase
- length: 162
- theoretical pI: 4.36649
- theoretical MW: 18101.7
- GRAVY: -0.110494
⊟Function[edit | edit source]
- reaction: EC 3.5.1.31? ExPASyFormylmethionine deformylase N-formyl-L-methionine + H2O = formate + L-methionine
- TIGRFAM: Protein fate Protein modification and repair peptide deformylase (TIGR00079; EC 3.5.1.88; HMM-score: 105.4)
- TheSEED :
- Peptide deformylase (EC 3.5.1.88)
Carbohydrates Central carbohydrate metabolism Dehydrogenase complexes Peptide deformylase (EC 3.5.1.88)and 1 more - PFAM: no clan defined Pep_deformylase; Polypeptide deformylase (PF01327; HMM-score: 132)and 1 more4H_Cytokine (CL0053) CNTF; Ciliary neurotrophic factor (PF01110; HMM-score: 12.8)
⊟Structure, modifications & cofactors[edit | edit source]
- domains:
- modifications:
- cofactors:
- effectors:
⊟Localization[edit | edit source]
- PSORTb: Cytoplasmic
- Cytoplasmic Score: 7.5
- Cytoplasmic Membrane Score: 1.15
- Cellwall Score: 0.62
- Extracellular Score: 0.73
- Internal Helices: 0
- LocateP: Intracellular
- Prediction by SwissProt Classification: Cytoplasmic
- Pathway Prediction: No pathway
- Intracellular possibility: 1
- Signal peptide possibility: -1
- N-terminally Anchored Score: 1
- Predicted Cleavage Site: No CleavageSite
- SignalP: no predicted signal peptide
- SP(Sec/SPI): 0.009408
- TAT(Tat/SPI): 0.000392
- LIPO(Sec/SPII): 0.000424
- predicted transmembrane helices (TMHMM): 0
⊟Accession numbers[edit | edit source]
⊟Protein sequence[edit | edit source]
- MAIKKLVPASHPILTKKAQAVKTFDDSLKRLLQDLEDTMYAQEAAGLCAPQINQSLQVAIIDMEMEGLLQLVNPKIISQSNETITDLEGSITLPDVYGEVTRSKMIVVESYDVNGNKVELTAHEDVARMILHIIDQMNGIPFTERADRILTDKEVEAYFIND
⊟Experimental data[edit | edit source]
- experimentally validated: PeptideAtlas
- protein localization: Cytoplasmic [1] [2] [3]
- quantitative data / protein copy number per cell:
- interaction partners:
SACOL1760 (ackA) acetate kinase [4] (data from MRSA252) SACOL2657 (arcA) arginine deiminase [4] (data from MRSA252) SACOL0557 (cysK) cysteine synthase [4] (data from MRSA252) SACOL1016 (fabI) enoyl-ACP reductase [4] (data from MRSA252) SACOL1072 (folD) bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase [4] (data from MRSA252) SACOL0593 (fusA) elongation factor G [4] (data from MRSA252) SACOL1734 (gapA2) glyceraldehyde 3-phosphate dehydrogenase 2 [4] (data from MRSA252) SACOL1922 (hemL2) glutamate-1-semialdehyde aminotransferase [4] (data from MRSA252) SACOL1477 (ilvA1) threonine dehydratase [4] (data from MRSA252) SACOL0222 (ldh1) L-lactate dehydrogenase [4] (data from MRSA252) SACOL2092 (murAA) UDP-N-acetylglucosamine 1-carboxyvinyltransferase [4] (data from MRSA252) SACOL0793 (nrdF) ribonucleotide-diphosphate reductase subunit beta [4] (data from MRSA252) SACOL1102 (pdhA) pyruvate dehydrogenase complex E1 component subunit alpha [4] (data from MRSA252) SACOL1105 (pdhD) dihydrolipoamide dehydrogenase [4] (data from MRSA252) SACOL2128 (pdp) pyrimidine-nucleoside phosphorylase [4] (data from MRSA252) SACOL0204 (pflB) formate acetyltransferase [4] (data from MRSA252) SACOL1745 (pyk) pyruvate kinase [4] (data from MRSA252) SACOL0584 (rplA) 50S ribosomal protein L1 [4] (data from MRSA252) SACOL2232 (rplP) 50S ribosomal protein L16 [4] (data from MRSA252) SACOL1274 (rpsB) 30S ribosomal protein S2 [4] (data from MRSA252) SACOL2233 (rpsC) 30S ribosomal protein S3 [4] (data from MRSA252) SACOL2222 (rpsE) 30S ribosomal protein S5 [4] (data from MRSA252) SACOL2230 (rpsQ) 30S ribosomal protein S17 [4] (data from MRSA252) SACOL2057 (rsbU) sigma factor B regulator protein [4] (data from MRSA252) SACOL0594 (tuf) elongation factor Tu [4] (data from MRSA252) SACOL2104 (upp) uracil phosphoribosyltransferase [4] (data from MRSA252) SACOL0731 LysR family transcriptional regulator [4] (data from MRSA252) SACOL0834 hypothetical protein [4] (data from MRSA252) SACOL0944 NADH dehydrogenase [4] (data from MRSA252) SACOL1759 universal stress protein [4] (data from MRSA252) SACOL1793 hypothetical protein [4] (data from MRSA252) SACOL2293 NAD/NADP octopine/nopaline dehydrogenase [4] (data from MRSA252) SACOL2297 hypothetical protein [4] (data from MRSA252) SACOL2553 pyruvate oxidase [4] (data from MRSA252) SACOL2561 hydroxymethylglutaryl-CoA synthase [4] (data from MRSA252)
⊟Expression & Regulation[edit | edit source]
⊟Operon[edit | edit source]
⊟Regulation[edit | edit source]
- regulator:
⊟Transcription pattern[edit | edit source]
- S.aureus Expression Data Browser: data available for NCTC8325
⊟Protein synthesis (provided by Aureolib)[edit | edit source]
- Aureolib: no data available
⊟Protein stability[edit | edit source]
- half-life: no data available
⊟Biological Material[edit | edit source]
⊟Mutants[edit | edit source]
⊟Expression vector[edit | edit source]
⊟lacZ fusion[edit | edit source]
⊟GFP fusion[edit | edit source]
⊟two-hybrid system[edit | edit source]
⊟FLAG-tag construct[edit | edit source]
⊟Antibody[edit | edit source]
⊟Other Information[edit | edit source]
You are kindly invited to share additional interesting facts.
⊟Literature[edit | edit source]
⊟References[edit | edit source]
- ↑ Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
PLoS One: 2009, 4(12);e8176
[PubMed:19997597] [WorldCat.org] [DOI] (I e) - ↑ Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
J Proteome Res: 2011, 10(4);1657-66
[PubMed:21323324] [WorldCat.org] [DOI] (I p) - ↑ Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
The Staphylococcus aureus proteome.
Int J Med Microbiol: 2014, 304(2);110-20
[PubMed:24439828] [WorldCat.org] [DOI] (I p) - ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 4.13 4.14 4.15 4.16 4.17 4.18 4.19 4.20 4.21 4.22 4.23 4.24 4.25 4.26 4.27 4.28 4.29 4.30 4.31 4.32 4.33 4.34 Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.
J Proteome Res: 2011, 10(3);1139-50
[PubMed:21166474] [WorldCat.org] [DOI] (I p)