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m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "") |
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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> | ||
| Line 24: | Line 25: | ||
==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> | ||
| Line 38: | Line 40: | ||
==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> | ||
| Line 71: | Line 78: | ||
==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> | ||
| Line 90: | Line 97: | ||
==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> | ||
| Line 99: | Line 106: | ||
==Accession numbers== | ==Accession numbers== | ||
* <aureodatabase>protein GI</aureodatabase> | *<aureodatabase>protein GI</aureodatabase> | ||
* <aureodatabase>protein UniProt</aureodatabase> | *<aureodatabase>protein RefSeq</aureodatabase> | ||
* <aureodatabase>protein | *<aureodatabase>protein UniProt</aureodatabase> | ||
*<aureodatabase>protein STRING</aureodatabase> | |||
</protect> | </protect> | ||
| Line 107: | Line 115: | ||
==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> | ||
| Line 124: | Line 135: | ||
==Operon== | ==Operon== | ||
* <aureodatabase>operons</aureodatabase> | *<aureodatabase>operons</aureodatabase> | ||
</protect> | </protect> | ||
| Line 130: | Line 141: | ||
==Regulation== | ==Regulation== | ||
*<aureodatabase>regulators</aureodatabase> | |||
* <aureodatabase>regulators</aureodatabase> | |||
</protect> | </protect> | ||
| Line 137: | Line 147: | ||
==Transcription pattern== | ==Transcription pattern== | ||
* <aureodatabase>expression browser</aureodatabase> | *<aureodatabase>expression browser</aureodatabase> | ||
</protect> | </protect> | ||
| Line 143: | Line 153: | ||
==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 13:45, 11 March 2016
NCBI: 03-AUG-2016
⊟Summary[edit | edit source]
- organism: Staphylococcus aureus NCTC8325
- locus tag: SAOUHSC_00004
- pan locus tag?: SAUPAN000010000
- symbol: recF
- pan gene symbol?: recF
- synonym:
- product: recombination protein F
⊟Genome View[edit | edit source]
⊟Gene[edit | edit source]
⊟General[edit | edit source]
- type: CDS
- locus tag: SAOUHSC_00004
- symbol: recF
- product: recombination protein F
- replicon: chromosome
- strand: +
- coordinates: 3912..5024
- length: 1113
- essential: no DEG other strains
⊟Accession numbers[edit | edit source]
- Gene ID: 3919177 NCBI
- RefSeq: YP_498612 NCBI
- BioCyc: G1I0R-4 BioCyc
- MicrobesOnline: 1288504 MicrobesOnline
⊟Phenotype[edit | edit source]
Share your knowledge and add information here. [edit]
⊟DNA sequence[edit | edit source]
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1081ATGAAGTTAAATACACTCCAATTAGAAAATTATCGTAACTATGATGAGGTTACGTTGAAA
TGTCATCCTGACGTGAATATCCTCATTGGAGAAAATGCACAAGGAAAGACAAATTTACTT
GAATCAATTTATACCTTAGCTTTAGCAAAAAGTCATAGAACGAGTAATGATAAGGAACTC
ATACGTTTTAATGCTGATTATGCTAAAATAGAAGGTGAGCTTAGTTATAGACACGGCACG
ATGCCATTAACAATGTTTATAACTAAAAAAGGTAAACAAGTCAAAGTGAATCACTTAGAG
CAAAGTCGTCTAACTCAATATATTGGACACCTCAATGTGGTTCTATTTGCGCCAGAAGAT
TTGAATATTGTAAAAGGCTCTCCTCAAATAAGACGACGCTTTATAGATATGGAGTTGGGC
CAAATTTCTGCTGTTTACTTAAATGATTTAGCTCAATACCAACGTATTTTAAAGCAAAAG
AATAATTACTTAAAGCAGTTACAATTAGGCCAAAAAAAGGACTTAACAATGTTGGAAGTA
TTAAATCAGCAGTTTGCTGAATATGCAATGAAAGTAACTGATAAACGTGCACATTTTATT
CAAGAGCTAGAGTCGTTAGCTAAACCGATTCATGCTGGTATCACAAATGATAAAGAAGCG
TTGTCGCTGAATTATTTACCTAGTCTTAAATTTGATTATGCTCAAAATGAAGCGGCACGA
CTTGAAGAAATTATGTCTATTCTTAGCGATAATATGCAAAGAGAAAAAGAACGAGGCATT
AGCTTATTCGGACCACATCGAGATGATATAAGTTTTGATGTGAATGGCATGGATGCTCAA
ACATATGGTTCTCAAGGACAGCAACGTACAACGGCTTTGTCCATTAAATTAGCTGAAATT
GAGTTAATGAATATCGAAGTTGGGGAATATCCCATCTTATTATTAGACGATGTACTCAGT
GAATTAGATGATTCGCGTCAAACGCATTTATTAAGTACGATTCAGCATAAAGTACAAACA
TTTGTCACTACGACATCTGTAGATGGTATTGATCATGAAATCATGAATAACGCTAAATTG
TATCGTATTAATCAAGGTGAAATTATAAAGTAA60
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⊟Protein[edit | edit source]
⊟General[edit | edit source]
- locus tag: SAOUHSC_00004
- symbol: RecF
- description: recombination protein F
- length: 370
- theoretical pI: 6.44688
- theoretical MW: 42415.1
- GRAVY: -0.444054
⊟Function[edit | edit source]
- TIGRFAM: DNA metabolism DNA replication, recombination, and repair DNA replication and repair protein RecF (TIGR00611; HMM-score: 474.6)and 1 moreTransport and binding proteins Amino acids, peptides and amines urea ABC transporter, ATP-binding protein UrtE (TIGR03410; HMM-score: 13.2)
- TheSEED :
- DNA recombination and repair protein RecF
- PFAM: P-loop_NTPase (CL0023) SMC_N; RecF/RecN/SMC N terminal domain (PF02463; HMM-score: 60.4)and 8 moreAAA_15; AAA ATPase domain (PF13175; HMM-score: 46)AAA_23; AAA domain (PF13476; HMM-score: 37.4)AAA_21; AAA domain, putative AbiEii toxin, Type IV TA system (PF13304; HMM-score: 28.3)AAA_27; AAA domain (PF13514; HMM-score: 21.9)AAA_29; P-loop containing region of AAA domain (PF13555; HMM-score: 21.6)DUF2813; Protein of unknown function (DUF2813) (PF11398; HMM-score: 16.3)no clan defined ERp29; Endoplasmic reticulum protein ERp29, C-terminal domain (PF07749; HMM-score: 11.4)P-loop_NTPase (CL0023) ABC_tran; ABC transporter (PF00005; HMM-score: 10.7)
⊟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): 0.007642
- TAT(Tat/SPI): 0.000271
- LIPO(Sec/SPII): 0.001318
- predicted transmembrane helices (TMHMM): 0
⊟Accession numbers[edit | edit source]
⊟Protein sequence[edit | edit source]
- MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIYTLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGTMPLTMFITKKGKQVKVNHLEQSRLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQKNNYLKQLQLGQKKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDKEALSLNYLPSLKFDYAQNEAARLEEIMSILSDNMQREKERGISLFGPHRDDISFDVNGMDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLSELDDSRQTHLLSTIQHKVQTFVTTTSVDGIDHEIMNNAKLYRINQGEIIK
⊟Experimental data[edit | edit source]
- experimentally validated: PeptideAtlas [1] [2]
- protein localization: data available for COL
- quantitative data / protein copy number per cell: data available for COL
- interaction partners:
SAOUHSC_00799 (eno) phosphopyruvate hydratase [3] (data from MRSA252) SAOUHSC_02117 (gatA) aspartyl/glutamyl-tRNA amidotransferase subunit A [3] (data from MRSA252) SAOUHSC_01246 (infB) translation initiation factor IF-2 [3] (data from MRSA252) SAOUHSC_01786 (infC) translation initiation factor IF-3 [3] (data from MRSA252) SAOUHSC_00519 (rplA) 50S ribosomal protein L1 [3] (data from MRSA252) SAOUHSC_02509 (rplB) 50S ribosomal protein L2 [3] (data from MRSA252) SAOUHSC_02512 (rplC) 50S ribosomal protein L3 [3] (data from MRSA252) SAOUHSC_02511 (rplD) 50S ribosomal protein L4 [3] (data from MRSA252) SAOUHSC_02500 (rplE) 50S ribosomal protein L5 [3] (data from MRSA252) SAOUHSC_02496 (rplF) 50S ribosomal protein L6 [3] (data from MRSA252) SAOUHSC_00520 (rplJ) 50S ribosomal protein L10 [3] (data from MRSA252) SAOUHSC_00518 (rplK) 50S ribosomal protein L11 [3] (data from MRSA252) SAOUHSC_00521 (rplL) 50S ribosomal protein L7/L12 [3] (data from MRSA252) SAOUHSC_02492 (rplO) 50S ribosomal protein L15 [3] (data from MRSA252) SAOUHSC_02484 (rplQ) 50S ribosomal protein L17 [3] (data from MRSA252) SAOUHSC_01211 (rplS) 50S ribosomal protein L19 [3] (data from MRSA252) SAOUHSC_01757 (rplU) 50S ribosomal protein L21 [3] (data from MRSA252) SAOUHSC_02507 (rplV) 50S ribosomal protein L22 [3] (data from MRSA252) SAOUHSC_02510 (rplW) 50S ribosomal protein L23 [3] (data from MRSA252) SAOUHSC_01232 (rpsB) 30S ribosomal protein S2 [3] (data from MRSA252) SAOUHSC_02506 (rpsC) 30S ribosomal protein S3 [3] (data from MRSA252) SAOUHSC_01829 (rpsD) 30S ribosomal protein S4 [3] (data from MRSA252) SAOUHSC_02494 (rpsE) 30S ribosomal protein S5 [3] (data from MRSA252) SAOUHSC_02498 (rpsH) 30S ribosomal protein S8 [3] (data from MRSA252) SAOUHSC_02503 (rpsQ) 30S ribosomal protein S17 [3] (data from MRSA252) SAOUHSC_01418 (sucA) 2-oxoglutarate dehydrogenase E1 component [3] (data from MRSA252) SAOUHSC_00187 formate acetyltransferase [3] (data from MRSA252) SAOUHSC_00206 L-lactate dehydrogenase [3] (data from MRSA252) SAOUHSC_00529 elongation factor G [3] (data from MRSA252) SAOUHSC_00530 elongation factor Tu [3] (data from MRSA252) SAOUHSC_00878 hypothetical protein [3] (data from MRSA252) SAOUHSC_01035 hypothetical protein [3] (data from MRSA252) SAOUHSC_01040 pyruvate dehydrogenase complex, E1 component subunit alpha [3] (data from MRSA252) SAOUHSC_01041 pyruvate dehydrogenase complex, E1 component subunit beta [3] (data from MRSA252) SAOUHSC_01043 dihydrolipoamide dehydrogenase [3] (data from MRSA252) SAOUHSC_01150 cell division protein FtsZ [3] (data from MRSA252) SAOUHSC_01416 dihydrolipoamide succinyltransferase [3] (data from MRSA252) SAOUHSC_01451 threonine dehydratase [3] (data from MRSA252) SAOUHSC_01794 glyceraldehyde 3-phosphate dehydrogenase 2 [3] (data from MRSA252) SAOUHSC_01801 isocitrate dehydrogenase [3] (data from MRSA252) SAOUHSC_01806 pyruvate kinase [3] (data from MRSA252) SAOUHSC_01819 hypothetical protein [3] (data from MRSA252) SAOUHSC_01845 formate--tetrahydrofolate ligase [3] (data from MRSA252) SAOUHSC_02316 DEAD-box ATP dependent DNA helicase [3] (data from MRSA252) SAOUHSC_02441 alkaline shock protein 23 [3] (data from MRSA252) SAOUHSC_02486 30S ribosomal protein S11 [3] (data from MRSA252) SAOUHSC_02860 HMG-CoA synthase [3] (data from MRSA252) SAOUHSC_02927 malate:quinone oxidoreductase [3] (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: [4]
Multi-gene expression profiles
⊟Protein synthesis (provided by Aureolib)[edit | edit source]
⊟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]
- ↑ Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
Proteomics: 2015, 15(21);3648-61
[PubMed:26224020] [WorldCat.org] [DOI] (I p) - ↑ Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
Sci Rep: 2017, 7(1);9718
[PubMed:28887440] [WorldCat.org] [DOI] (I e) - ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 3.12 3.13 3.14 3.15 3.16 3.17 3.18 3.19 3.20 3.21 3.22 3.23 3.24 3.25 3.26 3.27 3.28 3.29 3.30 3.31 3.32 3.33 3.34 3.35 3.36 3.37 3.38 3.39 3.40 3.41 3.42 3.43 3.44 3.45 3.46 3.47 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) - ↑ 4.0 4.1 Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
PLoS Genet: 2016, 12(4);e1005962
[PubMed:27035918] [WorldCat.org] [DOI] (I e)