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m (Text replacement - "gene Genbank" to "gene RefSeq") |
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> | ||
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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 RefSeq</aureodatabase> | *<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 03:16, 11 March 2016
NCBI: 10-JUN-2013
⊟Summary[edit | edit source]
- organism: Staphylococcus aureus USA300_FPR3757
- locus tag: SAUSA300_1143 [new locus tag: SAUSA300_RS06185 ]
- pan locus tag?: SAUPAN003548000
- symbol: topA
- pan gene symbol?: topA
- synonym:
- product: DNA topoisomerase I
⊟Genome View[edit | edit source]
⊟Gene[edit | edit source]
⊟General[edit | edit source]
- type: CDS
- locus tag: SAUSA300_1143 [new locus tag: SAUSA300_RS06185 ]
- symbol: topA
- product: DNA topoisomerase I
- replicon: chromosome
- strand: +
- coordinates: 1252764..1254839
- length: 2076
- essential: unknown other strains
⊟Accession numbers[edit | edit source]
- Gene ID: 3915296 NCBI
- RefSeq: YP_493840 NCBI
- BioCyc: GH3C-1138 BioCyc
- MicrobesOnline: 1292658 MicrobesOnline
⊟Phenotype[edit | edit source]
Share your knowledge and add information here. [edit]
⊟DNA sequence[edit | edit source]
- 1
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2041ATGACATTGGCAGATAATTTAGTCATTGTTGAATCGCCTGCAAAAGCAAAAACCATTGAA
AAGTATTTAGGTAAGAAATATAAAGTTATAGCTTCAATGGGACACGTCAGAGACTTACCA
AGAAGTCAAATGGGTGTCGACACTGAAGATAATTACGAACCAAAATATATAACAATACGC
GGAAAAGGTCCTGTTGTAAAAGAATTGAAAAAACATGCAAAAAAAGCGAAAAACGTCTTT
CTCGCAAGTGACCCCGACCGTGAAGGTGAAGCAATTGCTTGGCATTTATCAAAAATTTTA
GAGCTTGAAGATTCTAAAGAAAATCGCGTTGTTTTCAACGAAATAACTAAAGACGCTGTT
AAAGAAAGTTTTAAAAATCCTAGAGAAATTGAAATGAACTTAGTCGATGCACAACAAGCG
CGTCGAATATTAGATAGATTAGTTGGCTATAACATCTCGCCAGTTCTTTGGAAAAAAGTA
AAAAAAGGGTTGTCAGCGGGTCGAGTTCAATCTGTTGCACTTCGTTTAGTCATTGACCGT
GAAAATGAAATTCGAAACTTTAAACCAGAAGAATATTGGACTATTGAAGGAGAATTTAGA
TACAAAAAATCAAAATTCAATGCTAAATTCCTTCATTATAAAAATAAACCTTTTAAACTA
AAAACGAAAAAAGATGTTGAGAAAATTACAGCTGCATTAGATGGAGATCAATTCGAAATT
ACAAACGTGACTAAAAAAGAAAAAACGCGTAATCCAGCAAACCCATTTACAACTTCTACA
TTACAACAAGAGGCGGCACGTAAATTAAACTTTAAAGCAAGAAAAACAATGATGGTCGCA
CAACAATTATATGAAGGTATAGATTTGAAAAAACAAGGTACGATTGGTTTAATAACATAT
ATGAGAACCGATTCTACACGTATTTCAGATACTGCCAAAGTTGAAGCAAAACAGTATATA
ACTGATAAATACGGTGAATCTTACACTTCTAAACGTAAAGCATCAGGGAAACAAGGTGAC
CAAGATGCCCATGAGGCTATTAGACCTTCAAGTACTATGCGTACGCCAGATGATATGAAG
TCATTTTTGACGAAAGACCAATACCGATTATACAAATTAATTTGGGAACGATTTGTTGCT
AGTCAAATGGCTCCAGCAATACTTGATACAGTCTCATTAGACATAACACAAGGTGACATT
AAATTTAGAGCGAATGGTCAAACAATCAAGTTTAAAGGATTTATGACACTTTATGTAGAA
ACTAAAGATGATAGTGATAGCGAAAAGGAAAATAAACTGCCTAAATTAGAGCAAGGTGAT
AAAGTCACAGCAACTCAAATTGAACCAGCTCAACACTATACACAACCACCTCCAAGATAT
ACTGAGGCGAGATTAGTAAAAACACTAGAAGAATTGAAAATTGGGCGACCATCAACTTAT
GCACCGACAATAGATACGATTCAAAAGCGTAACTATGTCAAATTAGAAAGTAAGCGTTTT
GTTCCTACTGAGTTGGGAGAAATAGTTCATGAACAAGTGAAAGAATACTTCCCAGAGATT
ATTGATGTGGAATTCACAGTGAATATGGAAACGTTACTTGATAAGATTGCAGAAGGCGAC
ATTACATGGAGGAAAGTAATCGACGGTTTCTTTAGTAGCTTTAAACAAGATGTTGAACGT
GCTGAAGAAGAGATGGAAAAGATTGAAATCAAAGATGAGCCAGCCGGTGAAGACTGTGAA
ATTTGTGGTTCTCCTATGGTTATAAAAATGGGACGCTATGGTAAGTTCATGGCTTGCTCA
AACTTCCCGGATTGTCGTAATACAAAAGCGATAGTTAAGTCTATTGGTGTTAAATGTCCA
AAATGTAATGATGGTGACGTCGTAGAAAGAAAATCTAAAAAGAATCGTGTCTTTTATGGA
TGTTCGAAATATCCTGAATGCGACTTTATCTCTTGGGATAAGCCGATTGGAAGAGATTGT
CCAAAATGTAACCAATATCTTGTTGAAAATAAAAAAGGCAAGACAACACAAGTAATATGT
TCAAATTGCGATTATAAAGAGGCAGCGCAGAAATAA60
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2076
⊟Protein[edit | edit source]
⊟General[edit | edit source]
- locus tag: SAUSA300_1143 [new locus tag: SAUSA300_RS06185 ]
- symbol: TopA
- description: DNA topoisomerase I
- length: 691
- theoretical pI: 9.4884
- theoretical MW: 79326.5
- GRAVY: -0.719247
⊟Function[edit | edit source]
- reaction: EC 5.99.1.2? ExPASyDNA topoisomerase ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
- TIGRFAM: DNA metabolism DNA replication, recombination, and repair DNA topoisomerase I (TIGR01051; EC 5.99.1.2; HMM-score: 859.4)and 6 moreDNA metabolism DNA replication, recombination, and repair DNA topoisomerase I (TIGR01057; EC 5.99.1.2; HMM-score: 311.8)DNA metabolism DNA replication, recombination, and repair reverse gyrase (TIGR01054; EC 3.6.4.12,5.99.1.3; HMM-score: 309.9)DNA metabolism DNA replication, recombination, and repair DNA topoisomerase III (TIGR01056; EC 5.99.1.2; HMM-score: 211.2)Transcription RNA processing ribonuclease M5 (TIGR00334; EC 3.1.26.8; HMM-score: 15.2)conserved hypothetical protein (TIGR02443; HMM-score: 5.8)Energy metabolism Methanogenesis methyl coenzyme M reductase system, component A2 (TIGR03269; HMM-score: 5.6)
- TheSEED :
- DNA topoisomerase I (EC 5.99.1.2)
- PFAM: no clan defined Topoisom_bac; DNA topoisomerase (PF01131; HMM-score: 446.1)and 10 moreZn_Beta_Ribbon (CL0167) zf-C4_Topoisom; Topoisomerase DNA binding C4 zinc finger (PF01396; HMM-score: 108.3)Toprim-like (CL0413) Toprim; Toprim domain (PF01751; HMM-score: 106.4)Toprim_4; Toprim domain (PF13662; HMM-score: 18.5)Toprim_2; Toprim-like (PF13155; HMM-score: 15.5)Zn_Beta_Ribbon (CL0167) RNA_POL_M_15KD; RNA polymerases M/15 Kd subunit (PF02150; HMM-score: 14.8)Auto_anti-p27; Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) (PF06677; HMM-score: 12.1)IHF-likeDNA-bdg (CL0548) Bac_DNA_binding; Bacterial DNA-binding protein (PF00216; HMM-score: 11.8)no clan defined HypA; Hydrogenase/urease nickel incorporation, metallochaperone, hypA (PF01155; HMM-score: 10)Zn_Beta_Ribbon (CL0167) zf-TFIIB; Transcription factor zinc-finger (PF13453; HMM-score: 9.5)RING (CL0229) IBR; IBR domain, a half RING-finger domain (PF01485; HMM-score: 7.1)
⊟Structure, modifications & cofactors[edit | edit source]
- domains:
- modifications:
- cofactors: Mg2+
- effectors:
⊟Localization[edit | edit source]
- PSORTb: Cytoplasmic
- Cytoplasmic Score: 9.97
- Cytoplasmic Membrane Score: 0
- Cellwall Score: 0.01
- Extracellular Score: 0.02
- 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): 0.009849
- TAT(Tat/SPI): 0.000672
- LIPO(Sec/SPII): 0.001226
- predicted transmembrane helices (TMHMM): 0
⊟Accession numbers[edit | edit source]
⊟Protein sequence[edit | edit source]
- MTLADNLVIVESPAKAKTIEKYLGKKYKVIASMGHVRDLPRSQMGVDTEDNYEPKYITIRGKGPVVKELKKHAKKAKNVFLASDPDREGEAIAWHLSKILELEDSKENRVVFNEITKDAVKESFKNPREIEMNLVDAQQARRILDRLVGYNISPVLWKKVKKGLSAGRVQSVALRLVIDRENEIRNFKPEEYWTIEGEFRYKKSKFNAKFLHYKNKPFKLKTKKDVEKITAALDGDQFEITNVTKKEKTRNPANPFTTSTLQQEAARKLNFKARKTMMVAQQLYEGIDLKKQGTIGLITYMRTDSTRISDTAKVEAKQYITDKYGESYTSKRKASGKQGDQDAHEAIRPSSTMRTPDDMKSFLTKDQYRLYKLIWERFVASQMAPAILDTVSLDITQGDIKFRANGQTIKFKGFMTLYVETKDDSDSEKENKLPKLEQGDKVTATQIEPAQHYTQPPPRYTEARLVKTLEELKIGRPSTYAPTIDTIQKRNYVKLESKRFVPTELGEIVHEQVKEYFPEIIDVEFTVNMETLLDKIAEGDITWRKVIDGFFSSFKQDVERAEEEMEKIEIKDEPAGEDCEICGSPMVIKMGRYGKFMACSNFPDCRNTKAIVKSIGVKCPKCNDGDVVERKSKKNRVFYGCSKYPECDFISWDKPIGRDCPKCNQYLVENKKGKTTQVICSNCDYKEAAQK
⊟Experimental data[edit | edit source]
⊟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.