| Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching O17482 from www.uniprot.org...
The NucPred score for your sequence is 0.98 (see score help below)
1 MDWLLATPQLQSVFSSLGSLVGGTYVVSPNALAILEEINHKLTYEDQTLR 50
51 TFRRAIGFGQNVRVDLIPLLENAKDDAVLESVIRILVNLTVPVECLFSVD 100
101 LMYRTEVGRHTIFELNKLLYNSKEAFTDPKSTKSVVEYMKHILESDPKLS 150
151 PHKCDQINNCLLLLRNILHIPETHAHFLMPRLQPGSGHQVSMQNTILWNL 200
201 FIQSIDKLLLYLMTCPQRSLWGVTMVQLIALIYKDQHVSTLQKLLNLWFE 250
251 ASLSESSDDNESNTTPPKQASGDSSPMLTSDPTSDSSDNGSGGKKESCEE 300
301 RRQALREGTDATLHEVSRKGHEYQNAMASSNAANYILEGPCSAQQPWSDC 350
351 EMQEYKQMTAVISEPLNLSQPADNVNYTTNANYARTTSTDILTKTTSLKH 400
401 EGFKPPAPRRNTLSAILSDNYAPLSFISAVKLGQKSPHAGQLQLIKGKCC 450
451 PQKRECPSSQSEHSDCGYGTQMENPESISTSSNDDDGPQGKPQHQKPPCS 500
501 SKHRSKQRIFAVPQDTKDLRRKKLVKRSKSSLINMKGLVLHTPNDDDISN 550
551 LLKEFTVDFLLKGYNYLVEELHSQLLSNAKMPIDTSHFFWLVTFFLKFAA 600
601 QLELDMEHIDTILTFDVLSFLTYEGVSLCEQLELNARQEGADLRPYLRRM 650
651 HLVVTAIREFLQAIEAYNKVTHLSEDDRYRLRQLQLQISATTDLRCLFVL 700
701 LLRRFNPSIHSKQYLQDLVVTNHILLLILDNAAKLEGGQTIGLSEHISQF 750
751 ATLEVMHYYGILLEDFSNNGEYVNDCIFTMMHHIGGDLDQVGVLYQPIIL 800
801 KAYSRIWEADYDICDDWSDLIEYVIHKFLNTPPKSPMAIPTASLTELTKE 850
851 QNQEHTACPWSQEDMDSLCWYFVQSKRQNDVIGNIAKLFSNNGNKIKTRI 900
901 SIIQQLLQQDIITLLEYDDLMKFEDAEYQRTLLATPTSLTTDSGIELKES 950
951 AYGKPSDDVQVLLDLIRKENKSQHLVWLQKLLLECCYVKMMIKCGSCQTD 1000
1001 VEPIMEPVVYHCMFKQKPIPVVQWNNEQSSTMLYQPFMLLLHKLGIQLPA 1050
1051 DAGLIFARIPDFWTPETMYGLAKKLGPLDKLTLKFDPRDLEDAPPSRHHT 1100
1101 GARNSLSSISSLEADFGDSEGLALIPEVDPAVEKAAAAASAIPNNEIFAL 1150
1151 PRVKHCNSIIRYTPDPTPPVPSWLQLVMRTKCSKRRSPATDASDCTSTST 1200
1201 MIADDEIKSYASMAQASHTKLNSGYPTSTLVCMNKLSNCSFAAPPNENSS 1250
1251 SSGCGGTASSMSMPNMPDGNSDALMKTSFERLAVTGARYLRPSNTDQDYS 1300
1301 ALVASVYENEFANSDNVSVASDLTRMYVSDEDEKHELQLQQVE 1343
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
What does the NucPred score mean?
You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper. |
NucPred score threshold | Specificity | Sensitivity |
see above | fraction of proteins predicted to be nuclear that actually are nuclear | fraction of true nuclear proteins that are predicted (coverage) |
0.10 | 0.45 | 0.88 |
0.20 | 0.52 | 0.83 |
0.30 | 0.57 | 0.77 |
0.40 | 0.63 | 0.69 |
0.50 | 0.70 | 0.62 |
0.60 | 0.71 | 0.53 |
0.70 | 0.81 | 0.44 |
0.80 | 0.84 | 0.32 |
0.90 | 0.88 | 0.21 |
1.00 | 1.00 | 0.02 |
Sequences which score >= 0.8 with NucPred and which
are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.) |
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