| Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching P33748 from www.uniprot.org...
The NucPred score for your sequence is 0.99 (see score help below)
1 MTVDHDFNSEDILFPIESMSSIQYVENNNPNNINNDVIPYSLDIKNTVLD 50
51 SADLNDIQNQETSLNLGLPPLSFDSPLPVTETIPSTTDNSLHLKADSNKN 100
101 RDARTIENDSEIKSTNNASGSGANQYTTLTSPYPMNDILYNMNNPLQSPS 150
151 PSSVPQNPTINPPINTASNETNLSPQTSNGNETLISPRAQQHTSIKDNRL 200
201 SLPNGANSNLFIDTNPNNLNEKLRNQLNSDTNSYSNSISNSNSNSTGNLN 250
251 SSYFNSLNIDSMLDDYVSSDLLLNDDDDDTNLSRRRFSDVITNQFPSMTN 300
301 SRNSISHSLDLWNHPKINPSNRNTNLNITTNSTSSSNASPNTTTMNANAD 350
351 SNIAGNPKNNDATIDNELTQILNEYNMNFNDNLGTSTSGKNKSACPSSFD 400
401 ANAMTKINPSQQLQQQLNRVQHKQLTSSHNNSSTNMKSFNSDLYSRRQRA 450
451 SLPIIDDSLSYDLVNKQDEDPKNDMLPNSNLSSSQQFIKPSMILSDNASV 500
501 IAKVATTGLSNDMPFLTEEGEQNANSTPNFDLSITQMNMAPLSPASSSST 550
551 SLATNHFYHHFPQQGHHTMNSKIGSSLRRRKSAVPLMGTVPLTNQQNNIS 600
601 SSSVNSTGNGAGVTKERRPSYRRKSMTPSRRSSVVIESTKELEEKPFHCH 650
651 ICPKSFKRSEHLKRHVRSVHSNERPFACHICDKKFSRSDNLSQHIKTHKK 700
701 HGDI 704
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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