SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q96J92 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MLASPATETTVLMSQTEADLALRPPPPLGTAGQPRLGPPPRRARRFSGKA    50
51 EPRPRSSRLSRRSSVDLGLLSSWSLPASPAPDPPDPPDSAGPGPARSPPP 100
101 SSKEPPEGTWTEGAPVKAAEDSARPELPDSAVGPGSREPLRVPEAVALER 150
151 RREQEEKEDMETQAVATSPDGRYLKFDIEIGRGSFKTVYRGLDTDTTVEV 200
201 AWCELQTRKLSRAERQRFSEEVEMLKGLQHPNIVRFYDSWKSVLRGQVCI 250
251 VLVTELMTSGTLKTYLRRFREMKPRVLQRWSRQILRGLHFLHSRVPPILH 300
301 RDLKCDNVFITGPTGSVKIGDLGLATLKRASFAKSVIGTPEFMAPEMYEE 350
351 KYDEAVDVYAFGMCMLEMATSEYPYSECQNAAQIYRKVTSGRKPNSFHKV 400
401 KIPEVKEIIEGCIRTDKNERFTIQDLLAHAFFREERGVHVELAEEDDGEK 450
451 PGLKLWLRMEDARRGGRPRDNQAIEFLFQLGRDAAEEVAQEMVALGLVCE 500
501 ADYQPVARAVRERVAAIQRKREKLRKARELEALPPEPGPPPATVPMAPGP 550
551 PSVFPPEPEEPEADQHQPFLFRHASYSSTTSDCETDGYLSSSGFLDASDP 600
601 ALQPPGGVPSSLAESHLCLPSAFALSIPRSGPGSDFSPGDSYASDAASGL 650
651 SDVGEGMGQMRRPPGRNLRRRPRSRLRVTSVSDQNDRVVECQLQTHNSKM 700
701 VTFRFDLDGDSPEEIAAAMVYNEFILPSERDGFLRRIREIIQRVETLLKR 750
751 DTGPMEAAEDTLSPQEEPAPLPALPVPLPDPSNEELQSSTSLEHRSWTAF 800
801 STSSSSPGTPLSPGNPFSPGTPISPGPIFPITSPPCHPSPSPFSPISSQV 850
851 SSNPSPHPTSSPLPFSSSTPEFPVPLSQCPWSSLPTTSPPTFSPTCSQVT 900
901 LSSPFFPPCPSTSSFPSTTAAPLLSLASAFSLAVMTVAQSLLSPSPGLLS 950
951 QSPPAPPSPLPSLPLPPPVAPGGQESPSPHTAEVESEASPPPARPLPGEA 1000
1001 RLAPISEEGKPQLVGRFQVTSSKEPAEPLPLQPTSPTLSGSPKPSTPQLT 1050
1051 SESSDTEDSAGGGPETREALAESDRAAEGLGAGVEEEGDDGKEPQVGGSP 1100
1101 QPLSHPSPVWMNYSYSSLCLSSEESESSGEDEEFWAELQSLRQKHLSEVE 1150
1151 TLQTLQKKEIEDLYSRLGKQPPPGIVAPAAMLSSRQRRLSKGSFPTSRRN 1200
1201 SLQRSEPPGPGIMRRNSLSGSSTGSQEQRASKGVTFAGDVGRM 1243

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

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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