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

NucPred

Fetching Q9BQF6 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MDKRKLGRRPSSSEIITEGKRKKSSSDLSEIRKMLNAKPEDVHVQSPLSK    50
  51  FRSSERWTLPLQWERSLRNKVISLDHKNKKHIRGCPVTSKSSPERQLKVM   100
 101  LTNVLWTDLGRKFRKTLPRNDANLCDANKVQSDSLPSTSVDSLETCQKLE   150
 151  PLRQSLNLSERIPRVILTNVLGTELGRKYIRTPPVTEGSLSDTDNLQSEQ   200
 201  LSSSSDGSLESYQNLNPHKSCYLSERGSQRSKTVDDNSAKQTAHNKEKRR   250
 251  KDDGISLLISDTQPEDLNSGSRGCDHLEQESRNKDVKYSDSKVELTLISR   300
 301  KTKRRLRNNLPDSQYCTSLDKSTEQTKKQEDDSTISTEFEKPSENYHQDP   350
 351  KLPEEITTKPTKSDFTKLSSLNSQELTLSNATKSASAGSTTETVENSNSI   400
 401  DIVGISSLVEKDENELNTIEKPILRGHNEGNQSLISAEPIVVSSDEEGPV   450
 451  EHKSSEILKLQSKQDRETTNENESTSESALLELPLITCESVQMSSELCPY   500
 501  NPVMENISSIMPSNEMDLQLDFIFTSVYIGKIKGASKGCVTITKKYIKIP   550
 551  FQVSLNEISLLVDTTHLKRFGLWKSKDDNHSKRSHAILFFWVSSDYLQEI   600
 601  QTQLEHSVLSQQSKSSEFIFLELHNPVSQREELKLKDIMTEISIISGELE   650
 651  LSYPLSWVQAFPLFQNLSSKESSFIHYYCVSTCSFPAGVAVAEEMKLKSV   700
 701  SQPSNTDAAKPTYTFLQKQSSGCYSLSITSNPDEEWREVRHTGLVQKLIV   750
 751  YPPPPTKGGLGVTNEDLECLEEGEFLNDVIIDFYLKYLILEKASDELVER   800
 801  SHIFSSFFYKCLTRKENNLTEDNPNLSMAQRRHKRVRTWTRHINIFNKDY   850
 851  IFVPVNESSHWYLAVICFPWLEEAVYEDFPQTVSQQSQAQQSQNDNKTID   900
 901  NDLRTTSTLSLSAEDSQSTESNMSVPKKMCKRPCILILDSLKAASVQNTV   950
 951  QNLREYLEVEWEVKLKTHRQFSKTNMVDLCPKVPKQDNSSDCGVYLLQYV  1000
1001  ESFFKDPIVNFELPIHLEKWFPRHVIKTKREDIRELILKLHLQQQKGSSS  1050

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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