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

NucPred

Fetching Q2U6D4 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MGPAKKPAMAGVNSKAEREADLVMGTNNSSIVSKRSVEMLYYSKPHFFRY    50
  51  FVKKPQRRSPLINRGYWLRMHAMAETVRKFMREPSDKPKFVLNLGCGFDP   100
 101  LPYMLLSADNDLCRDTTFVDIDYEKLMVNKKTAIRKTDEITQLLEDVEFL   150
 151  PDDSAVQIRSKPYLAIGCDLKNLTKLDTVLRAEVLPSECAVLFLAEVSLT   200
 201  YMDVKSANAVVSWASGLSNDAQFCILEQFFPDGPDHPFASTMMKHFKKLG   250
 251  APLYSIHEYPSLNEQEQRFKDAGWNHAHARSLWDLWSDDEFVDGSLRASL   300
 301  DAIEPFDEWEEFALFGSHYFLLHASTRPRVSETATRTLTGLDPQTDKSGH   350
 351  FRLLAKCPPGSGQRRFGAVIPDSDKAVGHHSGLGRQTRLSSTELYTKSEG   400
 401  TTKTHEFPPGDIPARMCHTVTCLSNQDCLLVGGRASPASGFKDCWVRQGN   450
 451  QWRSTQSLPVPRFRHSAVKVTLDSEYVLVYGGKTSDGTTLNTWLAWSSKK   500
 501  QDWQQVETNSIHIKARFGACLGSINDTSGVLFGGIGAEGTILGDFFTWKL   550
 551  HQRSDGSLFMELTDHTDDLRRTSSLFNQIHRFGATVNQTAWGLVIVGGIV   600
 601  PRGIITHDKEIMLLDSTELTKCIASGWPSNHTIISALGLGNRLDGPRPLL   650
 651  VGHVSCAIDSKEILILGGGAVCFSFGTYWTEGTWLLQDVSSTTENDWTLI   700
 701  PESVEPNKSQSEKATSKPSAQSQNEPYRAAEVITPIPRVCVQNPAQFQDI   750
 751  LAEGRPVIIEGSDVGPCTELWTKEYLTSAVGGDRKIVVHEAQSAHMSFQT   800
 801  KNFSYATKTFGTFMDEVYAGDRQYLRSISAEQPTKLPANLAVDFPSLSHD   850
 851  FRLPESLSIVTDNTHSSPLRISGPVTLWLHYDVMANVLCQIRGEKRLILF   900
 901  PPSDVQYLQVPPGASSSTINIFQSNGSVASIPHTSPQEAVLKRGDILFIP   950
 951  PLWLHTASPTGDVSVAVNVFFRNLSKGYAAGRDVYGNRDLQAYEKARNDI  1000
1001  QKMAKSFDGLPSEMARFYLLRLAQELKDKAEK                    1032

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.)

Go back to the NucPred Home Page.