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

NucPred

Fetching Q9NRP7 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MEKYHVLEMIGEGSFGRVYKGRRKYSAQVVALKFIPKLGRSEKELRNLQR    50
  51  EIEIMRGLRHPNIVHMLDSFETDKEVVVVTDYAEGELFQILEDDGKLPED   100
 101  QVQAIAAQLVSALYYLHSHRILHRDMKPQNILLAKGGGIKLCDFGFARAM   150
 151  STNTMVLTSIKGTPLYMSPELVEERPYDHTADLWSVGCILYELAVGTPPF   200
 201  YATSIFQLVSLILKDPVRWPSTISPCFKNFLQGLLTKDPRQRLSWPDLLY   250
 251  HPFIAGHVTIITEPAGPDLGTPFTSRLPPELQVLKDEQAHRLAPKGNQSR   300
 301  ILTQAYKRMAEEAMQKKHQNTGPALEQEDKTSKVAPGTAPLPRLGATPQE   350
 351  SSLLAGILASELKSSWAKSGTGEVPSAPRENRTTPDCERAFPEERPEVLG   400
 401  QRSTDVVDLENEEPDSDNEWQHLLETTEPVPIQLKAPLTLLCNPDFCQRI   450
 451  QSQLHEAGGQILKGILEGASHILPAFRVLSSLLSSCSDSVALYSFCREAG   500
 501  LPGLLLSLLRHSQESNSLQQQSWYGTFLQDLMAVIQAYFACTFNLERSQT   550
 551  SDSLQVFQEAANLFLDLLGKLLAQPDDSEQTLRRDSLMCFTVLCEAMDGN   600
 601  SRAISKAFYSSLLTTQQVVLDGLLHGLTVPQLPVHTPQGAPQVSQPLREQ   650
 651  SEDIPGAISSALAAICTAPVGLPDCWDAKEQVCWHLANQLTEDSSQLRPS   700
 701  LISGLQHPILCLHLLKVLYSCCLVSEGLCRLLGQEPLALESLFMLIQGKV   750
 751  KVVDWEESTEVTLYFLSLLVFRLQNLPCGMEKLGSDVATLFTHSHVVSLV   800
 801  SAAACLLGQLGQQGVTFDLQPMEWMAAATHALSAPAEVRLTPPGSCGFYD   850
 851  GLLILLLQLLTEQGKASLIRDMSSSEMWTVLWHRFSMVLRLPEEASAQEG   900
 901  ELSLSSPPSPEPDWTLISPQGMAALLSLAMATFTQEPQLCLSCLSQHGSI   950
 951  LMSILKHLLCPSFLNQLRQAPHGSEFLPVVVLSVCQLLCFPFALDMDADL  1000
1001  LIGVLADLRDSEVAAHLLQVCCYHLPLMQVELPISLLTRLALMDPTSLNQ  1050
1051  FVNTVSASPRTIVSFLSVALLSDQPLLTSDLLSLLAHTARVLSPSHLSFI  1100
1101  QELLAGSDESYRPLRSLLGHPENSVRAHTYRLLGHLLQHSMALRGALQSQ  1150
1151  SGLLSLLLLGLGDKDPVVRCSASFAVGNAAYQAGPLGPALAAAVPSMTQL  1200
1201  LGDPQAGIRRNVASALGNLGPEGLGEELLQCEVPQRLLEMACGDPQPNVK  1250
1251  EAALIALRSLQQEPGIHQVLVSLGASEKLSLLSLGNQSLPHSSPRPASAK  1300
1301  HCRKLIHLLRPAHSM                                     1315

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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