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

NucPred

Fetching P34544 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MDQQEPSNNVDTSSILSDDGMETQEQSSFVTATIDLTVDDYDETEIQEIL    50
  51  DNGKAEEGTDEDSDLVEGILNANSDVQALLDAPSEQVAQALNSFFGNESE   100
 101  QEAVAAQRRVDAEKTAKDEAELKQQEEAEDLIIEDSIVKTDEEKQAVRRL   150
 151  KINEFLSWFTRLLPEQFKNFEFTNPNYLTESISDSPVVNVDKCKEIVKSF   200
 201  KESESLEGLSQKYELIDEDVLVAAICIGVLDTNNEEDVDFNVLCDDRIDD   250
 251  WSIEKCVTFLDYPNTGLNSKNGPLRFMQFTVTSPASAILMLTLIRLREEG   300
 301  HPCRLDFDSNPTDDLLLNFDQVEFSNNIIDTAVKYWDDQKENGAQDKIGR   350
 351  ELNDFFHEIESTSAEFKQHFENAVGSRNEIIQLVNEKIPDFDGTEAAVNE   400
 401  SFTSDQRTEIINSRAIMETLKAEMKLAIAEAQKVYDTKTDFEKFFVLTVG   450
 451  DFCLARANPSDDAELTYAIVQDRVDAMTYKVKFIDTSQIRECNIRDLAMT   500
 501  TQGMYDPSLNTFGDVGLRVACRQVISSSQFGKKTIWLTGTAAGRRRAHRS   550
 551  DFLIFFDNGTDAYVSAPTMPGEPGYEVASEKKSVFSLKEMIAKMNAAQIA   600
 601  IMVGQPVGKEGNLDYFLTFHWIRQSHRSAYIRDFMKEFPEWPLLKMPVGM   650
 651  RICLYNSLVDRRKKMVTVIGTDRAFAIVRHEAPNPLAPGNRCTDFPCNDR   700
 701  NHQHIDEKIYRGSHRLEGAAHKKHMISTNNNLSQRRKDQLQSQFEPTDMI   750
 751  RSMPERNHQQVVKKKTTGTNQNVASTNDAKSKREIEIRKKNQFLFNKIIV   800
 801  PIPVLTPLENLKAHAQCGPDCLQKMDADPYEARFHRNSPIHTPLLCGWRR   850
 851  IMYTMSTGKKRGAVKKNIIYFSPCGAALHQISDVSEYIHVTRSLLTIDCF   900
 901  SFDARIDTATYITVDDKYLKVADFSLGTEGIPIPLVNSVDNDEPPSLEYS   950
 951  KRRFQYNDQVDISSVSRDFCSGCSCDGDCSDASKCECQQLSIEAMKRLPH  1000
1001  NLQFDGHDELVPHYQNRLLSSKVISGLYECNDQCSCHRKSCYNRVVQNNI  1050
1051  KYPMHIFKTAQSGWGVRALTDIPQSTFICTYVGAILTDDLADELRNADQY  1100
1101  FADLDLKDTVELEKGREDHETDFGYGGDESDYDDEEGSDGDSGDDVMNKM  1150
1151  VKRQDSSESGEETKRLTRQKRKQSKKSGKGGSVEKDDTTPRDSMEKDNIE  1200
1201  SKDEPVFNWDKYFEPFPLYVIDAKQRGNLGRFLNHSCDPNVHVQHVMYDT  1250
1251  HDLRLPWVAFFTRKYVKAGDELTWDYQYTQDQTATTQLTCHCGAENCTGR  1300
1301  LLKS                                                1304

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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