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

NucPred

Fetching Q9LK64 from www.uniprot.org...

The NucPred score for your sequence is 0.26 (see score help below)

   1  MDFLGSTTGSGTLAMLFSFSESILPLDSRSFLLKPLFLRWLSGFLHSVLL    50
  51  LVLFFSWVRKKIRGDSGVTESLKDRRDFGFKSALFCSLALSLLNLVLMSL   100
 101  SGFYWYESGWLDNEQLVSSLGFLLGMVSWGVLSICLHRCRDCEHKKAPFL   150
 151  LRLWLVFYLVVSCYSLVVDFVMYERRETVPVHLLVFDIVAFIAAVFLGYV   200
 201  AVLKKDRSNSNGVLEEPLLNGGDSRVGGDDSVELNKTNGSGEATPYSRAG   250
 251  ILSLLTFSWMSPLIDIGNKKTLDLEDVPQLHDTDSVVGLAPKFRSMLESP   300
 301  DGGERSGVTTFKLIKALYFTAQWEILVTAFFAFIYTVASYVGPALIDTFV   350
 351  QYLNGRRQYNHEGYVLVITFFAAKIVECLSQRHWFFRLQKVGIRMRSALV   400
 401  AMIYEKGLTLSCQSKQGRTSGEIINFMTVDAERIGNFSWYMHDPWMVLLQ   450
 451  VGLALWILYRNLGLASIAALVATIIVMLINFPFGRMQERFQEKLMEAKDS   500
 501  RMKSTSEILRNMRILKLQGWEMKFLSKIFDLRKSEEGWLKKYVYNSAVIS   550
 551  FVFWGAPTLVSVSTFGACILLGIPLESGKILSALATFRILQEPIYNLPDT   600
 601  ISMIVQTKVSLDRLASYLCLDNLQPDIVERLPKGSSDVAVEVINSTLSWD   650
 651  VSSSNPTLKDINFKVFPGMKVAVCGTVGSGKSSLLSSLLGEVPKVSGSLK   700
 701  VCGTKAYVAQSPWIQSGKIEDNILFGKPMERERYDKVLEACSLSKDLEIL   750
 751  SFGDQTVIGERGINLSGGQKQRIQIARALYQDADIYLFDDPFSAVDAHTG   800
 801  SHLFKEVLLGLLCSKSVIYVTHQVEFLPAADLILVMKDGRISQAGKYNDI   850
 851  LNSGTDFMELIGAHQEALAVVDSVDANSVSEKSALGQENVIVKDAIAVDE   900
 901  KLESQDLKNDKLESVEPQRQIIQEEEREKGSVALDVYWKYITLAYGGALV   950
 951  PFILLGQVLFQLLQIGSNYWMAWATPVSEDVQAPVKLSTLMIVYVALAFG  1000
1001  SSLCILLRATLLVTAGYKTATELFHKMHHCIFRSPMSFFDSTPSGRIMSR  1050
1051  ASTDQSAVDLELPYQFGSVAITVIQLIGIIGVMSQVSWLVFLVFIPVVAA  1100
1101  SIWYQRYYIAAARELSRLVGVCKAPLIQHFSETISGATTIRSFSQEFRFR  1150
1151  SDNMRLSDGYSRPKFYTAGAMEWLCFRLDMLSSLTFVFSLVFLVSIPTGV  1200
1201  IDPSLAGLAVTYGLSLNTLQAWLIWTLCNLENKIISVERILQYASVPSEP  1250
1251  PLVIESNRPEQSWPSRGEVEIRDLQVRYAPHMPLVLRGITCTFKGGLRTG  1300
1301  IVGRTGSGKSTLIQTLFRIVEPSAGEIRIDGVNILTIGLHDLRLRLSIIP  1350
1351  QDPTMFEGTMRSNLDPLEEYTDDQIWEALDKCQLGDEVRKKEQKLDSSVS  1400
1401  ENGDNWSMGQRQLVCLGRVLLKRSKILVLDEATASVDTATDNLIQKTLRE  1450
1451  HFSDCTVITIAHRISSVIDSDMVLLLSNGIIEEYDTPVRLLEDKSSSFSK  1500
1501  LVAEYTSRSSSSFD                                      1514

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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