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

NucPred

Fetching Q6IV68 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MVSKRSRLDFEDKETLAEDASKIMKQPLSKLAKKSCGSHEVEENGSVFVR    50
  51  LLKASGLTLKTGDNQNQLGVDQIIFQRKLFQALRKHPSYPKVIEEFVNGL   100
 101  ESYTEDIDSLRNCLLSCERLQDEEASMGTFYSKSLIKLLLGIDILQPAII   150
 151  KMLFEKVPQFLFESESRDGISMPRLIISQLKWLDRIVDSKDLTTQMMQLI   200
 201  SVAPVNLQHDFITSLPEILGDSQHANVGKELSELLVQNTSLTVPILDVFS   250
 251  SLRLDPNFLSEIRQLVMGKLSSVRLEDLPVIVKFILHSVTDSTSLEVIAE   300
 301  LREKLNVQHFTLPSRIQASQSKLKSKGLASSSGNQENSDKDCIVLLFDVI   350
 351  KSAIRYEKTISEAWIKAIERIQSAAEHKALDVAMLLIIYGTSTQTKKGVE   400
 401  RLLRNKIQSDCIQEQLLDSTFSTHCLVLKDICPSILLLAQTLFHSQDQRI   450
 451  ILFGSLLCKYAFKFFDTYCQQEVVGALVTHVCSGNEAEVDAALDVLLELI   500
 501  VLNASAMRLNAAFIKGILDYLENMSPQQIRKIFCILSTLAFSQQPGTSNH   550
 551  IQDDMHLVIRKQLSSTVFKYKLIGIIGAVTMAGIMAEDRTMPSNSTQRSA   600
 601  SVSSEQHTQVTSLLQLVHSCTEHSPWASSLYYDEFANLIQERKLAPKTLE   650
 651  WVAQTIFNDFQDAFVVDFCAVPEGDFPFPVKALYGLEECNTQDGIVINLL   700
 701  PLFFQEFAKDVSQVTSQESSQKSMSPLCLASHFRLLRLCVARQHNGNLDE   750
 751  IDALLDCPLFLPDLEPGEKLESMSAKDRSLMCSLTFLTFNWFREVVNAFC   800
 801  QQTSPEMKGKVLSRLKDLVELQEILEKYLAVIPDYVPPFTSVDLDTLDVI   850
 851  PRSNSAVAAKSRHKGKTGGKKQKADSSTASCTDTLLTEDTSECDVAPSGK   900
 901  SQVDKESTGKEGKTFVSLQNYRAFFRELDIEVFSILHSGLVTKFILDTEM   950
 951  HTEATEVVQLGPAELLFLLEDLSQKLENRLTPSFTKRVCFFKNKGSRNIG  1000
1001  FSHLHQRSVQDIVHCVVQLLTPMCNHLENIHNFFQCLGAENLSVNDKARV  1050
1051  TAQEHYTMSSCYQKLLQVFHALLAWKGFTHQSNHRLLRSALEVLASRLKQ  1100
1101  TEEGQPLEELLSQSFSYLQNLQHSIPSFQCGLYLLRLLMALLEKSAVPTQ  1150
1151  KKEKLASLAKQLLCRAWPHGDKEKNPTFNDHLHDLLCIYLEHTDNVLKAI  1200
1201  EEITGVGVPELVNAPKDASSSTFPTLTRHTFVIFFRVMMAELEKTVKGLQ  1250
1251  AGTATDSQQVHEEKLLYWNMAVRDFSILINLMKVFDSYPVLHVCLKYGRR  1300
1301  FVEAFLKQCMPLLDFSFRKHRDDVLSLLQTLQLNTRLLHHLCGHSKIHQD  1350
1351  TRLTKHVPLLKKSLELLVCRVKAMLVLNNCREAFWLGTLKNRDLQGEEII  1400
1401  SQHPSSPENTSEDSEDGMTSYVSRNRAIEDGEDEANDGQDRDSDESDDSS  1450
1451  S                                                   1451

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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