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

NucPred

Fetching Q8K4G1 from www.uniprot.org...

The NucPred score for your sequence is 0.60 (see score help below)

   1  MRRPGLGGPCPLLLLLLLPAATSASGSSPSPSPSPIEKAVVPSHQAGVAA    50
  51  CHCCLDQTPKSSRCTRASCRVRNCPPAKCTGLEGCLTPTPSVPSPSRSPV   100
 101  EKSQVSLNWQPLTLQEARALLRQRRPRGPWARALLKRRPPHRAPAGQARV   150
 151  LCPLICHNGGVCVKPDRCLCPPDFAGKFCQLHSSGARPPAPAMPGLTRSV   200
 201  YTMPLANHRDDEHGVASMVSVHVEHPQEASVVVHQVERVSGPWEEANPEA   250
 251  LARAEAAARAEAAAPYTVLAQSAPREDGYSDASGFGYCFRELRGSECASP   300
 301  LPGLRTQEVCCRGEGLAWGVHDCHPCAEHLRNSNQVSGPNGPCPPGFERV   350
 351  NGSCVDVDECATGGRCQHGECANTRGGYTCVCPDGFLLDSSRSSCISQHV   400
 401  ISEAKGPCYRVLHDGGCSLPILRNITKQICCCSRVGKAWGRGCQLCPPYG   450
 451  SEGFREICPAGPGYHYSASDLRYNTRPLNQDPPRVTFNQPRVPPATPRPP   500
 501  TGFLPTRRPEPRPDPGPQPEPRPRPEPRPRPESRPRPEPRPRPEPRPQPE   550
 551  SQPRPESRPRPESQPWPEFPLPSIPAWTGPEIPESGPSSSMCQRNPQVCG   600
 601  PGRCVPRPSGYTCACDPGFRLGPQGTRCIDIDECRRVPTPCAPGRCENTP   650
 651  GSFRCVCGTGFQAGPRATECLDVDECRRVPPPCDRGRCENTPGSFLCVCP   700
 701  AGYQAAPHGASCQDVDECTQSPGLCGRGVCENLPGSFRCVCPAGFRGSAC   750
 751  EEDVDECAQQPPPCGPGRCDNTAGSFHCACPAGFRSRGPGAPCQDVDECS   800
 801  RSPSPCAYGRCENTEGSFKCVCPTGFQPNAAGSECEDVDECENRLACPGQ   850
 851  ECVNSPGSFQCRACPVGHHLHRGRCTDVDECSSGTPCGLHGQCTNTKGSF   900
 901  HCSCSTGYRAPSGQPGPCADINECLEGDFCFPHGECLNTDGSFTCTCAPG   950
 951  YRPGPRGASCLDVDECSEEDLCQSGICTNTDGSFECICPPGHRAGPDLAS  1000
1001  CLDIDECRERGPALCGSQRCENSPGSYRCVRDCDPGYHPGPEGTCDDIDE  1050
1051  CREYGSAICGAQRCENTPGSYRCTPACDPGYQPTPGGGCQDVDECRNRSF  1100
1101  CGAHAMCQNLPGSFQCVCDQGYEGARDGRHCVDVNECETLQGVCGSALCE  1150
1151  NVEGSFLCVCPNSPEEFDPMTGRCVPPRAPAGTFPGSQPQAPASPSLPAR  1200
1201  PPAPPPPRRPSPPRQGPVSSGRRECYFDTAAPDACDNILARNVTWQECCC  1250
1251  TVGEGWGSGCRIQQCPGTETAEYQSLCPHGRGYLVPSGDLSARRDVDECQ  1300
1301  LFQDQVCKSGVCVNTAPGYSCYCSNGFYYHAHRLECVDNDECADEEPACE  1350
1351  GGRCVNTVGSYHCTCEPPLVLDGSRRRCVSNESQSLDDNLGVCWQEVGPD  1400
1401  LVCSRPRLDRQATYTECCCLYGEAWGMDCALCPAQDSDDFEALCNVLRPP  1450
1451  AYGPPRPGGFGIPYEYGPDIGPPYQSLPYGPDLYPPPVLPYDPYPPPPGP  1500
1501  FARREAPYGAPPFDMPDFEDDGGPYGESETPDPPSRGTGWPYRSRDTRGS  1550
1551  FPEPEESSERGSYTGALSEPYEGLEAEECGILDGCPHGRCVRVPEGFTCD  1600
1601  CFDGYRLDITRMSCVDVNECDEAEATSPLCVNARCVNTDGSFRCICRPGF  1650
1651  APTHQPHHCAPARPRA                                    1666

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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