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

NucPred

Fetching Q9VXG1 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MCDAAAATATTTTTAAVAAAVATTTASVALEATATQPGTTTTTVATASAG    50
  51  TTSPEAAIPTAATATSARNSNSERSARQNCCRLCIAPQTECISIINSYAA   100
 101  DKEPLSTKIHNCVGIKVTPQDRLSQQICHACISYLNSWQSFKNRCFSSQA   150
 151  KQRQWLDTNKSKLLNYLDLNSAENGGGGFFDQHLHQQQQHHQHLENELEA   200
 201  EKEKATPTAASTAANILDGIHSLKKRKSLTVYPLPAMPIKDEPIDTDDDY   250
 251  QMKSIDESDDMVDPTMFLERSEHEGDVPLTASDYDYTAQHGVNASSVAAS   300
 301  LPPNAVANVAAAGDSKVASCRACSLQFSTRANARRHERNLHPNLFQLSTD   350
 351  SPHNTPITKPTPALAAALEMQRAAAAAATAEANRAAGAAGGNISTQKYRQ   400
 401  VVMNAFIKCEGGGYDYDNPEQYRPLLTRDKVEFIEQNDEFLEQYQTMTCR   450
 451  CCNKYFSTYKNFMAHVRKKYPQLPRNLCFNCLKMNDSKALFISHLKKRNC   500
 501  INLFRVLNALRGKTTTVVVPIADDVADDGATGSIPVADAGAGVVAMNSPT   550
 551  VTASGEVVTPGGGSERPEKLRAKELLVNKLYECKLCPKGFRTKHEFRTHV   600
 601  YDKHADVQRKDNNSIQCSFCGLDFADPVDRRRHYNNMDCIVRLRCMTCDA   650
 651  KLETHQRFLDHVYQDHLGGVGGGAVSDNASTTGSGMARSNSMEHSPGKRS   700
 701  LLGALGVGSSAEESRSSSAAPPLTSTPKLAGGNQVGGGGSTSASAAAAAQ   750
 751  SSANRDASAPKSQYFSRMPQVCPICGQQYNNYNNVLRHMESKHPNKLPET   800
 801  YKCVRCGLGYPRISYLREHMINVHGVDKNRHSGGFEYIVNADAVKLADGS   850
 851  TPNVYTGRYDYVMKDLMSITNGGTLDDEEEEPGSVAKKMRLDDSSNNSSL   900
 901  VGVASQQKECPICNAVFSNNIGLSNHMRSHYTASNAVNAALAAANRMTPK   950
 951  SLTITATPATDSELGVGGTMSESAPATPANVPPAMANQTPQEQAVFRRSL  1000
1001  DQAADRRFRRMRCRICQRRFSSKKSYRYHMLTDHQVQNVQFIKCKLCNAE  1050
1051  FAYEKGLKVHLFKVHGKAIKDEMIIKQFECDVCSIVYSSESELQQHKRSV  1100
1101  HKLTSASASTSASTSSKIDDDSLMDDGKPTSSDLADLSTLAAGGSTASAP  1150
1151  LYWYQCKYCPSNFNTNKKLAIHINSHDEFDSNDYSCKDCGNVYSGRKSLW  1200
1201  VHRYKKHPQVPNPAECSLCRKVFFDRQMHDNHTPTCNRKPITSTGAHQQQ  1250
1251  DGQLHSHHTAKRTIFRHKTGDDDDEEDDDEQQQLEERANSDGNGTTVGVA  1300
1301  SGSTAAAGTSLKIRIPEVACTICGARFTDQEHFSKHIQKHEQELYVDNPL  1350
1351  AAMFDDGPADAGQFQVERQNENGEYACDLCAKTFPQVIALKVHRKWHFRG  1400
1401  DSKQNPIDGEATQLTNNNHTTNNNNNNSMHLRELHAVGLMPNQQQQSLNN  1450
1451  SCNSSMNHNNNSSSNRSKSMKRKRELKCEYCASTFISNNNLRRHMYELHK  1500
1501  HEVSNLPEPPVIVVDDHLTCRRCQLKFDTKELWIEHKLADAKVVRPFCPF  1550
1551  QWGCDLCGEYLSRKEKLMNHINNHLKEEVIVPVATKAAIERTAAMESAAA  1600
1601  DANAAATLSALGEGAETEDQFAEKVEAAGATTTDKLTNPDEEDSDDLDED  1650
1651  SSGDDDDSSGTGDDDDDDDSDDDEDGEGEDEDEEGDGGEGEDEEGVQPPA  1700
1701  QLLPQQQHKTDLNLNQDDDDLVEEVISSDDDEDDDGEVESDDDDEDDDDE  1750
1751  EDDVEEPEPVGLTVRPLMNGKSKMPPLIVASSDDEDDGVMPIEDIIEEEF  1800
1801  DEDADPDPEDAIEEVDEDDLDEGEVEDEPNVVSTASFSESESSTTTTSNS  1850
1851  HSHSHSTGERRKKAVDQLNDPGFTCDLCQLCFDSQELLQSHIKSHILNGP  1900
1901  KLSTVSAAAAAAAAAATASSKATALLTAAKAKPDSKSAVLANNNNSKTSS  1950
1951  KTVAAGATN                                           1959

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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