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

NucPred

Fetching P38938 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MKHIKNEREEVFLEDDQAQHSQAELLSSKDENLQPSIPLSPVAFELDFSG    50
  51  NFQFISDNSSELLDIPKDKIIGHSVAEVLGTDGYNAFMRAVNCLLKDDSH   100
 101  SYHVRFQHSINANHANQNYYTAKGDLPSDEKITKPFDAIGILIRHPGSAI   150
 151  PAHTMWVVNPATNSLGSVSPLVTKLLDVIGFGASLLDKYLCDLRTSYHKH   200
 201  NSLDALPLPTPEFCQICEREIQSWFFELHSKFCLSTSTYESVVQAAQDSL   250
 251  LYFRSTLLEIQEGMQKDSSLVPVYKNEPLIVDADDYFFTDENKQTLSLCS   300
 301  FLSQVMYYLEVAIDITIPPVKIIVNFDKVDSLRVQSPRSEKATIELDNYN   350
 351  PSLENCSSAVIALWEDIKTAVDTKITGVLRLRNAIYYSERIRLEIDHHVQ   400
 401  EIIDDVVSNLVTNHSSTSLGHLESKLAPSITFPDACDALEAEECITRPGS   450
 451  ATNTPQSDRSLDINDLSRSSSYSRHLSHVSLSNPDFAIGSPMSQDSSNYS   500
 501  SPLHRRKASDSNFSDPRFDDLKYLSPNSSPRFVASDGPNRPASNGRSSLF   550
 551  SRGRASNLGDVGLRLPSPSPRIHTIVPNSAPEHPSINDYKILKPISKGAF   600
 601  GSVYLAQKRTTGDYFAIKILKKSNMIAKNQVINVRAERAILMSQGESPFV   650
 651  AKLYYTFQSKDYLYLVMEYLNGGDCGSLLKTMGVLDLDWIRTYIAETVLC   700
 701  LGDLHDRGIIHRDIKPENLLISQNGHLKLTDFGLSRVGYMKRHRRKQSSS   750
 751  IPVLDLRDRSSAISDLSLSTASSVLEAQSLITPERPKRPSLNEKLLSLDG   800
 801  TSIRLAGQSFNYENSAEDSPTATNTPTSQVDESNIFRSTDSPRVQPFFEN   850
 851  KDPSKRFIGTPDYIAPEVILGNPGIKASDWWSLGCVVFEFLFGYPPFNAE   900
 901  TPDQVFQNILARRINWPAEVFTAESSVALDLIDRLLCMNPANRLGANGVE   950
 951  EIKAHPFFKSVNWDTILEEDPPFVPKPFSPEDTVYFDSRGLKGFDFSEYY  1000
1001  NQPTVTEAQKLEEERPASSIPQHVSGNRKGRLRSNTISTPEFGSFTYRNL  1050
1051  DFLNKANRNTIQKLRKEHMAVKSAKTSVDDTFSQYMSRFKAKLSTSQSVG  1100
1101  PVKSSRRASMADYEASTTTRVQDITTDSIDSIDDFDSLKEGRMLSFFDNL  1150
1151  ALEDHKGVSSTMSASQSQSSMHTALPDVTEGTSSDEHTTIQKGRIDNLQA  1200
1201  QSLTHKRNAISYPGLFQLDRLQMIIPKDEIELAEILKKIFPKLTLVLIDD  1250
1251  PWSILKKLLQNEQFNVVFLHFGNDKVSSSRLMYSVRTSATINSRVPFVYI  1300
1301  CEDETCIPTDLQSDGVLLKPITCENIESCLRKLDVWHS              1338

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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