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

NucPred

Fetching Q03468 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MPNEGIPHSSQTQEQDCLQSQPVSNNEEMAIKQESGGDGEVEEYLSFRSV    50
  51  GDGLSTSAVGCASAAPRRGPALLHIDRHQIQAVEPSAQALELQGLGVDVY   100
 101  DQDVLEQGVLQQVDNAIHEASRASQLVDVEKEYRSVLDDLTSCTTSLRQI   150
 151  NKIIEQLSPQAATSRDINRKLDSVKRQKYNKEQQLKKITAKQKHLQAILG   200
 201  GAEVKIELDHASLEEDAEPGPSSLGSMLMPVQETAWEELIRTGQMTPFGT   250
 251  QIPQKQEKKPRKIMLNEASGFEKYLADQAKLSFERKKQGCNKRAARKAPA   300
 301  PVTPPAPVQNKNKPNKKARVLSKKEERLKKHIKKLQKRALQFQGKVGLPK   350
 351  ARRPWESDMRPEAEGDSEGEESEYFPTEEEEEEEDDEVEGAEADLSGDGT   400
 401  DYELKPLPKGGKRQKKVPVQEIDDDFFPSSGEEAEAASVGEGGGGGRKVG   450
 451  RYRDDGDEDYYKQRLRRWNKLRLQDKEKRLKLEDDSEESDAEFDEGFKVP   500
 501  GFLFKKLFKYQQTGVRWLWELHCQQAGGILGDEMGLGKTIQIIAFLAGLS   550
 551  YSKIRTRGSNYRFEGLGPTVIVCPTTVMHQWVKEFHTWWPPFRVAILHET   600
 601  GSYTHKKEKLIRDVAHCHGILITSYSYIRLMQDDISRYDWHYVILDEGHK   650
 651  IRNPNAAVTLACKQFRTPHRIILSGSPMQNNLRELWSLFDFIFPGKLGTL   700
 701  PVFMEQFSVPITMGGYSNASPVQVKTAYKCACVLRDTINPYLLRRMKSDV   750
 751  KMSLSLPDKNEQVLFCRLTDEQHKVYQNFVDSKEVYRILNGEMQIFSGLI   800
 801  ALRKICNHPDLFSGGPKNLKGLPDDELEEDQFGYWKRSGKMIVVESLLKI   850
 851  WHKQGQRVLLFSQSRQMLDILEVFLRAQKYTYLKMDGTTTIASRQPLITR   900
 901  YNEDTSIFVFLLTTRVGGLGVNLTGANRVVIYDPDWNPSTDTQARERAWR   950
 951  IGQKKQVTVYRLLTAGTIEEKIYHRQIFKQFLTNRVLKDPKQRRFFKSND  1000
1001  LYELFTLTSPDASQSTETSAIFAGTGSDVQTPKCHLKRRIQPAFGADHDV  1050
1051  PKRKKFPASNISVNDATSSEEKSEAKGAEVNAVTSNRSDPLKDDPHMSSN  1100
1101  VTSNDRLGEETNAVSGPEELSVISGNGECSNSSGTGKTSMPSGDESIDEK  1150
1151  LGLSYKRERPSQAQTEAFWENKQMENNFYKHKSKTKHHSVAEEETLEKHL  1200
1201  RPKQKPKNSKHCRDAKFEGTRIPHLVKKRRYQKQDSENKSEAKEQSNDDY  1250
1251  VLEKLFKKSVGVHSVMKHDAIMDGASPDYVLVEAEANRVAQDALKALRLS  1300
1301  RQRCLGAVSGVPTWTGHRGISGAPAGKKSRFGKKRNSNFSVQHPSSTSPT  1350
1351  EKCQDGIMKKEGKDNVPEHFSGRAEDADSSSGPLASSSLLAKMRARNHLI  1400
1401  LPERLESESGHLQEASALLPTTEHDDLLVEMRNFIAFQAHTDGQASTREI  1450
1451  LQEFESKLSASQSCVFRELLRNLCTFHRTSGGEGIWKLKPEYC         1493

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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