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

NucPred

Fetching P08096 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MSIDADFSDYEDEASGDENVLPNTTTKRKASTTSSKSRAKKASTPDLRQT    50
  51  SLTSMTASEQIPLVTNNGNGNSNVSTQYQRLTPREHVLRRPDTYIGSIEP   100
 101  TTSEMWVFDSEKNKLDYKAVTYVPGLYKIFDEIIVNAADNKVRDPNMNTL   150
 151  KVTLDPEANVISIYNNGKGIPIEIHDKEKIYIPELIFGNLLTSSNYDDNQ   200
 201  KKVTGGRNGYGAKLCNIFSTEFVVETADKERMKKYKQTWYDNMSRKSEPV   250
 251  ITSLKKPDEYTKITFKPDLAKFGMDKIDDDMVSIIKRRIYDMAGTVRETK   300
 301  VYLNNERISISGFKKYVEMYLASDTKPDEEPPRVIYEHVNDRWDVAFAVS   350
 351  DGQFKQVSFVNNISTIRGGTHVNYVANKIVDAIDEVVKKENKKAPVKAFQ   400
 401  IKNYVQVFVNCQIENPSFDSQTKETLTTKVSAFGSQCTLSDKFLKAIKKS   450
 451  SVVEEVLKFATAKADQQLSKGDGGLRSRITGLTKLEDANKAGTKESHKCV   500
 501  LILTEGDSAKSLAVSGLSVVGRDYYGVFPLRGKLLNVREASHSQILNNKE   550
 551  IQAIKKIMGFTHKKTYTDVKGLRYGHLMIMTDQDHDGSHIKGLIINYLES   600
 601  SYPSLLQIPGFLIQFITPIIKCTRGNQVQAFYTLPEYEYWKEANNNGRGW   650
 651  KIKYYKGLGTSDHDDMKSYFSDLDRHMKYFHAMQEKDAELIEMAFAKKKA   700
 701  DVRKEWLRTYRPGIYMDYTQPQIPIDDFINRELIQFSMADNIRSIPSVVD   750
 751  GLKPGQRKVVYYCFKRNLVHETKVSRLAGYVASETAYHHGEVSMEQTIVN   800
 801  LAQNFVGSNNINLLMPNGQFGTRSEGGKNASASRYLNTALSPLARVLFNS   850
 851  NDDQLLNYQNDEGQWIEPEYYVPILPMVLVNGAEGIGTGWSTFIPNYNPK   900
 901  DITANLRHMLNGEPLEIMTPWYRGFRGSITKVAPDRYKISGIINQIGENK   950
 951  VEITELPIRFWTQDMKEYLEAGLVGTEKIRKFIVDYESHHGEGNVHFNVT  1000
1001  LTEAGMKEALNESLEVKFKLSRTQATSNMIAFDASGRIKKYDSVEDILTE  1050
1051  FYEVRLRTYQRRKEHMVNELEKRFDRFSNQARFIHMIIEGELVVSKKKKK  1100
1101  DLIVELKEKKFQPISKPKKGHLVDLEVENALAEEEQSGDVSQDEDSDAYN  1150
1151  YLLSMPLWSLTYERYVELLKKKDEVMAELDALIKKTPKELWLHDLDAFEH  1200
1201  AWNKVMDDIQREMLEEEQSSRDFVNRTKKKPRGKSTGTRKPRAIAGSSSS  1250
1251  TAVKKEASSESKPSTTNRKQQTLLEFAASKEPEKSSDINIVKTEDNSHGL  1300
1301  SVEENRISKSPGLDSSDSGKSRKRSQSVDSEDAGSKKPVKKIAASASGRG  1350
1351  RKTNKPVATTIFSSDDEDDLLPSSLKPSTITSTKASAKNKGKKASSVKKQ  1400
1401  SPEDDDDDFIIPGSSSTPKASSTNAEPPEDSDSPIRKRPTRRAAATVKTP  1450
1451  IYVDPSFDSMDEPSMQDDSFIVDNDEDVDDYDESD                 1485

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.)

Go back to the NucPred Home Page.