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

NucPred

Fetching P40105 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEKASARP    50
  51  NDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIF   100
 101  SAYQASLPGEKKVDTERLKRDLCPRKPTEIKYFSQICNDMMNKKDRLGDI   150
 151  LHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRS   200
 201  PNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHE   250
 251  VAQETALKDSYRITLVPSSDGVSVCGKLFNREYVRGFYFACKAQFDNLWE   300
 301  ELNDCFYMPTVVDIASLILRNREVLFREPKRGIDEYLENDSFLQMIPVKY   350
 351  REIVLPKLRRDTNKMTAALKNKVTVAIDELTVPLMWMIHFAVGYPYRYPE   400
 401  LQLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVF   450
 451  YFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPDQVTNRDISRIVLYS   500
 501  YMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVG   550
 551  SRFETDLYESATSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERA   600
 601  SERWIQWLGLESDYHCSFSSTRNAEDVVAGEAASSDHHQKISRVTRKRPR   650
 651  EPKSTNDILVAGQKLFGSSFEFRDLHQLRLCHEIYMADTPSVAVQAPPGY   700
 701  GKTELFHLPLIALASKGDVKYVSFLFVPYTVLLANCMIRLSRCGCLNVAP   750
 751  VRNFIEEGCDGVTDLYVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKL   800
 801  GYLIVDEFHNFETEVYRQSQFGGITNLDFDAFEKAIFLSGTAPEAVADAA   850
 851  LQRIGLTGLAKKSMDINELKRSEDLSRGLSSYPTRMFNLIKEKSEVPLGH   900
 901  VHKIWKKVESQPEEALKLLLALFEIEPESKAIVVASTTNEVEELACSWRK   950
 951  YFRVVWIHGKLGAAEKVSRTKEFVTDGSMRVLIGTKLVTEGIDIKQLMMV  1000
1001  IMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKGELPPIKEGC  1050
1051  ITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQA  1100
1101  TASMSIVALPSSFQESNSSDRCRKYCSSDEDSDTCIHGSANASTNATTNS  1150
1151  STNATTTASTNVRTSATTTASINVRTSATTTESTNSSTNATTTASTNVRT  1200
1201  SATTTASINVRTSATTTESTNSNTSATTTESTDSNTSATTTESTDSNTSA  1250
1251  TTTASTNSSTNATTTASTNSSTNATTTESTNASAKEDANKDGNAEDNRFH  1300
1301  PVTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLGFRSDEIK  1350
1351  HLFLYGIDVYFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRMAWEA  1400
1401  LAVERMLRNDEEYKEYLEDIEPYHGDPVGYLKYFSVKRGEIYSQIQRNYA  1450
1451  WYLAITRRRETISVLDSTRGKQGSQVFRMSGRQIKELYYKVWSNLRESKT  1500
1501  EVLQYFLNWDEKKCREEWEAKDDTVFVEALEKVGVFQRLRSMTSAGLQGP  1550
1551  QYVKLQFSRHHRQLRSRYELSLGMHLRDQLALGVTPSKVPHWTAFLSMLI  1600
1601  GLFCNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADNTRVPLYMLM  1650
1651  VAVHKELDSDDVPDGRFDILLCRDSSREVGE                     1681

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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