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

NucPred

Fetching O95255 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MAAPAEPCAGQGVWNQTEPEPAATSLLSLCFLRTAGVWVPPMYLWVLGPI    50
  51  YLLFIHHHGRGYLRMSPLFKAKMVLGFALIVLCTSSVAVALWKIQQGTPE   100
 101  APEFLIHPTVWLTTMSFAVFLIHTERKKGVQSSGVLFGYWLLCFVLPATN   150
 151  AAQQASGAGFQSDPVRHLSTYLCLSLVVAQFVLSCLADQPPFFPEDPQQS   200
 201  NPCPETGAAFPSKATFWWVSGLVWRGYRRPLRPKDLWSLGRENSSEELVS   250
 251  RLEKEWMRNRSAARRHNKAIAFKRKGGSGMKAPETEPFLRQEGSQWRPLL   300
 301  KAIWQVFHSTFLLGTLSLIISDVFRFTVPKLLSLFLEFIGDPKPPAWKGY   350
 351  LLAVLMFLSACLQTLFEQQNMYRLKVLQMRLRSAITGLVYRKVLALSSGS   400
 401  RKASAVGDVVNLVSVDVQRLTESVLYLNGLWLPLVWIVVCFVYLWQLLGP   450
 451  SALTAIAVFLSLLPLNFFISKKRNHHQEEQMRQKDSRARLTSSILRNSKT   500
 501  IKFHGWEGAFLDRVLGIRGQELGALRTSGLLFSVSLVSFQVSTFLVALVV   550
 551  FAVHTLVAENAMNAEKAFVTLTVLNILNKAQAFLPFSIHSLVQARVSFDR   600
 601  LVTFLCLEEVDPGVVDSSSSGSAAGKDCITIHSATFAWSQESPPCLHRIN   650
 651  LTVPQGCLLAVVGPVGAGKSSLLSALLGELSKVEGFVSIEGAVAYVPQEA   700
 701  WVQNTSVVENVCFGQELDPPWLERVLEACALQPDVDSFPEGIHTSIGEQG   750
 751  MNLSGGQKQRLSLARAVYRKAAVYLLDDPLAALDAHVGQHVFNQVIGPGG   800
 801  LLQGTTRILVTHALHILPQADWIIVLANGAIAEMGSYQELLQRKGALMCL   850
 851  LDQARQPGDRGEGETEPGTSTKDPRGTSAGRRPELRRERSIKSVPEKDRT   900
 901  TSEAQTEVPLDDPDRAGWPAGKDSIQYGRVKATVHLAYLRAVGTPLCLYA   950
 951  LFLFLCQQVASFCRGYWLSLWADDPAVGGQQTQAALRGGIFGLLGCLQAI  1000
1001  GLFASMAAVLLGGARASRLLFQRLLWDVVRSPISFFERTPIGHLLNRFSK  1050
1051  ETDTVDVDIPDKLRSLLMYAFGLLEVSLVVAVATPLATVAILPLFLLYAG  1100
1101  FQSLYVVSSCQLRRLESASYSSVCSHMAETFQGSTVVRAFRTQAPFVAQN  1150
1151  NARVDESQRISFPRLVADRWLAANVELLGNGLVFAAATCAVLSKAHLSAG  1200
1201  LVGFSVSAALQVTQTLQWVVRNWTDLENSIVSVERMQDYAWTPKEAPWRL  1250
1251  PTCAAQPPWPQGGQIEFRDFGLRYRPELPLAVQGVSFKIHAGEKVGIVGR  1300
1301  TGAGKSSLASGLLRLQEAAEGGIWIDGVPIAHVGLHTLRSRISIIPQDPI  1350
1351  LFPGSLRMNLDLLQEHSDEAIWAALETVQLKALVASLPGQLQYKCADRGE  1400
1401  DLSVGQKQLLCLARALLRKTQILILDEATAAVDPGTELQMQAMLGSWFAQ  1450
1451  CTVLLIAHRLRSVMDCARVLVMDKGQVAESGSPAQLLAQKGLFYRLAQES  1500
1501  GLV                                                 1503

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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