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

NucPred

Fetching P20193 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MDRDSSMQAKNLDAQCNPDLKMASANSETLASATHELKIMDVEGGALVDP    50
  51  DHIEEVETSMVIVVDDDDGDVAMVVEEDKHPMRDDPCIEDIMDDEHAPLV   100
 101  AELQSALNNPDDKQASEDPLLEDQEREPDAMSTKTEPSSDAESSHSYHDP   150
 151  MGLLERIEIHDPGDSQDDDDEDDESSNGGGVDGGMRRKMPRAQRWLLWMK   200
 201  RWPWILHEDSDGTLAFCLYCNISINVNNRSRHIQQHNVSLSHQERECNYL   250
 251  AFKKSEEETRGAISDNEIKHEFGTKSYVAAMKQKRISETEAFNNFNWLRW   300
 301  LRWHPWLERSMPTGTIGTCRICSVRMNVEFVYLRKRHETTKGHMEALRNL   350
 351  DSDKRSRKRKRSKSNSVTNSGGDEAEREKESEPEVGPEDAQDTPVVMMNG   400
 401  DVDSGDDPGKWCALIPDTNPQQCRCTLCNCTMAITSFLRHCKTRAHCHML   450
 451  STPAEKGSSDIRGIWAVFADMHPWLIADPEDPSIGYCSVCRKRFMYGNSE   500
 501  IKRKNHEKSEKHTLALASAKAGIEVGSADGRGGDNMDEEEAAASDQAQSS   550
 551  QTDDSEDNDDDNWSEIQKLGKGFAHKSSSEPRKATVRAGVRFYPWLCYSK   600
 601  DRKTQICKFCRVRFHNEAAKARHELSARHVKLVKQFKMRQAKLHQGTNTQ   650
 651  TKHNAQDDEESQEQDEEYGEEEEDAEEDSQSNFDLGTVQARKTARADNKL   700
 701  FVKPIPATMKGKVMVWKGRFPWLSYKKNEQRGNYAWCKLCEVSLYLPSSK   750
 751  WASKHQRTSRHIRLRIDRKRNGGNPLKTSNKNSGEISTVVATASALASAE   800
 801  ARQKAAMAELQAKYDWLDPDANDENHCHCRVCDSRLPIKVFYLRQHDASR   850
 851  KHVENKERQRANAAAAANAPSVSPTSTVDAERQESGMDKESENDMSVRSD   900
 901  GSTAEPLAKRSRRSMEVRRIIRALRDSMGKRQEERSQMDMARDMICSSFD   950
 951  IVTRLRTLERESVAHNESMAQAPPSVTVSPIKPPEPRHVMDLFFDSISPT  1000
1001  MKSLPPDLAAEGKSKIMQLVCSLELRAMQRNATTPTPATVSASSKWPSST  1050
1051  TVTPVKTPPAPISAPLASVDADLHSSVVTTPHEYNNGQNNNNDKETVPKE  1100
1101  PVTGASSAQVTINGSAKDLPENIRRILTSNQTQVTNRLETDSVRCVPLDK  1150
1151  LTTQSRTNVNGRLSQGGTSEAPSTPQADLSNGNTLAMIRQIRVNNNNSSK  1200
1201  ITVTNTPQMQQPQQAQASITSSTPIMRGGPSSNGCQITTFRTMVNHNRRP  1250

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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