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

NucPred

Fetching Q22670 from www.uniprot.org...

The NucPred score for your sequence is 0.62 (see score help below)

   1  MSVTPVILEAYCAVSDEVAKQVKKYLLGDFAEESKFERKNSESSDGSETQ    50
  51  FCRATEKKENVEVWDDWGDKEEGAAENSLESDESIRNWLFRCDLKTYSDA   100
 101  EYLLVTWESRFVVLRKPPDEPVYKIVCKQYIEGDPISNEITASSIFGLSN   150
 151  VRHIELLDSIIIALGTLDGHVYFFTEQGTMLYFDRFSIFEPVNSLQFEVV   200
 201  KTGQTFIVVFTKGFFMINPISLKSVLYQAKVLIAKCEKTVKQISESIELQ   250
 251  SELLAPDIKGNIIHVIFTGLHKPSTLEQYISASYDSFYAKVEKPSLPLYS   300
 301  TFMVTTEKEFAVFVWHDREEQDKLIDDVIKYGKSLVPSFGIRKFFGISTE   350
 351  PARIASHMRSAVHAPTRSIIMETRVAQNVSRSPDCQYVAVTDRMARVLVI   400
 401  DIASRQVVLIFKGYRDASISWVSVTEDDRVAQFLTIFAPRRSLLEVWTVL   450
 451  GNVRVCAQHVPSSECNVVTGGENKMLCGRCHVHTDSNSFFIDEKGEFHRI   500
 501  ALPFHLALTSRSRQDQHDHLLLKQLENTKTGGEDWFQTFSDLKMATSRKT   550
 551  TFQNALHNLSTAEEAHQFIARIRSIPTSASLGDLPNSAEKSIGFYARTVA   600
 601  ETKPPVGEYDDKDTSNYKLDSIVERILECHMQKFGERTDMLNDSEVMKVG   650
 651  EWLKYVDLSQEDIDVFSEHWSEKQRHCLANLIFGPLFGSFEIDEYYDTVL   700
 701  EKIPVKRKNIVKLFYMRFEKTTTHIDWRIFNRIVEMFLNLEKSETGILEQ   750
 751  VDQMAMDSKDVPLGMILLSICWCARIQIRILKGNDEDEVENDHDLEEEDE   800
 801  KNKTIDEWDAISPEAEHLDCIIMCLHCVSLAQSLLKDDSNILRISDVVPR   850
 851  IDSYIRENVAKWIVSTPIDTDTIEKLFPRDPSENLAEKGNEEDRRKQMII   900
 901  DFPDDKEVVIQRMYQIIPRVFEHDLVVADVCWEMMSQWFREKDDNFSYIK   950
 951  DCTTLLPQSIVDPRLRHGIARLIWDKFIFMVFQSIVNMVEKTGRRPKDKE  1000
1001  TRKEIGFGEVKLEEFLMECEKFLEVLMDSVRDMPPPIDFKQDLLVEMASS  1050
1051  SFAAHLHQSKTAYRQDQFAILASRQPLVNFHLVLHHQHLALALRLQLTTG  1100
1101  LRFHPLRNLFCVTGNRAFFASLDSHPLIPLDRVDDATMEKRHAFLVKVAE  1150
1151  QGSMEERRLARHLEMEWKLTVNEISFMQALSSFRLGNDHQGSLELASCVR  1200
1201  DDRSAVALARVLAARLIQLANEANKRYSTAHSQYLCALAGEEAARVELYE  1250
1251  NSPDDPLVDSNPKTWKDAVTSLGRAGNSVPQSAQAAIPFVRMNDIAKLYF  1300
1301  GAQWVNN                                             1307

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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