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

NucPred

Fetching Q90693 from www.uniprot.org...

The NucPred score for your sequence is 0.35 (see score help below)

   1  MASAADALEPESGSSTAGGGSHPVRAARSARGRRRRSGGTRRAAAPDREY    50
  51  LQRPSYCDAAFALEQIAKGRATGRRAPLWLRAKFQRLLFNLGCYIQKNCG   100
 101  KFLVVGLLYSAFAVGLRAANLETNVEELWVEVGGRVSRELNYTRQKIGEE   150
 151  AMFNPQLMIQTPQEDGTNVLTTEALRQHLDSALQASRVHVYMYNRQWKLE   200
 201  HLCYKSGELITEAGYMDQIIEYLYPCLIITPLDCFWEGAKLQSGTAYLLG   250
 251  KPPLQWINFDPLEFLEELKKINYQVESWEEMLNKAEVGHGYMDRPCLNPA   300
 301  DPDCPITAPNKNSTKPLDVALVLSGGCYGLSRKYMHWQEELIIGGTVKNS   350
 351  SGKLVSAQALQTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAWQ   400
 401  RMYVEVVHQSVAQNSTQKVLSFTTTTLDDILKSFSDVSVIRVASGYLLML   450
 451  AYACLTMLRWDCAKSQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATT   500
 501  QVLPFLALGVGVDDVFLLAHAFSETGQNKRIPFEDRTGECLKRTGASVAL   550
 551  TSISNVTAFFMAALIPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDL   600
 601  YRREDRRLDIFCCFTSPCVTRVIQIEPQAYAENDNICYSSPPPYSSHSFA   650
 651  HETQITMQSTVQLRTEYDPHTQAYYTTAEPRSEISVQPVTVTQDSLSCQS   700
 701  PESASSTRDLLSQFSDSSVHCLEPPCTKWTLSTFAEKHYAPFLLKPKAKV   750
 751  VVIFLFLGLLGLSLYGTTRVRDGLDLTDIVPRDTREYDFIAAQFKYFSFY   800
 801  NMYIVTQKADYPNVQHLLYELHRSFSNVTYVLLEGDRQLPKMWLHYFRDW   850
 851  LQGLQDAFDSDWETGKITYSNYKNGSDDAVLAYKLLVQTGNRAKPIDISQ   900
 901  LTKQRLVDADGIINPNAFYIYLTAWVSNDPVAYAASQANIRPHRPEWVHD   950
 951  KADYMPETRLRIPAAEPIEYAQFPFYLNGLRETSDFVEAIEKVRAICNNY  1000
1001  TSLGIASYPNGYPFLFWEQYIGLRHWLLLSISVVLACTFLVCALFLLNPW  1050
1051  TAGIIVVVLALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHIA  1100
1101  LAFLTAIGDKNRRAVLALEHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRY  1150
1151  FFAVLAILTILGVLNGLVLLPVLLSFFGPYPEVSPACGRNRLPTPSPEPP  1200
1201  PSIVRFALPPGHTNNGSDSSDSEYSSQTTVSGISEELHHYEATQSPGIPV  1250
1251  HQVVVEATENPVFARSTVVQPESRHQSSPRLQSNPEAGTQQVWHQGRQPK  1300
1301  QEVREGLRPPPYRPRRDAFEISTEGHSGPSNKDRLNHKAHSHNMRSPAFG  1350
1351  AMGVPGSAYCQPITTVTASASVTVAVHPAVHSHNSCRGSFPSCEEYNEDD  1400
1401  RGMFEDPHVPFNVRCERRNSKVEVIELQDVECEERTAGKISE          1442

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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