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

NucPred

Fetching P10676 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MMYLPYAQLPDPTDKFEIYEEIAQGVNAKVFRAKELDNDRIVALKIQHYD    50
  51  EEHQVSIEEEYRTLRDYCDHPNLPEFYGVYKLSKPNGPDEIWFVMEYCAG   100
 101  GTAVDMVNKLLKLDRRMREEHIAYIIRETCRAAIELNRNHVLHRDIRGDN   150
 151  ILLTKNGRVKLCDFGLSRQVDSTLGKRGTCIGSPCWMAPEVVSAMESREP   200
 201  DITVRADVWALGITTIELADGKPPFADMHPTRAMFQIIRNPPPTLMRPTN   250
 251  WSQQINDFISESLEKNAENRPMMVEMVEHPFLTELIENEDEMRSDIAEML   300
 301  ELSRDVKTLYKEPELFVDRGYVKRFDEKPEKMYPEDLAALENPVDENIIE   350
 351  SLRHRILMGESYSFIGDILLSLNSNEIKQEFPQEFHAKYRFKSRSENQPH   400
 401  IFSVADIAYQDMLHHKEPQHIVLSGESYSGKSTNARLLIKHLCYLGDGNR   450
 451  GATGRVESSIKAILMLVNAGTPVNNDSTRCVLQYCLTFGKTGKMSGAVFN   500
 501  MYMLEKLRVATTDGTQHNFHIFYYFYDFINQQNQLKEYNLKADRNYRYLR   550
 551  VPPEVPPSKLKYRRDDPEGNVERYREFENILRDIDFNHKQLETVRKVLAA   600
 601  ILNIGNIRFRQNGKYAEVENTDIVSRIAELLRVDEKKFMWSLTNFIMVKG   650
 651  GIAERRQYTTEEARDARDAVASTLYSRLVDFIINRINMNMSFPRAVFGDT   700
 701  NAIIIHDMFGFECFNRNGLEQLMINTLNEQMQYHYNQRIFISEMLEMEAE   750
 751  DIDTINLNFYDNKTALDNLLTKPDGLFYIIDDASRSCQDQDLIMDRVSEK   800
 801  HSQFVKKHTATEISVAHYTGRIIYDTRAFTDINRDFVPPEMIETFRSSLD   850
 851  ESIMLMFTNQLTKAGNLTMPFEAVQHKDESERKSYALNTLSAGCISQVNN   900
 901  LRTLAANFRFTCLTLLKMLSQNANLGVHFVRCIRADLEYKPRSFHSDVVQ   950
 951  QQMKALGVLDTVIARQKGFSSRLPFDEFLRRYQFLAFDFDEPVEMTKDNC  1000
1001  RLLFLRLKMEGWALGKTKVFLRYYNDEFLARLYELQVKKVIKVQSMMRAL  1050
1051  LARKRVKGGKVFKLGKKGPEHHDVAASKIQKAFRGFRDRVRLPPLVNEKS  1100
1101  GQLNENTADFIRPFAKKWREKSIFQVLLHYRAARFQDFVNLSQQVHIYNQ  1150
1151  RMVAGLNKCTRAVPFERINMREVNSSQLGPLPVPIKKMPFRLDQIPFYDT  1200
1201  QYMVDPANSISRQAFPNQLLTQHMEDDEPWDSPLQRNPSMTSCALTYNAY  1250
1251  KKEQACQTNWDRMGESDNIYNQGYFRDPQQLRRNQMQMNMNAYNNAYNSY  1300
1301  NSNYNNQNWGVHRSGSRRNSLKGYAAPPPPPPPMPSSNYYRNNPNQQQRN  1350
1351  YQQRSSYPPSDPVRELQNMARNEGDNSEDPPFNFKAMLRKTNYPRGSETN  1400
1401  TYDFNNRRGSDSGDQHTFQPPKLRSTGRRYQDDEGYNSSSGNYGVSRKFG  1450
1451  QQQRAPTLRQSPASVGRSFEDSNARSFEEAGSYVEEEIAPGITLSGYAVD  1500
1501  I                                                   1501

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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