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

NucPred

Fetching Q2KN96 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MRKASRSVGAAPKVPANNKSQATERSKSESSAPTASKVSRPGSSLSKAKS    50
  51  NDDLLAGMAGGLPASNSVKVKKNSTTSYPNSGTAMSGQEGRTRSSAGSSS   100
 101  NTKRSGSSGAKEVGSSRERLRERSRLTANKKPQGLGVGTGEVSAPSKRSR   150
 151  GRTDSDMIRMSKSKSDNQISDRAALEAKVKELMNLAKNKDAEILLLRTEL   200
 201  RDTRSQLGQDVSDKSPDDLPLIHLQEQNTTVCEELQQLKSENRMLKDRLN   250
 251  ALGFSLGQQPDDPDKLYGFQSLGINPGSHSDCGGGTLTSSVEGSAPGSME   300
 301  DLLSQDESTLTGERRSSSMDNLDSECSEVYQPLTSSDDALDAPSSSSESE   350
 351  GLPSTERSRKGSSGNASEVSVACLTERIHQMEENQHSTAEELQATLQELA   400
 401  DLQQITQELNSENERLGEEKVILMDSLCQQSDKLELFSRQLEYAQALLDE   450
 451  HHIAYSLDEDLKSSRYLDLEQRYMDLAENGRFEREQLLGVQQHLSNSLKM   500
 501  AEQDNKDAQDVIRALKERNHHMERIAEAEQLSKQALAATLEEYKATLNSE   550
 551  QGECARLKALLEQEKQRVAELYSIHSSGDASHIQNLLESVRSDKEKAESL   600
 601  ASSLQEELLHARTDVNRMQDAFGKLEDEYRAFREEAQKQVSELTLALEKV   650
 651  RHELEEKETELSDMKETIFELEDEVEQHRAVKLHDNLIISDVENAVKKLQ   700
 701  DQKHDMEREIKILNRKLREESAEWRQFQADLQTAVVIANDIKSEAQEEIG   750
 751  ELKRQLQEALEKNEKLAKEMENATSRKQEEERGRVYNYMNAVERDLAALR   800
 801  QGMGLNRRSSTSSDPAPTVKTLIKSFDNASSQAAAVAAAAATPISRTPLS   850
 851  PSPMKTPPAAAVSPMQRHSISGPISVAKSLPGLSEKRPSYAEIPVQEHML   900
 901  RSSSSSRSAASLPRVPAIDNAKSISVSRRSSEELKRDISVPDGSSAPSLM   950
 951  VMTSPSPQLSLSSSSPTASVTPTARSRIREERKDPLAALAREYGGSKRNA  1000
1001  LLKWCQKKTEGYPNIDITNFSSSWNDGLAFCALLHTYLPAHIPYQELTNQ  1050
1051  DKRRNFTLAFQAAESVGIKSTLDINEMVRTERPDWQCLMTYVTSIYKYFE  1100
1101  T                                                   1101

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.)

Go back to the NucPred Home Page.