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

NucPred

Fetching P53121 from www.uniprot.org...

The NucPred score for your sequence is 0.25 (see score help below)

   1  MRFLQVYKSSALIGLIILLASKVNLAEAKRKLVATSLVTCMENSQLSANS    50
  51  FDVVFNPDDRSLHYDLDMSTQIDSYIFADIDVYAYGFKIITKNVDLCSIN   100
 101  WKQFCPVHPGNIQIDSIEYISSEYVNEIPGIAYQVPDIDAYARVKITNNV   150
 151  SEYLACIQIYFSNGKTVSQIGVKWATAVVAGIGLLLSAILSTFGNSTAAS   200
 201  HISANTMSLFLYFQSVVVVAMQHVHRVPPIAAAWAENLVWSMGLIRISFM   250
 251  QRIFRWYVQSTGGTPSLYLTSTSMSVLAQRSWQYLMELPLIKRATNVLYG   300
 301  NANTLIFRGIKRLGYKMGIENTSIVCTGFTFFVLCGYVLAGFIIVFKCCV   350
 351  ELATRLGWIQKARFWEFRKQWRMILKGALLRYIYIGFVQLTILSFWEFTE   400
 401  RDSPAVIVIACLFILLSCGLMLWAAWRTVFFARRSVALYNNPAALLYGDE   450
 451  YVLHKYGFFYTMFNANHYWWNIVLLSYIFVKSLLVGFAQASGQTQVLFMF   500
 501  ILDLFYFVAIIYYKPYLDRPTNIMNILIATVTVVNSFLFMFFSDLFNQSY   550
 551  KVAAIMGWIFFIMNAAFSFILLMMILAFAGMMLFSKNPDLRFKPAKDDRT   600
 601  SFQRNTMKPEGTVNRSVANELLALGNVAKDHDDNSDYESNDTGVNDELKQ   650
 651  AQDETTPTTVTSSDDNKPTFSEKILSKFSRPKNENASTDALRVEAPKQQT   700
 701  FPHNLTNLSRENLSTLGSKPYPGHTRSQSDAHNGLINSFEEEDTSSNTDP   750
 751  FHDSTEGDLLDTSSSDGGFRSQNYVRDDSINSLGNNKQPLRKPPGFFDEG   800
 801  FM                                                   802

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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