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

NucPred

Fetching Q19981 from www.uniprot.org...

The NucPred score for your sequence is 0.22 (see score help below)

   1  MISAREVFPCFIFRVFLLFQVFSRVHTLTNHANFEFEKSLSSCDKPCYNG    50
  51  VCLNKACVCSKGWYGSQCDHCFGRIRISDNASYISDGPLDYSPSAKCTWL   100
 101  IEPENSATPLKIRINSFFTECGWDYLYIYDGDSVYGKQLAALCGEQPSQE   150
 151  FTAASGKALVHFFSDLAINLNGFNVSYESNRCAYNCSNHGSCLNGKCDCE   200
 201  DGYKGLNCEYQVCQLSGKSTESPCHEGQCVDGRCECLSARVHGETCQMPV   250
 251  SSSVWDLIHPTNNAPTGKASHASIAIDDVVWSIGGEFFDGSSDPNNIDVY   300
 301  NVTSRIWSKVEVSGDMPKPRFDHTVVKYKNKLYMFGGVTKTQVRHQTTQA   350
 351  ATNELWIFDMGSKKWAQQIHKNETIIAAPFAVAGHSAHVIRSEMFVIFGY   400
 401  NPLFGFMHHVQIYNFETEEWTVANTSDHVYGRFKHSAVEYTTPTGATAIL   450
 451  VYGGSMWNNTITDSLMQFDTSTKKWSNLPQSGVQLYLHAAAYLNGLMVVV   500
 501  GGRGSNVTAGSKSECFSNMVQSYDVACKQWSNMSTAPVDLKRFGHSVHVI   550
 551  GQKLYALGGFNGKMKSDVWTLSPAKCSSATRPDECRLITDGTKCVFVDSS   600
 601  CVPFDPTVSYKSSFASMIKSSTPKSFDECTNTPLRLALKTCEEQTDCVSC   650
 651  ASKSGCGWCSSGEQCLPNEQECVDGPGMLTSWEKCPQRNSVATMRPCNME   700
 701  NNCGSCRISPHCTWYPIDKASPCVSKEDLIAVVYEYETKSVLADRNKFLS   750
 751  PSHFPSFFRNATECPMPCAQRNNCSDCTDLEQCMWCPSTNRCINLEAYTL   800
 801  SFAYGQCHSWVTSGSGSVINRVCQAESVVCEEHKTCGECQRDPGCGWLAD   850
 851  DSKTGLGLCIRGTSTGPLEPKPENSTWYFIDCPACQCNGHSTCFTSVGSF   900
 901  PPVTIEKCQSCQNHTTGAHCERCAPGFYGDARNGGVCSPCDCHHQADMCD   950
 951  PVSGQCFCKTKGVTGDRCDKCEAKYVGNPRNGTPCFYELAVDFIFTFKLR  1000
1001  SDDKDNHTSEIYLYSVPYKKDTDVTFQISCESPKGNALVALNMTSSYVNG  1050
1051  LADKSQAMMVDTICDSKGFRRVYVASDKGYPFGPDSNTTFFVRVYNFNTP  1100
1101  VQIVVSFAQSPPINWVLFFVIFAACFIVLLVVAGLLWMIKVRIEAYRRNQ  1150
1151  RRIDEIEHMASRPFASTKMELSMLSQFSSAGGPTPLSIEPCSNYRAGVFT  1200
1201  LAVRLPTGGKAVTPSGTSGLAVASSLCLLTPQQVGVLQAQDNGESNSGRK  1250
1251  SNFRNLLRLTIRQRPNNND                                 1269

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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