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

NucPred

Fetching Q75E74 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MSSWLPQNVQKRLLIYLLQQISIFSQIDTTNLDVSLGCRSQFAFHDVELN    50
  51  VDHMRVPHITVESGHISELELGLVVSGGLDITGDGLCFVVRPELSEVAGS   100
 101  HDLAQSLARSIMDLTNSMMQPLPEVLEGDEVLANSCSEAGDAQQPASSSA   150
 151  LDKMRNKVLERALSNLTVRIINVRIQVLFPGQQSITVLVGSVELSTVDKT   200
 201  RRVDLQDICISHSELVPSPEQPDEFMSTSASNSIYMSAIDSLPFGSRSKM   250
 251  EENARNVRALLQMDKLHVTFQGISSVEDISIRDLMLHMGRVDVFLDAIIA   300
 301  VDIGVFEVLVQFVAEFQQDTEVSETSNTLQNYKRFRQEQNLEEDLQITGF   350
 351  TIEELRITLSQSVKVSVIDIQLRNRYIENSTVTVGRVTICDYDLDLLHID   400
 401  AGSKPCLELTVDSRKLQRIISVDGDIHMDISSTFVSSLIPLIFRLQELGR   450
 451  GLHFVGTNNCKMSQEFKTQVETKTIILSLPVGDDTLQMIIQPISYELSLH   500
 501  TVFTDFISISKVQSSETRDIAIIREIKIGYQTANFQVKSYNLKLSETLLT   550
 551  SKLRGSVSSVELYCSDSDIKWLFDGLSPYQDMITPYMHSKPEVRKPIMNK   600
 601  SVRILSASSVIHRQNVFSDMVLLIERITCSLSADSISSFGNVKTELNSSL   650
 651  LSLNTDNSIIFHSSCVKGSTVFSDVKYCLFEPIKTKDVTKPALFVQRFEN   700
 701  GKLKVNVQNTCIYYHAKWLDILDESKGTKSTPQQESAVPVPLQQRIEVKF   750
 751  HDCALSMHPYRLKSALLICVNRCILDISVPPANFKCIIRSPTFMLADDCS   800
 801  NMKTSITESWESLVRYYSKAGFAVIGKSGLLSCTIKQSGGQICLDIDVDR   850
 851  IDLSICADSFQCLIQTLIDIKPPVSFPDEKKYRTEPCSIPVFENVDDEFF   900
 901  VPKGTSNLPALNDMHIVDDFINNSNNSFSEVQVIEETEEGSPLKLEDNGL   950
 951  LFDEGHFNKEDIPVATDSKFFPFGPVAIVLHLFVRKASIKLHDGYDWVYT  1000
1001  RRSISKVVDDLEDEVHKQDQPGRVETSLFDSIYLYATPDSNIKKAVSSNI  1050
1051  QSEDIIAENYSSKMKLRPSKHHKILIELTNMKLTFSGYSYDEPTEDIADW  1100
1101  STDLLNSIDVEVKTFEIVDNVATSTWNKFLTELKEAHGGSPSMLALSISL  1150
1151  VRPIDFLYATELIISAQVSPLRLHVDQDTLDFLIRFSEFKDARFDLIDDY  1200
1201  PDIVYIQRFEVNSIDVKLDYKPKKVDYVGLKSGHTSELMNFFTLDGAKMT  1250
1251  LKRVVLYGVDGLGELHNCLSSIWTPDITRSQLSGVLKGVTPLKSIITLGS  1300
1301  GVKALVTVPLKEYRQDQRLTRSLQKGARDFLKTTSGELIRLGVRMASGTQ  1350
1351  AILENTEEFFGGQGARARCMSARLPEDELSPVPSACDEFDLFRSSIPRKQ  1400
1401  SPIVPIPSEEDDIEPLKAISLYADQPQNAQKGVKEAYGSLGKNLTIAYGA  1450
1451  VRRAQRDARHSISAQDAATAFARATPIAFIRPMIGATEAVSKTLQGISNQ  1500
1501  MDRDQLVHMRDKYKQSSHYQRKRER                           1525

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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