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

NucPred

Fetching Q24020 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MSVLPFVRGVDFTKNDFSATFPSSMRQMSRVQWLTLDRTQLAEIPEELGH    50
  51  LQKLEHLSLNHNRLEKIFGELTELSCLRSLDLRHNQLKNSGIPPELFHLE   100
 101  ELTTLDLSHNKLKEVPEGLERAKNLIVLNLSNNQIESIPTPLFIHLTDLL   150
 151  FLDLSHNRLETLPPQTRRLINLKTLDLSHNPLELFQLRQLPSLQSLEVLK   200
 201  MSGTQRTLLNFPTSIDSLANLCELDLSHNSLPKLPDCVYNVVTLVRLNLS   250
 251  DNELTELTAGVELWQRLESLNLSRNQLVALPAALCKLPKLRRLLVNDNKL   300
 301  NFEGIPSGIGKLGALEVFSAANNLLEMVPEGLCRCGALKQLNLSCNRLIT   350
 351  LPDAIHLLEGLDQLDLRNNPELVMPPKPSEASKATSLEFYNIDFSLQTQL   400
 401  RLAGAAVPPSMPSSATPKDSTARKIRLRRGPRSEGDQDAAKVLKGMKDVA   450
 451  KDKDNEAGAVPEDGKPESLKPKRWDESLEKPQLDYSKFFEKDDGQLPGLT   500
 501  IWEIENFLPNKIEEVVHGKFYEGDCYIVLKTKFDDLGLLDWEIFFWIGNE   550
 551  ATLDKRACAAIHAVNLRNFLGARCRTVREEQGDESEQFLSLFETEVIYIE   600
 601  GGRTATGFYTIEEMIHITRLYLVHAYGATIHLEPVAPAITSLDPRHAFVL   650
 651  DLGTHIYIWMGERSKNTLNSKARLMAEKISKTERKNKCEIQLERQGEESA   700
 701  EFWQGLGMTSEEADAAEPPKEHVPEDYQPVQPRLYQVQLGMGYLELPQVE   750
 751  LPEQKLCHTLLNSKHVYILDCYTDLFVWFGKKSTRLVRAAAVKLSRELFN   800
 801  MMDRPDYALVMRVPEGNEMQIFRTKFAGWDEVMAVDFTRTAKSVAKTGAN   850
 851  LTQWARQQETRTDLAALFMPRQSAMPLAEAEQLEEEWNYDLEMMEAFVLE   900
 901  NKKFVRLPEEELGRFYTGECYVFLCRYCIPIEEPENGSEDGANPAADVSK   950
 951  SSANNQPEDEIQCVVYFWQGRNAGNMGWLTFTFTLQKKFKAMFGEELEVV  1000
1001  RIFQQQENLKFMSHFKRKFIIHTGKRKDKAHTAKGKSPVEFFHLRSNGGA  1050
1051  LTTRLIQINPDAVHLNSTFCYILHVPFETEDDSQSGIVYVWIGSKACNEE  1100
1101  AKLVQDIAEQMFNSPWVSLQILNEGDEPENFFWVALGGRKPYDTDAEYMN  1150
1151  YTRLFRCSNERGYYTVAEKCADFCQDDLADDDIMILDNGEHVFLWMGPRC  1200
1201  SEVEVKLAYKSAQVYIQHMRIKQPERPRKLFLTMKNKESRRFTKCFHGWS  1250
1251  AFKVYL                                              1256

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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