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

NucPred

Fetching Q6L3Y2 from www.uniprot.org...

The NucPred score for your sequence is 0.44 (see score help below)

   1  MIEIWKSQCTRILSISPDSGIQYWKKTESMKSQYLEEVGVALDSFVYWKE    50
  51  VIWKTKQEFRAEYSFPKTSLAANKVIDDDDINIDSLKFVKEVINVFVGNI   100
 101  NVLVKINDPRSWFFVPGLKEQIEQVLKEFKLLRFFVCFVSNKCIEPQYRC   150
 151  STFYSHVLIEASHIAMVVCLHLPIYGNGNQDLAPSEKMIDIWKSHCPDSF   200
 201  PYMKVISKTNVIIKTLYVDELRSCPSCNSYDSFDNWKEVIWKTKQEFRAE   250
 251  YSFPKTSLAVNKVDDVNTHSPKFVMEVIDVFVGNLNVLVEINDPSSWLFV   300
 301  PGHMKEQIEQVLKELKLLRFFVCFVSSKCIEPQYRCTTFYTLVLIEASHN   350
 351  AMVVWLHLPVYGNGNQDLAPSEVSRLFSDFMEMKIKSIEPGISRNSIYID   400
 401  VLQALKSTIPQAQKKQLDIPTHSLTVGFSGQMANLQEMLCLLRDNLIHLP   450
 451  ILDLEFHLQDMDSVIVDAGLLIYSLYDIKGEKEDTVLDDMNQALGFDLPR   500
 501  NIEPIKAMVYLVMQKAFHCNLPRIHGLGYVDFLLKNLNDFQGRYSDSLAF   550
 551  LKNQLQVIQTEFESLQPFLKVVAEEPHNKLKTLNEDCATQIIRKAYEVEY   600
 601  VVDACINKETPHWCLKCWLLDIIEENTCIKAKIQEKNTVEDTMKSVIART   650
 651  SSQLARTPRMNEEIVGFEDDLLLALLRDAIGEGSVRRELHANELSDMLRK   700
 701  TLLPRRYLILVDDVWENSVWDDLRGCFPDANNRSRIFGPSHPMLGPPKSK   750
 751  LPTHQMLSTGREVGEQVANNLGTHIHNDSRAIVDQSYHVLPCHLKSCFLY   800
 801  FGAFLEDRVIDISRLIRLWISEAFIKSSEGRSLEDIAEGYLENLIGRNLV   850
 851  MVTQRAISDGKVKACRLHDVLLDFCKERAAEENFLLWIKRDQTTKAVYSH   900
 901  KQHAHLAFTEMDNLVEWSASCSLVGSVLFKSYDPYFACRPLSSHAFAVSH   950
 951  ILLNFKFLKVLDLEHQIVIDFIPTELPYLRYFSALIDQNSIPSSKSNLWN  1000
1001  LETLILKRRSAATYKTLLLPSTVWDMVKLIYLYIPNFSPENKKALFKNSP  1050
1051  KLDDLETLSNPYFARVEDYLSETVDHLKHLEVLELYRVEFGDHGEWKVSS  1100
1101  GKFPKLKILKLDYVSLMKWIVADDAFPNLEQLVSLGCQNLMEIPSCFTDI  1150
1151  LSLKYIEVDICNKSVVKSAKYIQETQVEYNQNTNFKLVIIKKLVLKFDRF  1200
1201  HGDEEIRKRLSSLPGIKSISINRGEKKLTVGGDVDADEVRLVVGKLNKRD  1250
1251  ML                                                  1252

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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