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

NucPred

Fetching P25390 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MMMDILNTQQQKAAEGGRVLAPHTISSKLVKRLSSHSSHKLSRSDLKALG    50
  51  GSETISDGPSQLTFKDRYVFNESLYLKKLKKTALDDYYTRGIKLTNRYEE   100
 101  DDGDDEIIRLSNGDRIDEDLHSGVKFFSTTPYCRKMRSDSDELAWNEIAT   150
 151  ERFKWQSMLARVLKGDIVKGEKTRIANQVKKPGLNKELSDEIWLELKAWL   200
 201  NGRTMQEMEQSLTYLRDSSDSVFEEIMKFQIPQGKILSLDALEAILQDLM   250
 251  NRYHSVVSYWPNLKKMYKDKPITNTAEFTARIDVMNSWLNFKTNLTLRRQ   300
 301  ELDDWINRFSPISSSDNCQEDFDGVPQWNCKMKILAEQLMKEKNIESIFQ   350
 351  KKIFYPLSPWMFKLKLHFIVYRETLTKMNIKYPYERLRSLLAFPVYLIKE   400
 401  VILTRLSYARKLKNPTMMMIDQMIDDFNAFIRLSVQLKYTLTKYCSNLPF   450
 451  DVDFDPTFENTVIEAIRYLFFLLNLKLIDSSKQNFKAPDLLLKYWDHLKN   500
 501  TGHYINGAETVIPNEFLKLTLRLVHKLQFYLLKQQNFPPTFANASEAEKW   550
 551  LSSIFENLGAMKRKLNRFSNILVKAFQNSAVYQINHNAQLVKKLKDAHYF   600
 601  LVYSGNTFESSGVYMFAAPELLGCDNDTILRILRNKSIGCDLVPKLDIGN   650
 651  NLNVYDITTKETDLNILVSKGEDSKGIPYYRVVANSSSDLDRHAHQSKKK   700
 701  NFSTDPFDQHLDEKNNEVFELEVALSSLGALVVLYPGEPVVWDGPVYKLP   750
 751  GNNLFASNEMDLGKIGNPNTLILLNQGSNYALTYQIDKFNQTVGDSVSFI   800
 801  EKRCSLNSIESSLQKINKAYYKLTYTVLNNYKGILGSFMKQCPGNELLNS   850
 851  IFMFGRDFGRSFLKYNAFSSKRKYVIIFLMVKLGMNWLKFLVEECDPTDQ   900
 901  RTFRWCVLAMDFAMQMTSGYNILALNVKQFQELKERVSVCMSLLISHFDV   950
 951  MGARATEAENGMQQARLNIDTEENIDEEATLEINSRLRLEAIKTLEKTMK  1000
1001  RNPRQMGKVLDATDQGNKYLLSLASSLSNVSMRWQKRSFIGGGTFGQVYS  1050
1051  AINLENGEILAVKEIKIHDTTTMKKIFPLIKEEMTVLEMLNHPNIVQYYG  1100
1101  VEVHRDKVNIFMEYCEGGSLASLLDHGRIEDEMVTQVYTFELLEGLAYLH  1150
1151  QSGVVHRDIKPENILLDFNGIIKYVDFGTARTVVGSRTRTVRNAAVQDFG  1200
1201  VETKSLNEMMGTPMYMAPETISGSAVKGKLGADDVWALGCVVLEMATGRR  1250
1251  PWSNLDNEWAIMYHVAAGRIPQLPNRDEMTAAGRAFLERCLVQDPTMRAT  1300
1301  AVELLIDPWMIQIREIAFGNSEKDQVPILSS                     1331

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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