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

NucPred

Fetching Q62240 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MKPGSDDFLPPPECPVFEPSWAEFRDPLGYIAKIRPIAEKSGICKIRPPA    50
  51  DWQPPFAVEVDNFRFTPRIQRLNELEAQTRVKLNYLDQIAKFWEIQGSSL   100
 101  KIPNVERKILDLYSLNKIVMEEGGYEAICKDRRWARVAQRLNYPSGKNIG   150
 151  SLLRSHYERIIYPYEIFQSGANLVQCNTDPFDSEERDKEYKPHSIPLRQS   200
 201  VQPSKFSCYSRRGKRLQPEPEPTEEDIEKNPELKKLQIYGAGPKMIGLGL   250
 251  KAKEKTLRKKDSKQPDKEEVTCPATIVVKGEASEFGKVTSAFSDKNLNHS   300
 301  FEPCMKMTMQLRNNHSSTQFMNSYVCRICSRGDEVDKFLLCDGCSDNYHI   350
 351  FCLLPPLSEVPKGVWRCPKCILAECKSPPEAFGFEQATQEYTLQSFGEMA   400
 401  DSFKADYFNMPVHMVPTEVVEKEFWRLVSSIEEDVTVEYGADIHSKEFGS   450
 451  GFPVNNSKWDLSPEEKEYAACGWNLNVMPVLDQSVLCHINADISGMKVPW   500
 501  LYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEDVMKR   550
 551  LTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAY   600
 601  HSGFNQGYNFAEAVNFCTADWLPVGRQCIEHYRRLRRYCVFSHEELICKM   650
 651  AAFPEKLDLNLAVAVHKEMFIMVQEERRLRKTLLEKGITEAEREAFELLP   700
 701  DDERQCIKCKTTCFLSALACYDCPDSLVCLSHINDLCKCSRNRQYLRYRY   750
 751  TLDELPAMLQKLKIRAESFDNWANKVQAALEVEDGRKRSFEELRALESEA   800
 801  RDRRFPNSELLQRLKKCLTEAEACISQVLGLISNSEDRLQTPQITLTELQ   850
 851  LLLKQMGTLPCTMHQIDEVKDVLQQVESYQIETREALTSLPYSLEILQSL   900
 901  MEKGQQLRVEVPEAHQLEELLEQAQWLDQVKQALAPSGQRHSLVIMKKLL   950
 951  VMGTKVASSPSVNKARAELQELLTIAECWEEKAHFCLKASQKHSPATLEV  1000
1001  IIREAENIPVYLPNIQSLKEALTKAQAWIADVNEIQNGDHYPCLDDLEGL  1050
1051  VAVGRDLPVELEELRQLENQVLTAHSWKEKASKTFLKKNSCYTLLEVLCP  1100
1101  CADAGSVSTKRSRWIEKEMGLYKYDTELLGLSAQDLRDPGSVIMAFKEGE  1150
1151  EKEKEGILHLRHINSAKPSPMSSSMNASATSICICGQVCAGVESLQCDLC  1200
1201  HDWFHGQCVTVPHLLSSVRASHTSSQLLAWWEWDTKFLCPLCMRSRRPRL  1250
1251  ETILSLLVGLQRLSVRLPEGEALQCLTERAIGWQGRARQALASEDVTALL  1300
1301  KQLEKSRQQLQDELRHKKPPTLPSGFAFDCLTENSGKDILKEEEELVLNE  1350
1351  ERIKSSEKIVPKESSCKGDKELLPSLLSQLTGPVLELPEATRAPLEELMM  1400
1401  EGDLLEVTLDENYSIWQLLQAGQNPNLERIHTLLELEKPENPGNWSEEQT  1450
1451  PERRRQRRQKVVLSRKGEDFTQKELESKRVKSSRIKPKEEKFQKPILGDN  1500
1501  VLYTHHTEHTNILKEHINSVQGKDPSPSSSFPSLTPLLHLSYFHQQKL    1548

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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