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

NucPred

Fetching O95155 from www.uniprot.org...

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

   1  MEELSADEIRRRRLARLAGGQTSQPTTPLTSPQRENPPGPPIAASAPGPS    50
  51  QSLGLNVHNMTPATSPIGASGVAHRSQSSEGVSSLSSSPSNSLETQSQSL   100
 101  SRSQSMDIDGVSCEKSMSQVDVDSGIENMEVDENDRREKRSLSDKEPSSG   150
 151  PEVSEEQALQLVCKIFRVSWKDRDRDVIFLSSLSAQFKQNPKEVFSDFKD   200
 201  LIGQILMEVLMMSTQTRDENPFASLTATSQPIAAAARSPDRNLLLNTGSN   250
 251  PGTSPMFCSVASFGASSLSSLYESSPAPTPSFWSSVPVMGPSLASPSRAA   300
 301  SQLAVPSTPLSPHSAASGTAAGSQPSSPRYRPYTVTHPWASSGVSILSSS   350
 351  PSPPALASSPQAVPASSSRQRPSSTGPPLPPASPSATSRRPSSLRISPSL   400
 401  GASGGASNWDSYSDHFTIETCKETDMLNYLIECFDRVGIEEKKAPKMCSQ   450
 451  PAVSQLLSNIRSQCISHTALVLQGSLTQPRSLQQPSFLVPYMLCRNLPYG   500
 501  FIQELVRTTHQDEEVFKQIFIPILQGLALAAKECSLDSDYFKYPLMALGE   550
 551  LCETKFGKTHPVCNLVASLRLWLPKSLSPGCGRELQRLSYLGAFFSFSVF   600
 601  AEDDVKVVEKYFSGPAITLENTRVVSQSLQHYLELGRQELFKILHSILLN   650
 651  GETREAALSYMAAVVNANMKKAQMQTDDRLVSTDGFMLNFLWVLQQLSTK   700
 701  IKLETVDPTYIFHPRCRITLPNDETRVNATMEDVNDWLTELYGDQPPFSE   750
 751  PKFPTECFFLTLHAHHLSILPSCRRYIRRLRAIRELNRTVEDLKNNESQW   800
 801  KDSPLATRHREMLKRCKTQLKKLVRCKACADAGLLDESFLRRCLNFYGLL   850
 851  IQLLLRILDPAYPDITLPLNSDVPKVFAALPEFYVEDVAEFLFFIVQYSP   900
 901  QALYEPCTQDIVMFLVVMLCNQNYIRNPYLVAKLVEVMFMTNPAVQPRTQ   950
 951  KFFEMIENHPLSTKLLVPSLMKFYTDVEHTGATSEFYDKFTIRYHISTIF  1000
1001  KSLWQNIAHHGTFMEEFNSGKQFVRYINMLINDTTFLLDESLESLKRIHE  1050
1051  VQEEMKNKEQWDQLPRDQQQARQSQLAQDERVSRSYLALATETVDMFHIL  1100
1101  TKQVQKPFLRPELGPRLAAMLNFNLQQLCGPKCRDLKVENPEKYGFEPKK  1150
1151  LLDQLTDIYLQLDCARFAKAIADDQRSYSKELFEEVISKMRKAGIKSTIA  1200
1201  IEKFKLLAEKVEEIVAKNARAEIDYSDAPDEFRDPLMDTLMTDPVRLPSG  1250
1251  TIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVPELKEQIQAWMREKQNS  1300
1301  DH                                                  1302

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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