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

NucPred

Fetching Q7M6U3 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSRGAPFPVPCPVLLGTFTDDSLEAQLHEYAKQGNCVKLKKILKKGVCVD    50
  51  AVNTQGQSALFVAALLGHVKLVDVLVDYGSDPNHRCFDGSTPVHAAAFSG   100
 101  NQWILSKLLTAGGDLRLHDEKGRNPQAWALTAGKDRSTQMVEFMQRCTSH   150
 151  MKAIIQGFSYDLLKKIDSPQRLIGSPPWFGSLIQGSPNSSPNRQLKPGII   200
 201  SAQNIYSFGFGKFYLTSGMQLTYPGSLPVIGEKEVVQADDEPTFSFFSGP   250
 251  YMVMTNLVWNRSRVTVKELNLPTRPHCSRLRLADLLIAEQEHSSNLRHPN   300
 301  LLQLMAVCLSRDLEKIRLVYERITVGTLFSVLHERRSQFPVLHMEVIVHL   350
 351  LLQVADALIYLHSRGFIHRSLSSYAVHIVSAGEARLTNLEYLTESQDSGA   400
 401  HRNVTRMPLPTQLYNWAAPEVVLQKAATVKSDIYSFSVIIQEILTDSIPW   450
 451  NGLDGSLVKETIALGNYLEADVRLPEPYYDIVKSGIHAKQKNRTMNLQDI   500
 501  RYILKNDLKEFIGAQKTQPTESPRGQSYEPHPDVNICLGLTSEYQKDPPD   550
 551  LDIKELKEMGSQPHSPTDHSFLTVKPTLAPQTLDSSLSAQKPDNANVPSP   600
 601  PAACLAEEVRSPTASQDSLCSFEINEIYSGCLTLGTDKEEECLGTAASPE   650
 651  GDRPNQGDELPSLEEELDKMERELHCFCEEDKSISEVDTDLLFEDDDWQS   700
 701  DSLGSLNLPEPTREAKGKTSSWSKTDEYVSKCVLNLKISQVMMQQSAEWL   750
 751  RKLEQEVEELEWAQKELDSQCSSLRDASLKFANAKFQPAVGPPSLAYLPP   800
 801  VMQLPGLKQPENGGTWLTLARSPGNEREFQEGHFSKKPEKLSACGWKPFT   850
 851  QVSEESRGDCSELNNQLPTLRGPGKQSTGEQLPSTQEARESLEKNTNQNS   900
 901  RSMASVSSEIYATKSRNNEDNGEAHLKWRLAVKEMAEKAVSGQLLLPPWN   950
 951  PQSSAPFESKVENESTPLPRPPIRGPESTEWQHILEYQRENDEPKGNTKF  1000
1001  GKMDNSDCDKNKHSRWTGLQRFTGIRYPFFRNHEQPEQNEASQASCDTSV  1050
1051  GTEKFYSTSSPIGDDFERFQDSFAQRQGYVEENFQIREIFEKNAEILTKP  1100
1101  QFQAIQCAEDKQDETLGETPKELKEKNTSLTDIQDLSSITYDQDGYFKET  1150
1151  SYKTPKLKHAPTSASTPLSPESISSAASHYEDCLENTTFHVKRGSTFCWN  1200
1201  GQEAMRTLSAKFTTVRERAKSLESLLASSKSLPAKLTDSKRLCMLSETGS  1250
1251  SNVSAAFVTSTHATKRKSLPRELAEATSQQHLDELPPPAQELLDEIEQLK  1300
1301  QQQVSSLASHENTARDLSVTNKDKKHLEEQETNSSKDSSFLSSREIQDLE  1350
1351  DTERAHSSLDEDLERFLQSPEENTALLDPTKGSTREKKNKDQDVVEQKRK  1400
1401  KKESIKPERRESDSSLGTLEEDELKPCFWKRLGWSEPSRIIVLDQSDLSD  1450

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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