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

NucPred

Fetching Q9DGN1 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MITSELSVLQDSTNESAVMHTDMTAVSADLSTELVEDLEVKGKRKRGRPG    50
  51  RPPSAIKKPRKTPGDRSRAEPGSRGRGRANGHPQQNGEGDPVTLFEVVKM   100
 101  GKSAMQAVVDDWIESYKQDRDIALLDLINFFIQCSGCKGTVRIEMFRNMQ   150
 151  NAEIIRKMTEEFDEDSGDYPLTMPGPHWKKFRCNFCEFISVLIRQCQYSI   200
 201  IYDEYMMDTVISLLTGLSDSQVRAFRHTSTLAAMKLMTALVNVALNLSIH   250
 251  QDNTQRQYETERNKIINKRANERLELLLQKRKELQENQDEIENMMNSIFK   300
 301  GIFVHRYRDAIAEIRAICIEEIGVWMKMYSDAFLNDSYLKYVGWTLHDRQ   350
 351  GEVRLKCLKALQSLYTNRELFPKLELFTNRFKDRIVSMTLDKEYDVAVEA   400
 401  IRLVTLILHGSEEALSNEDCENVYHLVYSAHRPVAVAAGEFLHKKLFSRH   450
 451  DPQAEEALAKRRGRSSPNGNLVKMLVLFFLESELHEHAAYLVDSLWESSQ   500
 501  ELLKDWECMTELLVEEPMQGEEVMSERQESALVELMVCTIRQAAEAHPPV   550
 551  GRGTGKRVLTAKERKTQLDDKTKLTEHFIVALPVLLSKYSADAEKVANLL   600
 601  QIPQYFDLELYSTGRMEKHLDSLLKQIRFVVEKHIESDVLEACSKTYSIL   650
 651  CSEEYTIQNRVEIAHSQLIDELADRFSHAVEELLQEAEEADEDEIYNVMA   700
 701  SLKRLTCFHNAHDLTKWDFFGNCYRLLRAGIEHEGMMEQIVVQALQCSHY   750
 751  SILWQLVKITEGNPSKEEMLALRKTVKSFLAVCQQCLSSMTTLVKEQAFM   800
 801  LLCDLLMIFSHQLTTGGRENLLLLVFNPDVGLQSELLSFVMDHVFIDQDD   850
 851  ENQSMEGDEEDEANKIEALHKRRNLLASFCKLIIYDIVDMNAAADIFKHY   900
 901  MKYYNDYGDIIKETLSKTRQMDKIQCAKTLILSLQQLFNELVQEQGPNLD   950
 951  RTSAHVSGIKELARRFALTFGLDQIKTREAVATLHKDGIEFAFKYQNPKG  1000
1001  PEYPPLNLAFLEVLSEFSSKLLRQDKKTVHSYLEKFLTDLMMERREDVWL  1050
1051  PLISYRNSLVTGGDEDRLSVNSGGSNSKGSSVRSKKGRPPLHKKRVIEEE  1100
1101  SIDNSWVTRNDTIQTPGALTTPQLTSTVLRENPRQIPEQIPEQESEPSSE  1150
1151  PDFLHSPQMQMSWLGQQKLEDLNRKDRTSMSYMKVRSGVRHAVRGLMEDD  1200
1201  AEPIFEDVMMSSRGQLEDMNEEFEDTMVIDLPPSRNRRERAELRPDFFDS  1250
1251  AAIIEDDSGFGMPMF                                     1265

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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