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

NucPred

Fetching Q02384 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MQQAPQPYEFFSEENSPKWRGLLVPALRKVQEQVHPTLSANEESLYYIEE    50
  51  LIFQLLNKLCMAQPRTVQDVEERVQKTFPHPIDKWAIADAQSAIEKRKRR   100
 101  NPLLLPVDKIHPSLKEVLGYKVDYHVSLYIVAVLEYISADILKLAGNYVF   150
 151  NIRHYEISQQDIKVSMCADKVLMDMFDQDDDIGLVSLCEDEPCSSGELNY   200
 201  YDLVRTEIAEERQYLRELNMIIKVFREAFLLDRKLFKPSEIEKIFSNISD   250
 251  IHELTVKLLGLIEDTVEMTDESSPHPLAGSCFEDLAEEQAFDPYETLSQD   300
 301  ILAPEFNDHFSKLMARPAVALHFQSIADGFKEAVRYVLPRLMLVPVYHCW   350
 351  HYFELLKQLKACSEEQEDKECLNQAITALMNLQGSMDRIYKQHSPRRRPG   400
 401  DPVCLFYNRQLRSKHLAIKKMNEIQKNIDGWEGKDIGQCCNEFIMEGPLT   450
 451  RIGAKHERHIFLFDGLMISCKPNHGQTRLPGYSSAEYRLKEKFVMRKIQI   500
 501  CDKEDACEYRHAFELVSKDENSVIFAAKSAEEKNNWMAALISLHYRSTLD   550
 551  RMLDSVLLKEENEQPLRLPSPDMYRFVVTDSEENIVFEDNLQSRSGIPII   600
 601  KGGTVVKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLNLLIERFEIP   650
 651  EPEPTEADKLALEKGEQPISADLKRFRKEYVQPVQLRVLNVFRHWVEHHY   700
 701  YDFERDLELLERLESFISSVRGKAMKKWVESIAKIIKRKKQAQANGISHN   750
 751  ITFESSPPPVEWHISRTGQFETFDLMTLHPIEIARQLTLLESDLYRKVQP   800
 801  SELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVEAENFEERVAV   850
 851  LSRIVEILQVFQDLNNFNGVLEIVSAVNSVSVYRLDHTFEALQERKRRIL   900
 901  DDAVELSQDHFKKYLVKLKSINPPCVPFFGIYLTNILKTEEGNSDFLKRK   950
 951  GKDLINFSKRRKVAEITGEIQQYQNQPYCLRTEPEMRRFFENLNPMGILS  1000
1001  EKEFTDYLFNKSLEIEPRNCKQPPRFPRKSTFSLKSPGIRPNAGRHGSTS  1050
1051  GTLRGHPTPLEREPYKISFSRIAETELESTVSAPTSPNTPSTPPVSASSD  1100
1101  HSVFLDVDLNSSCGSNTIFAPVLLPHSKTFFSSCGSLHKLSEEPLIPPPL  1150
1151  PPRKKFDHDALNSKGAVKSDDDPPAIPPRQPPPPKVKPRVPVLMGTFDGP  1200
1201  VPSPPPPPPRDPLPDTPPPVPLRPPEHFINCPFNLQPPPLGHPHRDPDWL  1250
1251  RDVSTCPNSPSTPPTTPSPRIPRSCHLLSSSHSSLAHLPAPPVPPRQNSS  1300
1301  PLLPKLPPKTYKRELSHPPLYRLPLLENAETPQ                   1333

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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