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

NucPred

Fetching P28349 from www.uniprot.org...

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

   1  MNSSDVQMMSSQDAPGSAGLAPDNIASSLPSKKKSRRGADPTNQKRRCVS    50
  51  TACIACRRRKSKCDGALPSCAACASVYGTECIYDPNSDHRRKGVYREKND   100
 101  SMKAQNATLQILIEAILNASEEDVIDIVRRIRTCDDLDEVAESIRRDEKN   150
 151  ATATNDNDDSDEPTQPGRDDATSQAVEGERDLARKMGELRIENGSVRFIG   200
 201  GTSHLIYLSEPTDASEEPELETRLSTCDENPITTWTEVTKNPQLIIHLVN   250
 251  MYFNWHYPYFTTLSRSLFYRDFIKGKPAGQPRSTVYCSSLLVNAMLALGC   300
 301  HFTSVDGAFAVPGDSRTKGDHFFAEAKRLIVQNDEYEKPRLTTVQALALM   350
 351  SVREAGCGREAKGWVYSGMSFRMAQDIGLNLDIGSLDEKEVDARRITFWG   400
 401  CFVFDKCWSNYLGRLPQLPKNTYNVPKYDVFPDEDAELWSPYTDAGFDQS   450
 451  CKQPSRTRAIGLQLSKLCEISSDLLLFFYHPSHIGRSSGKSAELKKLSEL   500
 501  HRRLEDWRTELPKEFEPKDGQLPNVILMHMFYHLQYIHLFRPFLKYTKEA   550
 551  SPLEKVQPRRICTTNANSISKLMRLYKKLYNLRQICNIAVYMLHSACTIH   600
 601  MLNLPEKTARRDITHGVRQLEEMAEDWPCARRTLGIISVLARKWNVELPE   650
 651  EAAIVLKRTDEKYGMFSTSEVPSPNRTAPSLAPSSPAPPYTPEASLLFST   700
 701  TAAAVLEQQPYSPMTLYSHPTPPHLGPESISDPGMSPNIVTFSDLPDPSA   750
 751  PIIPQQQQNMQAISSLSQNNMLHQHHHHLQNQHQPQQPHHNHMTYQQQQH   800
 801  NLLTHPVSASSMSMSDTLATITAWGIPTSSPGNNNNNNIVSQHPHHQKQP   850
 851  QQQQQPQAQRYPTVGSVGTNTVKPPAAATQTFTPAQLHANNLATATRSTA   900
 901  SNHKSVGRHVSPSSIYAIDGQDWYLKDGVTWQQGFQGWDLEGGGAGTATS   950
 951  TGGIGDGGGPTGGAGDSMARLAPRGNIGGGGGGGGGSTGQRQQQQQRQQQ  1000
1001  QQQQQQQQQQQQQQQQQQQQQQQQEANMFAYHHGAERGGGGIESTGMGMT  1050
1051  TVGGGGGGFDPIGGSGLLDDLVGLDELGSLDGLGHLPGLD            1090

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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