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

NucPred

Fetching Q9BXX3 from www.uniprot.org...

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

   1  MEEISAAAVKVVPGPERPSPFSQLVYTSNDSYIVHSGDLRKIHKAASRGQ    50
  51  VRKLEKMTKRKKTINLNIQDAQKRTALHWACVNGHEEVVTFLVDRKCQLD   100
 101  VLDGEHRTPLMKALQCHQEACANILIDSGADINLVDVYGNTALHYAVYSE   150
 151  ILSVVAKLLSHGAVIEVHNKASLTPLLLSITKRSEQIVEFLLIKNANANA   200
 201  VNKYKCTALMLAVCHGSSEIVGMLLQQNVDVFAADICGVTAEHYAVTCGF   250
 251  HHIHEQIMEYIRKLSKNHQNTNPEGTSAGTPDEAAPLAERTPDTAESLVE   300
 301  KTPDEAAPLVERTPDTAESLVEKTPDEAASLVEGTSDKIQCLEKATSGKF   350
 351  EQSAEETPREITSPAKETSEKFTWPAKGRPRKIAWEKKEDTPREIMSPAK   400
 401  ETSEKFTWAAKGRPRKIAWEKKETPVKTGCVARVTSNKTKVLEKGRSKMI   450
 451  ACPTKESSTKASANDQRFPSESKQEEDEEYSCDSRSLFESSAKIQVCIPE   500
 501  SIYQKVMEINREVEEPPKKPSAFKPAIEMQNSVPNKAFELKNEQTLRADP   550
 551  MFPPESKQKDYEENSWDSESLCETVSQKDVCLPKATHQKEIDKINGKLEE   600
 601  SPNKDGLLKATCGMKVSIPTKALELKDMQTFKAEPPGKPSAFEPATEMQK   650
 651  SVPNKALELKNEQTLRADEILPSESKQKDYEENSWDTESLCETVSQKDVC   700
 701  LPKAAHQKEIDKINGKLEGSPVKDGLLKANCGMKVSIPTKALELMDMQTF   750
 751  KAEPPEKPSAFEPAIEMQKSVPNKALELKNEQTLRADEILPSESKQKDYE   800
 801  ESSWDSESLCETVSQKDVCLPKATHQKEIDKINGKLEESPDNDGFLKAPC   850
 851  RMKVSIPTKALELMDMQTFKAEPPEKPSAFEPAIEMQKSVPNKALELKNE   900
 901  QTLRADQMFPSESKQKKVEENSWDSESLRETVSQKDVCVPKATHQKEMDK   950
 951  ISGKLEDSTSLSKILDTVHSCERARELQKDHCEQRTGKMEQMKKKFCVLK  1000
1001  KKLSEAKEIKSQLENQKVKWEQELCSVRLTLNQEEEKRRNADILNEKIRE  1050
1051  ELGRIEEQHRKELEVKQQLEQALRIQDIELKSVESNLNQVSHTHENENYL  1100
1101  LHENCMLKKEIAMLKLEIATLKHQYQEKENKYFEDIKILKEKNAELQMTL  1150
1151  KLKEESLTKRASQYSGQLKVLIAENTMLTSKLKEKQDKEILEAEIESHHP  1200
1201  RLASAVQDHDQIVTSRKSQEPAFHIAGDACLQRKMNVDVSSTIYNNEVLH  1250
1251  QPLSEAQRKSKSLKINLNYAGDALRENTLVSEHAQRDQRETQCQMKEAEH  1300
1301  MYQNEQDNVNKHTEQQESLDQKLFQLQSKNMWLQQQLVHAHKKADNKSKI  1350
1351  TIDIHFLERKMQHHLLKEKNEEIFNYNNHLKNRIYQYEKEKAETENS     1397

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.)

Go back to the NucPred Home Page.