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

NucPred

Fetching P31563 from www.uniprot.org...

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

   1  MTLKMFLPVNLVSVCMKLNNSVVMVGLYYGFISAFSIGSSYLFLLRPRFL    50
  51  NDDPDAIEKKASETAGFFTGQLLIFISILYGPLHLALGRPHTILLLLAPY   100
 101  FFFHFLSSNSGQYPSQRFAFPLLTKSMRNRSFQLVFLHSLLFQLFSLSVL   150
 151  GRPMLTRLSYIYIFRSNNKMLFVLSSFVGWLIGHILVLKWAGLVFVWLLK   200
 201  FIRSKTMKYITCNVLIPATKYIIEKWRNSFVAGLIREILAMKQVESALVR   250
 251  IKNSRLLDDVRWWIRGSGLISGLKINIRFYARLILRGFENVYVGAKFRQD   300
 301  MEHLFSIILFAFFLLYLDRTPLLYADPADKKLQLQRKLSNETQAAREEKE   350
 351  LEERLTEKFEAQRRAQRAAQRKALQEFKQGVVESYLANQAAKDENQIQAQ   400
 401  KDEKQIQAEKKATIRAEQVVQYTFGLIEAQRREMEIEAARAMQEAYKGML   450
 451  AAEEEDVEEGVQEKQEGFPEEPISPSEEREENPKLLILKEKISILTEKIS   500
 501  ILTEKNDLFSFEIPIITSLFDPQKPLRPLRYIKTCAGVEKAVKNEMSQYF   550
 551  FYPCRSDGKQRLCFTYPPSLATFWEMIQRKMASRFPRIYTKAKWRALRGS   600
 601  APGSYRQWISRNKKKKNSLSTEFQNRIQTLDQKKSLLNVLARRKRSSLQN   650
 651  VLETRKRLCNYKTKKEYLPEIADPFLTGALRGKSDPEVYDGVRKTSEIKV   700
 701  VFLKNNITMATLGNKNDDDLREEKNAISLLSRMKNPVNKLHLLFVNERDY   750
 751  PFVKPLVNRINGPAVPKKKKTISKSKQNEIKSKQKKVKSKQKKVKSKQKK   800
 801  VKSKQKKVKSKQNEIKSKQNEIKSKQKKVKRKQNEIKSKLNEVKRKQNEI   850
 851  YPKGVKFNATPKTEINPHGIRFDAATIEKYSFATGYSYRPPSFHDIIFKA   900
 901  FVTEPQRNKKKVIELEEEINKQVPRWSYQLIDELEQLEGAEGETQFSDHE   950
 951  IRILPFKRVSVFTEKEAKKKPLIDEEGNYVRHKKTYAVRFLGHMSDFRRG  1000
1001  LIKGS                                               1005

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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