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

NucPred

Fetching P04920 from www.uniprot.org...

The NucPred score for your sequence is 0.51 (see score help below)

   1  MSSAPRRPAKGADSFCTPEPESLGPGTPGFPEQEEDELHRTLGVERFEEI    50
  51  LQEAGSRGGEEPGRSYGEEDFEYHRQSSHHIHHPLSTHLPPDARRRKTPQ   100
 101  GPGRKPRRRPGASPTGETPTIEEGEEDEDEASEAEGARALTQPSPVSTPS   150
 151  SVQFFLQEDDSADRKAERTSPSSPAPLPHQEATPRASKGAQAGTQVEEAE   200
 201  AEAVAVASGTAGGDDGGASGRPLPKAQPGHRSYNLQERRRIGSMTGAEQA   250
 251  LLPRVPTDEIEAQTLATADLDLMKSHRFEDVPGVRRHLVRKNAKGSTQSG   300
 301  REGREPGPTPRARPRAPHKPHEVFVELNELLLDKNQEPQWRETARWIKFE   350
 351  EDVEEETERWGKPHVASLSFRSLLELRRTLAHGAVLLDLDQQTLPGVAHQ   400
 401  VVEQMVISDQIKAEDRANVLRALLLKHSHPSDEKDFSFPRNISAGSLGSL   450
 451  LGHHHGQGAESDPHVTEPLMGGVPETRLEVERERELPPPAPPAGITRSKS   500
 501  KHELKLLEKIPENAEATVVLVGCVEFLSRPTMAFVRLREAVELDAVLEVP   550
 551  VPVRFLFLLLGPSSANMDYHEIGRSISTLMSDKQFHEAAYLADEREDLLT   600
 601  AINAFLDCSVVLPPSEVQGEELLRSVAHFQRQMLKKREEQGRLLPTGAGL   650
 651  EPKSAQDKALLQMVEAAGAAEDDPLRRTGRPFGGLIRDVRRRYPHYLSDF   700
 701  RDALDPQCLAAVIFIYFAALSPAITFGGLLGEKTQDLIGVSELIMSTALQ   750
 751  GVVFCLLGAQPLLVIGFSGPLLVFEEAFFSFCSSNHLEYLVGRVWIGFWL   800
 801  VFLALLMVALEGSFLVRFVSRFTQEIFAFLISLIFIYETFYKLVKIFQEH   850
 851  PLHGCSASNSSEVDGGENMTWAGARPTLGPGNRSLAGQSGQGKPRGQPNT   900
 901  ALLSLVLMAGTFFIAFFLRKFKNSRFFPGRIRRVIGDFGVPIAILIMVLV   950
 951  DYSIEDTYTQKLSVPSGFSVTAPEKRGWVINPLGEKSPFPVWMMVASLLP  1000
1001  AILVFILIFMETQITTLIISKKERMLQKGSGFHLDLLLIVAMGGICALFG  1050
1051  LPWLAAATVRSVTHANALTVMSKAVAPGDKPKIQEVKEQRVTGLLVALLV  1100
1101  GLSIVIGDLLRQIPLAVLFGIFLYMGVTSLNGIQFYERLHLLLMPPKHHP  1150
1151  DVTYVKKVRTLRMHLFTALQLLCLALLWAVMSTAASLAFPFILILTVPLR  1200
1201  MVVLTRIFTDREMKCLDANEAEPVFDEREGVDEYNEMPMPV           1241

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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