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

NucPred

Fetching Q80TJ7 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MASVPVYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHC    50
  51  PNCEVLHGPSIMKKRRGSSKGHDNHKGKPLKTGSSMFIRELRGRTFDSSD   100
 101  EVILKPTGSQLTVEFLEENSFSVPILVLKKDGLGMTLPSPSFTVRDVEHY   150
 151  VGSDKEIDVIDVARQADCKMKLGDFVKYYYSGKREKVLNVISLEFSDTRL   200
 201  SNLVETPRIVRKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDF   250
 251  GGTSVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVEKC   300
 301  YKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIE   350
 351  KRLSTADLFKFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKAL   400
 401  NLAFRAWTKKEALPDHEDEIPETVRTVQLIKDLAREIRLVEDIFQQNVGK   450
 451  TSNIFGLQRIFPAGSIPLTKPAHSTSVSMSKLSLPSKNGSKKKGLKPKDI   500
 501  FKKAERKGKQSSALGPAGQLSYNLMDPYSHQALKTGPSQKAKFNMSGTSL   550
 551  NDSDDDSADMDLDGSENPLALLMANGSTKRMKSVSKSRRAKIAKKVDSAR   600
 601  LVAEQVMGDEFDLDSDDELQIDERLGKEKANLLIRSKFPRKLPRAKPCSD   650
 651  PNRIREPGEVEFDIEEDYTTDEDMVEGVESKLGNGSGAGGILDLLKASRQ   700
 701  VGGPDYAALTEAPASPSTQEAIQGMLCMANLQSSSSSPATSSLQAWWTGG   750
 751  QERSSGSSSSGLGTVSSSPASQRTPGKRPIKRPAYWKNESEEEENASLDE   800
 801  QDSLGACFKDAEYIYPSLESDDDDPALKSRPKKKKNSDDAPWSPKARVTP   850
 851  TLPKQDRPVREGTRVASIETGLAAAAAKLAQQELQKAQKKKYIKKKPLLK   900
 901  EVEQPRPQDSNPIMTMPAPTVATTPQPDTSSSPQPPPEPKQEALSGSLAD   950
 951  HEYTARPNAFGMAQANRSTTPMAPGVFLTQRRPSVGSQSSQAGQGKRPKK  1000
1001  GLATAKQRLGRILKIHRNGKLLL                             1023

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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