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

NucPred

Fetching Q6PB44 from www.uniprot.org...

The NucPred score for your sequence is 0.60 (see score help below)

   1  MEAVPRMPMIWLDLKEAGDFHFQSAVKKFVLKNYGENPEAYNEELKKLEL    50
  51  LRQNAIRVARDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVAVTWTEIF   100
 101  SGKSVSHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCA   150
 151  AGAFAYLREHFPQAFSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKS   200
 201  FLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAA   250
 251  VAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRF   300
 301  AMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPA   350
 351  VTGPDIFAKLVPMAAHEASSLYSEEKAKLLREMLAKIEDKNEVLDQFMDS   400
 401  MQLDPETVDNLDAYNHIPPQLMEKCAALSVRPDTVKNLVQSMQVLSGVFT   450
 451  DVEASLKDIRDLLEEDELQEQKLQETLGQAGAGPGPSVAKAELAEVRREW   500
 501  AKYMEVHEKASFTNSELHRAMNLHVGNLRLLSGPLDQVRAALPTPALTPE   550
 551  DKAVLQNLKRILAKVQEMRDQRVSLEQQLRELIQKDDITASLVTTDHSEM   600
 601  KKLFEEQLKKYDQLKVYLEQNLAAQDNVLRALTEANVQYAAVRRVLSELD   650
 651  QKWNSTLQTLVASYEAYEDLMKKSQEGKDFYADLESKVATLLERAQSICR   700
 701  AQEAARQQLLDRELKKKAPPPRPTAPKPLLSRREEGEAVEAGDTPEELRS   750
 751  LPPDMMVGPRLPDPFLGTTAPLHFSPGPFPSSTGPATHYLSGPLPPGTYS   800
 801  GPTQLMQPRAAVPMAPATVLYPAPAYTSELGLVPRSSPQHGIVSSPYAGV   850
 851  GPPQPVVGLPSAPPPQLSGPELAMTVRPATTTVDSVQAPISSHTAPRPNP   900
 901  TPALPQPCFPVPQPVPQSVPQPQPLPVPYTYSIGTKQPLPAPYTYSIGTK   950
 951  QHLTGPLPQHQFPPGIPTGFPVPRTGPQAQAQPQPQPQPQPQPQPQPQPQ  1000
1001  PQPQSQSQPQPQPQPQPQRPAFGPQPTQQPLPFQHPHLFPSQAPGILPPP  1050
1051  PPTPYHFTPQPGVLGQPPPTLHTQLYPGPSQDPLPPHSGALPFPSPGPPH  1100
1101  PHPTLAYGPAPSPRPLGPQATPVSIRGPPPASQPTPSPHLVPSPAPSPGP  1150
1151  GPVPSRPPTAEPPPCLRRGAAAADLLSSSPESQHGGTQPPGGGQPLLQPT  1200
1201  KVDAAEGRRPQALRLIEQDPYEHPERLQQLQQELEAFRGQLGDAGALDAI  1250
1251  WRELQEAQEHDARGRSIAIARCYSLKNRHQDVMPYDSNRVVLRSGKDDYI  1300
1301  NASCVEGLSPYCPPLVATQAPLPGTAADFWLMVHEQKVSVIVMLVSEAEM  1350
1351  EKQKVARYFPTERGQPMVHGALSVALSSIRTTETHVERVLSLQFRDQSLK  1400
1401  RSLVHLHFPTWPELGLPDSPGNLLRFIQEVHAHYLHQRPLHTPIVVHCSS  1450
1451  GVGRTGAFALLYAAVQEVEAGNGIPELPQLVRRMRQQRKHMLQEKLHLKF  1500
1501  CHEALVRHVEQVLQRHGVPPPGKPVASVNISQKNHLPQDSQDLVLGGDVP  1550
1551  ISSIQATIAKLSIRPLGGLDSPAASLPGLVEPPGLPPASLPESTPVPSSS  1600
1601  PPPLSSPLPEAPQPEEEPSVPEAPSLGPPSSSLELLASLTPEAFSLDSSL  1650
1651  RGKQRMSKQNFLQAHNGQGLRAAQPTDDPLSLLDPLWTLNKT          1692

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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