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

NucPred

Fetching O88902 from www.uniprot.org...

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

   1  LNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPD    50
  51  TASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQS   100
 101  ALDKLNEAIKLAKGQPDTVQDALRFAMDVIGGKYNSAKKDNDFIYHEAVP   150
 151  ALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLVPMAAHEASSLYSEE   200
 201  KAKLLREMLAKIEDKNEVLDQFMDSMQLDPDTVDNLDAYNHIPPQLMEKC   250
 251  AALSVRPDTVKNLVQSMQVLSGVFTDVEASLKDIRDLLEEDELQEQKLQE   300
 301  TLGQAGAGPGPSVTKAELGEVRREWAKYTEVHEKASFTNSELHRAMNLHV   350
 351  GNLRLLSGPLDQVRAALPTPALTPEDKAVLQNLKRILAKVQEMRDQRVSL   400
 401  EQQLRELIQKDDITASLVTTDHSEMKKLFEEQLKKYDQLKVYLEQNLAAQ   450
 451  DNVLRALTEANVQYAAVRRVLSELDQKWNSTLQTLVASYEAYEDLMKKSQ   500
 501  EGKDFYADLESKVAALLERAQSLCRAQEAARQQLLDRELKKKAPPPRPTA   550
 551  PKPLLSRREEGEAAEAGDQPEELRSLPPDMMAGPRLPDPFLGTAAPLHFS   600
 601  PGPFPGSTGPATHYLSGPLPPGTYSGPTQLMQPRAAVPMAPGPVLYPAPV   650
 651  YTSELGLVPRSSPQHGIVSSPYAGVGPPQPIVGLPSAPPPQFSGPELAMD   700
 701  VRPATTTVDSVQAPISSHMALRPGPAPAPPQPCFPVPQPVPQSVPQPQPL   750
 751  PTPYTYSIGTKQHLTGPLPQHHFPPGIPTSFPAPRIGPQPPPQLQPQPQP   800
 801  QPQPQPPPQPQPQPQPQPQPQPQPQPQRPVFGPQPTQQPLPFQHPHLFPS   850
 851  QAPGILTPPPPYPFTPQPGVLGQPPPTRHTQLYPGPPPDTLPPHSGALPF   900
 901  PSPGPPHPHPTLAYGPAPSPRPLGPQATPVSIRGPPPANQPAPSPHLVPS   950
 951  PAPSPGPGPVPSRPPTAEPPPCLRRGAAAADLLSSSPESQHGGTQPPGGG  1000
1001  QPLLQPTKVDAAERPTAQALRLIEQDPYEHPERLQKLQQELESFRGQLGD  1050
1051  AGALDAVWRELQEAQEHDARGRSIAIARCYSLKNRHQDVMPYDSNRVVLR  1100
1101  SGKDDYINASCVEGLSPYCPPLVATQRPLPGTAADFWLMVHEQKVSVIVM  1150
1151  LVSEAEMEKQKVARYFPIERGQPMVHGALSVALSSVRTTDTHVERVLSLQ  1200
1201  FRDQSLKRSLVHLHFPTWPELGLPDSPGNLLRFIQEVHAHYLHQRPLHTP  1250
1251  IVVHCSSGVGRTGAFALLYAAVQEVEAGSRIPELPQLVRRMRQQRKHMLQ  1300
1301  EKLHLKFCHEALVRHVEQVLQRHGVPPPGKPVASMSVSQKSHLPQDSQDL  1350
1351  VLGGDVPISSIQATIAKLSIRPLGGLDSPAASLPSLVEPPGLPPASLPEP  1400
1401  TPAPPSSPPPPSSPLPEPPQPEEEPSVPEAPSLGPPSSSLELLASLTPEA  1450
1451  FSLDSSLRGKQRMSKQNFLQAHNGQGLRAAQPTDDPLSLLDPLWTLNKT   1499

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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