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

NucPred

Fetching Q09237 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MSSVSSAEPTAQQNFNPSCHFRMRPNAANRGGSISSGNNRSSGFGGGGFD    50
  51  DGGDEISSSAIAAAAAAVLSSPVVSEFSYTRERLLELAPTGSIMPDALRD   100
 101  QLFFNEKNLPLVSNTPLSEHEQKLQHNINSSKAMSLLSHADRASIAAGAA   150
 151  YGSGYGAASGALQNGQSPTSRWAPKSSWNKGTPDRGTGTTPRGGGSVGRA   200
 201  SGAFFAGRGGGRIGGENGFGGATNGGSPAAQNEDSPGTYQSKFNALRRGG   250
 251  GAGSVGRGGSTTGSAFNTRADALYNPNDPTDRPKAVNPAATRSESDEEEE   300
 301  EGWSKVGSTSRTSTNAAPQSSERPAWARSESWIQRTQQQQQQQQQQSTQQ   350
 351  QAQPPITLWNNREVGSDSTVWKDRNHMVAAVRKASTENHPPQQQQQQQQR   400
 401  SSAPVSAPSRQESESTDVPNLPIPTYPSDPSAWSNNSMGGGIFYQPTPQP   450
 451  PAPIVKEEPVQFYYMDPTETRRGPFPKDQMNVWFKAGYFTDESLRVQRGE   500
 501  NGEYKTIGDLKKLHGSSTPFEYLEDIEPPRPILPSIPYPSATNPLYPAAF   550
 551  GGVNMWSSMGQPTDVYMMQTNFEQQLVAERNRLLDDHNRRLAEEAEKMAK   600
 601  FQEAMYRQLTMQHEQRVREQELLLQKRAEEIEKREAESKREEAARLQKLE   650
 651  QEAREIEERKAALEAEDRRKREIEEYNRMCEKKKNEIIAKEAADRMRLEE   700
 701  ATERERRRLEAESRVAEEKIRRDRVRAELEAREREEERKRAAERERIARE   750
 751  TASLQQQAELDAAWAGKKIATVTTSNSAFTGAPKQVSPSGSEESDEWIST   800
 801  SKEVKHTKTAPWAAKVEAPQKSEKTLLEIQKEEERKFKVEQEKNAKLKAK   850
 851  EQASNITSAAAIAGDKSGGLWGASKTWAAPESNSSKSYVSPFLDGPSLEA   900
 901  ANKMALQKKNSQPKIAVPAKSAPTSAKVATPVKAKATAVAVSSPATNQKT   950
 951  KKTKEQVATDELQQWFVKRFQQFSTQVDSSTLFDCIMSLENPNEVEDIVM  1000
1001  SYLDESKTVKEFVREFIKRRIAMRAAGGRPDADDLTSARTAAAAPSDSNS  1050
1051  GSNSNSGNGQGKKKKKTQKQVLDGNILGFRGTAAADRLNKGEIDAVPSAP  1100
1101  VNPSRR                                              1106

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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