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

NucPred

Fetching Q09743 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MKPVRRGQTDTALDISSHAKTNGDFIKKMNTTDSKRLKLLEDLKGKLEVE    50
  51  CKIRDGAETLLQVFDTNFKKETKERKEMLKKKCTDELESSKKKIEELVSS   100
 101  IESFQGENGEAKTGSTSLTRSASATVSRKSSLQEKYSTRFSYKAGCSDSC   150
 151  SVTVSGTGELIGPTRNAHSNLTPTVIQRIDFENVNEKNNSSSEDTQPNGK   200
 201  RPSSLQSNFSQFPLNPWLDNIYKACLEGSMKDVIDSSNNLCEYLHEHSDP   250
 251  AYAKNFSLITPTILSMLELNVSEVTASVYRLLRHLFLDATAFSCCQMLNL   300
 301  PWILSKSLLSGTDAYQIEREQAFRLIRTLYFLSSTEGHEDYLSGITRTII   350
 351  SICEHVSDVSRGIAVETLIELMIIRPKILFKANGLRVLMISLIDGSISEN   400
 401  LAASAALALVYLLDDPESACYVNLPYDIGILLSPFTSSSSRDTFNSSEEQ   450
 451  SEQAAKAMKSSAKVASVLLNSWSGLLALSTNDFQALRSIVDTLRVPSFAP   500
 501  RSDVIDLFFLIFQVEYSSWSESFLAGKRLTVVKNQAVSNDDNINMVNIPD   550
 551  GSNKKYMSLRQHFTAVLLFIFLELGLVESIVCMIRASDDPSASRKATYLL   600
 601  GEVLRLSDELLPIHLGAKIQSLPSLFNMASQFTAEDRFVATSVLQSIESL   650
 651  NRVKFHSATQPFSQTTSLLFKEQKTDGSFRGQRQVEHVKLKMGMQIDDSH   700
 701  FRSMLAETNVLATKNYQKWRWDTLVQIMEGPLLSPKRIDETLRTTKFMRR   750
 751  LLAFYKPFSNRFSSIQNTKPNQKFIKVGCLVFRTLLANPEGVKYLSESKV   800
 801  IKQIAESLSQIDGYSEQVSEPIFSNSRLQKTLTHGYFPMLKVLSSQKEGH   850
 851  AIMERWRIFTTLYHLTELRNRDDLIIIFLTNLDYRLEGHTRIIFSKALNT   900
 901  GQQAVRLTATKHLAALINSESANDNLNHWAISLLIFQLYDPCLEVCKTAV   950
 951  KVLNEVCARNENLLAQVVQLQPSLAHLGEIGSPLLLRFLATTVGFHYLSE  1000
1001  INFIEHELDNWYHHRNIDYVDLLEQNFFLSFVSNLKIIDKKNNEPDENIL  1050
1051  PLHFYGELVKSPQGCEVLESSGHFESFMGTLVEFYDKPLGNEAIRQLKSA  1100
1101  LWAIGNIGKTDQGITFLINHDTIPLIVKYAENSLIPTVRGTAYFVLGLIS  1150
1151  RTSKGVEILESLHWYSLMSLMGTSQGICIPRHAGQVLSTPRRNVEFVNER  1200
1201  VPTPEFSSLLSSLTNSEREVIRLVSNLSNHVLTNESARQLTKIRSKNAKV  1250
1251  FSSKRLVKACMTILGKFHYRVQIQQFVFELFPYSVLLSSSTSQDLNESPS  1300
1301  RPNNLSISA                                           1309

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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