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

NucPred

Fetching P30573 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MSNFRDSSSPRRGYSEFDPESGEGLGRKKSLIRPERSRMDESHPRFHYTQ    50
  51  VANQESNHIKVQPSSTGVDPRKSNELSTSRSHLSNYATPPHQEEEEDEGI   100
 101  PLMDIHNASPNVSSDQNNDLKGGREVYGLNDEINDYGSSPKKNQVISSSR   150
 151  PMNNEKPAKPKHDIYFWKVYCYAITFWAPAPLLKLFGLPTKDRQFAWREK   200
 201  IGLISCILYVGAFVAYLTFGFTKTVCSSQVVRTQINHVNGGYLIINGRAY   250
 251  DLTSSQHPKAAGIQAGSNVLYPPMNAGGKDASFLFQNVNGNCKGLIKPRD   300
 301  NCSIPYDGDELAWYMPCRLFNQDGSTKPNNTFAYYKGWACHTSETARDAY   350
 351  YKLKVNGDVYFTWDDVKNSSRNLVVYSGNVLDLDLINWIETDDVTYPELF   400
 401  DKLRDDETYRGLDISLVLTNSEERQAARCLTEIIKVGSIDTDTIGCIASK   450
 451  VVLYMSLVFILSVVVVKFIMACWFKWVTSRKQGATMYDSKAWAKRNREIE   500
 501  DWVDHDHGIGAEVKTVPVKARANYKAAKTNRQSVFHRAQKLSLGPNADLS   550
 551  QYYDNPNALSKTFKYTTMSTQAALLGRNGYGKRGNNANKSVSGGFNGRQS   600
 601  NLYLTDQGSSTDLLNRPVSSYNPFDSMGDDSIVINGLSPDIIHPDVVPQP   650
 651  PVEYQPFGYPLAHTINLVTCYSEDEEGIRITLDSIATTDYPNSHKLILVI   700
 701  CDGIIKGSGNDETTPDIVLDMMSDLTVPRDEVEAYSYVAVAQGSKRHNMA   750
 751  KVYAGFYKYNDETVPPEKQQRIPMITIVKCGTPEEASAPKPGNRGKRDSQ   800
 801  IILMSFLQKVVFDERMTSLEYEMLQSIWRITGLMAEFYEIVLMVDADTKV   850
 851  FPDSLTHMVAEMVKDPTIMGLCGETKISNKAQTWVTAIQVFEYYISHHQA   900
 901  KAFESIFGGVTCLPGCFCMYRIKAPKGSDGYWVPILANPDIVERYSDNVV   950
 951  DTLHRKNLLLLGEDRYLSSLMLRTFPTRKQVFVPKAACKTVVPDKFKVLL  1000
1001  SQRRRWINSTVHNLFELVLVKDLCGTFCFSMQFVIFIELIGTLVLPAAIT  1050
1051  FTIYVIIVAIVSKPTPVMSLVLLAVIFGLPGCLIVITVSSLSYLVYFVIY  1100
1101  LFALPIWNFVLPSYAYWKFDDFSWGETRTVAGGDKGDHSAVEGKFDSSKI  1150
1151  AMKRWREWERERRSTENRKQQQQQQLTNNSSNNLAVPGAAWDPSNTGGNL  1200
1201  IDDLSQGSSSGSS                                       1213

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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