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

NucPred

Fetching Q8T498 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MGRRTYLSRSSTISYPSRIEGWLDVCETEGELTRLIKTLPWGPLYCVLQQ    50
  51  DDQTFTAYCSEEISLGDVCYEDIPRVRLDRVRRPAKALWDGPPTLVEENE   100
 101  DSDSCVGGSGGMSGINDIVLNTTLYSELGEYKSKTLPRIHFDTALNDTSL   150
 151  NEDTSYEKACRRGSAPTTPILGSKQHQTEHNATSRFTNFFSKKSNPLKRT   200
 201  KSVTKLERTKRGSGGLRGSRSHESLLSSHAVMSTIDLSCTGAVGVAPVHQ   250
 251  SVLGRRHCFQVRGGPRGERYYSCGSRQERDLWIYSLRKSIAPNAEHTRRT   300
 301  DNSLKMWVYEAKNLPPKKRYFCELQLDKTLYGRTSVKLQTDLLFWGEHFD   350
 351  FPDIPEINVITVNVFREVDKKKKRDKYQFVGSVKIPVHDVTSRLPCEQWY   400
 401  PILSDKAGDSLGRTSGGGGSGSKDKEQLPTLRIKCRFQSTDILPINVYGN   450
 451  FLTYLKENYKRVCETLEPVIGVKAKEDIGQALVLLMHAQGLAGAFLTDVV   500
 501  ALDLLRVGDQRLTFRGNSLATKSMEAFLKLTGEQYLQDTLSAPINELIQS   550
 551  ERDCEVDPTKTSGSSAGSLQRQQAALRGAVRGAWQCIFESHKHFPAQLRN   600
 601  CFATFRERLQQLGRQDMADNLISASIFLRFLCPAILSPSLFNITSELPSA   650
 651  RATRNLTLVAKTLQTLANFTRFQGKENFMEFLNDFLEQEAARMQQFLEII   700
 701  STRPEHPAPDSILDWAGYIDQGKQLSILHSLLSESLAKLPEARQHELDPL   750
 751  QHILDEISRAKEHGMGTALPGGYLPATSSTHSIASENQENRNPGSSGSHA   800
 801  GSNSEQLLPQQSQLAQPQHAIVSKPLSAERGIMRGVLTPNSLEKNIFRYN   850
 851  DPTVNGLLQQQQQQQQQQQQQQQQHQQLQQHGHQQQPHHQHPLQMLSNSQ   900
 901  TSIAGNQYMSSPGGLQHAQSQTSMASSSLNGSSSNLLHGHQQHAHHPQQL   950
 951  HPHHCPPAPQTSASSTMERMDRMNYPYMSHNGNDYETSTPSSTRSRTLPR  1000
1001  NGNPNANGNVGSSNNNQSGSYDDMHGEFQIQISGFDTSSAFVCKSPTPMM  1050
1051  KSSLGPAGAGRSHHKLNLGIPDHSGGYVRGNNLNPNSNMPKNLEDLDDLF  1100
1101  KYAEEHDVAEPANHHNHNQGQQNHQGHLKPAAVPGKEQLSAKSSHCSSGY  1150
1151  QSISTNPSPSQSSSPVESQLKAAMGSHNAPLAFKNPSYQLQPQTGSSRSS  1200
1201  AQSNTHQQQQQQQQQQFGSRLKPIGGGLVAARAAFLNSGGALEAATLTPS  1250
1251  SSDEQLSADNYFSYAAAAAAGAGIATKLEAQRSLSGGSSSSTSASASTSN  1300
1301  LGKSGGSSAYGRLNGPLKREDVYGSGYGGSSGNVGYGLSTSSAAGHHQHP  1350
1351  HQQQQNPMQQQQQRERDQEHKQYAGSVAGSVGSATSAAQRRLSLDSARTL  1400
1401  SDSSTDTEGHCNQLQEGKRRRQLRSSGGSGGGGAGSEQGLGKSYDQNGEI  1450
1451  QLLQQTLDTLCHTLDRDEAELRDSSDELFGLQRPAGSNGSNNLSLQSEST  1500
1501  MRSIIDRLITMEEELRREQLKMSLALSHKQRVIEEQGQQIAALDAANSRL  1550
1551  LSALTALRQRYETQQQQQQHQAPPKTQKPQ                      1580

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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