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

NucPred

Fetching P48415 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MTPEAKKRKNQKKKLKQKQKKAAEKAASHSEEPLELPESTINSSFNDDSV    50
  51  NRTESDIASKSDVPPVSSSTNISPANETQLEIPDTQELHHKLLNDSDQHD   100
 101  ITADSNDLPDNSIVEHDSVITQTKPAMSQEYEETAAHLSSRNPSLDVVAG   150
 151  ELHNNNEHTQKIAVSAVEEDSFNEEEGENHDSIIISSLNDATPSQYNHFL   200
 201  PSDGNLLSPELSSGDTPTHNVPLGTKDNEINDDEYCNDKEISLNANNVLP   250
 251  DELSKEEDERLKLETHVSTEEKKQDIADQETAENLFTSSTEPSENKIRNS   300
 301  GDDTSMLFQDDESDQKVPWEEDVKKDFHNENTNNTQESAPNTDDRDKGYE   350
 351  GNEALKKSESCTAADERSYSEETSEDIFHGHDKQVVEGQNDFTGKNIENE   400
 401  SQKLMGEGNHKLPLSAEADIIEPGKDIQDQAEDLFTQSSGDLGEVLPWES   450
 451  TDKNADVTSKSQEKHEDLFAASGNDEKLPWEVSDGEVSSGKTENSMQTST   500
 501  EKIAEQKFSFLENDDDLLDDDDSFLASSEEEDTVPNTDNTTNLTSKPVEE   550
 551  KKASRYKPIIEEEAGMRQEQVHFTNTTGIVTPQQFHGLTKTGLGTPNQQV   600
 601  SVPNIVSPKPPVVKDNRSNFKINEEKKKSDAYDFPLEIISESSKKGHAKP   650
 651  VAVPTQRFGSGNSFSSLDKPIPQSRKGSNNSNRPPVIPLGTQEPRSSRTN   700
 701  SAISQSPVNYAFPNPYKIQQLQQAPIQSGMPLPNTNIPPPALKVETTVSA   750
 751  PPIRARGVSNASVGSSASFGARHATQYGLNNGVPPVSPYGQATINLPTAN   800
 801  KYAPVSPTVQQKQYPSVVQNLGASAVNTPNFVKTHRGHTSSISSYTPNQN   850
 851  EHASRYAPNYQQSYQVPYTSQPVGPVAGNSSYQSQTRSSYAVPMMPQAQT   900
 901  SASIQPHANIQPPTGILPLAPLRPLDPLQAATNLQPRASNITAANSLPLA   950
 951  NLPLAENILPEIITHRATSSVAPPRQENNPIKIDNEALLRRQFPIFHWSA  1000
1001  ANKVVYAVPPIPDQSQYMISSSIVQEIKVTPIDQIIKPNDMLKSFPGPLG  1050
1051  SAKLKKKDLTKWMETTIKSISENESSTDMTIWQLLEMKLNDKVNWKNISK  1100
1101  LLYNSDELLMYLSQPFPNGDMIPNAYRLDINCQMRVLAFLQTGNHDEALR  1150
1151  LALSKRDYAIALLVGSLMGKDRWSEVIQKYLYEGFTAGPNDQKELAHFLL  1200
1201  LIFQVFVGNSKMAIKSFYTNNETSQWASENWKSIVAAVLINIPENNEDPL  1250
1251  LIPPVVLEFLIEFGIFLTKKGLTAAASTLFIIGNVPLSNEPVMADSDVIF  1300
1301  ESIGNMNTFESILWDEIYEYIFSYDPKFKGFSSILPQKIYHASLLQEQGL  1350
1351  NSLGTKYTDYLSSSVRKLPKKDILTINLTRELSEVASRLSESNTGWLAKP  1400
1401  KLSSVWGQLDKSFNKYIGGDDIDALNKKNDKKKVFDGFTPGSSANSSTVD  1450
1451  LTQTFTPFQAQVTSQSYVDTTALLHNAHNVPSHSVLHSKPSNVSKGLVEA  1500
1501  NLPYTHRIGDSLQGSPQRIHNTQFAAAEPQMASLRRVRTDQHTNEKALKS  1550
1551  QQILEKKSTAYTPQFGQNHSVPMEKSNSNVPSLFADFPAPPKLGTVPSNY  1600
1601  VSSPDLVRRESIISTGSEFLPPPKIGVPTKANSSQGSLMYSPSVEALPID  1650
1651  PVVPQVHETGYNDFGNKHSQKSMPEDESHTSHDNSNADQNTLKDSADVTD  1700
1701  ETMDIEGPGFNDVKNLLPMEPNHQPTSTVNPIQTISDDIQPILQTNVEVR  1750
1751  GTDASKMENSLPSIENERSSEEQPENISKSASSAYLPSTGGLSLENRPLT  1800
1801  QDENSISETVQSTYLPAGSISMEAKPISQVQDVPRNVNNKASKLVEQHMA  1850
1851  PPKPKSTDATKMNYSPYVPQSTAASADGDESTILKTSPAIYARTHQAHAS  1900
1901  NPSQYFPLVNQANETASFELSESTSQAQSNGNVASENRFSPIKKAEVVEK  1950
1951  DTFQPTIRKASTNQYRAFKPLESDADKYNDVIEDESDDDNMSTDEAKNRK  2000
2001  EEKKNVNMKKETKPSNKDIDDKSNGWFGWLKKDTGDKKVYKAKLGHKNTL  2050
2051  YYDEKLKRWVNKDATEEEKQKIIESSAPPPPPIVKRKDGGPKTKPRSGPI  2100
2101  NNSLPPVHATSVIPNNPITGEPLPIKTSPSPTGPNPNNSPSPSSPISRIS  2150
2151  GVNLTSKKANGLDDLLSLAGGPKPASTRRKKKTARGYVNVMDNIQ       2195

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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