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

NucPred

Fetching Q9VWF2 from www.uniprot.org...

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

   1  MNDLRQQQMVAATSSSGSESGTAVESAAATSTAGSAGAAGRPQSNCSANS    50
  51  NAKSVAASSTSEEEQRVSSTSSPAQRDQQLNADRDREQEPEPQQQQQREE   100
 101  ALQHQHNQPGHITSTTASPPPTLPPPTTPCDDAPSTTGASASASSASGEA   150
 151  PSAASAAGAAGGPMAATALEVESEERDGHKIILKLSKHANPNSNANESQP   200
 201  GGDERRVEPLRIQLPCGGAEGGLVAKQQDAFDADASSCSSSCAEDEVATT   250
 251  LGQQLRNTPHIVPKLTIRAANERRVGSVVPKLTIKLPENPAASGSNSNSG   300
 301  SCSAAVSGAQSAMPAKNDAHLSSLSPASASSSSASSSSSSSSSSSLAEMQ   350
 351  TVPKLMIKTTLAGSSCISSSEELPQQQQQIPKLTIKTGGGGQEHVHTVIM   400
 401  THDLNNAQSIPKLTIKTKSIEMIEDEQAAKLEQQLQPLPKLTIKNLCSPK   450
 451  HKVRAVLEEKPPTAASKLAIPKPTPNPTPAPMTNGGESNSSSQEFCGFSD   500
 501  PDADIAAPASDDVRRNSDDMVIDDSLSKEHDPKIFHNLPPMPASNGIASG   550
 551  GSKASKASKSAQSQHNVVDMVDLTSSPSPGSSPTHVPNNFTGRISPKGLL   600
 601  IDCLRMQTAIGCYVPEEADSRVRPAASPNSNILLSQLTAPAKSFTTTTPK   650
 651  SKSSKYPQLTERLMANGSGTGGGSVIAAESEAVVGPLPAANPAQSIIESI   700
 701  EILDTPDGSPRVAYMDEDSNPMLNKHLQTIHKLAMDHGVEQRMDTQDNNN   750
 751  ENHLKRTNSEGNESPSSRLPPSKQRRLDNDENDQQTQNCHDPARKCSESL   800
 801  QALPPSHRSRKQKHERILNTDLEGSLFPPTQQQSISTPDQNGALSSEVEG   850
 851  EDAKAQDPLEPATPQPPPVATPAGTGKKRGRPKRIQNQSSPDGGGAVTPK   900
 901  PGTPQEEANSAVKSRRVQLLRKRLAIDMVSVGQEQADMKAKEKESSVGVP   950
 951  NARVEDGLAETLESPKTRDHRPLRATRRTTTSTNTNLQPTPKSTRKRQSK  1000
1001  ASVQQSQLPPPTMAQFGSSESESNNNNNSSISFALSAQIDLTMCSSSSST  1050
1051  SSGAAANQQVIGGSGSSSMLPPTTILSSSDPLPDVIFQPNDFSSIMATQQ  1100
1101  LRSSRPSSISCGSTGGSQPDCHDEDNYTSALDNSGDETALPMPPTRGRGR  1150
1151  GRRSRGGRGRGSSSVDRAVSVGGTASTTPATQPRAPRMSRGASAVAKAIA  1200
1201  MSRPRCVGGLKHQPDPERLKGLFSPSPQVFEEDTRMSADLSNSNQSMASL  1250
1251  MEPPLTPQKQPDFLNNEESQSSMVSNVSMMDSNQGQSADAILGSALKRPK  1300
1301  KKKMETCVAEDTDYSASSIAEYDWPPPKGCCPSKNRDTFMIQEQVALYLG  1350
1351  ITSFKRKYPDLPRRSVDMEERNWLQEKGLVSEKLCDLGITAVWASDILDI  1400
1401  MYADFFDKYEEYKEYIRRKHLREIEAKQKALGLTVGAGRGLQARDRAMLS  1450
1451  ATKWNAYFNKSRKDERQSCMDLQTFTINQPQPRTAPTCTRLERSTSDLIR  1500
1501  AVAEEANIPAPPNLLPPRDYDEAFRNSDYAYPLTVVPDQFSMAYRQFEPA  1550
1551  ELRAYPLDTALDKPPTDLMAQLLQAKSEAVGSDEIKTSAPAPKDLGQEQS  1600
1601  AIKSVTVTAPVRRSRRSTRQQTDKVRTASSSSTSSAQSVSSASSGNGSSS  1650
1651  DTESGDESDFSSTSSCSSSTGASSGAGSEDEDGNECSSSVRLSTCGVCLR  1700
1701  SQHRNARDMPEAFIRCYTCRKRVHPSCVDMPPRMVGRVRNYNWQCAGCKC  1750
1751  CIKCRSSQRPGKMLYCEQCDRGYHIYCLGLRTVPDGRWSCERCCFCMRCG  1800
1801  ATKPEGLPQVAALSQASGGPSANGDRSKAARNKRLKWVHEYRIDHVTKIR  1850
1851  EHAAMFCVPCARNKPAKRQSAAGAAGAAAVTPVLEATSAQTDDSPMPSPG  1900
1901  LTTNGGRALSPTAALSPKAAVPVASLPPVLEATTVTTNIAGTIGRRQAGN  1950
1951  AVNITTMQCSSSSSSNFSGNGVTEDAANVTATGTATAAAGAPAATPIGIA  2000
2001  PPPVVA                                              2006

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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