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

NucPred

Fetching Q9VM75 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MSTALAQQLQKLAAPQSSVTLADARSRASILFDPKEAATKDRRSIYEIGL    50
  51  TGLQELTDFNPAFKEFQLTLFDEATLTLERSVELPEINKMLDAAIAKFLR   100
 101  LLSPYLLLRPAHMAFEWLLRRFQVHEYNRSEVMALILPYHETMIFVQIVK   150
 151  TMRLRSSDGDWYWLRPLQRPGVPLAKTAIINRAASNPAFLGFICQSTQKA   200
 201  VKELGPRAHQLQAQINFYATVVVGALQTAKPLQDWHITTILESLLRGLIS   250
 251  DNIDFMAAAYVIVAQLVSRTKLKSKVCNALLERVANCPFERLHSESLLLL   300
 301  VCIYGKQQAALPHFKPETILNLVGKKWLISTLSSLAKGNIAIQSICMPLM   350
 351  TGAVAAIRDDDASSNSCKLFLDNLLSEVPMPKPTAQQLINCFLDTYVETA   400
 401  IDAPEPMETNSNEDDDTIVIDSDDEIETEKTTFQAWYSTYLEKLERRYPE   450
 451  AFDLSVKEALRSKSSTSNRQKALKLALGFRLNTTDEKAKHAYEKLYHYSA   500
 501  DWRLSAVQKLLQNLNVTKKRERSVKLLQECLPDRINDDSGAVVSTLLSLP   550
 551  TEELAEMLGPLPLAQTLCHLLYRAQSEKDEEWQPVVPLAVRHLTSALVSG   600
 601  SYDTNLVLLALMPLLFPGEALAEHQHKALRILLGSDFVSKVPFLAELKVS   650
 651  NKFSDFNVGEHRQHFLDIIASSNQELSSQERALLQSVEDHGGELYIQKAS   700
 701  QLTHLLLLLTAYAKRELQPRESLHMLEKIGLYSRRLQFRVVNGSQNTQNC   750
 751  APLQLYVDFLLTLVKNTKWTALASTPWNQMTDELRLCLRLLEIICAQVFS   800
 801  EKADQPERQEWTRALQQSLQLILPEAQDRLEVLSNFYVFERLPELWPRDS   850
 851  DYAVFRLQGFIILEAVLSNPKSQIDCGLVHVLRVANACGSPLQTLRVQAI   900
 901  NILQLISNRKLVSHVEQLVRSLLQRKSELSMDHEQYALILYTILEPEKAT   950
 951  AKERLVLSKLKRSVLALASDPKQSPICTASLLAALKHVNDENFLNELLPL  1000
1001  GLDSLKTITAGEDNQNIKQLPWPHSEIYKSVIERFEGRVALNVLLRKDLA  1050
1051  WKLFEDSFAQYDTYVQLEQKLQPLPCVLLNSLTPETFEQMHAKHKIALIK  1100
1101  LIVESATNSDNDSIFLASHRLLKRCRLDCQPLVPILLEMANTKVEKKQPV  1150
1151  KRRSVQATQLDLTSPYWKQGMTLLELLEHKKQLVGAELLIPPLFELLQAC  1200
1201  LTMEEHSAAEYPKQLILSSLLHCCQTAQSAGVQLVKAMPESSFRIELVVQ  1250
1251  SLRNTRNPQTQQHALLFLTHCAGMYPQQVLHKIVEIFTFVGSTVARHDDA  1300
1301  FSLHIIHNVVESIIPILLLNTGHNELVIPVLKVFADICTDVPVHRRLPLY  1350
1351  ATLFRVLEPKEHLWQFLCIIFESQVLLEQVPQKVSTDKSRLDFARELTLM  1400
1401  FEDPTVAIQTCIRLLDYLAKLPATKSSLSGGSGSSVLSTEQQLFDVRTRT  1450
1451  FKQLRHYKYLIMDFLSGISSCNEWEKKMKRPDPNELLPYYQEFILKTLAY  1500
1501  VGVLNGALEAASETPSLEKFWRVLANHAHDVLDNAIGLLAPQHFISVITE  1550
1551  LLKHDHVYVRIKVMDLLVTKLSPSSDYFQQSNAEHFGVLFAPLQEIINGI  1600
1601  LEGSSNSAQQAKLQQTALHALQLLALRHGRDYIEECRSLLATLTKITKRR  1650
1651  ANVPKAVVGNVVLTLVEICASLKAHALAQLPKFAPQLTELLKEQVHQMAS  1700
1701  LKQGPDYVCSTLVTALHKLFKALPLFLGPYLVDIIGGLARLSVQLENPQL  1750
1751  LQDKRTQVLKQKLADVWSAVAQGVEVRILVPSCAKAFSSLLEQQAYDELG  1800
1801  HLMQQLLLQSVRHNSAAQLQPVQDPLSELFLQALNFRLQVRGLGLQRQLV  1850
1851  SDVEASITETFVTWILKLSETSFRPMYSRVHKWALESTSRETRLTYFLLT  1900
1901  NRIAEALKSLFVLFASDFVEDSSRLLTEHNSIRPEFEVEEREDDVDLLMA  1950
1951  ILNTLHHVFLYCSEDFINDHRFNVLMPPLVNQLENDLVLGNESLQQVLSN  2000
2001  CIAQFAVATNDVMWKQLNSQVLLKTRTSNPEVRILAFNSCVAIARKLGES  2050
2051  YAALLPETVPFIAELLEDEHQRVEKNTRTGVQELETILGESVQKYL      2096

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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