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

NucPred

Fetching Q62968 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MELPFASVGTTNFRRFTPESLAEIEKQIAAHRAAKKARTKHRGQEDKGEK    50
  51  PRPQLDLKACNQLPKFYGELPAELVGEPLEDLDPFYSTHRTFMVLNKSRT   100
 101  ISRFSATWALWLFSPFNLIRRTAIKVSVHSWFSIFITITILVNCVCMTRT   150
 151  DLPEKVEYVFTVIYTFEALIKILARGFCLNEFTYLRDPWNWLDFSVITLA   200
 201  YVGAAIDLRGISGLRTFRVLRALKTVSVIPGLKVIVGALIHSVRKLADVT   250
 251  ILTVFCLSVFALVGLQLFKGNLKNKCIRNGTDPHKADNLSSEMAEYIFIK   300
 301  PGTTDPLLCGNGSDAGHCPGGYVCLKTPDNPDFNYTSFDSFAWAFLSLFR   350
 351  LMTQDSWERLYQQTLRASGKMYMVFFVLVIFLGSFYLVNLILAVVTMAYE   400
 401  EQSQATIAEIEAKEKKFQEALEVLQKEQEVLAALGIDTTSLQSHSGSPLA   450
 451  SKNANERRPRVKSRVSEGSTDDNRSPQSDPYNQRRMSFLGLSSGRRRASH   500
 501  GSVFHFRAPSQDISFPDGITDDGVFHGDQESRRGSILLGRGAGQTGPLPR   550
 551  SPLPQSPNPGRRHGEEGQLGVPTGELTAGAPEGPALDTTGQKSFLSAGYL   600
 601  NEPFRAQRAMSVVSIMTSVIEELEESKLKCPPCLISFAQKYLIWECCPKW   650
 651  RKFKMALFELVTDPFAELTITLCIVVNTVFMAMEHYPMTDAFDAMLQAGN   700
 701  IVFTVFFTMEMAFKIIAFDPYYYFQKKWNIFDCVIVTVSLLELSASKKGS   750
 751  LSVLRTFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLTFILAIIVFIF   800
 801  ALVGKQLLSEDYGCRKDGVSVWNGEKLRWHMCDFFHSFLVVFRILCGEWI   850
 851  ENMWVCMEVSQKSICLILFLTVMVLGNLVVLNLFIALLLNSFSADNLTAP   900
 901  EDDGEVNNLQLALARIQVLGHRASRAIASYISSHCRFRWPKVETQLGMKP   950
 951  PLTSSEAKNHIATDAVSAAVGNLTKPALSSPKENHGDFITDPNVWVSVPI  1000
1001  AEGESDLDELEEDMEQASQSSWQEEDPKGQQEQLPQVQKCENHQAARSPA  1050
1051  SMMSSEDLAPYLGESWKRKDSPQVPAEGVDDTSSSEGSTVDCPDPEEILR  1100
1101  KIPELADDLDEPDDCFTEGCTRRCPCCNVNTSKSPWATGWQVRKTCYRIV  1150
1151  EHSWFESFIIFMILLSSGALAFEDNYLEEKPRVKSVLEYTDRVFTFIFVF  1200
1201  EMLLKWVAYGFKKYFTNAWCWLDFLIVNISLTSLIAKILEYSDVASIKAL  1250
1251  RTLRALRPLRALSRFEGMRVVVDALVGAIPSIMNVLLVCLIFWLIFSIMG  1300
1301  VNLFAGKFSKCVDTRNNPFSNVNSTMVNNKSECHNQNSTGHFFWVNVKVN  1350
1351  FDNVAMGYLALLQVATFKGWMDIMYAAVDSGEINSQPNWENNLYMYLYFV  1400
1401  VFIIFGGFFTLNLFVGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKL  1450
1451  GSKKPQKPIPRPLNKYQGFVFDIVTRQAFDIIIMVLICLNMITMMVETDE  1500
1501  QGEEKTKVLGRINQFFVAVFTGECVMKMFALRQYYFTNGWNVFDFIVVIL  1550
1551  SIGSLLFSAILKSLENYFSPTLFRVIRLARIGRILRLIRAAKGIRTLLFA  1600
1601  LMMSLPALFNIGLLLFLVMFIYSIFGMASFANVVDEAGIDDMFNFKTFGN  1650
1651  SMLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGSRGNCGSPAVGI  1700
1701  IFFTTYIIISFLIVVNMYIAVILENFNVATEESTEPLSEDDFDMFYETWE  1750
1751  KFDPEATQFIAFSALSDFADTLSGPLRIPKPNQNILIQMDLPLVPGDKIH  1800
1801  CLDILFAFTKNVLGESGELDSLKTNMEEKFMATNLSKASYEPIATTLRWK  1850
1851  QEDLSATVIQKAYRSYMLHRSLTLSNTLHVPRAEEDGVSLPGEGYVTFMA  1900
1901  NSGLPDKSETASATSFPPSYDSVTRGLSDRANINPSSSMQNEDEVAAKEG  1950
1951  NSPGPQ                                              1956

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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