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

NucPred

Fetching Q9Y5Y9 from www.uniprot.org...

The NucPred score for your sequence is 0.45 (see score help below)

   1  MEFPIGSLETNNFRRFTPESLVEIEKQIAAKQGTKKAREKHREQKDQEEK    50
  51  PRPQLDLKACNQLPKFYGELPAELIGEPLEDLDPFYSTHRTFMVLNKGRT   100
 101  ISRFSATRALWLFSPFNLIRRTAIKVSVHSWFSLFITVTILVNCVCMTRT   150
 151  DLPEKIEYVFTVIYTFEALIKILARGFCLNEFTYLRDPWNWLDFSVITLA   200
 201  YVGTAIDLRGISGLRTFRVLRALKTVSVIPGLKVIVGALIHSVKKLADVT   250
 251  ILTIFCLSVFALVGLQLFKGNLKNKCVKNDMAVNETTNYSSHRKPDIYIN   300
 301  KRGTSDPLLCGNGSDSGHCPDGYICLKTSDNPDFNYTSFDSFAWAFLSLF   350
 351  RLMTQDSWERLYQQTLRTSGKIYMIFFVLVIFLGSFYLVNLILAVVTMAY   400
 401  EEQNQATTDEIEAKEKKFQEALEMLRKEQEVLAALGIDTTSLHSHNGSPL   450
 451  TSKNASERRHRIKPRVSEGSTEDNKSPRSDPYNQRRMSFLGLASGKRRAS   500
 501  HGSVFHFRSPGRDISLPEGVTDDGVFPGDHESHRGSLLLGGGAGQQGPLP   550
 551  RSPLPQPSNPDSRHGEDEHQPPPTSELAPGAVDVSAFDAGQKKTFLSAEY   600
 601  LDEPFRAQRAMSVVSIITSVLEELEESEQKCPPCLTSLSQKYLIWDCCPM   650
 651  WVKLKTILFGLVTDPFAELTITLCIVVNTIFMAMEHHGMSPTFEAMLQIG   700
 701  NIVFTIFFTAEMVFKIIAFDPYYYFQKKWNIFDCIIVTVSLLELGVAKKG   750
 751  SLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLTIILAIIVFV   800
 801  FALVGKQLLGENYRNNRKNISAPHEDWPRWHMHDFFHSFLIVFRILCGEW   850
 851  IENMWACMEVGQKSICLILFLTVMVLGNLVVLNLFIALLLNSFSADNLTA   900
 901  PEDDGEVNNLQVALARIQVFGHRTKQALCSFFSRSCPFPQPKAEPELVVK   950
 951  LPLSSSKAENHIAANTARGSSGGLQAPRGPRDEHSDFIANPTVWVSVPIA  1000
1001  EGESDLDDLEDDGGEDAQSFQQEVIPKGQQEQLQQVERCGDHLTPRSPGT  1050
1051  GTSSEDLAPSLGETWKDESVPQVPAEGVDDTSSSEGSTVDCLDPEEILRK  1100
1101  IPELADDLEEPDDCFTEGCIRHCPCCKLDTTKSPWDVGWQVRKTCYRIVE  1150
1151  HSWFESFIIFMILLSSGSLAFEDYYLDQKPTVKALLEYTDRVFTFIFVFE  1200
1201  MLLKWVAYGFKKYFTNAWCWLDFLIVNISLISLTAKILEYSEVAPIKALR  1250
1251  TLRALRPLRALSRFEGMRVVVDALVGAIPSIMNVLLVCLIFWLIFSIMGV  1300
1301  NLFAGKFWRCINYTDGEFSLVPLSIVNNKSDCKIQNSTGSFFWVNVKVNF  1350
1351  DNVAMGYLALLQVATFKGWMDIMYAAVDSREVNMQPKWEDNVYMYLYFVI  1400
1401  FIIFGGFFTLNLFVGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLG  1450
1451  SKKPQKPIPRPLNKFQGFVFDIVTRQAFDITIMVLICLNMITMMVETDDQ  1500
1501  SEEKTKILGKINQFFVAVFTGECVMKMFALRQYYFTNGWNVFDFIVVVLS  1550
1551  IASLIFSAILKSLQSYFSPTLFRVIRLARIGRILRLIRAAKGIRTLLFAL  1600
1601  MMSLPALFNIGLLLFLVMFIYSIFGMSSFPHVRWEAGIDDMFNFQTFANS  1650
1651  MLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGTRGDCGSPAVGII  1700
1701  FFTTYIIISFLIMVNMYIAVILENFNVATEESTEPLSEDDFDMFYETWEK  1750
1751  FDPEATQFITFSALSDFADTLSGPLRIPKPNRNILIQMDLPLVPGDKIHC  1800
1801  LDILFAFTKNVLGESGELDSLKANMEEKFMATNLSKSSYEPIATTLRWKQ  1850
1851  EDISATVIQKAYRSYVLHRSMALSNTPCVPRAEEEAASLPDEGFVAFTAN  1900
1901  ENCVLPDKSETASATSFPPSYESVTRGLSDRVNMRTSSSIQNEDEATSME  1950
1951  LIAPGP                                              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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