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

NucPred

Fetching Q9CPW0 from www.uniprot.org...

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

   1  MVMSLRAGYRAALSLWILSSFICRAWTAPSTFQKCDEPLISGLPHVSFSS    50
  51  SSSLSSSYAPGYAKINKRGGAGGWSPSDSDHYQWLQVDFGNRKQISAIAT   100
 101  QGRYSSSDWVTQYRMLYSDTGRNWKPYHQDGNIWAFPGNINSDSVVRHDL   150
 151  QHAVVARYVRIVPLDWNGEGHIGLRAEVYGCAYWADVINFDGHGVLPYRF   200
 201  RNKKMKTLKDVIALKFKTSESEGVLLHGEGQQGDYITLELKKAKLVLSLN   250
 251  LGSNQLGPIYGHTSVTSGSLLDDHHWHSVLIERQGRSINLTLDRSMQHFR   300
 301  TNGEFDYLDLDYEITFGGIPFSGKPSSSNRKNFKGCMESINYNGVNITDL   350
 351  ARRKKLGPSNMGNLSFSCVEPYTVPVFFNATSYLEVPGRLNQDLFSVSFQ   400
 401  FRTWNPSGLLLFSHFADNLGNVEIDLVESKVGVHINNTQTKTSQIDISSG   450
 451  SGLNDGQWHEVRFLAKENFAVLTIDGDEASAVRTNSPLQVKTGEKYFFGG   500
 501  FLNHMNNASYSALQPSFQGCMQLIQVDDQLVNLYEVAQRKPGSFANVTID   550
 551  MCAIIDRCVPNHCEHGGKCSQTWDSFKCTCDETGYSGATCHNSIYEPSCE   600
 601  AYKHLGQTSNYYWIDPDGSGPLGPLKVYCNMTEDKVWTIVSHDLQMQTTV   650
 651  VGYNPEKYSVTQLIYSASMDQISAITSSAEYCEQYVSYFCRMSRLLNTPD   700
 701  GSPYTWWVGKANEKHYYWGGSEPGIQKCACGIERNCTDPKYYCNCDADYK   750
 751  QWRKDAGFLSYKDHLPVSQVVVGDTDRQGSEAKLSVGPLRCQGDRNYWNA   800
 801  ASFPNPSSYLHFSTFQGETSADISFYFKTLIPRGVFLENLGNTDFIKLEL   850
 851  KSATEVSFSFDVGNGPVEIVVRSPSPLNDDQWHRVTAERNVKQASLQVDR   900
 901  LPQQIRKAPTEGHTRLELYSQLFVGGAGGQQGFLGCIRSLRMNGVTLDLE   950
 951  ERAKVTSGFKSGCSGHCTSYGANCENGGKCIEKYHGYSCDCSNTAYDGTF  1000
1001  CNKDVGAFFEEGMWLRYNFQAPAVTARDTGSRAENSADQQQHLAPDLAQE  1050
1051  QIHFSFSTTKAPCILLYVSSLTTDFLAVLVKPTGNLQIRYNLGGTREPFN  1100
1101  IDVDHRNMANGQPHSVNITRHERTIILKLDHYPAVGYHLPSSSDTLFNSP  1150
1151  KSLFLGKVIETGKIDQEIHKYNTPGFTGCLSRVQFNHIAPLKAALRQTNA  1200
1201  SAHVHIQGELVESNCGASPLTLSPMSSATDPWHLDHLDSASADFPYNPGQ  1250
1251  GQAIRNGVNRNSAIIGGVIAVVIFTILCTLVFLIRYMFRHKGTYHTNEAK  1300
1301  GAESAESADAAIMNNDPNFTETIDESKKEWLI                    1332

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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