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

NucPred

Fetching Q9VZF4 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MERGCPAASSESVTSAGERTQSAVTSSTSTWVKSQASTSRKTEASEESGL    50
  51  GAVDAEVGAGREAFVSMSTLREDVEDVCVSSNSQHGFAVVLDDESSTFEI   100
 101  SSSNSLPTSAGAASTVGVVAVDDSSSTDTLNGGHPDLGHPASSEHSRQGF   150
 151  FNEDNEDPPVVCLINDDDDDEEPEPEEDDEEELIEDEDEDAVDIVTGAIS   200
 201  CPNTSQLALADGTIMAADGSKIFLETPVVEEAQPHPGQVVTTGSQSELTG   250
 251  KPKRLSDEFLLGEEDQAENLALGRCIKSEPVNPVDDNPSEGDDGATCFSL   300
 301  HDRLMSVRLKQMSLTANTVSNPSPAASANAAAPEEASTSNSSSTSSSALS   350
 351  RADIESMDLIERRDFETEQRLTGGIILRTSSMVSQNKLNLSLIKSMAGGS   400
 401  KAANGSGTANSDDWPSSSNGRTVSSDSKYTYKDLSTTPTSSRKYTNSRLS   450
 451  KSTAKLNLGSSLGASSCSQHRSGSSSTSKSMESSTSCTGAARTDVYTNTN   500
 501  SNDYPSLAPTTSGSSTSGGSCQQDQEENVSASVSYSSVGSQTSQESGCSR   550
 551  TTAINPTAACSTGSACLGDSQASTSASTSSGAGASNRCQYATTSTTKAAR   600
 601  QVNASAQTQERFLTRSNPPAASGAGSVGANPTASVRQRRNGSSDVVHLEV   650
 651  VVEEGAGGGDGGVVEPGDFSAEEPWANCDEENNCSDLEEICTCQNGNGSS   700
 701  YGGSNASLSETFDMDAMDPDEPISLSLSSASAGFTEYSLTNPSSLMSHQR   750
 751  KRKFNEGRLLDGGDYSVTISSSGEVGGPGSGVSDNCRKRIAYDFASTPRS   800
 801  SQHLGPTAVLSVTPSSHLTSSTPGSALGRRTPRSVPSRDNPPPELQHWLA   850
 851  QFQRWSHVERLLALDRLIDHCDPSQVRHMMKVIEPQFQRDFISLLPRELA   900
 901  LFVLSYLEPKDLLRAAQTCRSWRFLCDDNLLWKEKCRKAQILAEPRSDRP   950
 951  KRGRDGNMPPIASPWKAAYMRQHIIEMNWRSRPVRKPKVLKGHDDHVITC  1000
1001  LQFSGNRIVSGSDDNTLKVWSAVNGKCLRTLVGHTGGVWSSQMSGNIIIS  1050
1051  GSTDRTLKVWDMDSGACVHTLQGHTSTVRCMHLHGSKVVSGSRDATLRVW  1100
1101  DIEQGSCLHVLVGHLAAVRCVQYDGKLIVSGAYDYMVKIWHPERQECLHT  1150
1151  LQGHTNRVYSLQFDGLHVVSGSLDTSIRVWDVETGNCKHTLMGHQSLTSG  1200
1201  MELRQNILVSGNADSTVKVWDITTGQCLQTLSGPNKHHSAVTCLQFNSRF  1250
1251  VVTSSDDGTVKLWDVKTGDFIRNLVALDSGGSGGVVWRIRANDTKLICAV  1300
1301  GSRNGTEETKLMVLDFDVEGACVKCS                          1326

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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