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

NucPred

Fetching Q8WI26 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MMVDQIKLLFYNKMMDRTAIKQLISRLIAQFGITYTTNILDQLKTLGFKQ    50
  51  ATNASVSLGIDDLLEAPSKAWLIQDAERQGSIFEQHHRFGSVHAVEKLRQ   100
 101  LIETWYATSEYLKREMIPNFRIIDPLNPVHMMSFSGARGSTSQVHQLVGM   150
 151  RGLMSDPQGQIIDLPIRSNLREGLSLTEYIISCYGARKGVVDTAVRTSDA   200
 201  GYLTRRLVEVVQHIVVRKMDCGSTRGIPFKMTQDRFKRNLYQQRLIGRVL   250
 251  ADNVYLEMRCIAMRNQDIGNELANRLITIQKQLVYVRSPLTRKSISWVCQ   300
 301  LCYGWSLTHQNLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGDIA   350
 351  EHIRIPFNGIISFAEDSVHPIRTRHGHPAWICQDNLSVSVKNKNRIHNVI   400
 401  IPYQSLILVQNNQYVESKQVIAEVRINQSLPKERVKKHIYSNSEGEMHWS   450
 451  TIVRHSPQHRQSNVYPVLKTGHIWILSGSLCNVIETSSSFYKEQDRFNIQ   500
 501  SVFTKPEFLPYSFGRNKGEKNQLTNLHKKGQELNHLKFDSSATIKTYKFP   550
 551  YLTSLFYCKIRKDKTENKVILSIKPIQRRNKYYRKTPYRDFVFQTPTNGI   600
 601  LNRGDILAIHENPEYRIHISGVIKYGTLKIDSIVENERIPNDREKTTFGS   650
 651  RYKVLRGGNFFFLPGEIYIVHESSAYILVSNNSIVQAGTQITPTLTSQLG   700
 701  GLVQIKNIQKSFEIRILPGTIHHPKRIPSISKQNNMLIPPGQSVFDNLKF   750
 751  DHWIYLQWITSPRKKTFALARPVIEYFVRKGSYPPILNLLKEQNTLRVKF   800
 801  LDYMLYEDGEEIQIKNNMSIQLVQTCLLLDWEKKSPIKAAKTSILELRIN   850
 851  KIIKTFLQISLLNSFDFYVKGSKFKRFFNNKKSFVADSIPKTLESQLSIK   900
 901  HQGTIRSVSNRKTSFLVLSPSDSFQNSLSTNFQYYDSKNRYGKKKELKWN   950
 951  TFFDTKKVSRSLKKNYLSSIKDSEKRSLNSKVGLTSVSSFDHTRQLQGMK  1000
1001  ILGLLGYLYSIANCFLYPKGIFRNEVFFHRDSSIDDLVGFDKLPNWYFLD  1050
1051  ENRKIYSFHLRNLIGKRFFYWTRNLSNFNEIPLVNLGQFICEGARLFENQ  1100
1101  ISSQSGQIIALSPEFLIIRLAKLYLATKGATIHNHYGDLLREGDTLITLT  1150
1151  YERFKSGDIIQGLPKVEQLLEARSVNAVSRNIEDNFKKCNRVIAKFIESP  1200
1201  WSFFFSAKISTEQSRKDLVDQIQGVYQSQGVQISDKHIEIIVRQMTSKVL  1250
1251  TLEDGIATVFLPGELIELPRAQRMNRALKQLIYYKPILLGITKASLNTTS  1300
1301  FLSEASFQETTRVLARAAIRGRIDWLKGLKENVIIGGIVPTGTGSREVTC  1350
1351  QMDLEKHKKGSNLKIKNTHSFSCEIKDLLFNHGKVSLTFKRSNIHRELKK  1400
1401  PLSENDSD                                            1408

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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