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

NucPred

Fetching Q85X62 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MKIWRFLLMKKQTRLPFDNLPFYNKVMDKTAIKKLISRLIDHFGMTYTSH    50
  51  ILDQLKTSGFKQATDTAISLGIDDLLTAPSKGWLVQDAEQQGSVSEKQNH   100
 101  YGNLHAVEKLRQSIEIWYATSEYLRKEMNTNFSMTDPLNPVHVMSFSGAR   150
 151  GNTSQVHQLVGMRGLMSDPQGQIIDLPIRRNLREGLSLTEYIISCYGARK   200
 201  GVVDTAVRTADAGYLTRRLVEVVQQIVVRRTDCGTVQGIFVSPIRGRERD   250
 251  INEVVVRTQILIGRVLADDVYINRRCIATRNQDIGVGLANQLRNIRPRPI   300
 301  YIRTPFTCKSISRICQLCYGRSTTHSHLIELGEAVGIIAGQSIGEPGTQL   350
 351  TLRTFHTGGVFTGDIAEHIRAPFNGKIEFNENLVYPTRTRNGHPAYLCHN   400
 401  NLSITIDGQNQVQNLTIPPQSLLLVQNDQYVESEQIIAEVRARTSSFKEK   450
 451  VRKNIYSDLEGEMHWSTNVCHAPEYVHGNVHSILRTGYLWILSGGIYGSG   500
 501  VVPFPFHKYQDQVDVQPFVAKHTDSYVDQVEHRSGDSNCYGKEEQIFSYS   550
 551  ETETDRTISNEHRDSIYVTFSPKNYNMKGKKQMNRFIVSLQCDKEWGKRI   600
 601  IPCPDAILRIPKSGILQINSIFGYSNVEHGIPDGPNMTTPFSLDLSREGD   650
 651  NLQIQISNSILYEDGERIQVMSDTSIPLVRTCLGFDWEQIDSIESEAYVS   700
 701  LISVRTNKIVNNMVQISLMKYPPFFMGRRDNKASSNLMFHNNLDHTNLFS   750
 751  SNGASQLISKHQGTICSLSNGEEDSGSFMVLSPSDCFRIVLFNDSKCYDT   800
 801  GNKSNRKDPMRKIIEFSGLLGHLHSITSRFPSSQFITDKKVLSKKHSIFH   850
 851  NYFMDENMRISHFDPCRNIISNLLGPNWCSSSSEFCKKTFPVVSLGQLIP   900
 901  ESVWISEDEPLPESGQIIAVDEESLVIRSAKPYLATRKATVHGHYGEILD   950
 951  KGDTLITLIYERLKSSDIIQGLPKVEQLSEARLNNSISMNLKESFENWTG  1000
1001  DMTRFLGSLWGLFISARITMEQSQIHLVNQIQKVYRSQGVRIGDKHIEII  1050
1051  VRQMTSKVLISEDGTANVFSPGELIGLSRAQRMDRALEETIYYQTMLLGI  1100
1101  TRASLNTQSFISEASFQETARVLAKAALQGRIDWLKGLKENVILGGMIPA  1150
1151  GTGQHIHRSGKRNGIDPRIGNRNLFSNKVKDILFHHDKVSFFSIQENYHN  1200
1201  ILKQPLKES                                           1209

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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