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

NucPred

Fetching P41606 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MKIWRFFLMKERTRLPFDNLPFYNKVMDKTAIKKLISRLIDHFGMTYTSH    50
  51  ILDQLKTSGFQQATDTAISLGIDDLLTAPSKGWLVQDAEQQGSVSEKQNH   100
 101  YGNVHAVEKLRQSIEIWYATSEYLRKEMNPNFSMTDPLNPVHVMSFSGAR   150
 151  GSTSQVHQLVGMRGLMSDPQGQIIDLPIRRNLREGLSLTEYIISCYGARK   200
 201  GVVDTAVRTADAGYLTRRLVEVVQHIVVRRTDCGTIQGIFVSPIRGRERD   250
 251  RNEIVVRTQILIGRVLADDVYINRRCIATRNQDIGVGLANQLINLRTQPI   300
 301  YIRTPFTCKSISRICQLCYGRSTTHSHLIELGEAVGIIAGQSIGEPGTQL   350
 351  TLRTFHTGGVFTGDIAEHIRAPFNGKIEFNENLVYPTRTRNGHPAYLCHN   400
 401  NLSITIDGQDQVQNLTIPPQSLLLVQNDQYVESEQLIAEVRARTSSFKEK   450
 451  VRKNIYSDLEGEMHWSTNVCHAPEYVQGNVHPILRTGYLWILSGGIYGSR   500
 501  VVPFPFHKYQDQVYVQPFVAKHQSLSDSYVDQVEHRSGDSNCYEKEEQIF   550
 551  SYSETETDRTISNKHRDSIYVFYPNNYNIKGKKQMNRFIVSLQCDKEWEK   600
 601  KIIPCPDAILRIPKSGILQRNSIFGYSNVEHGIPDGSNMTTPFSLDLSRE   650
 651  GDNLQIQISYSISYEDGERIQVMSDISIPLVRTCIGFDWEQIDSIESEAY   700
 701  VSLISVRTNKIVNNMVQISLMKYPPFFMGRRDNKTSPNLMFHNNLDHTNL   750
 751  LSSNGASQLISKHQGIICSLSNGEEDSGSFMVLSPSDYFRIVLFNDSKCY   800
 801  DTGNQSNRKDPMRKIIEFSGLLGNLHSITNRFPSSHFLTYKKVLSKKHSI   850
 851  FHNSFNTFQVPKYYFMDENMIIYHFDPCRNIISNLLGPNWCSSSSESEFC   900
 901  EKTFPVVSLGQLIPESVWISEDEPLPESGQIIAVDEESLVIRSAKPYLAT   950
 951  RKATVHSHYGKILDKGDTLITLIYERFKSSDIIQGLPKVEQLSEARLNNS  1000
1001  ISMNLKESFENWTGDMTRFLGSLWGLFISARITMEQSQIHLVNQIQKVYR  1050
1051  SQGVRIGDKHIEVIVRQMTSKVLISEDGTANVFSPGELIVLSRAQRMDRA  1100
1101  LEEAIYYQTMLLGITRASLNTQSFISEASFQETARVLAKAALQGRIDWLK  1150
1151  GLKENVILGGMIPAGTGQHIHRSGKRNGIDPRIGNRNLFSNKVKDILFHH  1200
1201  DKVDFFSFQDNSYKYHNILKQQLK                            1224

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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