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

NucPred

Fetching Q8BX17 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MKPEPRTLPPSPNWYCSRCSDAAPGGIFGFAARTSVFLVRVGPGAGASPG    50
  51  APPFRVVGELVGHTERVSGFTFSHHPGQYNLCATSSDDGTVKVWDVETKT   100
 101  VVTEHTLHQHTISALHWSPTVKDLIVSGDEKGVVFCYWLNRNDSQHLFTE   150
 151  PRTIFCLTCSPHHENLVAIGYKDGIVVIIDISKKGEVIHRLRGHDDEIHS   200
 201  IAWCPLSGEDCLSISQEENSEEPDIPNGKLIAETPITKGCYLATGSKDQT   250
 251  IRIWSCSRGRGVMVLKLPFLKRRSGGVDPTVKERLWLTLHWPKNQPTQLV   300
 301  SSCFGGELLLWDLTQSWRRKYTLFSTSAEGHNHSRIVFNLCSLKTEDGKQ   350
 351  LLLSTSMDRDVKCWDMATLECCWTLPSLGGFAYSLAFSPVDVGSLAIGVG   400
 401  DGMIRVWNTLSIKNNYDVKNFWQGVKSKVTALCWHPNKEGCLAFGTDDGK   450
 451  VGLYDTCSNKPPQISSTYHKKTVYRLAWGPPVPPMSLGGEGDRPSLTLYS   500
 501  CGGEGVVLQHNPWKLSGEAFDINKLVRDTNSIRYKLPVHTEISWKGDGKV   550
 551  LALGNEDGSIEIFQVPNLRLLCTIQQHHKLVNAIVWHHEHGSRPELSCLL   600
 601  ASGSNNAVIYVHNLKAVLESNPESPITITEPYRTLSGHTAKITSLAWSPH   650
 651  HDGRLVSACYDGTAQVWDALREEPLFNFRGHRGRLLCVAWSPVDPECIYS   700
 701  GADDFCVYRWLTSMQDHSRPPQGKKCIELEKKRLSQFKPKLKKKKKPTLR   750
 751  LPVKQDSSVGNEDESVKENSGPAENGLSDQDGEEEAQEPELPPSPVVCVE   800
 801  PVSCTDICSGFEKSKVTVSSKATSLKKEPAKEKPEALLKKRKARSMLPLS   850
 851  TSLDHRSKEELHRDCLVLATATHAKAELNEDVSADLEERFHLGLFTDRAT   900
 901  LYRMMETEGKGHLESGHPELFHQLMLWKGDLKGVLQAAAERGELTDSLVA   950
 951  VAPVAGYSVWLWAVEAFAKQLCFQDQYVKAASYLLSIHKVYEAVELLKSN  1000
1001  HLYREAIAVAKARLRPEDPVLKELYLSWGSILERDGHYAIAAKCYLGATS  1050
1051  AYDAAKVLARKGDAASLRTAAELAAIAGEHELAASLALRCAQELLLMKNW  1100
1101  VGAQEALGLHESLQGQRLVFCLLELLCRHLEEKQPLEVRGPSSIYHQWAT  1150
1151  GSEGTLVQRVTGVWRSAFSVDTPEQCQAALQKLQDVKYPSATSNTPFRQL  1200
1201  LLHVCHDLTLAMLSQQAAAWEEAVPALLQAVVRSYTSGNFTLMQEIYSAF  1250
1251  LPGGCDHLRDKLGDLSPAMAAYKSLEAFCIYGQLYEVWWSLCGPGPESSV  1300
1301  WVLSAESTVSDKQSKPEDSASAEDMEQPPGPGPRLSAESERLLSACKELF  1350
1351  SERHASLQTSQRTVAEVQETLAEMIRQHQKSQLCKATTNGPSRDEPSRDE  1400
1401  PSQEAERAPSQPPSPTEERNAPVSLPELTRRLTEANERIAEFPESVKAWP  1450
1451  FPDVLECCLVLLHIGSQCPDAVDPEMQQQAQELLHKYGHTRAYRRHCQSR  1500
1501  HT                                                  1502

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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