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

NucPred

Fetching Q7Z460 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MEPRMESCLAQVLQKDVGKRLQVGQELIDYFSDKQKSADLEHDQTMLDKL    50
  51  VDGLATSWVNSSNYKVVLLGMDILSALVTRLQDRFKAQIGTVLPSLIDRL   100
 101  GDAKDSVREQDQTLLLKIMDQAANPQYVWDRMLGGFKHKNFRTREGICLC   150
 151  LIATLNASGAQTLTLSKIVPHICNLLGDPNSQVRDAAINSLVEIYRHVGE   200
 201  RVRADLSKKGLPQSRLNVIFTKFDEVQKSGNMIQSANDKNFDDEDSVDGN   250
 251  RPSSASSTSSKAPPSSRRNVGMGTTRRLGSSTLGSKSSAAKEGAGAVDEE   300
 301  DFIKAFDDVPVVQIYSSRDLEESINKIREILSDDKHDWEQRVNALKKIRS   350
 351  LLLAGAAEYDNFFQHLRLLDGAFKLSAKDLRSQVVREACITLGHLSSVLG   400
 401  NKFDHGAEAIMPTIFNLIPNSAKIMATSGVVAVRLIIRHTHIPRLIPVIT   450
 451  SNCTSKSVAVRRRCFEFLDLLLQEWQTHSLERHISVLAETIKKGIHDADS   500
 501  EARIEARKCYWGFHSHFSREAEHLYHTLESSYQKALQSHLKNSDSIVSLP   550
 551  QSDRSSSSSQESLNRPLSAKRSPTGSTTSRASTVSTKSVSTTGSLQRSRS   600
 601  DIDVNAAASAKSKVSSSSGTTPFSSAAALPPGSYASLGRIRTRRQSSGSA   650
 651  TNVASTPDNRGRSRAKVVSQSQRSRSANPAGAGSRSSSPGKLLGSGYGGL   700
 701  TGGSSRGPPVTPSSEKRSKIPRSQGCSRETSPNRIGLARSSRIPRPSMSQ   750
 751  GCSRDTSRESSRDTSPARGFPPLDRFGLGQPGRIPGSVNAMRVLSTSTDL   800
 801  EAAVADALKKPVRRRYEPYGMYSDDDANSDASSVCSERSYGSRNGGIPHY   850
 851  LRQTEDVAEVLNHCASSNWSERKEGLLGLQNLLKSQRTLSRVELKRLCEI   900
 901  FTRMFADPHSKRVFSMFLETLVDFIIIHKDDLQDWLFVLLTQLLKKMGAD   950
 951  LLGSVQAKVQKALDVTRDSFPFDQQFNILMRFIVDQTQTPNLKVKVAILK  1000
1001  YIESLARQMDPTDFVNSSETRLAVSRIITWTTEPKSSDVRKAAQIVLISL  1050
1051  FELNTPEFTMLLGALPKTFQDGATKLLHNHLKNSSNTSVGSPSNTIGRTP  1100
1101  SRHTSSRTSPLTSPTNCSHGGLSPSRLWGWSADGLAKHPPPFSQPNSIPT  1150
1151  APSHKALRRSYSPSMLDYDTENLNSEEIYSSLRGVTEAIEKFSFRSQEDL  1200
1201  NEPIKRDGKKECDIVSRDGGAASPATEGRGGSEVEGGRTALDNKTSLLNT  1250
1251  QPPRAFPGPRARDYNPYPYSDAINTYDKTALKEAVFDDDMEQLRDVPIDH  1300
1301  SDLVADLLKELSNHNERVEERKGALLELLKITREDSLGVWEEHFKTILLL  1350
1351  LLETLGDKDHSIRALALRVLREILRNQPARFKNYAELTIMKTLEAHKDSH  1400
1401  KEVVRAAEEAASTLASSIHPEQCIKVLCPIIQTADYPINLAAIKMQTKVV  1450
1451  ERIAKESLLQLLVDIIPGLLQGYDNTESSVRKASVFCLVAIYSVIGEDLK  1500
1501  PHLAQLTGSKMKLLNLYIKRAQTTNSNSSSSSDVSTHS              1538

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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