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

NucPred

Fetching Q9M1C7 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MFKPFGFAAETGSHLLTTQWLQLGNSLCLKERISIAMQVTFLAFFLIHLA    50
  51  LKWFGVVRNRGSNDVEEDLKKQSITVKQSFSYNISLLCSVSILGTHCFIL   100
 101  LLLFRDSVVSRCDSSVSVFSAEVSQSFSWLFVSVVVVKIRERRLVKFPWM   150
 151  LRSWWLCSFILSFSFDAHFITAKHEPLEFQDYADLTGLLASLFLLAVSIR   200
 201  GKTGFHLLESSGNTEPLLLGDQTEQNKKDSYSSSSPYGNATLFQRITFSW   250
 251  INPLFSLGYKRPLEKDDVPDIDVKDSARFCSHAFDQKLKTTKEKEGPGNA   300
 301  FFYNSVLRYVWRKAAINAVFAVVNASTAYIGPYLINDFVEFLSEKQSQSL   350
 351  NHGYLLALGFLTAKIVETVTQRQWIFGARQLGLRLRAALISHIYQKGLVL   400
 401  SSQSRQSHTSGEIINYMSVDVQRITDFIWYVNNIWMLPIQIFSAIYILQK   450
 451  HLGLGALAALVTTLMVMACNYPLTRLQRNYQSDIMNAKDDRMKATSEILK   500
 501  NMKILKLQAWDNQFLNKVKTLRKKEYDCLWKSLRLQAFTTFILWGAPSLI   550
 551  SVVTFVTCMLMGVKLTAGAVLSALATFQMLQSPIFGLPDLLSALVQSKVS   600
 601  ADRIASYLQQSETQKDAVEYCSKDHTELSVEIENGAFSWEPESSRPTLDD   650
 651  IELKVKSGMKVAVCGAVGSGKSSLLSSILGEIQKLKGTVRVSGKQAYVPQ   700
 701  SPWILSGTIRDNILFGSMYESEKYERTVKACALIKDFELFSNGDLTEIGE   750
 751  RGINMSGGQKQRIQIARAVYQNADIYLLDDPFSAVDAHTGRELFEDCLMG   800
 801  ILKDKTVLYVTHQVEFLPAADLILVMQNGRVMQAGKFEELLKQNIGFEVL   850
 851  VGAHNEALDSILSIEKSSRNFKEGSKDDTASIAESLQTHCDSEHNISTEN   900
 901  KKKEAKLVQDEETEKGVIGKEVYLAYLTTVKGGLLVPFIILAQSCFQMLQ   950
 951  IASNYWMAWTAPPTAESIPKLGMGRILLVYALLAAGSSLCVLARTILVAI  1000
1001  GGLSTAETFFSRMLCSIFRAPMSFFDSTPTGRILNRASTDQSVLDLEMAV  1050
1051  KLGWCAFSIIQIVGTIFVMSQVAWQVCVIFIPVAVACVFYQRYYTPTARE  1100
1101  LSRMSGVERAPILHHFAESLAGATTIRAFDQRDRFISSNLVLIDSHSRPW  1150
1151  FHVASAMEWLSFRLNLLSHFVFAFSLVLLVTLPEGVINPSIAGLGVTYGL  1200
1201  SLNVLQATVIWNICNAENKMISVERILQYSKIPSEAPLVIDGHRPLDNWP  1250
1251  NVGSIVFRDLQVRYAEHFPAVLKNITCEFPGGKKIGVVGRTGSGKSTLIQ  1300
1301  ALFRIVEPSQGTIVIDNVDITKIGLHDLRSRLGIIPQDPALFDGTIRLNL  1350
1351  DPLAQYTDHEIWEAIDKCQLGDVIRAKDERLDATVVENGENWSVGQRQLV  1400
1401  CLGRVLLKKSNILVLDEATASVDSATDGVIQKIINQEFKDRTVVTIAHRI  1450
1451  HTVIESDLVLVLSDGRIAEFDSPAKLLQREDSFFSKLIKEYSLRSNHFAG  1500
1501  SNDLLS                                              1506

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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