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

NucPred

Fetching Q872I5 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MDHFSTVLQRPPHFDEDGTEGRGDRGNGAGPGPAPPPPPPRGGLRDILNP    50
  51  VSSNSAVQSQAAAAAPPPPPAVASSSLHGIAASVPPPSSTNSMRATPHSS   100
 101  SSFNLRSPTREPSEYRHPLSSLATPAPFAASPPTSIANANNTNNNNALGA   150
 151  AGSLSSQPPPPPPTGPRSILNPPTPSQQHQQQHHHPNPFVAASAPSLPPP   200
 201  PSSLQAPPAITPIAGLSAPAPASGSLPLSAGGIGNSITVSSSSQPPARAS   250
 251  QLHAPSAYYSPAESFRDRDSSVREKSSTGGSFYDPTAEASNGISGSSPRK   300
 301  DRDRDRDHRGTTRESQRRSVSGHSDTGSSWRNATQTSASNKTRDPYNYSP   350
 351  SSADYYNTRKKENYPVDNTTSSSIAAPSNFTVATRSPVAALSHPASIAAP   400
 401  ASVGSLTGSISPRLSLRPPSMASPTIRSAVLANPTNGTTSTALPALGRND   450
 451  SPPSKMSPGTSTNPSRAAGVMSFSNILSSSEPVPRPRATSPNNPDDDDDV   500
 501  PMKVERADSSEKVVKEKKERKPRQPKQPRISDIRHSESTPKGRRGSTKQE   550
 551  SPLPNIRIPAKRMANGAPKQQKTFSAENEEKIRKAMDRIETRELPHEDEF   600
 601  EEELRLWRERREYKRQQMNQRDLRQRRQRRADYTEVEAQKLKLHADFGKR   650
 651  RYDDLNYDDALQEVRERELFAEKERKKDMQRKRRREKSMATTMEAKAAAL   700
 701  ARASAAQDEAERQKYMREAERANKKVQQTRLILQKGIKGPSRNTGPIEPN   750
 751  LEGGTMATFQAENMEPGKTKGKGRAGARPKKSKEQKQAEKDAAEAAQAAL   800
 801  DAGLELPPKEETNKIRIKLTKTKAPKEADVDKDKENKEPQEPKEPKEPKE   850
 851  KVIKEKVVEEPKDPLELKFQSKGFNQIYDQIWRDLARKDVNKVFRLAIDS   900
 901  YSTKSSNLKKTAILASKEAKRWQLRTNKGTKDLQARAKRVMRDMMGFWKR   950
 951  NEREERDLRKAAEKQELENARKEEADREAARQKRKLNFLISQTELYSHFI  1000
1001  GKKIKTNEVERSTDHPDEIAAEKDKIPENEMDIEVPTGPIGAKVTNFENL  1050
1051  DFDAEDESTLRAAAMANAQNAIAEAQKKAREFNKEESKLDEDGEMNFQNP  1100
1101  TMMGDVEIEQPKLLNCQLKEYQLKGLNWLVNLYEQGINGILADEMGLGKT  1150
1151  VQSISVMAYLAEKYDIWGPFLVVAPASTLHNWQQEITKFVPQFKVLPYWG  1200
1201  TAGDRKVLRKFWDRKHTTYKKDAPFHVMITSYQLVVSDVAYFQKMKWQYM  1250
1251  ILDEAQAIKSSQSSRWKCLLGFHCRNRLLLTGTPIQNNMQELWALLHFIM  1300
1301  PSLFDSHDEFSEWFSKDIESHAQSNTKLNEDQLKRLHMILKPFMLRRVKK  1350
1351  HVQKELGDKIEMDVFCDLTYRQRAMYANLRNQISIMDLIEKATLGDDDSA  1400
1401  SLMNLVMQFRKVCNHPDLFERADTASPYSFGHFAETASFIREGSQVTVGY  1450
1451  STRSLIQYELPRLLWRDGGRLHKAGEDNQVAGWRNQWLNEKFNIWTPEHI  1500
1501  RESLAGTDNFSWLRFADTSYEEAYRASHKDLFARAVEMSTKKNRLAEIKI  1550
1551  AYDEPEDLNFTPAHALFHIREREDRRPLAEITEQGILGSLMNVSRSAFSE  1600
1601  TGLGRLEQAAAPKASAPPIEVVCDSRSAVVERENIMFNAPMRKVLFGPTL  1650
1651  AEEKALVVQKVPPSRYPPPALLPAPDKEKQKFTNITVPSMRRFVTDSGKL  1700
1701  AKLDELLRELKENGHRVLLYFQMTRMIDLMEEYLTYRNYKYCRLDGSTKL  1750
1751  EDRRDTVADFQTRPEIFIFLLSTRAGGLGINLTSADTVIFYDSDWNPTID  1800
1801  SQAMDRAHRLGQTKQVTVYRLITRGTIEERIRKRAMQKEEVQRVVITGGS  1850
1851  SAAGGGVDFSGRRAPENRNRDIAMWLADDEQAEMIEKRERELLESGELDK  1900
1901  MQKKSRGGNKRKRGGAGGEGKEVSLDEMYHEGEGNFDDGGNNIKGSGTAT  1950
1951  PNGAAGGEGGDGKGAVGGAAKKRKTGGSKKAKTTKQRLAIADGEIDI     1997

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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