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

NucPred

Fetching P20806 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MFWREDAAQQQQQQQQQQQQQQQQQQPPHPPKRLSFSFNVKIAVNVNTKM    50
  51  STTHINQERSKQQTTTGSRSRSRSNSNSSVSCKGDGDRRVRRHTTRLVGL   100
 101  RQQLLHLGRQLNPGQFLVTGHGGISTILIANLLLLLLLSLCCNVCCRSHI   150
 151  EPDQNLTPTTTSPAAVAVVPMLLPLAQTHMRPQLDSDVVEKVAVWTKHVG   200
 201  AAPPSIAEGIAISSVVRMPPSIQTPTETVRRQEQQRQQQQQQQEAAAAAA   250
 251  ADAAIDERIVLERVTRDCVQRCIVEEDLFLDEFGIKCEKADNSDKCYKTR   300
 301  CNKGCAQWYRALKEIEPCQEACASTQFYPYDMPCIGACETAQRDYWHMQR   350
 351  LAMARLVETTQPQLLEMTDESSTLTIKWAMQFPENYLASRPFNIQYQQVD   400
 401  NQSEPEWHNLADYDCDEYYVCEILEALVPYTRYKFRFELPFGESSEDVLY   450
 451  SPATPVYETPMEGAPISAPIIVALLALDEHHVFVHWRPGRYSNAPIEGYR   500
 501  VLLTSAGNTSREQLLPAQRTSCIFAQLQPLTNYTVALTMINKQGEGPSTV   550
 551  VSIVTKSPLEPQQLQSVLLASEHSIIWQSLEPAGETRLLYTSEPAAISDF   600
 601  TFSQREQRLWLLDELGQLHSQLLDETTTSAARRLRLELPSNGSSQWTPRK   650
 651  LSLDWLQRRLYIAAQANSSDGAEGGFELFSSNLEGGDVQMAGVQLGLVVE   700
 701  QLELDALNGWLFWCDADSLWRLDLSSKQQLRLTQPAGAPGRFMLEPQRWL   750
 751  LHVLLPQENQLLELSYDGGHKHALALSNDSWRGFAWSSDQAQLLLANETQ   800
 801  LQLLDGQTLVPLANWSPDGGCCALLPLERRRQPLSLEPPAPRELRALLGA   850
 851  QGAHITWQPPAANPYQTATAAARNFSYELEVLDVASQSAYNIRNIRVPHF   900
 901  GLERLQADNLYQLRVRANNAAGRAGVWTAPLATRTWPLGDHRLRWATQRG   950
 951  SLYTTNELGGQLQPLPVQLASSPGPLALVNASVAYYVSGREQSLHCVNLL  1000
1001  QPQLSCTDERLEHVGAVAYDWRGGLLYWTDLARDCVQRLDPFSGERELLP  1050
1051  IFGARHLALDSAQGHLYYSSSAHLARRSLSALSTHQPELEYYHVNGLAGQ  1100
1101  ISGFCLDLPQRHIYWLVAGNSALHLYRTALSAGGSQAAVPLQLLTTLPAA  1150
1151  DALPHTLQHLAPLGALLWLAADGRGAHLLRLAAQLETDTDTMRLLPEGLV  1200
1201  EPLSAVQLLERSAGPPPPPPDEGVRPLAVPPDSVHIDEGGHWNDFRVRWQ  1250
1251  PAASGGNHSVCYKLLLEHGSERLITLELLTPFARITQLAQAPLGLRISIT  1300
1301  PHTAWRAGSTTRVQLDTPVAAPTQPRRLRVFVERQAAPLQLAPNVSALLR  1350
1351  WDVPEEHAGSQSLQYRISCWRGSELHSELLLNQSTLEARVEHLQPEETYR  1400
1401  FQVQAHVAATGLAAGATSHALHVSPEVQSVPRLLYANAEHIGELDLDTGH  1450
1451  RKQLVHTASPVEHLVVLQGEQRLLWVNEHVELLSHVPGKAPAKLARMRAE  1500
1501  VLALTVDWVQRIVYWAELDAADGGCVIYSLDLCRFDGRILQGERLWSTPR  1550
1551  GQLLRDLVALPHARQLVWLQHDLDSRNATLQGRSLANGSALTFEGVTLPL  1600
1601  WRLFEGSQEPLAETLNLVDHLGRLCVYHVARQLCTSSALRAQLNLLNDDI  1650
1651  GQLAQDPGYLYALRNGSVRAYGRRRQQLEFLLELQPDEVRLLRAYNYQAY  1700
1701  PSRRCLLLPTTAAALESTPSSCEETQCSLQLPALSAAPDCPLPVPGLNYQ  1750
1751  LNLSSSSRSAQLELRSLHSAAGLTLNISQLQPYQAYELRAQVGSYYQQQL  1800
1801  GQEPLQLPVLTLHTAAATPSAPRNFSGRALSPSELELSWLAPLELRSASV  1850
1851  YYTLHWQLQLEDTEEQSQEQPAQEQRVETAGVQRLTGLQPARLYQVWLQA  1900
1901  HATPSKYNSSGRLLIRSYAPLPPLQLIELNAYGMTLAWPGTPDALSSLTL  1950
1951  ECQSLREQLQFNVAGNHTQMRLAPLQPKTRYSCRLALAYAATPGAPIYFG  2000
2001  PSHEYETLGDAPSAPGRPQLEHIAGEIFRVSWTPALDNGSPILLYNLEAL  2050
2051  QARRTNRRRRRRRETTLSLLPWAEEPLVIEDQWLDFCNTTELSCIVRELH  2100
2101  TRRLLLFRVRARNRPHGWGPYSEDSERIAEPFVSPEKRGSLVLAIIAPAA  2150
2151  IVSSCVLALVLVRKLQKRRHRAKKLLQQSRPSIWSNLSALQTQQQLLAAR  2200
2201  SRTFSMSLSDADIALLPQINWNRLTLLRFLGSGAFGEVYEGQLQAEDEAQ  2250
2251  PQRVAIKSLRKGASEFAELLQEAQLMSNFKHENIVCLIGICCDTDSISLI  2300
2301  MEHMEAGDLLSYLRAARPSSQEALSKLQLPELLSMCLDVANGCSYMEDMH  2350
2351  FVHRDLACRNCLVSDGAAIGGRRIVKIGDFGLARDIYKSDYYRKEGEGLL  2400
2401  PVRWMALESLVDGLFSTQSDVWAFGVLCWEIFTLGQQPYAARNNFEVLAH  2450
2451  VKEGGRLQQPERCPEKLYALLLQCWRSEPWERPSFKRCLSTLQALSSDLR  2500
2501  RTEMLATDETPLVSALCAFKPDAKVRFDDAPQRLTLHLDAKDTVSTTDAD  2550
2551  TTGSPTTPTAPTTPTTTTSTIAVVSTAPSSENGQLYANEGISGL        2594

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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