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

NucPred

Fetching P25870 from www.uniprot.org...

The NucPred score for your sequence is 0.60 (see score help below)

   1  MTNLPIRFQEVLQLTNLGIGSNSIGFSTLTMESEKYICIRETTPDDKNNV    50
  51  VIIDTDNPSQILRKQMKTDAAIMNPKEPILALKIGQVLQLISIEQKMQLK   100
 101  SCQMQEPLEFWKWISPNTLALVTATSVFHWTKEGNSDPVKVFDRHPDLQN   150
 151  TEIINYRSDSTQNWLVLVAIHQRDGRVVGRIQLYSVEKQISQSIEGHAAC   200
 201  FANYIVPGATRPSTLFAISSRTQNASKILVLEVSKGDGPNFQKRASDVFY   250
 251  PPEIGASDFPVAMQVSEKYEVIYMVTKLGYIHLFDLGTANLIYRNRISNE   300
 301  NIFVTAFEESTNGIIAVNRKGQVLSVSIDDKNIIPYICNTLNNLELAISM   350
 351  ACKNNLPGAEGLLTTQFERYFQQGQYKEAAKVAADSPGSILRNLQTIQKF   400
 401  QSIPPIPDQPSALLQYFGMLLEKGKLNKVESLELVRPVLAQGKKPILEKW   450
 451  LTEDKLECSEQLGDEVRPHDRKLALSIYYRANASDKVITLFAETGEFDKI   500
 501  IAYCKKFNYKPDFMFLLQRMANANPMGAADFAVKLVKEEGGPYIDANQVV   550
 551  ELFSARNMIQETSNFLFAILDGDRPQDANLQTKLLEINLLHAPQNADAIM   600
 601  GGQKFTHYNRLRIGGLCEKAGLYQRALEHYTDLADIKRVLSHAGHMVNQE   650
 651  FLVSYFGSLNPEDRMECMRDFLRTNPRQNLQLVVAIAVSYSDQITPEAII   700
 701  AMFESFRLYEGLYLYLTQVVVTSTSPEVHFKYIEAAAKINQFKEVERMCR   750
 751  DSNYYDPEKTRDFLKEAKLPDQLPLIIVCDRYEFISDLTNYLYKNNLSKY   800
 801  IEAYVQKINPVNTPLVVGALLDLDCQEDYLRNLIMSVRNMCPADSLVEQV   850
 851  EKRNRLKLLLPWLEARVAEGNIEPAIHNALAKIYIDSNKNPEAFLLHNQF   900
 901  YDSKVVGKYCEKRDPYLSFVAYKRGLCDYELIEVTNKNTLFKNQARYLVE   950
 951  RQDPDLWAYVLSDQNEYKRSLIDQVVQTALPESTNATEVSATVKAFMDAN  1000
1001  LPNELIELLEKIVLEGKEFKTAKELQNLLILTAIRADKSRVTDYINRLDN  1050
1051  FDGSKLAPIAIESQLYEEAFFMYKKFQFNVEAIDVLITHIGSIERAHDFA  1100
1101  ERCNQTEVYSKLGVAQLKAEMVKECIESFIKANDTEHYQEVVAAAERKDE  1150
1151  YEDLVKFLQMCRKKIKEPAIESELIFAYAKVNKLAEMEDFINSPNSAHIQ  1200
1201  VVGDRCFENGLYEAAKVLYTNISNFSRLTSCLVKLGQYQAAVDAARKANS  1250
1251  TKTWKEVSAACIDAKEFRLAQVCGINIIVHGDELEELIRQYEDRGYFNEL  1300
1301  ISLLESGLASERAHVGMFTELAILYSKYKEEKLMEHLKLFYSRLNVPKVI  1350
1351  KACQANQQWPQLTYLYIHYDEHDNAIQTMINHSIEAWDHVLFKETIPKVA  1400
1401  KLDLYYSAISFYLEEQPLLINDLLSVLSPRIDHTRAVTLIRSLGHLPLVK  1450
1451  PYLVSAQDQNVAALNEALNELYVEEEDYESLRSSIDANSNFGTIALAQKL  1500
1501  EKHELLEFRRIAAYLYKKNNRWAQSVELSKKDKLYKDAIQSASDSKNPAI  1550
1551  GEELLQYFVDQQNNSAFAACLYTCYDFLKPDAVIELAWRNNILNYSFPYL  1600
1601  IQYVKEYTTKVDQLVDDFKARQKKTEEEKEQQNIESSQYQPDLTNLSYGY  1650
1651  AATGGMLALPPAVGYQQQQQPQQMYNPNQMMGGFQQNYNQYGGF        1694

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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