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

NucPred

Fetching Q00333 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MDHNSNHHWYSQNRPRNDPRIPSQQSPNTNINHHGFTNAANQTVQHAQQM    50
  51  LAGFPMASATPALQPVRHIANMTMTAAPPSFVQPNYYSSQAQPDYTHVQQ   100
 101  HNSQHIPPPPYTEYDQHLSYLSAPQVPQNRTEHWHTARDQSVRLLNEQAS   150
 151  RSYPYQEPQQPSNWPASSYQSTPFAQSVFQRTTPNSAYPTPPPPGISTSS   200
 201  SSLAFALGGPPQPPPRQQTVTQPLFHPTQAPLPQPAPAPQPAPVPQATVF   250
 251  PPPSNPPAAQASQPTYNADDSASFFNSFLERKTREMNATMQQTTSAKSIF   300
 301  PPAPAKLPLPVPVASKPPARMKTPPPREQKAVPDSSPDPLSLSSNMALPS   350
 351  STPLKRKCVVEIHSPPPKRIQSYKPMTLISQPLTPSRGPPLTPTSRASNA   400
 401  SSVPTTASSSTSITSMSSSSKTTVPMTPTPQRIGRKYEDTPDLGGYGSSE   450
 451  DTPLRRGLMSSVKRTGERDDRGPLEKFVTVVDEIFESEDSLPADLGHEDL   500
 501  PQEFFSSWSPDCSKPLLNTSTIRKLLKYVGQVARPTKRMRQASAGGQGLL   550
 551  ATPRTRAGRMADVDIQTLSRLLKMLERSLKEGEEVDPFKATGSSSGLNGT   600
 601  VSARSSPVKKGSRKKKAKDSLDDDDSMEADEADELPQQHLKKGSTPPPND   650
 651  IELEKLTRLLDLARDSVLAADCCIAILASDRLPKQLYSEELITSCLNTVK   700
 701  NQLTKVLYPFIEGASPDSINSKLYNGALLQHLIKNAPADPNTSANSSISQ   750
 751  AYHRKQMSEIFQSLSSVLPRINALANAESVAMSDSIIIQTVYIAIGPFFV   800
 801  VEGAEESTAKSASKKEKESVVNRTLGKSAMRGLRLDALSLIRSIFSNHED   850
 851  QRSWIIEEILTSLIKLSDTKQKAGQFRLRDGRSIRTVSALLMQLVQTSAH   900
 901  DVRINARRLEKERQNALALKRQESISDLNGQPKSDEPFLDNIDMEEIRLY   950
 951  GGGLESATKAAKTIIFFLNSRAGKGKTTKNSNEAEYRAIFDNLIDDLLVV  1000
1001  LYWPEWPAASLLLNIASKFMVSSLDDVKSNAQIDTNAAKSMALDHLGVIA  1050
1051  ARIRSSILKVQKDEDGTSYRGLKPLDEIVNNLQSKQFAKFMDAHRDVAAH  1100
1101  LCKRSTEDQAYESARELTAAILGHELAASLKRVNVWLDHPEQDEDLDLRD  1150
1151  SSKALSFGQKLKTALREVWKDPATDVFDIGSQEEVSRIDRLSEEIGTIQS  1200
1201  LRNSFQPILNVILSALDAPVIFMRTKALRALGQIVTSDATILGTASVRQG  1250
1251  IENHLLDSSPAVRDAAVELIGKYMIDSPEVAGNYYQKIAERMADTGLAVR  1300
1301  KRVIKLLKSYYGVIDDTQRKIDISARLVLRMVDEDDGVKDLAMKTLEELW  1350
1351  FPPLPPPSAMKVKPTSSSNPNQDKAALLSKVAIIMGTAANFRDRQSPLED  1400
1401  MLHKIISDKEGNEAASLHQRYAEICETLIDGLVDATDLPGFTIINCIRTI  1450
1451  HLFTAAYPSILPGTHASTLLPYLKNASTTEELLTSDFLLKIFRASIPHMP  1500
1501  KTAAKFGQELQTSLQPLILKPFGGVNILQEAVGCMCAVVRHLTHDFKRLI  1550
1551  NLLKGCNARLLSYLRHPPTKQLNNVESKTLLMLLFIVALLGEHCNFDRLR  1600
1601  LEQPDLAPDIDSITQGSVMEHIYFTLLRIYDKFDFADIRPRILQCLGFLF  1650
1651  RAQPTLMTKEESAAIMDAIFASEEEEGRARLLKIMQDFLISESEKHSAKE  1700
1701  KESAKNKNKANTDVNMEELVGNTDGFADSGVSSAIVQRYLSHILDAALSQ  1750
1751  NSQIQMAAIDVLTFTIKQGLAHPLQSFPVIIALETSPHAVLSARAIALHS  1800
1801  ILNSKHASLLNTRYSISARKSFDYQKKIVDGVVHGFRTNGHPTALLQRWY  1850
1851  TLVREKRATRQDFLKSLVKVFSENDSYQATQDDVDFTRYMAENFASFEYK  1900
1901  TQEEVFTVIKHLTTVLSTTGMQLLDIISPAHLLSQIQPSHSQPSQHNGGD  1950
1951  EISSNAAEAVVPLATPNYGDRDPVSLMRTSVIVAMVMLLKSYLKTLYGLS  2000
2001  EDKCNKFVIGKKSAIGDRPATKRSDKPISWEKLPYAVQAIHTTQDVELQK  2050
2051  QRFLEIWNEDGVTAEPEDDEFL                              2072

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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