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

NucPred

Fetching Q9QY06 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSAHEAGSSGRRQQATYHLHIYPQLSSAGSQTSCRVTATKDSTTSDVIQD    50
  51  VVASLHLDGSKHYVLVEVKESGGEEWVLDASDSPVHRVLLWPRRAQDEHP   100
 101  QEDGYYFLLQERNADGSIQYLPIQLLAQPTAACRLVERGLLPRPQADFDD   150
 151  LCNLPELTEANLLQNLKLRFMQQKIYTYAGSILVAINPFKFLPIYNPKYV   200
 201  KMYENQQLGKLEPHVFALADVAYYAMLRKHVNQCIVISGESGSGKTQSTN   250
 251  FLIHCLTALSQKGYASGVERTILGAGPVLEAFGNAKTAHNNNSSRFGKFI   300
 301  QVNYLENGIVRGAVVEKYLLEKSRLVSQEKDERNYHVFYYLLLGVSEEER   350
 351  LEFQLKQPQDYFYLNQHNLNIEDGEDLKHDFERLQQAMEMVGFLPATKKQ   400
 401  IFSVLSAILYLGNVTYKKRATGRDEGLEVGPPEVLDTLSQLLKVKRETLV   450
 451  EVLTKRKTVTVNDKLILPYSLSEAITARDSMAKSLYSALFDWIVLRINHA   500
 501  LLNKKDMEEAVSCLSIGVLDIFGFEDFERNSFEQFCINYANEQLQYYFTQ   550
 551  HIFKLEQEEYQGEGISWHNIDYTDNVGCIHLISKKPTGLFYLLDEESNFP   600
 601  HATSHTLLAKFKQQHEDNKYFLGTPVLEPAFIIQHFAGRVKYQIKDFREK   650
 651  NMDYMRPDIVALLRGSDSSYVRQLIGMDPVAVFRWAVLRAAIRAMAVLRE   700
 701  AGRLRAERAEKAAGISSPATRSHMEELPRGASTPSEKLYRDLHNQIIKSL   750
 751  KGLPWQGEDPRRLLQSLSLLQKPRTSFLKSKGIKQKQIIPKNLLDSKSLR   800
 801  LIISMTLHDRTTKSLLHLHKKKKPPSISAQFQTSLNKLLEALGKAEPFFI   850
 851  RCIRSNAEKKELCFDDELVLQQLRYTGMLETVRIRRSGYSAKYTFQDFTE   900
 901  QFQVLLPKDVQPCREAIAALLEKLQVDRQNYQIGKTKVFLKETERQTLQE   950
 951  KLHGEVLRRILQLQSWFRMVLERKHFVQMKHAALTIQACWRSYRVRRALE  1000
1001  RTQAAVYLQAAWRGYLQRQAYHHQRHSIIRLQSLCRGHLQRRSFSQMVSE  1050
1051  KQKAEQAREAAGGKLSEGEPGPVAAGEQLSEHPVEDPESLGVEAETWMNK  1100
1101  SPDGMSPKKETPSPEMETAAQKTVPAESHEKVSSSREKRESRRQRGLEHV  1150
1151  ERQNKHIQSCREESSTHREPSRRASLEIGESFPEGTKGPREDGLEAWTET  1200
1201  TAPSSSKQAQVVGDPPGSPSPVQRPTTLALDSRVSPMLPSSSLESPKDKD  1250
1251  KDESSTKAQDKPESPSGSTQIQRYQHPDTERLATAVEIWRGKKLASAVLS  1300
1301  QSLDLSEKHRATGAALTPTEERRISFSTSDISKLSPVKTSAEIDGDFSSK  1350
1351  KPSIHKKKSGDPSAGPDAGLSPGSQGDSKSAFKRLFLHKAKDKKPSLEGV  1400
1401  EETESNGGQAAQETPARKTLDVPSSQQHRHTTGEKPLKGKKNRNRKVGQI  1450
1451  TVSEKWRESVFRKITNANELKFLDEFLLNKVNDLRSQKTPIESLFIEATE  1500
1501  RFRSNIKTMYSVPNGKIHVGYKDLMENYQIVVSNLAAERGEKDTNLVLNV  1550
1551  FQSLLDEFTRSYNKTDFERAKSKAQKKKRKQERAVQEHNGHVFASYQVNI  1600
1601  PQSCEQCLSYIWLMDKALLCSVCKMTCHKKCVHKIQSYCSYTGRRKSELG  1650
1651  AEPGHFGVCVDSLTSDKASVPIVLEKLLEHVEMHGLYTEGLYRKSGAANR  1700
1701  TRELRQALQTDPAAVKLEDFPIHAITGVLKQWLRELPEPLMTFAQYGDFL  1750
1751  RAVELPEKQEQLSAIYAVLDHLPEANHTSLERLIFHLVKVALLEDVNRMS  1800
1801  PGALAIIFAPCLLRCPDNSDPLTSMKDVLKITTCVEMLIKEQMRKYKMKM  1850
1851  EEINHLEAAESIAFRRLSLLRQNAPWPLKLGFSSPYEGVRIKSPRTPVVQ  1900
1901  DLELGALSEEAAGGDEDREKEILMERIQSIKEEKEDITYRLPELDPRGSD  1950
1951  EENLDSETSASTESLLEERGVRGAVEGPPAPALPCPISPTLSPLPEAAAP  2000
2001  PRGRPTSFVTVRVKTPRRTPIMPMANIKLPPGLPLHLTSWAPALQEAVVP  2050
2051  VKRREPPARRQDQVHSVYIAPGADLPSQSTLIALDHDTILPGTKRRYSDP  2100
2101  PTYCLPPSSGQANG                                      2114

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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