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

NucPred

Fetching Q63358 from www.uniprot.org...

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

   1  MSAHEAGSSGRRRPATFHLHIYPQLPSAGSQTSCRVTATKDSTTSDVIRD    50
  51  VVASLHLDGSKHYVLVEVKESGGEEWVLDASDSPVHRVLLWPRRAQKEHP   100
 101  REDGYYFLLQERNADGSIQYLHVQLLAQPTAACRLVERGLLPRPQADFDD   150
 151  LCNLPELNEANLLQSLKLRFVQQKIYTYAGSILVAINPFKFLPIYNPKYV   200
 201  KMYENQQLGKLEPHVFALADVAYYTMLRKHVNQCIVISGESGSGKTQSTN   250
 251  FLIHCLTALSQKGYASGVERTILGAGPVLEAFGNAKTAHNNNSSRFGKFI   300
 301  QVNYLESGIVRGAVVEKYLLEKSRLVSQEKDERNYHVFYYLLLGVSEEER   350
 351  QEFQLKQPQDYFYLNQHNLNIEDGEDLKHDFERLQQAMEMVGFLPATKKQ   400
 401  IFSVLSAILYLGNVTYKKRATGRDEGLEVGPPEVLDTLSQLLKVKRETLV   450
 451  EVLTKRKTITVNDKLILPYSLSEAITARDSMAKSLYSALFDWIVLRINHA   500
 501  LLNKKDMEEAVSCLSIGVLDIFGFEDFERNSFEQFCINYANEQLQYYFTQ   550
 551  HIFKLEQEEYQGEGISWHNIDYTDNVGCIHLISKKPTGLFYLLDEESNFP   600
 601  HATSHTLLAKFKQQHEDNKYFLGTPVLEPAFIIQHFAGRVKYQIKDFREK   650
 651  NMDYMRPDIVALLRGSDSSYVRQLIGMDPVAVFRWAVLRAAIRAMAVLRE   700
 701  AGRLRAERAEKAEAGVSSPVTRSHVEELPRGANTPSEKLYRDLHNQIIKS   750
 751  LKGLPWQGEDPRRLLQSLSRLQKPRTFFLKSKGIKQKQIIPKNLLDSKSL   800
 801  RLIISMTLHDRTTKSLLHLHKKKKPPSISAQFQTSLNKLLEALGKAEPFF   850
 851  IRCIRSNAEKKELCFDDELVLQQLRYTGMLETVRIRRSGYSAKYTFQDFT   900
 901  EQFQVLLPKDVQPCREAIAALLEKLQVDRQNYQIGKTKVFLKETERQALQ   950
 951  ERLHGEVLRRILLLQSWFRMVLERRHFVQMKHAALTIQACWRSYRVRRTL  1000
1001  ERTRAAVYLQAAWRGYLQRQAYHHQRHSIIRLQSLCRGHLQRRSFSQMML  1050
1051  EKQKAEQARETAGAEMSEGEPSPVAAGEQPSEHPVEDPESLGVETETWMN  1100
1101  SKSPNGLSPKKEIPSPEMETPAQKTVPAESHEKVPSSREKRESRRQRGLE  1150
1151  HVERQNKHIQSCREENSTLREPSRKASLETGESFPEDTKEPREDGLETWT  1200
1201  ETAAPSCPKQVPIVGDPPRSPSPLQRPASLDLDSRVSPVLPSSSLESPQD  1250
1251  EDKGENSTKVQDKPESPSGSTQIQRYQHPDTERLATAVEIWRGKKLASAM  1300
1301  LSQSLDLSEKPRTAGAALTPTEERRISFSTSDVSKLSPVKTSTEVDGDLS  1350
1351  AKKPAGHKKKSEDPSAGPDAGLPTGSQGDSKSAFKRLFLHKAKDKKPSLE  1400
1401  GVEETEGSGGQAAQEAPARKTLDVPSSQQHRHTTGEKPLKGKKNRNRKVG  1450
1451  QITVSEKWRESVFRKITNANELKFLDEFLLNKVNDLRSQKTPIESLFIEA  1500
1501  TERFRSNIKTMYSVPNGKIHVGYKDLMENYQIVVSNLAAERGEKDTNLVL  1550
1551  NVFQSLLDEFTRSYNKTDFEPVKGKAQKKKRKQERAVQEHNGHVFASYQV  1600
1601  NIPQSCEQCLSYIWLMDKALLCSVCKMTCHKKCVHKIQSYCSYTGRRKSE  1650
1651  LGAEPGHFGVCVDSLTSDKASVPIVLEKLLEHVEMHGLYTEGLYRKSGAA  1700
1701  NRTRELRQALQTDPATVKLEDFPIHAITGVLKQWLRELPEPLMTFAQYGD  1750
1751  FLRAVELPEKQEQLAAIYAVLDHLPEANHTSLERLIFHLVKVALLEDVNR  1800
1801  MSPGALAIIFAPCLLRCPDNSDPLTSMKDVLKITTCVEMLIKEQMRKYKV  1850
1851  KMEEINHLEAAESIAFRRLSLLRQNAPWPLKLGFSSPYEGVRTKSPRTPV  1900
1901  VQDLEELGALPEEAAGGDEDREKEILMERIQSIKEEKEDITYRLPELDPR  1950
1951  GSDEENLDSETSASTESLLEERAVRGAAEE                      1980

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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