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

NucPred

Fetching Q9ESD7 from www.uniprot.org...

The NucPred score for your sequence is 0.72 (see score help below)

   1  MLRVFILFAENVHTPDSDISDAYCSAVFAGVKKRTKVIKNSVNPVWNEGF    50
  51  EWDLKGIPLDQSSELLVVVKDHETMGRNRFLGEAKIPLQEVLATPSLSAS   100
 101  FNAPLLDAKQQPTGASLVLQVSYTPPPGAVPLFPPPASLAPSPTLPDMDL   150
 151  VPDTGGEEDTEDQGLTGDEAEPFLDQSAAVGPGGPTTPRKPPSHPPPHYP   200
 201  GAKRKRSSAPPRKLLSDKPQDFQIRVQVIEGRQLPGVNIKPVVKVTAAGQ   250
 251  TKRTRIQKGNSPLFNETLFFNVFDSPLELFDEPIFITVVDSRSLRTDALL   300
 301  GEFRMDVGTVYREPRHAYLRKWLLLSDPDDFSAGARGYLKASLCVLGPGD   350
 351  EAPLDKKDPSEDKEDIEGNLLRPTGVALRGAHFCLKLFRAEDLPQMDDAV   400
 401  MDNVKQIFGFDSNKKNLVDPFVEVSFAGKMLCSKILEKTANPQWNQNITL   450
 451  PAMFPSMCEKMRIRVMDWDRLTHNDTVATTYLGMSKISATGGEIEEEPAG   500
 501  VLKSPQATDLDDNLGFLPTFGPCYVNLYGSPREFTGFPDPYAELNTGKGE   550
 551  GVAYRGRVLLSLETKLVEHSEQKVEDLPADDILRVEKYLRRRKYSLFAAF   600
 601  YSATMLQDVDDAIQFEVSIGNYGNKFDTTCLPLASTTQYSRAVFDGGSLP   650
 651  LPVGCHYYYLPWGNVKPVVVLSSYWEDISHRIEIQNQLLRVADRLEANLE   700
 701  QVHLALKAQCSSEDVDALVAQLTDELLADCSQPLCDIHEIPSATHLDQYL   750
 751  LRLRTRHLSQIKEAALALKLGHSELSTALEQAEDWLLHLRALAEEPQNSL   800
 801  PDIIIWMLQGDKRVAYQRVPAHEVLFSRRGPSYCGRNCGKLQTIFLKYPM   850
 851  EGMPGARMPVQIRIKLWFGLSVDEKEFNQFAEGKLSVFAETYENQTKLAL   900
 901  VGNWGTTGLTYPKFSDVTGKIKLPKDSFRPSAGWAWAGDWFVCPEKTLLH   950
 951  DADAGHLSFVEEVFENQTRLPGGQWIYMSDNYTDVNGEKVLPKDDIECPL  1000
1001  GWKWEDEEWSTDLNRAVDEQGWEYSITIPPDRKPKHWVPVEKMYYTHRRR  1050
1051  RWVRLRRRDLSQMEALKRHRQAEAEGEGWEYASLFGWKFHLEYRKTDAFR  1100
1101  RRRWRRRMEPLEKTGPAAVFALEGALGGMVDDKSEDSMSVSTLSFGVNRP  1150
1151  TISCIFDYGNRYHLRCYLYQARDLPAMDKDSFSDPYAIVSFLHQSQKTVV  1200
1201  EKNTLNPTWDQTLIFYEIEIFGEPASIAEHPPCIVVELYDHDTYGADEFM  1250
1251  GRCICQPSLERMPRLAWFPLTRGSQPAGELLAAFELIQREKPAIHHIPGF  1300
1301  EMHETSRILDETEDTDLPYPPPQREANIYMVPQNIKPALQRTAIEILAWG  1350
1351  LRNMKSYQMASISSPSLVVECGGQTVQSCVIRNLRKNPNFDVCTLFMEVM  1400
1401  LPREDLYCPPIVVKVIDNRQFGRRPVVGQCTIRSLENFLCDPYSAESPSP  1450
1451  QGGPDDVSLLSPGEDVLIDIDDKEPLIPVQEEEFIDWWSKFFASVGEREK  1500
1501  CGSYLEKDFDTLKVYDTQLENVEAFGGLSDFCNTFKLYRGRTQEETDDPS  1550
1551  VIGEFKGLFKIYPLPEDPAIPMPPRQFHQLAAQGPQECLVRIYIVRAFGL  1600
1601  QPKDPNGKCDPYIKISIGKKSVSDQDNYIPCTLEPVFGKMFELTCTLPLE  1650
1651  KDLKITLYDYDLLSKDEKIGETVIDLENRLLSKFGARCGLPQTYCVSGPN  1700
1701  QWRDQLRPSQLLHLFCQQHRIKAPVYRTDRVTFQDKDYTIEEIEAGRLPN  1750
1751  PHLGPVEERLALHVLQQQGLVPEHVESRPLYSPLQPDIEQGKLQMWIDIF  1800
1801  PKVLGRPGPPFNITPRKARRFFLRCIIWNTKDVILDDLSLTGEKMSDIYV  1850
1851  KGWMVGFEEHKQKTDVHYRSLGGEGNFNWRFVFPFDYLPAEQVCAVAKKD  1900
1901  AFWRLDKTESKIPARVVFQIWDNDKFSFDDFLGSLQLDLNRMPKPAKTAE  1950
1951  KCSLDQLDDTFHPEWFVSLFEQKTVKGWWPCVTEEGEKKMLAGKLEMTLE  2000
2001  IVAESEHEERPAGQGRDEPNMNPKLEDPRRPDTSFLWFTSPYKTMKFILW  2050
2051  RRFRCAIILFIILFILLLFLGVFVYAFPNYAAMKLVKPFR            2090

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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