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

NucPred

Fetching Q8BYJ6 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MESPSCIQDEPFPHPLEPEPSAPAQPGATKPGDKRFRLWYVGGSCLDRRT    50
  51  TLPMLPWLMAEIRRRSQKPDAGGCGAPAAREVILVLSAPFLRCVPAPGAG   100
 101  VGGGAGSGAVQPNTGVFIFEHKAQHISRFIHNSHDLTYFAYLIKAQPDDP   150
 151  ESQMACHVFRATDPNQVPDVISSIRQLSKAAMKEDSKPSKDNEDAFYNSQ   200
 201  KFEVLYCGRVIVTHKKAPSSLIDDCKDKFSLHEQQRLKLQGERGGDPGDE   250
 251  MGVLEVESPVSPDDSLPEKADGTVNSPRALPSLASLPALASQPALASSRV   300
 301  CFPERILEDCGFDEQQEFRSRCSSVTGVMQKKVHENNQKTQPRRRHASAP   350
 351  SHVQPSDSEKNRTMLFQVGRFEINLISPDTKSVVLEKNFKDISSCSQGIK   400
 401  HVDHFGFICRESPEPGLSQYICYVFQCANESLVDEVMLTLKQAFSTAAAL   450
 451  QSAKTQIKLCETCPMHSLHKLCERIEGLYPPRAKLVIQRHLSSLTDNEQA   500
 501  DIFERVQKMKPISDQEENELVILHLRQLCEAKQRTHVHIGEGPAIISNST   550
 551  IPENVTSGGRFKLDVLKNKAKRSLTSSLENIFSRGANRMRGRLGSMDSFE   600
 601  RANSLASEKDFSPGDSPPGTPPASPLSSAWHAFPEEDSDSPQFRRRAHTF   650
 651  SHPPSSSRRKLNLQDGKAHGLRSPLLRQSSSEQCSIVPSARRMYKESNSS   700
 701  CSLPSLHTSFSAPSFTAPSFLKSFYQNSGRLSPQYENEIRQDTASESSDG   750
 751  EGRKRTSSTCSNESLNAGGTPVTPRRVSWRQRIFLRVASPVNKSPSAMQQ   800
 801  QKDGLDRTELLPLSPLSPTMEEEPLIIFLSGDEDTEKVEEKKKSKELKSL   850
 851  WKKAIHQQILLLRMEKENQKLEEARRDELQSRKVKLDYEEVGTCQKEILI   900
 901  AWDKKLLNCRTKIRCDMEDIHTSLKEGVPKSRRGEIWQFLALQYRLRHRL   950
 951  PNKHQPPDTSYKELLKQLTAQQHAILVDLGRTFPTHPYFSVQLGAGQLSL  1000
1001  FNLLKAYSLLDKEVGYCQGISFVAGVLLLHMSEEQAFEMLKFLMYDLGFR  1050
1051  KQYRPDMMSLQIQMYQLSRLLHDYHRELYNHLEENEISPSLYAAPWFLTL  1100
1101  FASQFPLGFVARVFDIIFLQGTEVIFKVALSLLSSQEALIMECENFENIV  1150
1151  EFLKSTLPDMNTTEMEKIITQVFEMDISKQLHAYEVEYHVLQDELLESSY  1200
1201  ACEDNESLEKLERANNQLKRQNMDLLEKLQVAHAKIQALESNLETLLTRE  1250
1251  TKMKALIRTLEQDKMAYQKTVEQIRKLLPADALANCELLLKDLTHPTNDK  1300
1301  AKAGNKP                                             1307

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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