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

NucPred

Fetching P12024 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MGLEFFFKFGYAFLTITLMIMIWMSLARASMFDREMEETHYPPCTYNVMC    50
  51  TCSKSSTDLGIVHCKNVPFPALPRMVNQSKVFMLHMENTGLREIEPYFLQ   100
 101  STGMYRLKISGNHLTEIPDDAFTGLERSLWELILPQNDLVEIPSKSLRHL   150
 151  QKLRHLDLGYNHITHIQHDSFRGLEDSLQTLILRENCISQLMSHSFSGLL   200
 201  ILETLDLSGNNLFEIDPNVFVDGMPRLTRLLLTDNILSEIPYDALGPLKS   250
 251  LRTLDISHNVIWSLSGNETYEIKASTKLNLDNLHLEYNHIEVLPPNSFKY   300
 301  FDTVNRTFFDGNPIHTLREDAFKPARIREIYMRYCGLTNISPVAFDSLVN   350
 351  SLQILDLSGNNLTKLHHKLFNNFDVLRVISMRDNKIKIQKPTETFNAVHY   400
 401  TLLKLDLSGDRNDPTNLQTLRNMTRMRNMRSLSISRLGSSSVGPEDFKDF   450
 451  GVELEDLQITRASLSGIQSHAFKHVRGLKRLDFSENGISSIENDAFHEIG   500
 501  HSLISLKMSHGYSGSALPAEPLRHLTSLQELDFSNNHISSMSDTSFHFLK   550
 551  NLRLLELHDNRIEQVLKGTFQGDIHSKLEEISLRFNHLTSISQHTFFDLE   600
 601  ALRKLHLDDNKIDKIERRAFMNLDELEYLSLRGNKINNLADESFQNLPKL   650
 651  EILDMAFNQLPNFNFDYFDQVGTLSNLNVNVSHNQIRQLMYNSSWSGRNE   700
 701  HGGMYHSNIKILDLSHNNISIIHPGYFRPAEISLTHLHLGYNSLMNTTRD   750
 751  VFGNMPHLQWLDLSYNWIHELDFDAFKNTKQLQLVFFGHNYLSDIPQDIF   800
 801  KPVQGLRIVDFSHNHLRGLPDNLFYNGGMEKLDVSHNMMLKIPSSSLSSL   850
 851  AALTLCELHLSNNFISTIHSMDLSNKFRSLRYLDISYNYLLRIDDAVFAT   900
 901  MPKLAVLDLSHNRDLKVMDKSFMGLENSLIKLGLENISLSTVPEIRLKYL   950
 951  REFRLGYNELPSIPQELAHNMSNLRMLDLSNNDLTNVPLMTQALPHLRRL  1000
1001  MLSGNPITSLNNNSFDGVNEDLEMLDISNFRLHYFEYGCLDSLPHLRSLK  1050
1051  LTAYSHLEHFNIPHLLRHHYNIRQLWIEAPQPFTRIVKKGSGPTQEMQTL  1100
1101  QLGNPTDLQREMEGHLPSKLTNITFSGPQFTNLNERILRGMRSPYLYMQL  1150
1151  FNTSLQALPPNFFKYMGRVRNISLDIRYHNRNLKKIPNPNTGAVPYLPNS  1200
1201  VFLTDLKMSHTDLNCDCDLGWVEFWQRKRRQYICSSQTWTDTVFRTFMNS  1250
1251  PCQVYGRHNCDEHDDDLRETRCENKGGQQLMEALKFDLECGWDNANCREA  1300
1301  AFVVVMVCVAMVFWM                                     1315

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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