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

NucPred

Fetching P41653 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MKKRRRPWIIKLEEIQSYQFLCNPWTKSNLIRLLIQILSRRERLIKLFDP    50
  51  RILSTLLLRDLRKSNPYFLVKGIVVLTLSILIYRFNHQSSMIDRKNFYSI   100
 101  KLFPIHNFMELGNETPEEYLKPFTQNWLRFPHLLLSFQLKRYYNRDFDPI   150
 151  SLNSGYGKNTNKKDEIISKNQGPSETHSENDEKDINLKIDSTLNSTENEY   200
 201  WKPEKYLCEDPFTRNKTEIEQRRKRSILWDLSFIEREQTKIESDLSSKCL   250
 251  SKDYPISWAKELFTEDQRYTEENSFPLERKRFIENFTKSIRYSFFYILPI   300
 301  DEPCMGGPSATKKPIEDFNLSKRLFKIKKNVFSQDLRDSKSYSLMNRIVD   350
 351  LWKIKTYFEIENPSLNCAMRSFTLPWNLFSAFCDQSKGKYILHKNCLEMT   400
 401  DQFTLSITKPSQVHDKISFFIYYNKNGSLRSDRIFNHREKWKNQSLWVLL   450
 451  NIIDKADDYLDQIIDKQLSQIDSKNCLEIGTPFNNYRTEALGWYESIKYN   500
 501  IDNRYSKNLLNRFYFINRLSRNLKDQIRTNFIENENLNNVTKDTIDRHSS   550
 551  SWKKIKREWFNHSIIRIDKHINRNLNVYKWSNQTEYFMKYLKQVFSKKNY   600
 601  FKIVFDPIELCTNTNRDSIGWSVFLSLSESTVKILNSKFDIISNLNSKFD   650
 651  ILISFFDFAFHGLQSMNYRLLNQLLDPIGTLIVRLKKFKTFLLYDHNLSQ   700
 701  RSKLLIDEGTIAPFVTNKIPINPLIIDFFDNENNRMESFDNTYFSTISND   750
 751  RDNWLNPVKLSDQSSLIASFHGANTLQFFDYLHHTRPNYRNRLPSDMKRF   800
 801  YIKRNNFTYGQLFNLLIIHNNLSSLPIGEIGPVHSEKETISFIKSQVSNI   850
 851  LLPKYLKRKRSGDQTFVLIYDLYRSFNLLTRLNPFVREKRYLSSIEEIST   900
 901  TPLTKEQIVNFEKNFCQPFFKRSDSEENNFDQCFKRGFSSNVGLIQTRSY   950
 951  QDDLLSEMFSNKNEEIFPRIQDWFVTECLKNKIVNEDIDGRSTLSNSSKE  1000
1001  EQNIYRISQIDSIFSKWDLFKTYMPWFFTSAWCKYIENMLLDTLSEILLH  1050
1051  GSNPFVSILQNIKHNILLKRNILWELSHPLWEPIQCKLRTNLINKFFFPS  1100
1101  NNFKDFFPYCKDFLIEETSDREKSSVPFIWAHMRLLNARGYKYGILIPFF  1150
1151  VLGYSILQYFKVISFTFINIKRYFELIKYLKHPSYVIELQKMINPPVPNS  1200
1201  FLYYTIDRDRSSSLPQIINSFFSMNMKRKRKTKRKTKNRNIKLLITIIRE  1250
1251  LNGLCSSMDISEKEMNLLVQFLMTEKALFKFESIFTYSPNLFKNEFGDQI  1300
1301  IRQPGLIHLRYLAYTYQKGLINYGFNPFCLAERWVFLAFCQKITSSQILC  1350
1351  QTNPTFHGKPFSLHSGSLLSKGILLIGPMGTGRSYLVKSLAADSYVPLIR  1400
1401  ISLKKLWYGEYLDYPLERIPTEFDPFVKDKMEDFHITLELAKRMSPCIIW  1450
1451  IPNIHELNLNDATNYLFGFGFTDLFLSVLMNNLFRFRDGEKDSMRNILVI  1500
1501  ASTHIPQRVDPALIAPNRLDRSINIRMLVIPQRQREFPILLCSKGLYSVK  1550
1551  FPDEFGSITIDYAVRDLAALADEALILSITRNKSVIDTNTIRSAIYRQIF  1600
1601  HLQSMDNQVGSSQNDERIIYKVGKAFIQNTLRRNSPMNPLSTKKELWKKR  1650
1651  FCYLSEWYLEPSIAETTMKELTILPHILGCLAGSAARDSWSISERNRENW  1700
1701  IPFDKLAEHDLDIASSLLESILVEFPFSRLGICRGKSDKDQITFAPQLKM  1750
1751  RDNLDLIRFMKEYELKFTPGAKQRDMDEELIKNVVWTPRIWRLSFLRSNR  1800
1801  FDHIKTPNSLGSSYQFGSLRKRQMDRSLFPIQYPKQYKYSKKPLFFIGRR  1850
1851  FLWDSFLFQEQRPVFSRREFFANEELLKRLYITYGARRLIAQPDFFPKKS  1900
1901  IQSFFRRYDSKSTINSVLVMNWWKPLSLRHRHIEHFKRIQAIGIQLERMQ  1950
1951  PYFPIYSYNRWLTENSRERVDRFQSLIHRQRWLGTNRLLSNESFLYNTLF  2000
2001  ESYQYLSNLFLSNRMLLDQITKTLLENKWLFPNEIEHSIHTTGLRFDISW  2050
2051  ENME                                                2054

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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