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

NucPred

Fetching P05659 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MAAQRRRKGGEVESDYIKYLKYKNTGFQVSASDKTLAWWPTKDADRAFCH    50
  51  VEVTKDDGKNFTVRLENGEEKSQPKNEKNFLGVNPPKFDGVEDMGELGYL   100
 101  NEPAVLHNLKKRYDADLFHTYSGLFLVVVNPYKRLPVYTPEIIDIYRGRQ   150
 151  RDKVAPHIFAISDAAYRAMLNTRQNQSMLITGESGAGKTENTKKVIQYLT   200
 201  AIAGRAEGGLLEQQLLEFNPILEAFGNAKTTKNNNSSRFGKFIELQFNAG   250
 251  GQITGANTFIYLLEKSRVTAQGAGERNFHIFYQILSKAMPEELKQKLKLT   300
 301  KPEDYFFLNQNACYTVDDMDDAKEFDHMLKAFDILNINEEERLAIFQTIS   350
 351  AILHLGNLPFIDVNSETAGLKDEVELNIAAELLGVSAAGLKAGLLSPRIK   400
 401  AGNEWVTRALNKPKAMASRDALCKALFGRLFLWIVQKINRILSHKDKTAL   450
 451  WIGVLDISGFEIFQHNSFEQLCINYTNEKLQQFFNHHMFTLEQQEYEREK   500
 501  IDWTFVDYGMDSQDCIDLIEKKPMGILPLLDEQTVFPDADDTSFTKKLFQ   550
 551  THENHRNFRRPRFDANNFKIVHYAGEVEYQTSAWLEKNRDPLEDDLSNLC   600
 601  KKSSVRFVTGLFDEDLMPSFKAAPAEEEKAAAGGSRNRSTGRGKGGAQFI   650
 651  TVAFQYKEQLAHLMSMLSSTAPHFIRCIIPNLGKKPGVVSDQLVLDQLKC   700
 701  NGVLEGIRIARKGWPNRLKYDEFLKRYFLLKPGATPTSPSTKDAVKDLIE   750
 751  HLIAKEPTKVNKDEVRFGVTKIFFRSGQLAAIEELREQAISKMVVSIQAG   800
 801  ARAFLARRMYDKMREQTVSAKILQRNIRAWLELKNWAWYQLYVKARPLIS   850
 851  QRNFQKEIDDLKKQVKDLEKELAALKDANAKLDKEKQLAEEDADKLEKDL   900
 901  AALKLKILDLEGEKADLEEDNALLQKKVAGLEEELQEETSASNDILEQKR   950
 951  KLEAEKGELKASLEEEERNRKALQEAKTKVESERNELQDKYEDEAAAHDS  1000
1001  LKKKEEDLSRELRETKDALADAENISETLRSKLKNTERGADDVRNELDDV  1050
1051  TATKLQLEKTKKSLEEELAQTRAQLEEEKSGKEAASSKAKQLGQQLEDAR  1100
1101  SEVDSLKSKLSAAEKSLKTAKDQNRDLDEQLEDERTVRANVDKQKKALEA  1150
1151  KLTELEDQVTALDGQKNAAAAQAKTLKTQVDETKRRLEEAEASAARLEKE  1200
1201  RKNALDEVAQLTADLDAERDSGAQQRRKLNTRISELQSELENAPKTGGAS  1250
1251  SEEVKRLEGELERLEEELLTAQEARAAAEKNLDKANLELEELRQEADDAA  1300
1301  RDNDKLVKDNRKLKADLDEARIQLEEEQDAKSHADSSSRRLLAEIEELKK  1350
1351  RVAKETSDKQKAQDQKANYQRENESLKADRDSIERRNRDAERQVRDLRAQ  1400
1401  LDDALSRLDSEKRAKEKSVEANRELKKVVLDRERQSLESLSKFNSALESD  1450
1451  KQILEDEIGDLHEKNKQLQAKIAQLQDEIDGTPSSRGGSTRGASARGASV  1500
1501  RAGSARAEE                                           1509

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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