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

NucPred

Fetching Q9JM52 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MGDPAPARSLDDIDLSALRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQL    50
  51  AAIKVMDVTEDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKSPPGNDDQ   100
 101  LWLVMEFCGAGSVTDLVKNTKGNALKEDCIAYICREILRGLAHLHAHKVI   150
 151  HRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVI   200
 201  ACDENPDATYDYRSDIWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPP   250
 251  PRLKSKKWSKKFTDFIDTCLIKTYLSRPPTEQLLKFPFIRDQPTERQVRI   300
 301  QLKDHIDRSRKKRGEKEETEYEYSGSEEEDDSHGEEGEPSSIMNVPGEST   350
 351  LRREFLRLQQENKSNSEALKQQQQLQQQQQRDPEAHIKHLLHQRQRRIEE   400
 401  QKEERRRVEEQQRREREQRKLQEKEQQRRLEDMQALRREEERRQAEREQE   450
 451  YKRKQLEEQRQSERLQRQLQQEHAYLKSLQQQQQQQQLQKQQQQQQQILP   500
 501  GDRKPLYHYGRGINPADKPAWAREVEERARMNKQQNSPLAKAKPSSAGPE   550
 551  PPISQASPSPPGPLSQTPPMQRPVEPQEGPHKSLVAHRVPLKPYAAPVPR   600
 601  SQSLQDQPTRNLAAFPASHDPDPAAVPTPTATPSARGAVIRQNSDPTSEG   650
 651  PGPSPNPPSWVRPDNEAPPKVPQRTSSIATALNTSGAGGSRPAQAVRASN   700
 701  PDLRRSDPGWERSDSVLPASHGHLPQAGSLERNRNRVGASTKLDSSPVLS   750
 751  PGNKAKPEDHRSRPGRPASYKRAIGEDFVLLKERTLDEAPKPPKKAMDYS   800
 801  SSSEEVESSEEEEEEGDGEPSEGSRDTPGGRSDGDTDSVSTMVVHDVEEI   850
 851  SGTQPSYGGGTMVVQRTPEEERSLLLADSNGYTNLPDVVQPSHSPTENSK   900
 901  GQSPPTKDGGSDYQSRGLVKAPGKSSFTMFVDLGIYQPGGSGDTIPITAL   950
 951  VGGEGGRLDQLQFDVRKGSVVNVNPTNTRAHSETPEIRKYKKRFNSEILC  1000
1001  AALWGVNLLVGTENGLMLLDRSGQGKVYGLIGRRRFQQMDVLEGLNLLIT  1050
1051  ISGKRNKLRVYYLSWLRNKILHNDPEVEKKQGWTTVGDMEGCGHYRVVKY  1100
1101  ERIKFLVIALKNSVEVYAWAPKPYHKFMAFKSFADLPHRPLLVDLTVEEG  1150
1151  QRLKVIYGSSAGFHAVDVDSGNSYDIYIPVHIQSQITPHAIIFLPNTDGM  1200
1201  EMLLCYEDEGVYVNTYGRIIKDVVLQWGEMPTSVAYICSNQIMGWGEKAI  1250
1251  EIRSVETGHLDGVFMHKRAQRLKFLCERNDKVFFASVRSGGSSQVYFMTL  1300
1301  NRNCIMNW                                            1308

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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