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

NucPred

Fetching P53094 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MPLLQPSTCFCYPLKLPPLPLTSDSNEFDECARKRLTLDYRTGSAVTLTR    50
  51  SNIFVHGGLTIPLNLPVVNSMQLQKELILFFAKEKNNGSSFRNLNEWISK   100
 101  ETFFLDLMSRTWYRVKTSFDQRTEELLKAESSSAKADNDTNEIRTDIKKG   150
 151  KSLESPLKERLFHSLCYLDGCLYIFGGLTVSPQSGYELIATNELWKLDLN   200
 201  TKKWSLLSDDPQIARRFNHTMHVKNENNDNRDTKLIIVGGLNNMDQPVKK   250
 251  IDIYNISQNCWQSETIPKQPMEITTNVNGIPLALSKDQNFSILVENNEAN   300
 301  VPALAFYMRSDQIDEYLGKDSSKIKENSPIVALPLLSESQGIRMPSNPAL   350
 351  PKKLLNVPYELLAPTGDYFGFNIIIGGFHPNYQSSNFHCFIYDINSGKWS   400
 401  RVATACPDCDINKHRFWRVFVWKSHHQTILLGTKTDDYYSPSVQRFDHLS   450
 451  TFGLPLVNIFNKTIQLPHHKISASSLPIPIENFAKHKDTPLKKVSFTSSA   500
 501  TSQFENYIRYIAPPLEMSSIQSVFPPYAMVLGKDALEIYGKPLSDFEFIT   550
 551  SEGDSIGIPCYLLRKRWGRYFDMLLSQSYTKVCADYETTDTQSTLIKFSP   600
 601  HSSRNSSKAVRQEGRLSSSGSLDNYFEKNFPIFARTSVSEAQNTQPQVAN   650
 651  ADAKAPNTPSTSDEPSSSSSSDLYSTPHYQRNNDEEDDEDPVSPKPVSKS   700
 701  NSIYRPIRKTESSSTTSSSNGMIFRVPFKEKAAVTSNTEALLESNLSLQE   750
 751  LSRRRSSLMSIPSGELLRSSISEAEHQRRASHPLTSSPLFEDSGTPCGKQ   800
 801  LQQLQQHTIQNPHNHLSPRRFSRSARSSISYVSSSSDRRGNSISSRSTSD   850
 851  SFGTPPVLGVLNVPLPPQTREPNEPPPPCPAMSTGSNTRRSNTLTDYMHS   900
 901  NKASPFSSRRSSHIGRRSSTPETENAFSATPRASLDGQMLGKSLKEGSTS   950
 951  QYTQPRMNSFPKANETIQTPTSSNNEWSRQSVTSNTDSFDSLQSNFALEL  1000
1001  EPLLTPRSLYMPWPTSTVRAFAEFFYTGQVNSKWLLAPVALDLLVMAKIY  1050
1051  EIPLLYKLILEVLYSILAKKEESLSLICTSLMETFRTKTLNSYKGDEEKT  1100
1101  NTYLTSNDNYQELLKLKVSLENIDNGYYDPDLLRKQSRAQSSSTQESSGS  1150
1151  ANGEKTATGAGSLETSSTNVPTVFAGGPRDSHNSVGSIGFPNSMNIQGSR  1200
1201  RSTSGFSPRVKMKSSLSKEIDPKTFYEEYEPKEGKSFDDNDDQQTNIGSF  1250
1251  NLHLFDMNYGSISSSSTNSISSSDLEEKEEQEQLQDLLEIEREDSAEILD  1300
1301  ARFRNKEDDKVTKDISNDKKRNYLPHEKNNLKAKEGKETRDVREEEEEFD  1350
1351  FGLGMLSLNKIKREAKHVDKVDDSVDPLFKSSAFPQSPIRAYGSTTRTSS  1400
1401  ASGKPFRDNRSFNAFSVLTLENMASANALPPVDYVIKSIYRTTVLVNDIR  1450
1451  LMVRCMDCIELSKNLRALKKKTMEDISKLKGISKPSP               1487

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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