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

NucPred

Fetching Q9LYS2 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MIENYWTSFCGNHHTSSNCTVRFLQICFGITLSFLTLCICLFHKEPPKRI    50
  51  HQFFCLRLVSALFNGIIGSLDLVLGIWVLRENHSKPLILWLVILIQGFTW   100
 101  LFINLIICVRGTRIRKSSLRLLSIFSFFYGLVSSCLSVNNAVFGDELAVR   150
 151  TILDVLLLPGSVLLLLSAYKGYRFDESGESSLYEPLNAGDSNGFSEKADF   200
 201  DNRVSQFAKAGLFSTLSFWWLNSLIKRGNVKDLEEEDIPELRKEERAETC   250
 251  YSLFEENLIEQKRRLGSSCQPSILKVTVLCVWRELLTSGFFAFMKIVAVS   300
 301  AGPLLLNAFILVAEGNASFRYEGLVLAVLLFFSKMIESLSQRQWYFRCRI   350
 351  VGLRVRSLLTAAINKKQLRLNNSSRLIHSGSEIMNYATVDAYRIGEFPYW   400
 401  FHQLWTTSFQLLIALGILFHSVGVATFSALAVIILTVLCNAPIAKLQNKF   450
 451  QSELMTSQDERLKACNESLVNMKVLKLYAWESHFKKVIEKLRNIELKSLK   500
 501  AVQMRKAYNAVLFWSSPVFVSAATFATCYFLDIPLRASNVFTFVATLRLV   550
 551  QDPVRMIPDVIGVTIQAKVAFSRIATFLEAPELQGGERRRKQRSEGNQNA   600
 601  IIIKSASFSWEEKGSTKPNLRNVSLEVKFGEKVAVCGEVGSGKSTLLAAI   650
 651  LGETPCVSGTIDFYGTIAYVSQTAWIQTGTIRDNILFGGVMDEHRYRETI   700
 701  QKSSLDKDLELLPDGDQTEIGERGVNLSGGQKQRIQLARALYQDADIYLL   750
 751  DDPFSAVDAHTASSLFQEYVMDALAGKAVLLVTHQVDFLPAFDSVLLMSD   800
 801  GEITEADTYQELLARSRDFQDLVNAHRETAGSERVVAVENPTKPVKEINR   850
 851  VISSQSKVLKPSRLIKQEEREKGDTGLRPYIQYMNQNKGYIFFFIASLAQ   900
 901  VTFAVGQILQNSWMAANVDNPQVSTLKLILVYLLIGLCSVLCLMVRSVCV   950
 951  VIMCMKSSASLFSQLLNSLFRAPMSFYDSTPLGRILSRVSSDLSIVDLDV  1000
1001  PFGLIFVVASSVNTGCSLGVLAIVTWQVLFVSVPMVYLAFRLQKYYFQTA  1050
1051  KELMRINGTTRSYVANHLAESVAGAITIRAFDEEERFFKKSLTLIDTNAS  1100
1101  PFFHSFAANEWLIQRLETVSAIVLASTAFCMILLPTGTFSSGFIGMALSY  1150
1151  GLSLNMGLVYSVQNQCYLANWIISVERLNQYTHLTPEAPEVIEETRPPVN  1200
1201  WPVTGRVEISDLQIRYRRESPLVLKGISCTFEGGHKIGIVGRTGSGKTTL  1250
1251  ISALFRLVEPVGGKIVVDGVDISKIGVHDLRSRFGIIPQDPTLFNGTVRF  1300
1301  NLDPLCQHSDAEIWEVLGKCQLKEVVQEKENGLDSLVVEDGSNWSMGQRQ  1350
1351  LFCLGRAVLRRSRVLVLDEATASIDNATDLILQKTIRREFADCTVITVAH  1400
1401  RIPTVMDCTMVLSISDGRIVEYDEPMKLMKDENSLFGKLVKEYWSHYNSA  1450
1451  DSR                                                 1453

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.)

Go back to the NucPred Home Page.