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

NucPred

Fetching P32768 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MTMPHRYMFLAVFTLLALTSVASGATEACLPAGQRKSGMNINFYQYSLKD    50
  51  SSTYSNAAYMAYGYASKTKLGSVGGQTDISIDYNIPCVSSSGTFPCPQED   100
 101  SYGNWGCKGMGACSNSQGIAYWSTDLFGFYTTPTNVTLEMTGYFLPPQTG   150
 151  SYTFKFATVDDSAILSVGGATAFNCCAQQQPPITSTNFTIDGIKPWGGSL   200
 201  PPNIEGTVYMYAGYYYPMKVVYSNAVSWGTLPISVTLPDGTTVSDDFEGY   250
 251  VYSFDDDLSQSNCTVPDPSNYAVSTTTTTTEPWTGTFTSTSTEMTTVTGT   300
 301  NGVPTDETVIVIRTPTTASTIITTTEPWNSTFTSTSTELTTVTGTNGVRT   350
 351  DETIIVIRTPTTATTAITTTEPWNSTFTSTSTELTTVTGTNGLPTDETII   400
 401  VIRTPTTATTAMTTTQPWNDTFTSTSTELTTVTGTNGLPTDETIIVIRTP   450
 451  TTATTAMTTTQPWNDTFTSTSTELTTVTGTNGLPTDETIIVIRTPTTATT   500
 501  AMTTTQPWNDTFTSTSTEITTVTGTNGLPTDETIIVIRTPTTATTAMTTP   550
 551  QPWNDTFTSTSTEMTTVTGTNGLPTDETIIVIRTPTTATTAITTTEPWNS   600
 601  TFTSTSTEMTTVTGTNGLPTDETIIVIRTPTTATTAITTTQPWNDTFTST   650
 651  STEMTTVTGTNGLPTDETIIVIRTPTTATTAMTTTQPWNDTFTSTSTEIT   700
 701  TVTGTTGLPTDETIIVIRTPTTATTAMTTTQPWNDTFTSTSTEMTTVTGT   750
 751  NGVPTDETVIVIRTPTSEGLISTTTEPWTGTFTSTSTEMTTVTGTNGQPT   800
 801  DETVIVIRTPTSEGLVTTTTEPWTGTFTSTSTEMTTITGTNGVPTDETVI   850
 851  VIRTPTSEGLISTTTEPWTGTFTSTSTEMTTITGTNGQPTDETVIVIRTP   900
 901  TSEGLISTTTEPWTGTFTSTSTEMTHVTGTNGVPTDETVIVIRTPTSEGL   950
 951  ISTTTEPWTGTFTSTSTEVTTITGTNGQPTDETVIVIRTPTSEGLISTTT  1000
1001  EPWTGTFTSTSTEMTTVTGTNGQPTDETVIVIRTPTSEGLVTTTTEPWTG  1050
1051  TFTSTSTEMSTVTGTNGLPTDETVIVVKTPTTAISSSLSSSSSGQITSSI  1100
1101  TSSRPIITPFYPSNGTSVISSSVISSSVTSSLFTSSPVISSSVISSSTTT  1150
1151  STSIFSESSKSSVIPTSSSTSGSSESETSSAGSVSSSSFISSESSKSPTY  1200
1201  SSSSLPLVTSATTSQETASSLPPATTTKTSEQTTLVTVTSCESHVCTESI  1250
1251  SPAIVSTATVTVSGVTTEYTTWCPISTTETTKQTKGTTEQTTETTKQTTV  1300
1301  VTISSCESDVCSKTASPAIVSTSTATINGVTTEYTTWCPISTTESRQQTT  1350
1351  LVTVTSCESGVCSETASPAIVSTATATVNDVVTVYPTWRPQTANEESVSS  1400
1401  KMNSATGETTTNTLAAETTTNTVAAETITNTGAAETKTVVTSSLSRSNHA  1450
1451  ETQTASATDVIGHSSSVVSVSETGNTKSLTSSGLSTMSQQPRSTPASSMV  1500
1501  GYSTASLEISTYAGSANSLLAGSGLSVFIASLLLAII               1537

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.