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

NucPred

Fetching Q9P6S0 from www.uniprot.org...

The NucPred score for your sequence is 0.10 (see score help below)

   1  MSVRRFLSTSARALLFTAALLPSLTSGLPSGNVRILQKGMEPEDYLSSAS    50
  51  QNEVPHDISLPKTELADPNFLVDDMPTLLGRDAAVDPSMFTSTFTVKNGN   100
 101  DANYITASPVSNDASMTAISTFTSGKEASYAIQASPSTFLPDSTTTSGSQ   150
 151  VSNAVEASSTFVADTTSTSCNPATVLIVTTSGSTSTSCPPPTTILIVTVP   200
 201  TTTTTTTVGYPGSVTTTLTGTPSNGTVIDTVEVPTTTNYGYTTITTGYTG   250
 251  STTLTTTVPHSGNETGPTTVYVETPYPTTVTTTTTVGYPGSVTTTLTGAP   300
 301  SNGTVIDTVEVPTTTNYGYTTVTTGYTGSTTLTTTVPHSGNETGPTTVYV   350
 351  ETPYPTTVTTTTTVGYPGSVTTTLTGAPSNGTVIDTVEVPTTTNYGYTTV   400
 401  TTGYTGSTTLTTTVPHSGNETGPTTVYVETPYPTTVTTTTTVGYPGSVTT   450
 451  TLTGAPSNGTVIDTVEIPTTTNYGYTTITTGYTGSTTLTTTVPHSGNETG   500
 501  PTTVYVETPYPTTVTTTTTVGYPGSVTTTLTGAPSNGTVIDTVEVPTTTN   550
 551  YGYTTITTGYTGSTTLTTTVPHSGNETGPTTVYVETPYPTTVTTTTTVGY   600
 601  PGSVTTTLTGAPSNGTVIDTVEVPTTTNYGYTTVTTGYTGSTTLTTTVPH   650
 651  SGNETGPTTVYVETPYPTTVTTTTTVGYSGSVTTTLTGSGSNSIVTETVD   700
 701  VPTTTSVNYGYTTITTGWTGSTTLTSIVTHSGSETGPTTVYIETPSVSAT   750
 751  TTTTTIGYSGSLTTTLTGSSGPVVTNTVEIPYGNSSYIIPTTIVTGTVTT   800
 801  VTTGYTGTETSTVTVIPTGTTGTTTVVIQTPTTVTATETDIVTVTTGYTG   850
 851  TETSTVTVTPTGTSTGTTTVVIQTPTTVTATETDIVTVTTGYTGTETSTV   900
 901  TVTPTGTSTGTTTVVIQTPTTVTATETDIVTVTTGYTGTETSTVTVTPTG   950
 951  TSTGTTTVVIQTPTTVTATETDIVTVTTGYTGTETSTVTVTPTGTSTGTT  1000
1001  TVVIQTPTTVTATETDIVTVTTGYTGTETSTVTVTPTGTSTGTTTVVIQT  1050
1051  PTTVTATETDIVTVTTGYTGTETSTVTVTPTGTSTGTTTVVIQTPTTVTA  1100
1101  TETDIVTVTTGYTGTETSTVTVTPTGTATGTTTVVINTPTTTGSEVLPTT  1150
1151  GATGTAGTETQLTTATEVQPTTGATGTAGTETQVTTGTETQATTATETQA  1200
1201  TTATEVQTTTGATGTAGTETQATTATEVQPTTGATGTAGTETQVTTATEV  1250
1251  QPTTGATGTAGTETQVTTGTETQATTATETQATTATEVQTTTGATGTAGT  1300
1301  ETQATTATEVQPTTGATGTAGTETQVTTATEVQPTTGATGTAGTETQVTT  1350
1351  GTETQATTATETQATTATEVQTTTGATGTAGTETQVTTATEVQPTTAVTE  1400
1401  TSSSGYYTTIVSSTVVSTVVPGSTVYPVTHVTTTTGVSGESSAFTYTTSS  1450
1451  TQYEPSTVVTTSYYTTSVYTSAPATETVSSTEAPESSTVTSNPIYQGSGT  1500
1501  STWSTVRQWNGSATYNYTYYTTGGFTGGNNTNVTGLYPSSAGANKPIAYL  1550
1551  TFVSLFVYIVTLI                                       1563

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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