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

NucPred

Fetching Q9JIB6 from www.uniprot.org...

The NucPred score for your sequence is 0.55 (see score help below)

   1  MAEHGESSEDRISEIDYEFLAELSARFGMNLVQLAKSQEEEDHKERMKMK    50
  51  KGFNSQMRSEAKRLKTFESYDTFRSWTPQEMAAAGFYHTGVKLGVQCFCC   100
 101  SLILFGNSLRKLPIERHKKLRPECEFLQGKDVGNIGKYDIRVKSPEKMLR   150
 151  GGKARYHEEEARLESFEDWPFYAHGTSPRALSAAGFVFTGKRDTVQCFSC   200
 201  GGSLGNWEEGDDPWKEHAKWFPKCEFLQSKKSSEEIAQYIQDYEGFVHVT   250
 251  GEHFVKSWVRRELPMVSAYCNDSVFTNEELRMDMFKDWPQESPVGFEALV   300
 301  RAGFFYTGKKDIVRCFSCGGCLEKWAEGDDPMEDHIKFFPECVFLQTLKS   350
 351  SAEVIPTLQSQYALPEATETTRESNHDDAAAVHSTVVDLGRSEAQWFQEA   400
 401  RSLSEQLRDTYTKTSFCHMNLPEVCSSLGTDHLLGCDVSIISKHVSQPVQ   450
 451  GALTIPEVFSNLSSVMCVEGEAGSGKTTFLKRIAFLWASGCCPLLYRFQL   500
 501  VFYLSLSSITPDQGLANIICTQLLGAGGCISEVCLSSSIQQLQHQVLFLL   550
 551  DDYSGLASLPQALHTLITKNYLFRTCLLIAVHTNRVRDIRPYLGTSLEIQ   600
 601  EFPFYNTVFVLRKFFSHDIICVEKLIIYFSENKDLQGVYKTPLFVAAVCN   650
 651  DWNQNASAQDDFQDVTLFHSYMQYLSLKYKATAESLQATVSSCGQLALTG   700
 701  LFSSCFEFNSDDLAEAGVDEDVKLTTFLMSKFTAQRLRPVYRFLGPLFQE   750
 751  FLAAVRLTELLSSDRQEDQDLGLYYLRQIDSPLKAINSFNIFLYYVSSHS   800
 801  SSKAAPTVVSHLLQLVDEKESLENMSENEDYMKLHPQTFLWFQFVRGLWL   850
 851  VSPESFSSFVSEHLLRLALIFAYESNTVAECSPFILQFLRGRTLALRVLN   900
 901  LEYFWDHPESLLLLRSLKVSINGNKMSSYVDYSFKTYFENLQPPAINEEY   950
 951  TSAFEHVSEWRRNFAQDEEIIKNYENIWPRALPDISEGYWNLSPKPCKIP  1000
1001  KLEVQVNNMGPADQALLQVLMEVFSASQSIEFHLFNSSGFLESIRPALEL  1050
1051  SKASVTKCSMSRLELSRAEQELLLTLPALQSLEVSETNQLPDQLFHNLHK  1100
1101  FLGLKELCVRLDGKPDVLSVLPEEFLNLHHMEKLSIRTSTESDLSKLVKF  1150
1151  IQNFPNLHVFHLKCDFLSNCESLMTALASCKKLREIEFSGQCFEAMTFVN  1200
1201  ILPNFVSLKILSLKGQQFADKETSEKFAQALGSLRNLEELLVPTGDGIHQ  1250
1251  VAKLIVRQCLQLPCLRVLAFHDILDDESVIEIARAATSGSFQKLENLDIS  1300
1301  MNHKITEEGYRNFFQALDNLPNLQMLNICRNIPGRIQVQATTVKALGHCV  1350
1351  SRLPSLTRLGMLSWLLDEEDMKVINDVKERHPQSKRLTIFWKWIVPFSPV  1400
1401  VLE                                                 1403

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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