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

NucPred

Fetching Q6CNY4 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MSLEKLLNREENDSSKRTDFMGRWYLKMSKICERDDREMDYQNWKFLSYQ    50
  51  EFELINEWNQQGKELTKDNCERLLVNMDKTHKEWVEYQKFKEQKDAIIAE   100
 101  LKESIQIIKQEPSIPSGADANSVVSSDTEQIQDSETTANSKKSPAINGIK   150
 151  TSGKSPTKSPATNGRRRGAGGNRRVKRPSNLSKTVRSRNATDGDENGNEN   200
 201  IENGGTTPKRRSRPKKILVSNVSKDVDAEEEDDIHTEKDASGSAADLDKD   250
 251  IVDESINDSENAPRKRPVSSTSLLSRNKSNKPTKSSPLTPDSAREKENVN   300
 301  GVTEGNEDMDHDSVLDADDSAIGSDDNPNDEQEEADDENVDEEAEDENDE   350
 351  AEVEDDIDDLGAPEDDGDDDFAPSYSAISKVKVNKKVNIDSPMPAIQKEL   400
 401  RKMAIKSSVAKAMKRKFTNCKVISYSPESQLEIKITLKQLHIRKYKRHLA   450
 451  EEERKRKAEEALIKAEEEAKKRKLAPPPPPPPQQVRRVEHDLPTYGMKIT   500
 501  LKEARAIQRHYDQTYITIWKDMARRDSGRISRQLQQIQSIRGQNFRKTSS   550
 551  LCAKEARRWQMRNFRQVKDFQTRARRGIREMSSFWKKNEREEREMKKKAE   600
 601  KEAIEQAKKEEEQRENLRAAKKLNFLLTQTELYSHFIGSKIKTNELEGTM   650
 651  TDDSLTSMSNNKNKVVDLTKTAASKTNVESIDFATEDDEKLRLMAAQNAS   700
 701  NALKETQDKARKFDEEDEEDGELNFQNPTSLGEITIDQPKMLACTLKEYQ   750
 751  LKGLNWLANLYDQGINGILADEMGLGKTVQSISVLAHLADRYNIWGPFIV   800
 801  VTPASTLHNWVNEISRFVPQFKILPYWGNANDRKTLRKFWDRKHLRYGRD   850
 851  APFHVMVTSYQMVVSDASYLQKMKWQYMILDEAQAIKSSQSSRWKTLLSF   900
 901  HCRNRLLLTGTPIQNNMQELWALLHFIMPSLFDSHDEFSDWFSKDIESHA   950
 951  ESNTELNQEQLRRLHMVLKPFMLRRIKKNVQSELGDKIEIDVLCDLTFRQ  1000
1001  AKLYQVLKSQVSGGYDAIENAAGNDDVTSDQKLVNLVMEFRKVCNHPDLF  1050
1051  ERADVMSPFSFVSFGESASLSREGDFVEVNYSAKNLINYNLPRLIYDELV  1100
1101  VPNYNNDVDVRAKLLYHTMNIFHPANSFQLCFILSKLTDTSPNKFATLLE  1150
1151  QNVINRAIDLQNDGYFNTAKYSIAYDEGEKIFSSNLLINDKLKYLHLLKN  1200
1201  STSGSVLKNLLEIPSSVYENEYFNSISPAYHPAASAPPINIDVLASNNFV  1250
1251  QKKQYEMFNPSISSALSSIPSSVQHKLIVEKGIPIEELPVTEMAPKAFNN  1300
1301  SFTSYIEMPSMDRFITESAKLKKLDELLVKLKEEDHRVLIYFQMTKMMDL  1350
1351  MEEYLTYRQYTHIRLDGSSKLDDRRDLVHDWQTKPDIFIFLLSTRAGGLG  1400
1401  INLTAADTVIFYDSDWNPTIDSQAMDRAHRLGQTRQVTVYRLLIRGTIEE  1450
1451  RMRDRAKQKEHVQQVVMEGKAKENKQKIIEVEKEHSESA             1489

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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