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

NucPred

Fetching Q70E73 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MEQLSDEEIDHGAEEDSDKEDQDLDKMFGAWLGELDKLTQSLDSDKPMEP    50
  51  VKRSPLRQETNMANFSYRFSIYNLNEALNQGETVDLDALMADLCSIEQEL   100
 101  SSIGSGNSKRQITETKATQKLPVSRHTLKHGTLKGLSSSSNRIAKPSHAS   150
 151  YSLDDVTAQLEQASLSMDEAAQQSVLEDTKPLVTNQHRRTASAGTVSDAE   200
 201  VHSISNSSHSSITSAASSMDSLDIDKVTRPQELDLTHQGQPITEEEQAAK   250
 251  LKAEKIRVALEKIKEAQVKKLVIRVHMSDDSSKTMMVDERQTVRQVLDNL   300
 301  MDKSHCGYSLDWSLVETVSELQMERIFEDHENLVENLLNWTRDSQNKLIF   350
 351  MERIEKYALFKNPQNYLLGKKETAEMADRNKEVLLEECFCGSSVTVPEIE   400
 401  GVLWLKDDGKKSWKKRYFLLRASGIYYVPKGKAKVSRDLVCFLQLDHVNV   450
 451  YYGQDYRNKYKAPTDYCLVLKHPQIQKKSQYIKYLCCDDVRTLHQWVNGI   500
 501  RIAKYGKQLYMNYQEALKRTESAYDWTSLSSSSIKSGSSSSSIPESQSNH   550
 551  SNQSDSGVSDTQPAGHVRSQSIVSSVFSEAWKRGTQLEESSKARMESMNR   600
 601  PYTSLVPPLSPQPKIVTPYTASQPSPPLPPPPPPPPPPPPPPPPPPPPLP   650
 651  SQSAPSAGSAAPMFVKYSTITRLQNASQHSGALFKPPTPPVMQSQSVKPQ   700
 701  ILVPPNGVVPPPPPPPPPPTPGSAMAQLKPAPCAPSLPQFSAPPPPLKIH   750
 751  QVQHITQVAPPTPPPPPPIPAPLPPQAPPKPLVTIPAPTSTKTVAPVVTQ   800
 801  AAPPTPTPPVPPAKKQPAFPASYIPPSPPTPPVPVPPPTLPKQQSFCAKP   850
 851  PPSPLSPVPSVVKQIASQFPPPPTPPAMESQPLKPVPANVAPQSPPAVKA   900
 901  KPKWQPSSIPVPSPDFPPPPPESSLVFPPPPPSPVPAPPPPPPPTASPTP   950
 951  DKSGSPGKKTSKTSSPGGKKPPPTPQRNSSIKSSSGAEHPEPKRPSVDSL  1000
1001  VSKFTPPAESGSPSKETLPPPAAPPKPGKLNLSGVNLPGVLQQGCVSAKA  1050
1051  PVLSGRGKDSVVEFPSPPSDSDFPPPPPETELPLPPIEIPAVFSGNTSPK  1100
1101  VAVVNPQPQQWSKMSVKKAPPPTRPKRNDSTRLTQAEISEQPTMATVVPQ  1150
1151  VPTSPKSSLSVQPGFLADLNRTLQRKSITRHGSLSSRMSRAEPTATMDDM  1200
1201  ALPPPPPELLSDQQKAGYGGSHISGYATLRRGPPPAPPKRDQNTKLSRDW  1250

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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