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

NucPred

Fetching Q9UEF7 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MPASAPPRRPRPPPPSLSLLLVLLGLGGRRLRAEPGDGAQTWARFSRPPA    50
  51  PEAAGLFQGTFPDGFLWAVGSAAYQTEGGWQQHGKGASIWDTFTHHPLAP   100
 101  PGDSRNASLPLGAPSPLQPATGDVASDSYNNVFRDTEALRELGVTHYRFS   150
 151  ISWARVLPNGSAGVPNREGLRYYRRLLERLRELGVQPVVTLYHWDLPQRL   200
 201  QDAYGGWANRALADHFRDYAELCFRHFGGQVKYWITIDNPYVVAWHGYAT   250
 251  GRLAPGIRGSPRLGYLVAHNLLLAHAKVWHLYNTSFRPTQGGQVSIALSS   300
 301  HWINPRRMTDHSIKECQKSLDFVLGWFAKPVFIDGDYPESMKNNLSSILP   350
 351  DFTESEKKFIKGTADFFALCFGPTLSFQLLDPHMKFRQLESPNLRQLLSW   400
 401  IDLEFNHPQIFIVENGWFVSGTTKRDDAKYMYYLKKFIMETLKAIKLDGV   450
 451  DVIGYTAWSLMDGFEWHRGYSIRRGLFYVDFLSQDKMLLPKSSALFYQKL   500
 501  IEKNGFPPLPENQPLEGTFPCDFAWGVVDNYIQVDTTLSQFTDLNVYLWD   550
 551  VHHSKRLIKVDGVVTKKRKSYCVDFAAIQPQIALLQEMHVTHFRFSLDWA   600
 601  LILPLGNQSQVNHTILQYYRCMASELVRVNITPVVALWQPMAPNQGLPRL   650
 651  LARQGAWENPYTALAFAEYARLCFQELGHHVKLWITMNEPYTRNMTYSAG   700
 701  HNLLKAHALAWHVYNEKFRHAQNGKISIALQADWIEPACPFSQKDKEVAE   750
 751  RVLEFDIGWLAEPIFGSGDYPWVMRDWLNQRNNFLLPYFTEDEKKLIQGT   800
 801  FDFLALSHYTTILVDSEKEDPIKYNDYLEVQEMTDITWLNSPSQVAVVPW   850
 851  GLRKVLNWLKFKYGDLPMYIISNGIDDGLHAEDDQLRVYYMQNYINEALK   900
 901  AHILDGINLCGYFAYSFNDRTAPRFGLYRYAADQFEPKASMKHYRKIIDS   950
 951  NGFPGPETLERFCPEEFTVCTECSFFHTRKSLLAFIAFLFFASIISLSLI  1000
1001  FYYSKKGRRSYK                                        1012

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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