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

NucPred

Fetching Q64455 from www.uniprot.org...

The NucPred score for your sequence is 0.50 (see score help below)

   1  MKPAARETRTPPRSPGLRWALLPLLLLLRQGQVLCAGAAPNPIFDIEAVV    50
  51  SPTSVLLTWKHNDSGASECRIENKMESNLTFPVKNQTSCNITGLSPGTSY   100
 101  TFSIISVTTNETLNKTITTEPWPVSDLHVTSVGVTQARLTWSNANGTASY   150
 151  RMLIEELTTHSSVNISGLKPGTNNSFAFPESNETQADFAVAEEVPDANGT   200
 201  KRIPVTNLSQLHKNSLVSVDPPSGQDPSLTEILLTDLKPDTQYNATIYSQ   250
 251  AANGTEGQPRNKVFKTNSTQVSDVRAMNISASSMTLTWKSNYDGSRTSIV   300
 301  YKIHVAGGTHSVNQTVNKTEAIILGLSSSTLYNITVHPFLGQTEGTPGFL   350
 351  QVYTSPDQVSDFRVTNVSTRAIGLAWRSNDSKSFEIFIKQDGGEKHRNAS   400
 401  TGNQSYMVEDLKPGTSYHFEIIPRGPDGTEGLSSTVNGSTDPSAVTDIRV   450
 451  VNISTTEMQLEWQNTDDASGYTYHLVLESKSGSIIRTNSSQKWITVGSLT   500
 501  PGTLYNVTIFPEVDQIQGISNSITQYTRPSSVSHIEVNTTTTTAAIRWKN   550
 551  EDAASASYAYSVLILKTGDGSNVTSNFTKDPSILIPELIPGVSYTVKILT   600
 601  QVGDGTTSLVPGWNLFCTEPEPVTSFHCEVVPKEPALVLKWACPFGMYTG   650
 651  FELGVRSDSWDNMTRLENCTSDDDTECRTEVAYLNFSTSYNISIATLSCG   700
 701  KMALPAQNICTTGITDPPTPDGSPNITSVSHNSVKVKFSGFEASHGPIKA   750
 751  YAVILTTGEAAQPSADVLKYTYEDFKRGASDTYVTYLIRIEEKGQSQGLS   800
 801  EVLNYEIDVGNQSTTLGYYNGRLEPLGSYRACVAGFTNITYNLQNDGLIN   850
 851  GDESYVSFSPYSEAVFLPQDPGVICGAVFGCIFGALAITAVGGFIFWRKK   900
 901  RTDAKNNEVSFSQIKPKKSKLIRVENFEAYFKKQQADSNCGFAEEYEDLK   950
 951  LIGISLPKYTAEIAENRGKNRYNNVLPYDISRVKLSVQTHSTDDYINANY  1000
1001  MPGYHSKKDFIATQGPLPNTLKDFWRMVWEKNVYAIVMLTKCVEQGRTKC  1050
1051  EEYWPSKQAQDYGDITVAMTSEVVLPEWTIRDFVVKNMQNSESHPLRQFH  1100
1101  FTSWPDHGVPDTTDLLINFRYLVRDYMKQIPPESPILVHCSAGVGRTGTF  1150
1151  IAIDRLIYQIENENTVDVYGIVYDLRMHRPLMVQTEDQYVFLNQCVLDII  1200
1201  RAQKDSKVDLIYQNTTAMTIYENLEPVSMFGKTNGYIA              1238

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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