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

NucPred

Fetching Q6C8M8 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MLSASQFLKHRVSCLPMLNKVESDSTDGDPDDACQHPHDCNIFSVLVNGA    50
  51  TDRLEGFFDESDEEDGDEVETPSTTTTAVSPSATMSAPSPTATAPTPHSG   100
 101  THTPKSPLHSISHCPSFNSVAQALPHSLSPHSLCHTSSHEASRRGSAEQP   150
 151  SRTQSELARRIKTENILNSFHDSLEAAYEKCHGGANPEEHQSNKTEYFQQ   200
 201  KLKGFAALDVDEQLIADYPVWLLKNVLIQGHLYITAKHMCFLSYLPRRQN   250
 251  ANIRSGTLVKARKRSLREGTRYWCVLKNDSFSYYPDSTDVYFPAGTIDLS   300
 301  EALAAELCDDEGDVTEPESFRIVMPKKSVLFKADSHSAAHEWVKALQKEI   350
 351  FRAHNQGDTVRIVIPLQNIVDLEKTKIFEFATTIKTSVVESNETYAIDEY   400
 401  IFTFFKFGDDVLRTLTENGVEISGGNFSPRQSQLAVGHKHVTESVRDSTL   450
 451  LHASGHHHHFFHSAHHESDGKSNSKSHTSSRSHTPRNLTPQVTGEQPHER   500
 501  DEKRDSKLPRLPKFLRRFKDKVDDKCDDKPTLVPSFLKSRASSRRNSAEG   550
 551  SDRPNLASQRTSSSTLFPSAPPTPGSQPTTPGVHAPGSSTPGGSYGTTTP   600
 601  GTPASADSVSLAGTPGVAAPVGDIEGLNGNPMPAGIAAELKEKRKSGGAT   650
 651  SSGAATGATTPGGAAAPGSTGNSSPGTPGGLGGPGAVGAGGPGVMGGAES   700
 701  APAGTVPQQSHHAGISVVAPHDPAAAAAAADAAAPFTRGPGSGIPEIQDD   750
 751  SDSSDDDHWGHIGTAEVDEDPEQDTFKKKNKRFSTLSKVSDLWSGSTKHY   800
 801  GKHHTERLGDDDDKHLASAEEITESNERFQKRFALGTEERLIASYHCHLH   850
 851  RGGIPTYGKMYVSTNYVTFRSFLRTKTLMIVPLKVVENATKDSGFKFGYS   900
 901  GLVLTIQGYEEIFFEFASASHRDDAEVMLLRQLDIIRPHINDDIKSDDQY   950
 951  MLQSARLCTYEDALKAEANVEMPPVIIDGNLASVLPGLVTPQSKMLFTLL  1000
1001  TIGSRGDVQPYISLGKALIEEGHRVRIATHSEFKDWIEGYGIEFKEVAGD  1050
1051  PSELMKIMVDHGVFSVSFLRDAASKFRGWINELLASSWEACQGSDVLIES  1100
1101  PSAMAGIHIAEALQIPYFRAFTMPWSRTRAYPHAFIVPDQKMGGSYNYLT  1150
1151  YVMFDNVFWKGISGQVNRWRKKTLHLPRTNLDHMEQNKVPFLYNVSPAVL  1200
1201  PPPVDFPDWIKITGYWFLDEGSKDYTPDDKLCRFMEKARNDGKKLVYIGF  1250
1251  GSIVVSDPTALTKSVVESVLKADVRCILNKGWSDRLGKKDAKEPEIPLPE  1300
1301  EVLQITNCPHDWLFPQIDACVHHGGSGTTGAGLRAGLPTIIKPFFGDQFF  1350
1351  YANRVEDLGAGIHLRKLNVSQFSKALWEATHNERIIAKAAAVGRQIRSEN  1400
1401  GVISAIQAIYRDLDYARSLVQKKRGYTPTSDKEEETWTLVDDIERQMQDE  1450
1451  VEKHNL                                              1456

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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