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

NucPred

Fetching Q86UK5 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MDPSGSRGRPTWVLAGGLLAVALALGGRGCLGASSRPRWRPLGAQPPRDP    50
  51  QVAPRSGPGLRIPPGRSGAGPESSTQDLPCMIWPKVECCHFKTAVEAPLG   100
 101  MKLDKKMEVFIPLSTSAASSGPWAHSLFAFIPSWPKKNLFKRESPITHRL   150
 151  YGDISREVQGTSENGVIFQKCALVSGSSEAQTARIWLLVNNTKTTSSANL   200
 201  SELLLLDSIAGLTIWDSVGNRTSEGFQAFSKKFLQVGDAFAVSYAATLQA   250
 251  GDLGNGESLKLPAQLTFQSSSRNRTQLKVLFSITAEENVTVLPHHGLHAA   300
 301  GFFIAFLLSLVLTWAALFLMVRYQCLKGNMLTRHRVWQYESKLEPLPFTS   350
 351  ADGVNEDLSLNDQMIDILSSEDPGSMLQALEELEIATLNRADADLEACRT   400
 401  QISKDIIALLLKNLTSSGHLSPQVERKMSAVFKKQFLLLENEIQEEYDRK   450
 451  MVALTAECDLETRKKMENQYQREMMAMEEAEELLKRAGERSAVECSNLLR   500
 501  TLHGLEQEHLRKSLALQQEEDFAKAHRQLAVFQRNELHSIFFTQIKSAIF   550
 551  KGELKPEAAKMLLQNYSKIQENVEELMDFFQASKRYHLSKRFGHREYLVQ   600
 601  NLQSSETRVQGLLSTAAAQLTHLIQKHERAGYLDEDQMEMLLERAQTEVF   650
 651  SIKQKLDNDLKQEKKKLHQKLITKRRRELLQKHREQRREQASVGEAFRTV   700
 701  EDAGQYLHQKRSLMEEHGATLEELQERLDQAALDDLRTLTLSLFEKATDE   750
 751  LRRLQNSAMTQELLKRGVPWLFLQQILEEHGKEMAARAEQLEGEERDRDQ   800
 801  EGVQSVRQRLKDDAPEAVTEEQAELRRWEHLIFMKLCSSVFSLSEEELLR   850
 851  MRQEVHGCFAQMDRSLALPKIRARVLLQQFQTAWREAEFVKLDQAVAAPE   900
 901  LQQQSKVRKSRSKSKSKGELLKKCIEDKIHLCEEQASEDLVEKVRGELLR   950
 951  ERVQRMEAQEGGFAQSLVALQFQKASRVTETLSAYTALLSIQDLLLEELS  1000
1001  ASEMLTKSACTQILESHSRELQELERKLEDQLVQQEAAQQQQALASWQQW  1050
1051  VADGPGILNEPGEVDSERQVSTVLHQALSKSQTLLEQHQQCLREEQQNSV  1100
1101  VLEDLLENMEADTFATLCSQELRLASYLARMAMVPGATLRRLLSVVLPTA  1150
1151  SQPQLLALLDSATERHVDHAAESDGGAEQADVGRRRKHQSWWQALDGKLR  1200
1201  GDLISRGLEKMLWARKRKQSILKKTCLPLRERMIFSGKGSWPHLSLEPIG  1250
1251  ELAPVPIVGAETIDLLNTGEKLFIFRNPKEPEISLHVPPRKKKNFLNAKK  1300
1301  AMRALGMD                                            1308

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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