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

NucPred

Fetching Q9LRR5 from www.uniprot.org...

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

   1  MANSYLSSCANVMVERINTSQELVELCKGKSSSALLKRLKVALVTANPVL    50
  51  ADADQRAEHVREVKHWLTGIKDAFFQAEDILDELQTEALRRRVVAEAGGL   100
 101  GGLFQNLMAGREAIQKKIEPKMEKVVRLLEHHVKHIEVIGLKEYSETREP   150
 151  QWRQASRSRPDDLPQGRLVGRVEDKLALVNLLLSDDEISIGKPAVISVVG   200
 201  MPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTVTKAVLQDITS   250
 251  SAVNTEDLPSLQIQLKKTLSGKRFLLVLDDFWSESDSEWESFQVAFTDAE   300
 301  EGSKIVLTTRSEIVSTVAKAEKIYQMKLMTNEECWELISRFAFGNISVGS   350
 351  INQELEGIGKRIAEQCKGLPLAARAIASHLRSKPNPDDWYAVSKNFSSYT   400
 401  NSILPVLKLSYDSLPPQLKRCFALCSIFPKGHVFDREELVLLWMAIDLLY   450
 451  QPRSSRRLEDIGNDYLGDLVAQSFFQRLDITMTSFVMHDLMNDLAKAVSG   500
 501  DFCFRLEDDNIPEIPSTTRHFSFSRSQCDASVAFRSICGAEFLRTILPFN   550
 551  SPTSLESLQLTEKVLNPLLNALSGLRILSLSHYQITNLPKSLKGLKLLRY   600
 601  LDLSSTKIKELPEFVCTLCNLQTLLLSNCRDLTSLPKSIAELINLRLLDL   650
 651  VGTPLVEMPPGIKKLRSLQKLSNFVIGRLSGAGLHELKELSHLRGTLRIS   700
 701  ELQNVAFASEAKDAGLKRKPFLDGLILKWTVKGSGFVPGSFNALACDQKE   750
 751  VLRMLEPHPHLKTFCIESYQGGAFPKWLGDSSFFGITSVTLSSCNLCISL   800
 801  PPVGQLPSLKYLSIEKFNILQKVGLDFFFGENNSRGVPFQSLQILKFYGM   850
 851  PRWDEWICPELEDGIFPCLQKLIIQRCPSLRKKFPEGLPSSTEVTISDCP   900
 901  LRAVSGGENSFRRSLTNIPESPASIPSMSRRELSSPTGNPKSDASTSAQP   950
 951  GFASSSQSNDDNEVTSTSSLSSLPKDRQTEDFDQYETQLGSLPQQFEEPA  1000
1001  VISARYSGYISDIPSTLSPYMSRTSLVPDPKNEGSILPGSSSYQYHQYGI  1050
1051  KSSVPSPRSSEAIKPSQYDDDETDMEYLKVTDISHLMELPQNLQSLHIDS  1100
1101  CDGLTSLPENLTESYPNLHELLIIACHSLESFPGSHPPTTLKTLYIRDCK  1150
1151  KLNFTESLQPTRSYSQLEYLFIGSSCSNLVNFPLSLFPKLRSLSIRDCES  1200
1201  FKTFSIHAGLGDDRIALESLEIRDCPNLETFPQGGLPTPKLSSMLLSNCK  1250
1251  KLQALPEKLFGLTSLLSLFIIKCPEIETIPGGGFPSNLRTLCISLCDKLT  1300
1301  PRIEWGLRDLENLRNLEIDGGNEDIESFPEEGLLPKSVFSLRISRFENLK  1350
1351  TLNRKGFHDTKAIETMEISGCDKLQISIDEDLPPLSCLRISSCSLLTETF  1400
1401  AEVETEFFKVLNIPYVEIDGEIFS                            1424

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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