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

NucPred

Fetching Q6V3W0 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MSADIVKQLKGTRSDVKAAATTIELKFKEFSKGIGINDASFPLRYELSVL    50
  51  RQLCLALKDNLHQHADLYCGIAATMLPHVEPYEEKPSLWEAHLTSLRYIH   100
 101  HGLCQEKSLTECQKMYGLIRSQPCRLQEEADYKFYLDIHLTHFNGIYLQM   150
 151  QKETLPLAATDELYYALEAMGVLFDTMHQRKVAKNAALLVQLNDSLFSKR   200
 201  SKAFLKYLSALPPESTTKMYDPLLKLLSCSWATPSSELTNQFTEYLGLVL   250
 251  ALVQIDMFSIEAPLEQQLALKLLRICRDLYKDVSPQNYSIQLLYYYVKLM   300
 301  YVREATADFKQTYIDLCKKFVYFFEHKGATHAKEQWFMDLLVFFQRLQTL   350
 351  LHQSSNKPPLDIFWQQLEGDDSSEVYTAHFQLLHGCLGLAVNVVRSPLGT   400
 401  SCSNEACKSIRRHCLLYFGMCALEAYINWQPTTEQKADKAPYKPLLGILG   450
 451  YTLDVAKSMKCLGPSAMELVKLVRLLALVAEKVSCPEQMSLVLAFLEPLQ   500
 501  HLRPLIASQDMLSVLRRIYKASVHCKSSDMANRLQSTYLAALTNPSRLRS   550
 551  QLFAHYHNANNTEKCVYEWHESSPMPNPLTPAQTKQLYDVDLLAVLHFLS   600
 601  APPVPLLQSLLRCRHNDYHLALLARKMRTDSEVVRQCEELRSQLHSTALK   650
 651  QPLSRMQQLAIGHTSISVLLEALEAQKTKFSIKETAENCLEELIVKNNLL   700
 701  ELNIKREHRLVELATSAIAGFAAFFERADTEPLGCDDTPIDWEALIDDAV   750
 751  AAAMALSTMGYMAQADEAWLLILRIGQMLDERFTYLRALTHFLGQDHLNS   800
 801  NQQLQLSEEVDRAQELLDDLWPQLQNGWFFKRQHTIVMLCLCHMASYYAR   850
 851  QDCLCHAQLLLLQAEELRAQFDERVGKSDIVQITIQTVRFRLEYLRNKRC   900
 901  SSLPRRPTPLRQLDTLVDSVRNYCTVSSVDLGALQLLLADLVRESTECAA   950
 951  NRLTERFAFYGTMLNLVLQSGMALRTIEVLISWLWMNLQMEYLDQAQSKL  1000
1001  RLLDHLLAIKPLSRTLVEQTSATYVPAIAAKEDLKANAMSELTSNMLLMQ  1050
1051  LVEPIRKQNQMDVATIKSLPMHEPIPTSHQLQRYVSKQGTPPHLRDSMQL  1100
1101  QCIYFIVGCLHARFSFLKRENDQLDDFYVGAGNWLQEDPVRTATLGSMLL  1150
1151  VHELYHLNYLRFRKKHKEALSYAEAGLKSVYQTADINYSFNFMVQLKTAR  1200
1201  LELHPVGKARAKTIRRALAFNTSPEDKRRKGVVEGSIKAKSSARKTPRFK  1250
1251  IYTELELRPPIGCSNSSSSSSKSGNENTPPSDHVDLNACQAIEISDDDAA  1300
1301  SVSASTPAPSQLKRSQSVPAKATKTRSARVGSQLKVPEIIELDDTMEETP  1350
1351  STSTAATVKRYPTTDARSSRARNRQLEETPATTRGRPRRKVPEPAPQQET  1400
1401  VSLRPRQRN                                           1409

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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