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

NucPred

Fetching Q9TUQ2 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSADSADNLS    50
  51  EKLEREWDRELASKKNPKLINALRRCFFWRFMFYGILLYLGEVTKAVQPL   100
 101  LLGRIIASYDPDNKEERSIAIYLGIGLCLLFIVRTLLLHPAIFGLHHIGM   150
 151  QMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHF   200
 201  VWIVPLQVALLMGLIWELLQASAFCGLGFLIVLALFQAGLGRMMMKYRDQ   250
 251  RAGKINERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAA   300
 301  YVRYFNSSAFFFSGFFVVFLSVLPYALIKGIVLRKIFTTISFCIVLRMAV   350
 351  TRQFPWAVQTWYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVVMENVTAF   400
 401  WEEGFGELFEKAKQNNSNRKTSNDDDSLFFSNFSLLGTPVLKDINFKIER   450
 451  GQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSWIMPG   500
 501  TIKENIIFGVSYDEYRYRSVINACQLEEDISKFAEKDNIVLGEGGITLSG   550
 551  GQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTR   600
 601  ILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLRPDFSSKLMGYDSF   650
 651  DQFSAERRNSILTETLRRFSLEGDAPVSWTETKKQSFKQTGEFGEKRKNS   700
 701  ILNPINSIRKFSIVQKTPLQMNGIEEDSDEPLERRLSLVPDSEQGEVILP   750
 751  RISVISTGPTLQARRRQSVLNLMTHSVNQGQSIHRKTAASTRKVSLAPQA   800
 801  NLTELDIYSRRLSQETGLEISEEINEEDLKECFFDDMESIPAVTTWNTYL   850
 851  RYITVHKSLIFVLIWCLVIFLAEVAASLVVLWFLGNTPPQDKGNSTYSRN   900
 901  NSYAVIITRTSSYYVFYIYVGVADTLLAMGFFRGLPLVHTLITVSKILHH   950
 951  KMLHSVLQAPMSTLNTLKAGGILNRFSKDIAILDDLLPLTIFDFIQLLLI  1000
1001  VIGAIAVVAVLQPYIFVATVPVIVAFIMLRAYFLQTSQQLKQLESEGRSP  1050
1051  IFTHLVTSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWFQ  1100
1101  MRIEMIFVIFFIAVTFISILTTGEGEGTVGIILTLAMNIMSTLQWAVNSS  1150
1151  IDVDSLMRSVSRVFKFIDMPTEEGKPTRSTKPYKNGQLSKVMVIENSHVK  1200
1201  KDDIWPSGGQMTVKDLTAKYTEGGNPILENISFSISPGQRVGLLGRTGSG  1250
1251  KSTLLSAFLRLLNTEGEIQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGT  1300
1301  FRKNLDPYEQWSDQEIWKVADEVGLRSVIEQFPGKLDFVLVDGGCVLSHG  1350
1351  HKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQIIRRTLKQAFADCTVIL  1400
1401  CEHRIEAMLECQQFLVIEENKVRQYDSIQKLLNERSLFQQAISPSDRVKL  1450
1451  FPHRNSSKCKTQPQIAALKEETEEEVQDTRL                     1481

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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