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

NucPred

Fetching Q6PQZ2 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MQRSPLEKASIFSKLFFSWTRPILRKGYRQRLELSDIYHISSSDSADNLS    50
  51  EKLEREWDRELASKKNPKLINALRRCFFWRFMFYGIILYLGEVTKAVQPL   100
 101  LLGRIIASYDPDNKAERSIAIYLGVGLCLLFIVRTLLLHPAIFGPHHIGM   150
 151  QMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHF   200
 201  VWIAPLQVTLLMGLLWELLQASAFCGLAFLVVLALFQAGLGKMMMKYRDQ   250
 251  RAGKINERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAA   300
 301  YVRYFNSSAFFFSGLFVVFLSVLPYALLKGIMLRKIFTTISFCIVLRMAV   350
 351  TRQFPWAVQTWYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVVMENVTAF   400
 401  WEEGFGKLFEKAKQNNNSRKISNGDNSLFFSNFSLLGTPVLKDISFKIER   450
 451  GQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSWIMPG   500
 501  TIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSG   550
 551  GQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTR   600
 601  ILVTSKMEHLKKADKILILHEGSSYFYGTFSELQSQRPDFSSKLMGYDTF   650
 651  DQFTAERRNSIITETLRRFSLEGDASVSWNETKKQSFKQTGEFGEKRKNS   700
 701  ILNSINSIRKFSIVQKTPLQMNGFEEDSGEPLERRLSLVPDSEHGEAILP   750
 751  RSNVINAGPTFQGRRRQSVLNLMTRSSVNQGQSIHRKTATSTRKMSLVPQ   800
 801  ANLTEIDIYSRRLSQDTGLEISEEINEEDLRECFFDDVESIPTVTTWNTY   850
 851  LRYVTVHKSLIFVLIWCLVVFLAEVAACLVVLCLLKKTSPQDKGNSTKGA   900
 901  NNSYAVIITSTSAYYVFYIYVGVADGLLALGLFRGLPLVHTLITVSKILH   950
 951  RKMLHSVLQAPMSTLNTLKAGGILNRFSKDIAVLDDLLPLTIFDFIQLLL  1000
1001  IVIGAVAVVSVLKPYIFLATVPVIVAFILLRAYFLHTSQQLKQLESEGRS  1050
1051  PIFTHLITSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWF  1100
1101  QMRIEMIFVIFFIAVTFISILTTGEGEGTVGIILTLAMNIMSTLQWAVNS  1150
1151  SIDVDSLMRSVSRVFKFIDMPAEGDQPNRSFKPSKDGQLSKVMIIENQHV  1200
1201  KKDDIWPSGGQMTVKDLTAKYVDGGNAVLENISFSISPGQRVGLLGRTGS  1250
1251  GKSTLLLAFLRLLNTEGEIQVDGVSWDSITLQQWRKAFGVIPQKVFIFSG  1300
1301  TFRKNLDPYGQWNDQEIWKVAEEVGLRSVIEQFPGKLDFVLVDGGCVLSH  1350
1351  GHKQLMCLARSVLGKAKILLLDEPSAHLDPITYQIIRRTLKQAFADCTVI  1400
1401  LSEHRIEAMLECQRFLVIEENKVRQYDSIQRLLSEKSLFRQAISPLDRLK  1450
1451  LLPHRNSSKQRSRSKIAALKEETEEEVQETRL                    1482

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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