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

NucPred

Fetching Q00555 from www.uniprot.org...

The NucPred score for your sequence is 0.61 (see score help below)

   1  MQRSPLEKASVVSKLFFSWTRPILKKGYRQRLELSDIYHISSSDSADNLS    50
  51  EKLEREWDRELASKKNPKLINALRRCFFWRFMFYGIILYLGEVTKAVQPL   100
 101  LLGRIIASYDPDNKVERSIAIYLGIGLCLLFIVRTLLLHPAIFGLHHIGM   150
 151  QMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHF   200
 201  VWIAPLQVTLLMGLLWDLLQAFTFCGLAFLVVLALLQAGLGKMMMKYRDQ   250
 251  RAGKINERLVITSEMIENIQSVKAYCWEEAMEKIIENLRQTELKLTRKAA   300
 301  YVRYLNSSAFFFSGFFVVFLSVLPYALLKGIILRKIFTTISFCIVLRMAV   350
 351  TRQFPWAVQTWYDSLGAINKIQDFLQKQEYKTLEYNLTTTDVVMENVTAF   400
 401  WEEGFSKLFEKAKENNNNRKISNCDTSLFFSNLLLGTPVLKDISFKIERG   450
 451  QLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQYSWIMPGT   500
 501  IKDNIIFGVSYDEYRYRSVIKACQLEEDISKFSEKDNIVLGEGGITLSGG   550
 551  QRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRI   600
 601  LVTSKMEHLKKADKILILHEGSVYFYGTFSELQNQRPDFSSKLMGCDTFD   650
 651  QFTAERRNSIITETLRRFSLEGDTSVSWNETKKPSFKQTGEFGEKRKNSI   700
 701  LNSINSIRKFSVVQKTSLQMNGIDGASDEPLERRLSLVPHSEPGEGILPR   750
 751  SNAVNSGPTFLGGRRQSVLNLMTCSSVNQGQSIHRKTATSTRKMSLAPQA   800
 801  SLAEIDIYSRRLSQDTGLEISEEINEEDLRDCFFDDVENIPAVTTWNTYL   850
 851  RYITVHKSLMFVLIWCLVVFLVEVAASLVVLCLFPKILLQDKGNSTKNAS   900
 901  NSYAVIITSTSSYYIFYIYVGVADTLLALGLFRGLPLVHTLITVSKTLHH   950
 951  KMLQSVLQAPMSTLNTLKTGGILNRFSKDIAVLDDLLPLTIFDFIQLLLI  1000
1001  VIGAVVVVSVLQPYIFLATVPVIAAFILLRGYFLHTSQQLKQLESEGRSP  1050
1051  IFTHLVTSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWFQ  1100
1101  MRIEMIFVIFFIAVTFISILTTGEGEGRVGIILTLAMNIMGTLQWAVNSS  1150
1151  IDVDSLMRSVSRVFKFIDMPTEDGKPNNSFRPSKDSQPSKVMIIENQHVK  1200
1201  KDDIWPSGGQMTVKDLTAKYIDGGNAILENISFSISPGQRVGLLGRTGSG  1250
1251  KSTLLLAFLRLLNTKGEIQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGT  1300
1301  FRKNLDPYEQWSDQEIWKVADEVGLRSVIEQFPGKLDFVLVDGGCVLSHG  1350
1351  HKQLMCLARSVLSKAKILLLDEPSAHLDPITYQIIRRTLKQAFADCTVIL  1400
1401  SEHRIEAMLECQRFLVIEENKVRQYDSIQRMLSEKSLFRQAISPADRLKL  1450
1451  LPHRNSSRQRSRANIAALKEETEEEVQETKL                     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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