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

NucPred

Fetching Q00552 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MQKSPLVKASVISKLFFSWTRPILKKGYRKRLEVSDIYQVPSADSADNLS    50
  51  EELEREWDRELASKKNPKLINALRRCFLWRFIFYGILLYLGEVTKAVQPL   100
 101  LLGRIIASYDPDNKEERSIAIYLAIGLCLLFIVRTLLLHPAIFGLQHIGM   150
 151  QMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHF   200
 201  VWIAPLQVTLLMGLLWDLLQASAFCGLAVLIVLALFQAWLGKMMMKYRDQ   250
 251  RAGKINERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAA   300
 301  YMRYFNSAAFFFSGFFVVFLSVLPYAFLQGIILRKIFTTISFCIVLRMAI   350
 351  TRQFPGAVQTWYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVVMENVTAF   400
 401  WEEQGFGELLEKAKLNNNNRKISNGDNKLFFSNFSLLGSPVLKDINFKIE   450
 451  KGQLLAVAGSTGAGKTSLLMMILGELEPSEGKIKHSGRVSFCSQFSWIMP   500
 501  GTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLS   550
 551  GGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKQIFESCVCKLMANKT   600
 601  RILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLRPDFSSKLMGYDS   650
 651  FDQFSAERRNSILTETLRRFSLEGDPSVSFNETKKQSFKQTGEFGEKRKN   700
 701  SILNSINSIRKFSIVPKTPLQISGIEEDSDDPVERRLSLVPDSEQSDGLL   750
 751  LRSNVIHTGPTFQGSRRQSVLNLITHSVNQGQSFRRTTTAPSRKMSLAPQ   800
 801  ASLTEMDIYSRRLSQDSSLEINEEINEEDLKECFFDDVENIPTVTTWNTY   850
 851  LRYITVHKSLILVLIWCLIIFLAEVAASLVVLWLLKNNTPQQEMNSTQSG   900
 901  NRSYPVIITNTSFYYIFYIYVGVADTLLALGLFRGLPLVHTLITVSKILH   950
 951  HKMLRSVLQAPMSTLNALKAGGILNRFSKDIAILDDLLPLTIFDFIQLLL  1000
1001  IVIGAIAVVSVLQPYIFLATVPVIAAFIMLRAYFLHTSQQLKQLESEGRS  1050
1051  PIFTHLVTSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWF  1100
1101  QMRIEMIFVIFFIAVTFISILTTGEGQGSVGIILTLAMNIMSTLQWAVNS  1150
1151  SIDVDSLMRSVSRVFKFIDMPEEGAPVKSIKPSRDDQLSKVMIIENQHVK  1200
1201  KDDIWPSGGQMIVKDLTAKYVDGGIAILENISFSISPGQRVGLLGRTGSG  1250
1251  KSTLLSAFLRLLNTEGEIQIDGVSWDSTPLQQWRKAFGVIPQKVFIFSGT  1300
1301  FRKNLDPFGQWSDQEIWKVADEVGLRSVIEQFPGKLDFVLVDGGYVLSHG  1350
1351  HKQLMCLARSVLSKAKILLLDEPSAHLDPITYQIIRRTIKQAFADCTVIL  1400
1401  CEHRIEAMLECQRFLVIEENKVRQYDSIQKLLSEKSLFRQAISSSDRLKL  1450
1451  FPHRNSSKHKSRSQITALKEETEEEVQETRL                     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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