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

NucPred

Fetching Q5U820 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MQRSPLEKASVLSKLFFSWTRPILIKGYRQRLELSDIYQVPSTDSADHLS    50
  51  EKLEREWDRELASKKNPKLINALRRCFFWRFAFYGILLYLGEVTKAVQPL   100
 101  LLGRIIASYDPDNKQERSIAIYLAIGLCLLFIMRPLLLHPAIFGLHHIGM   150
 151  QIRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHF   200
 201  VWIAPLQVTLLMGLLWDLLQASAFCGLAFLIVLALVQAGLGRMIMKYRDQ   250
 251  RAGKINERLVITSEVIENIQSVKAYCWEEAMEKIIENIRQTELKLTRKAA   300
 301  HVRYFNSSAFFFSGFFVVSLSVLPYALIKTIILRKIFTTISFCIVLRMAV   350
 351  TRQFPWAVQTWYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVMMENVTAF   400
 401  WEEGFGELLEKAKENSNDRKISNGDNSLFFSNFSLLGTPVLKDINFKIER   450
 451  GQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSWIMPG   500
 501  TIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGVTLSG   550
 551  GQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTR   600
 601  ILVTSKMEHLKKADKVLILHEGSCYFYGTFSELQSLRPDFSSKLMGYDSF   650
 651  DQFSPERRNSIITETLRRFSLEGDAAVPWNETKKQSFKQTGEFGEKRKNS   700
 701  ILNPINSIRKFSIVQKTPLPMNGIEGESEVPVERRLSLFPDCEQGEAILP   750
 751  RSNMINTGPTLRRQRRQSVLNLMTRSSVNQGQSIHRRTTASTRKMSLAPQ   800
 801  ANLTEMDIYSRRLSQDSGLEISEEINEEDLKECFFDDVESIPPVTTWNTY   850
 851  LRYITVHKNLIFVLIWCLVIFLAEVAVSLVVLWILRNLSSQDKGNSTQSV   900
 901  NSSYAVIFTSTSAYYIFYIYVGVADTLLALGLFRGLPLVHTLITVSKILH   950
 951  HKMLHSVLQAPMSTLNTLKAGGILNRFSKDIAILDDLLPLTIFDFIQLLL  1000
1001  IVIGAVAVVSVLQPYIFLATVPVIAAFIILRAYFLHTSQQLKQLESEGRS  1050
1051  PIFTHLLTSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWF  1100
1101  QMRMEIIFVIFFIAVTFISILTTGEGEGTVGIILTLAMNIMGTLQWAVNS  1150
1151  SIEVDSLMRSVSRVFKFIDMPTEESKPPTKSFKPSKDAQLSKVTITENRH  1200
1201  VREDDIWPSGGQMTVKDLTAKYIDGGNAILENISFSISPGQRVGLLGRTG  1250
1251  SGKSTLLSALLRLVNTEGEIQIDGVSWDSIPLQEWRRAFGVIPQKVFIFS  1300
1301  GTFRKNLDPYGQWNDQEIWKVADEVGLRSVIEQFPGKLDFVLVDGGYVLS  1350
1351  HGHKQLMCLARSVLRKAKILLLDEPSAHLDPITYQIIRRTLKQAFADCTV  1400
1401  ILSEHRIEAMLECQRFLVIEDSRLRQFESIQRLLSERSAFRQAIGPPERP  1450
1451  GLLPHRLSSRQRSPSRIAALKEETEDEVQDTRL                   1483

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.)

Go back to the NucPred Home Page.