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

NucPred

Fetching Q6BVE1 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MAKEDIEEEREIRNDASENSSDEEGDDVLDSSEEDDDDDDEEAIKRVREG    50
  51  FIVDDDEDESQKRKRRKHKKRKREERTNDDENNALDQDDLELLMENSGAR   100
 101  PQPSSNKLKRLKRAYTEDTEGAEEEEIGAKSGRGGLTDIFSDEDNNEEER   150
 151  ADLGETRVDDDRNILDEFEDFIEEDEYSDEDEERQRKLTQQRERAQKKGP   200
 201  RLDTSKLSNVDRESLQQLFEVFGNGAEYEWALEAQEMEDEGNGENLEPTS   250
 251  LDEVFEHAELKERMLTEEDNLIRIVDIPERFQKYRANLNYIDLEGEELKS   300
 301  EQGWVANILFMEKQGSFSGFLEEPFKEAVSKVVEFISKDVYEVPFIWTHR   350
 351  RDFLLYSEEIKNEDGSVTNSVHKLLFEDDLWRIFQLDIEYHSLYEKRVNI   400
 401  EKLIESLNLDDDLVKDVKSLETMVAIQDLQDYINFTYSTEIRKLYDDKET   450
 451  EGIDANITKKHSKYAIFERIKSNVLYDAVNAFGISAKEFGENVQDQSSKK   500
 501  FEVPYRIHATDDHIESPEDLIERLCEDDEVLFKDPKNALNAVRKTFAEEI   550
 551  FHNPKIRHEVRTTFKDFASIRVAVTEKGKAIDNHSPYADIKYAINRSPAD   600
 601  LVRNPDVLLRMLEAEAAGLVVVKVETKDYDSWFQCIFNCLKSDGSSEIFE   650
 651  KWNKEREFVLNMAFKRLTSMVSMNTKEDLRRECERLIASEVRRRFLARID   700
 701  QAPFTPFGFDKGTKPNVLALSFGKGDFDSAVIGAFLRESGKVDEFFKSED   750
 751  NPIRDRESEDKFSGQLKEFFDKNLRNQKPDVIVVSGYNAISKKLFDSVKS   800
 801  FVETNNVTANTEELTDVQNPPLIQVIWGQSETATLFQNSERARIEFSDKP   850
 851  TLAKYCVGLARYVQSPLLEYLSLGEGILSLTFFEHQKLISTDLVMEAIES   900
 901  AYVDIINMVGVEINEAIRDPYIAQLLPYVAGLGPRKASGLLRNINSKLGS   950
 951  TLANRSDLIENELSTANIFINCSSFLNIPYDEGLSMRDSSVELLDATRIH  1000
1001  PEDYDLARKMAADALDLDEEDMAHVEEQGGIIYQLMQDGVNKVDDLNLTA  1050
1051  YGKELESKFGKKKYATLQSIKEELVNNFEEIRRSFHILESHEVFHMLTGE  1100
1101  TTESFTRNTIVPVTVNKVGQNFRDFENSKIKFAKVTTSSFIQGNIEEASI  1150
1151  PQGIDLAQGQVVQAVVLDAYYDSFTASFSLLEADIQKGAAPKFHKDPLKW  1200
1201  NFEAEQADKQKEMAKERAQLAKTRNIQHPLFHNFSYKQAEEFLAPQAVGD  1250
1251  CVLRPSSKGPNYLTVTWKVSNNLFQHLSIQENTQGMGKEYIVEHKKYADL  1300
1301  DQLIFQHVQAIAKHVDEMCRHPKFREGTMSEVNEWLESYTKANPKNSAYV  1350
1351  FCFDHKAPGWFLLLFKVNVNTPITTWHVKTECDGYRLKGFSYPSMLRLCN  1400
1401  GFKQTFKSYVKGIADRSRSTKPAPVNNQAQASTYGGYGY             1439

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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