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

NucPred

Fetching Q876G9 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MSFEVGTRCWYPHKELGWIGAEVIKNEVKDGKYHLELSLEDDEVVSVDTE    50
  51  DLNDDKNQSLPLLRNPPILEATEDLTSLSYLNEPAVLHAIKQRYSQLNIY   100
 101  TYSGIVLIATNPFDRVDQLYTQDMIQAYAGKRRGELEPHLFAIAEEAYRL   150
 151  MKNDKQNQTIVVSGESGAGKTVSAKYIMRYFASVEEENSTTIQHQVEMSE   200
 201  TEQRILATNPIMEAFGNAKTTRNDNSSRFGKYLEILFDKETSIIGARIRT   250
 251  YLLERSRLVYQPPIERNYHIFYQLMAGLPAQTKEELHLTDASDYFYMNQG   300
 301  GDTKIAGIDDAEEYQTTVDALTLVGITTATQHQIFKILAALLHIGNIEIK   350
 351  KTRNDASLSADEPSLKLACELLGIDSYNFAKWITKKQIVTRSEKIVSNLN   400
 401  FNQAMVAKDSVAKFIYSALFDWLVENINTVLCNPDVDDQINSFIGVLDIY   450
 451  GFEHFEKNSFEQFCINYANEKLQQEFNQHVFKLEQEEYVAEEIEWSFIEF   500
 501  NDNQPCIDLIENKLGILSLLDEESRLPAGSDESWTQKLYQTLDKSPTNEV   550
 551  FSKPRFGQTKFIVSHYALDVAYDVEGFIEKNRDTVSDGHLEVLKASTNET   600
 601  LINILEGLENAAKKLEETKKAELEQNNPGNKKPGPARTVNRKPTLGSMFK   650
 651  QSLIELMSTINSTNVHYIRCIKPNADKEAWQFDNLMVLSQLRACGVLETI   700
 701  RISCAGFPSRWTFEEFVLRYYILIPHEEWDLIFQKKETTEDDIISVVKMI   750
 751  LDATVKDKTKYQIGNTKIFFKAGMLAYLEKLRSNKMHNSIVTIQKKIRAK   800
 801  YYRNQYLKISQAIKIWQSNTRGFIIRHRVYHEMKVHSATLIQATYRGYAI   850
 851  RKNVFNVLITIINLQTRIREELKRKQLKREHEYNAAVTIQSKVRTFEPRS   900
 901  TFLNTKRDTVVVQSLIRRRAAQGRLRQLKSDAKSVHHLKEVSYKLENKVI   950
 951  ELTQNLASKVKENKEMTERIKELQVQVEESAKLQETLENMKKEHLVNIDN  1000
1001  QKNKDMELQKTIEDNLQSTEQNLKNAQLELEEMVKQHNELKEESRKQLDE  1050
1051  LDETKKALVEHQTLNGDLQNEVKSLKEEISRLQTAMSLGTVTTSVLPQTP  1100
1101  LKDVMGGSTANYNSLMLDNAELSPGKSRTTPMSGNHIDSLNIDQDNGANA  1150
1151  TQINEELYRLLEDTEILNQEITEGLLKGFEVPDAGVAIQLSKRDVVYPAR  1200
1201  ILIIVLSEMWRFGLTKQSESFLAQVLTTIQKVVTQLKGNDLIPSGVFWLA  1250
1251  NVRELYSFVVFALNSILTEETFKNGMTDEEYKEYVSLVTELKDDFEALSY  1300
1301  NIYNIWLKKLQKQLQKKAINAVVISESLPGFSAGETSGFLNKIFANTEEY  1350
1351  TMDDILTFFNSIYWCMKSFHIETEVFHAVVTTLLNYVDAICFNELIMKRN  1400
1401  FLSWKRGLQLNYNVTRLEEWCKTHGLTGGTECLQHLIQTAKLLQVRKYTI  1450
1451  EDIDILRGICYSLTPAQLQKLISQYQVADYESPIPQEILRYVADIVKKEA  1500
1501  ALSNDSKGHEHSSGIFITPETGPFTDPFSLIKTRKFDQVEAYIPAWLSLP  1550
1551  ATKRIVDLVAQQVVQDGH                                  1568

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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