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

NucPred

Fetching P19524 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MSFEVGTRCWYPHKELGWIGAEVIKNEFNDGKYHLELQLEDDEIVSVDTK    50
  51  DLNNDKDQSLPLLRNPPILEATEDLTSLSYLNEPAVLHAIKQRYSQLNIY   100
 101  TYSGIVLIATNPFDRVDQLYTQDMIQAYAGKRRGELEPHLFAIAEEAYRL   150
 151  MKNDKQNQTIVVSGESGAGKTVSAKYIMRYFASVEEENSATVQHQVEMSE   200
 201  TEQKILATNPIMEAFGNAKTTRNDNSSRFGKYLEILFDKDTSIIGARIRT   250
 251  YLLERSRLVYQPPIERNYHIFYQLMAGLPAQTKEELHLTDASDYFYMNQG   300
 301  GDTKINGIDDAKEYKITVDALTLVGITKETQHQIFKILAALLHIGNIEIK   350
 351  KTRNDASLSADEPNLKLACELLGIDAYNFAKWVTKKQIITRSEKIVSNLN   400
 401  YSQALVAKDSVAKFIYSALFDWLVENINTVLCNPAVNDQISSFIGVLDIY   450
 451  GFEHFEKNSFEQFCINYANEKLQQEFNQHVFKLEQEEYVKEEIEWSFIEF   500
 501  NDNQPCIDLIENKLGILSLLDEESRLPAGSDESWTQKLYQTLDKSPTNKV   550
 551  FSKPRFGQTKFIVSHYALDVAYDVEGFIEKNRDTVSDGHLEVLKASTNET   600
 601  LINILEGLEKAAKKLEEAKKLELEQAGSKKPGPIRTVNRKPTLGSMFKQS   650
 651  LIELMNTINSTNVHYIRCIKPNADKEAWQFDNLMVLSQLRACGVLETIRI   700
 701  SCAGFPSRWTFEEFVLRYYILIPHEQWDLIFKKKETTEEDIISVVKMILD   750
 751  ATVKDKSKYQIGNTKIFFKAGMLAYLEKLRSNKMHNSIVMIQKKIRAKYY   800
 801  RKQYLQISQAIKYLQNNIKGFIIRQRVNDEMKVNCATLLQAAYRGHSIRA   850
 851  NVFSVLRTITNLQKKIRKELKQRQLKQEHEYNAAVTIQSKVRTFEPRSRF   900
 901  LRTKKDTVVVQSLIRRRAAQRKLKQLKADAKSVNHLKEVSYKLENKVIEL   950
 951  TQNLASKVKENKEMTERIKELQVQVEESAKLQETLENMKKEHLIDIDNQK  1000
1001  SKDMELQKTIENNLQSTEQTLKDAQLELEDMVKQHDELKEESKKQLEELE  1050
1051  QTKKTLVEYQTLNGDLQNEVKSLKEEIARLQTAMSLGTVTTSVLPQTPLK  1100
1101  DVMGGGASNFNNMMLENSDLSPNDLNLKSRSTPSSGNNHIDSLSVDRENG  1150
1151  VNATQINEELYRLLEDTEILNQEITEGLLKGFEVPDAGVAIQLSKRDVVY  1200
1201  PARILIIVLSEMWRFGLTKQSESFLAQVLTTIQKVVTQLKGNDLIPSGVF  1250
1251  WLANVRELYSFVVFALNSILTEETFKNGMTDEEYKEYVSLVTELKDDFEA  1300
1301  LSYNIYNIWLKKLQKQLQKKAINAVVISESLPGFSAGETSGFLNKIFANT  1350
1351  EEYTMDDILTFFNSIYWCMKSFHIENEVFHAVVTTLLNYVDAICFNELIM  1400
1401  KRNFLSWKRGLQLNYNVTRLEEWCKTHGLTDGTECLQHLIQTAKLLQVRK  1450
1451  YTIEDIDILRGICYSLTPAQLQKLISQYQVADYESPIPQEILRYVADIVK  1500
1501  KEAALSSSGNDSKGHEHSSSIFITPETGPFTDPFSLIKTRKFDQVEAYIP  1550
1551  AWLSLPSTKRIVDLVAQQVVQDGH                            1574

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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