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

NucPred

Fetching Q9U2G0 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MADELARIQQYEYRQNSNLVLSVDYNLTDRRGREEPTGEVLPITDKEMRK    50
  51  MKMGDRAIKGKAPVQDQKKKRKKKDDEKAQQFGRNVLVDNNELMGAYKPR   100
 101  TQETKQTYEVILSFILDALGDVPREVLCGAADEVLLTLKNDKFRDKEKKK   150
 151  EVEALLGPLTDDRIAVLINLSKKISDFSIEEENKPEGDGDIYENEGVNVQ   200
 201  FDSDEEEDDGGMVNEIKGDSEEESEEEEGVDTDYTATLKGDGHLTEDEQK   250
 251  ARGILHPRDIDAHWIQRSLAKYFKDPLIAQQKQTEVIGILKNAADDRDAE   300
 301  NQLVLLLGFDQFEFIKCLRQNRLMILYCTLLRQANEKERLQIEDDMRSRP   350
 351  ELHPILALLQETDEGSVVQVEKSKRDAEKSKKAATAANEAISAGQWQAGR   400
 401  KMLDLNDLTFSQGSHLMSNKRCELPDGSYRRQKKSYEEIHVPALKPRPFA   450
 451  EGEKLVSVSELPKWAQPAFDGYKSLNRIQSRLCDSALRSKEHLLLCAPTG   500
 501  AGKTNVALLTMLQEIGNHLAEDGSVKLDEFKIVYIAPMKSLVQEMVGSFS   550
 551  KRLAPFGITVGEMTGDAQMSKEQFMATQVIVCTPEKYDVVTRKGGERAYN   600
 601  QMVRLLIIDEIHLLHDDRGPVLESIVVRTIRQMEQNHDECRLVGLSATLP   650
 651  NYQDVATFLRVKPEHLHFFDNSYRPVPLEQQYIGVTEKKALKRFQAMNEV   700
 701  VYDKIMEHAGKSQVLVFVHSRKETAKTAKAIRDACLEKDTLSAFMREGSA   750
 751  STEILRTEAEQAKNLDLKDLLPYGFAIHHAGMNRVDRTLVEDLFADRHIQ   800
 801  VLFSTATLAWGVNLPAHTVIIKGTQIYNPEKGRWTELGALDIMQMLGRAG   850
 851  RPQYDDRGEGILITNHSELQYYLSLMNQQLPVESQMVSRLTDMLNAEVVL   900
 901  GTVSSVSEATNWLGYTFLFVRMLKNPTLYGITHEQARADPLLEQRRADLI   950
 951  HTACVLLDKAGLIKYDKRSGIIQATELGRIASHFYCTYESMQTYNKLLVE  1000
1001  TCSDIDLFRIFSMSSEFKLLSVRDEEKLELQKMAEHAPIPIKENLDEASA  1050
1051  KTNVLLQAYISQLKLEGFALQADMVFVAQSAGRLFRALFEIVLWRGWAGL  1100
1101  AQKVLTLCKMVTQRQWGSLNPLHQFKKIPSEVVRSIDKKNYSFDRLYDLD  1150
1151  QHQLGDLIKMPKMGKPLFKFIRQFPKLEMTTLIQPITRTTMRIELTITPD  1200
1201  FKWDEKVHGSAEGFWIFIEDTDGEKILHHEFFLLKQKFCSDEHVVKMIVP  1250
1251  MFDPMPPLYYVRIVSDRWIGAETVLPISFRHLILPEKYPPPTELLDLQPL  1300
1301  PISAVTNKEFQTVFAESGFKVFNPIQTQVFRTVFESNENVIVCAPNGSGK  1350
1351  TAIAELAVLRHFENTPEAKAVYITPMEDMATKVYADWKRRLEPAIGHTIV  1400
1401  LLTGEQTMDLKLAQRGQLIISTPERWDNISRRWKQRKSVQNVKLFIADDL  1450
1451  HMIGASNGAVFEVVCSRTRYISSQLESAVRVVALSSSLTNARDLGMWLGC  1500
1501  SASATFNFMPSTRPVPLDLEIKSFNLSHNASRFAAMERPVYQAICRHAGK  1550
1551  LEPKPALVFVPVRRQTRPVAVALLTMALADGAPKRFLRLAEHDDTFQALL  1600
1601  ADIEDESLRESVSCGVGFLHEGTAPKDVHIVQQLFESNAIQVCVVPRGMC  1650
1651  YQIEMSAYLVVVMDTQFYNGKYHVYEDYPIADMLHMVGLANRPILDSDAK  1700
1701  CVVMCQTSKRAYYKKFLCDPLPVESHLDHCLHDHFNAEIVTKTIENKQDA  1750
1751  IDYLTWTLLYRRMTQNPNYYNLQGTTHRHLSDALSELVELTLKDLENSKC  1800
1801  IAVKDEMDTVSLNLGMIASYYYISYQTIELFSMSLKEKTKTRALIEIISA  1850
1851  SSEFGNVPMRHKEDVILRQLAERLPGQLKNQKFTDPHVKVNLLIHAHLSR  1900
1901  VKLTAELNKDTELIVLRACRLVQACVDVLSSNGWLSPAIHAMELSQMLTQ  1950
1951  AMYSNEPYLKQLPHCSAALLERAKAKEVTSVFELLELENDDRSDILQMEG  2000
2001  AELADVARFCNHYPSIEVATELENDVVTSNDNLMLAVSLERDNDIDGLAP  2050
2051  PVVAPLFPQKRKEEGWWLVIGDSESNALLTIKRLVINEKSSVQLDFAAPR  2100
2101  PGHHKFKLFFISDSYLGADQEFDVAFKVEEPGRSNRKRKHEKEED       2145

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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