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

NucPred

Fetching Q9URX8 from www.uniprot.org...

The NucPred score for your sequence is 0.62 (see score help below)

   1  MDINDPSFSSTENGIYELLSRGYAAIEAATERDLKLPELGDIIGQVHAPE    50
  51  YISQVLSGWKPFYLRSVVNIPDRIFEQYNRTECFTQMGLFAEIQRAWITV   100
 101  DNRLFLWDYLSGQNFQAYEDLSHTIVNVKLVRPKANVFVSEIQHLLVIAT   150
 151  SQEMLLLGVTIDEKTGELSFFSTGIQISVQGINVNCIVSSEDGRIFFSGN   200
 201  KDPNLYEFSYQLEEGWFSRRCSKINITGSVFDNFIPSFFSFGTHGDGIKQ   250
 251  IAVDDSRSLLYVLRETSSVSCYELTKNGVNRCVFYSFSSMISQAQMLNAT   300
 301  SPLLDPRTTQIVSIVPIPAYESQQIYCVAITSTGCRFYMRGGRGPISHYA   350
 351  PSNSTLSSTPPSTLQLTFVRFPPPMQVENYASSRNYPANPFFLQNQSTSQ   400
 401  QQPERSSAVKTTPMKCSSLSNIYTSDLFFAISSSNTNEGDVVCCTAPEVG   450
 451  RIANAWQSGTQPSLIESSMYVPIKGFVQDIKCIQNSRERNELVSQFNTPP   500
 501  PTFAILTNTGVYVVVHRRPIDVLASAIRMGPSLSSGIDGQVQLFFESVGR   550
 551  AEGCATCLGIVSGCLDQGDFSHAAANFSGSTTKLAQADLLDIVKKYYIEF   600
 601  GGKAFIDQSRYNNQYDSSSLEFVRLSGCHDGLASSISRIIRNVWKNHVII   650
 651  AKKMQNKRIHYAPAFNATEILKIQSGLLYLSTFLENNKSFIEGLNSPNTL   700
 701  IGSSNVADEIAVQAEHRALSALLLVLQQIVEGISFLLFLNDTGVSDFHEI   750
 751  VSSTSIDIQKSCSNMTFGEFFTSKRGREVTKELVNSLVNRHLQSGGNIDM   800
 801  VSQLLRKKCGSFCSADDVLIFKAVESLKKAKDTVDIEERQSLIELSYTLF   850
 851  KKAAHVFTPEDLRLAVEEYKSLNAYTTAVNLALHVASARDDRNQALSYLV   900
 901  DGMPENDPRREPFESRTKCYSYIFEILDSLESQMSNDSSAIKVDVYDTIQ   950
 951  RSKDELFHYCFYDWYSFKGLTDRLIEIDSPYIQSYLERNSTKDMKIADLL  1000
1001  WQYYAKREQYYQASIVLYDLATTHLAFSLEQRIEYLTRAKGFGSCHVPNS  1050
1051  LRHKMNKVMLSVLEQLDVASIQDDVLIAIRGDMRIPTSKREELSKQLDGE  1100
1101  IIPLSDLFNNYADPLGYGEICLSIFQCADYRGINEILNCWESIIKTTHEN  1150
1151  AIISPVGSSPVEAVSSTLKNLTLRFSQSENVFPIEQIIDITERYAFDQQG  1200
1201  EAVATGWVIDTFLGAGVSHELIFIVLNQLYDRREKPWQGKDRLFFLIKEV  1250
1251  THLLKLWHEVSVRAGVAQTSKPSFDAPLVLEAIEKYKNALGAPDTATKSC  1300
1301  KENLISLDSEIRQTY                                     1315

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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