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

NucPred

Fetching O70173 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MAYNWQTEPNRAEPQEGGHDHQQCHHADQHLSSRQVRLGFDQLVEELSNK    50
  51  TPLPEDEKEGTCFVPDTPNLDSKWQSIYGPHPRHFNEFTSQSPHFSQLPF   100
 101  GKASAIGFNPAVLPAHQFIHEGASWRNPTRKYHGGEDPRFSALTPSSTGL   150
 151  DKCHQQGQSGTEHCNYYVEPENNVPHHYSPYSMDSIPDSEEKGSGDADLV   200
 201  EPSLVFSKDSFLPRASENMSVESTEPIGCPLEIVEAPQGSNKSLASFCNN   250
 251  VTKIRGLYHASDTNSNSGKIWAITTAYPSRLFADTQFRVKISTDNSAQLL   300
 301  LLKPPANYLVKDLIAEILLLCANEQLSPKEYLLSICGSEEFLQTDHCLGS   350
 351  HKIFQKSKSVIQLHLQRSRDTPGKLSRKRDDDRSRVHLNQLLEFTHIWKI   400
 401  SRQCLSTVMKSYNLHVEHLLKTQEDVEEKPLSSMFSCGRHPPQPHGNDII   450
 451  EDVRNICSVLGCIETKQVSDAVKELTLILQRPSQNFHQNSETSKKGFIEN   500
 501  VTSELSRSLHQLVDVYCSSFCTDFRPARAPGGVSRDHAGLHSHLSFTVCS   550
 551  LHNVPETWAHSYKAFSFSCWLTYAGKKLCQVKSCRSLPVTKSFSFSVNWN   600
 601  EIINFPLEIKSLPRESMLVIKLFGIDSATHSANLLAWTCLPLFPKEKSPL   650
 651  GSRLLSMTLQSEPPIEMMAPGVWDGSQPTPLTLQIDFPAATWEYVKPETE   700
 701  ENRTDHQEPPRECLKHIARLSQKQPPLLLSVEKRRYLWFYRFYCNNENSS   750
 751  LPLVLGSAPGWDEGTVSEMHAVLRRWTFSHPLEALGLLTSRFPDQDIREV   800
 801  AVQQLDNFLTDELLDCLPQLVQAVKFEWSLESPLVELLLHRSLQSIRVAH   850
 851  RLFWLLRDAQGEDYFKSWYQELLAALQFCAGEALIEELSKEQKLVKLLGD   900
 901  IGEKVKSAGDAQRKDVLKKEIGSLEEFFKDIKTCHLPLNPALCVKGIDRD   950
 951  ACSYFTSNALPLKITFINANPMGKNISVIFKAGDDLRQDMLVLQIIQVMD  1000
1001  NVWLQEGLDMQMIIYGCLATGKAQGFIEMVPDAVTLAKIHLHSGLIGPLK  1050
1051  ENTIKKWFSQHNHLKEDYEKALRNFFYSCAGWCVVTFILGVCDRHNDNIM  1100
1101  LTKSGHMFHIDFGKFLGHAQTFGGIKRDRAPFIFTSEMEYFITEGGKNTQ  1150
1151  HFQDFVELCCRAYNIVRKHSQLLLSLLEMMLHAGLPELRGIEDLKYVHDN  1200
1201  LRPQDTDLEATSHFTTKIKQSLECFPVKLNNLIHTLAQMPAFSLARPAPQ  1250
1251  TPPQECCVLNKTRTIQRVTILGFSKTHSNLYLIEVTRSDNRKNLAKKSFE  1300
1301  QFYRLHSQIQKQFPLLTLPEFPHWWHLPFTDSHHERIRDLSHYVEQVLHG  1350
1351  SYEVANSDCVLSFFLSEHIQQTLEDSPFVDPGDHSPDKSPQVQLLMTYED  1400
1401  TKLTILVKHLKNIHLPDGSAPSAHVEIYLLPHPSEVRRKKTKCVPKCTDP  1450
1451  TYNEIVVYDDVSGLQGHVLMLIVKSKTVFVGAVNIQLCSVPLNEEKWYPL  1500
1501  GNSII                                               1505

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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