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

NucPred

Fetching O70167 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MAYSWQTEPNRTEPQEDGSDTQQFHHTNQHLSSRQVRLGFDQLVEEINNK    50
  51  TPLSESEKEEDTYFVPDAPNLGSKWPSIYETHPRYFSEFTSQSPDSSQLR   100
 101  FGKLSAIGFNPAVLPTHQLIHEGASWRNPSGKYHGIEYPRFDALPPSSTG   150
 151  QGECNPQGQSGTKHHNYCGEHEGNLPHHHSSYSIDSIPNREKRRSGDVNL   200
 201  VEPSLEFSKDSFLPRTSENVSVESTEPIGCPIEIVEVPQGSNKNLASFCN   250
 251  KVKKIRESYHASDINSNSGKIWAITTAYPSRLFADTKFRVKISIDNSAQL   300
 301  LLLMPHANYLVKDLIAEILLLCANEPLSPKEYLLSVCGSEEFLQMDHSLG   350
 351  SHKIFQKNKSVIQLHLQKNRDTPGKLSRKSEDDHSPFHLNQLLEFTHIWK   400
 401  ISRQCLSTVMKKYNLHVEHLLKPQKDMEEKHLSSMVSGNQHTSQPHVNNV   450
 451  LEEVKNICSVLGCIETKQVSDAVKELNLILQRPSQNFHQNSETSKKGFIE   500
 501  RVTAELSRSIYQLIDVYCSSFCTDFQPVHTPGGVSHVHAGLQSHLSFTVC   550
 551  SLHNVPETWAHSYKAFSFSCWLTYAGKKLCQVKSCRPLPVTKSFSLLVNW   600
 601  NEIINFPLEIKSLPRESMLVIKLFGIDSATHSTNLLAWTCLPLFPRQESV   650
 651  LGSRLFSVTLQSEPPIEMIAPGVWDGSQPSPLTLQIDFPDAGWEYLKPES   700
 701  EENRTDHEEPPRECLKHIAKLSQKKSPLLLSEEKRRYLWFYRLYCNNENS   750
 751  SLPLVLGSAPGWDEETVSEMHAILRRWTFSHPWEALGLLTSRFPDQDIRE   800
 801  VAVQQLDTLLTDELLDCLPQLVQAVKFEWNLESPLVELLPRRPLQSIRVA   850
 851  HCLYWLLRDAQGEAYFKSWYQELLAALQFCAGEALNEELSKEQKLVKLLG   900
 901  DIGEKVKSASDPQRKDVLKKEIGSLEEFFKDIKTCHLPLNPALCIKGIDR   950
 951  DACSYFTSNASPLKITFINANPMGKNISVIFKAGDDLRQDMLALQIIQVM  1000
1001  DNAWLQEGLDMQMITYGCLSTGRAQGFIEMVPDAVTLAKIHLHSGLIGPL  1050
1051  KENTIKKWFSQHNHLKEDYEKALRNFFYSCAGWCVVTFILGVCDRHNDNI  1100
1101  MLTKSGHMFHIDFGKFLGHAQTFGGIKRDRAPFIFTSEMEYFITEGGKNI  1150
1151  QHFQDFVELCCRAYNIVRKHSQLILSLLEMMLHAGLPELRGIEDLKYVHN  1200
1201  NLRPQDTDLEATSHFTKKIKESLECFPVKLNNLIHTLAQMPALSLAKPAP  1250
1251  QTLLQESCILNKTRTIQRVTILGFSKTHSNLYLMEVTCSDNRRSLTKKSF  1300
1301  EQFYRLHSQMQKQFSSLALPEFPHWWHLPFTDSDHKRIRDLSHYVEQVLR  1350
1351  GSYEVANSDCVLSFFLSEHIQPTLEDSPFVDPGENSLDKSPKVQLLMTYE  1400
1401  DSRLTILVKHLKNIHLPDGSVPSAHVEIYLLPHPSEVRRKKTKCVPKCTD  1450
1451  PTYNEIVVYDEVLGLQGHVLMLIVKSKTVFVGAVNIQLCSVPLNEEKWYP  1500
1501  LGNSII                                              1506

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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