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

NucPred

Fetching P54816 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MPRSDGFSPRKNLRRSARDHSRSYAGQCNEDFDDMYAPSSRRRSSGGVDG    50
  51  NGYTRSGRKINHNRYYEEEYHEAISSEEDERRYRTRRSSNSMTYRQQVMQ   100
 101  AIDESKRNQKVPPAKRKRIYLSDEEEEDFAEAAHVENTVPERATRRSTRR   150
 151  RSSMHEELGVSEQEESPVRRTRKAAKRLGSEQPEENLAADDPLPMEGGGE   200
 201  IVLPIAEIDGMAEQENEDLIEKIGREEEEEGAEEDEQSGEKDPEEEEDDS   250
 251  SNAESSEESTAPRQYSLRRRQPVVQFNASEARENRRARLEHHRVANQNRH   300
 301  HRNRNGSRRRRSDSDSDSDDMVLPRPDKRQSRPHMHNRGERERGRFMPIN   350
 351  MTEKELQSAQHILMDRMRKTDAGQGASDIDPMSVDSSVGFDQVGGLGHHI   400
 401  QSLKEVVLFPMLYPEVFEKFRINPPKGVVFYGPPGTGKTLVARALANECR   450
 451  RGANKVAFFMRKGADCLSKWVGESERQLRLLFDQAYAMRPSIIFFDEIDG   500
 501  LAPVRSSKQDQIHASIVSTLLALMDGLDGRGEVVVIGATNRLDTLDPALR   550
 551  RPGRFDRELRFSLPDLNARRQILDIHTSKWEENKPIPETLDAIAERTSGY   600
 601  CGADLKFLCTEAVLIGLRSRYPHIYMCSERLKLDVATIKITSEHFGHAMR   650
 651  RITPASRRDLTIPSRPLDERTSILLGDTVSNLISLRIPQGYRCVENAMAT   700
 701  ASSELEQVVRALEPNPTVPAIRLLLCGSEQLADGGQTSYVLPAILAKLDH   750
 751  LPVFSLSVSSLLTDGRPEEAFSNAIQSAMRASATGPCIMLLPSIDEWIKV   800
 801  IPVSVQHMLITCLESMTGFTPILFLSTLDTSFEDAPEYVTEIFRHANCIT   850
 851  LNPSRRTIRQKYFEHVIEKINTPPKVFDPTVYEMPLPDDDSPDSKPSRKL   900
 901  NDDETRELLKMYTALQRQMRLFFKERLTRLMRDRRFVEFVEPVDPDEAED   950
 951  YYEIIETPICMQDIMEKLNNCEYNHADKFVADLILIQTNALEYNPSTTKD  1000
1001  GKLIRQMANTLRDAIDDLIECELDESFVERIETVSRMLQDAGVTPTSDKL  1050
1051  LTEIPKGFARKKAWSMTNSLAKEIEQWTSEREAENQKMLSKLGVAAPTLE  1100
1101  LVVVPVEDMKSEEGTSTSTDGVPASAGNKKKLLKKKKGQKKSKTGESEEH  1150
1151  DEDSTVEDAGEDTIVENLEIKKNQETPNSEHDIEMKDASKDSTPSVQISI  1200
1201  AEKELIVSKPATCELIQCCVEKSEGWSVSELERLSSVLSHTIERFRDEWN  1250
1251  RENLPAQLTQIVREWQTADDSNNTIVNGTLNKSNGNLANGH           1291

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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