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

NucPred

Fetching Q9Y6R4 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MREAAAALVPPPAFAVTPAAAMEEPPPPPPPPPPPPEPETESEPECCLAA    50
  51  RQEGTLGDSACKSPESDLEDFSDETNTENLYGTSPPSTPRQMKRMSTKHQ   100
 101  RNNVGRPASRSNLKEKMNAPNQPPHKDTGKTVENVEEYSYKQEKKIRAAL   150
 151  RTTERDRKKNVQCSFMLDSVGGSLPKKSIPDVDLNKPYLSLGCSNAKLPV   200
 201  SVPMPIARPARQTSRTDCPADRLKFFETLRLLLKLTSVSKKKDREQRGQE   250
 251  NTSGFWLNRSNELIWLELQAWHAGRTINDQDFFLYTARQAIPDIINEILT   300
 301  FKVDYGSFAFVRDRAGFNGTSVEGQCKATPGTKIVGYSTHHEHLQRQRVS   350
 351  FEQVKRIMELLEYIEALYPSLQALQKDYEKYAAKDFQDRVQALCLWLNIT   400
 401  KDLNQKLRIMGTVLGIKNLSDIGWPVFEIPSPRPSKGNEPEYEGDDTEGE   450
 451  LKELESSTDESEEEQISDPRVPEIRQPIDNSFDIQSRDCISKKLERLESE   500
 501  DDSLGWGAPDWSTEAGFSRHCLTSIYRPFVDKALKQMGLRKLILRLHKLM   550
 551  DGSLQRARIALVKNDRPVEFSEFPDPMWGSDYVQLSRTPPSSEEKCSAVS   600
 601  WEELKAMDLPSFEPAFLVLCRVLLNVIHECLKLRLEQRPAGEPSLLSIKQ   650
 651  LVRECKEVLKGGLLMKQYYQFMLQEVLEDLEKPDCNIDAFEEDLHKMLMV   700
 701  YFDYMRSWIQMLQQLPQASHSLKNLLEEEWNFTKEITHYIRGGEAQAGKL   750
 751  FCDIAGMLLKSTGSFLEFGLQESCAEFWTSADDSSASDEIRRSVIEISRA   800
 801  LKELFHEARERASKALGFAKMLRKDLEIAAEFRLSAPVRDLLDVLKSKQY   850
 851  VKVQIPGLENLQMFVPDTLAEEKSIILQLLNAAAGKDCSKDSDDVLIDAY   900
 901  LLLTKHGDRARDSEDSWGTWEAQPVKVVPQVETVDTLRSMQVDNLLLVVM   950
 951  QSAHLTIQRKAFQQSIEGLMTLCQEQTSSQPVIAKALQQLKNDALELCNR  1000
1001  ISNAIDRVDHMFTSEFDAEVDESESVTLQQYYREAMIQGYNFGFEYHKEV  1050
1051  VRLMSGEFRQKIGDKYISFARKWMNYVLTKCESGRGTRPRWATQGFDFLQ  1100
1101  AIEPAFISALPEDDFLSLQALMNECIGHVIGKPHSPVTGLYLAIHRNSPR  1150
1151  PMKVPRCHSDPPNPHLIIPTPEGFSTRSMPSDARSHGSPAAAAAAAAAAV  1200
1201  AASRPSPSGGDSVLPKSISSAHDTRGSSVPENDRLASIAAELQFRSLSRH  1250
1251  SSPTEERDEPAYPRGDSSGSTRRSWELRTLISQSKDTASKLGPIEAIQKS  1300
1301  VRLFEEKRYREMRRKNIIGQVCDTPKSYDNVMHVGLRKVTFKWQRGNKIG  1350
1351  EGQYGKVYTCISVDTGELMAMKEIRFQPNDHKTIKETADELKIFEGIKHP  1400
1401  NLVRYFGVELHREEMYIFMEYCDEGTLEEVSRLGLQEHVIRLYSKQITIA  1450
1451  INVLHEHGIVHRDIKGANIFLTSSGLIKLGDFGCSVKLKNNAQTMPGEVN  1500
1501  STLGTAAYMAPEVITRAKGEGHGRAADIWSLGCVVIEMVTGKRPWHEYEH  1550
1551  NFQIMYKVGMGHKPPIPERLSPEGKDFLSHCLESDPKMRWTASQLLDHSF  1600
1601  VKVCTDEE                                            1608

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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