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

NucPred

Fetching Q8BXA7 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MKHNGSRTCLNRRSRFGSRERDWLREDVKRGCVYLYGADTTTATTTTSSS    50
  51  SSSSSSSDLHLVLCTVETPASEICAGEGRESLYLQLHGDLVRRLEPSERP   100
 101  LQIVYDYLSRLGFEDPVRIQEEATNPDLSCMIRFYGEKPCQMDHLDRILL   150
 151  SGIYNVRKGKTQLHKWAERLVVLCGTCLIVSSVKDCQTGKMHILPLVGGK   200
 201  IEEVKRRQHSLAFSSAGAQAQTYHVSFETLAEYQRWQRQASKVVSQRMST   250
 251  VDLSCYSLEEVPEHLFYSQDITYLNLRHNFMQLERPGGLDTLHKFSQLKG   300
 301  LNLSHNKLGLFPVLLCEISTLTELSLSCNGFHDLPSQIGKLLNLQTLSLD   350
 351  GNGLTALPDELGNLRQLTSLGISFNDFRHIPEVLEKLTMLDKVAMAGNRL   400
 401  EVLNLGALTRMSQVKHVDLRMNHLKTVITENMEGNKHITHMDLRDNQLTD   450
 451  LDLSSLCSLEQLHCERNQLRELTLSGFSLRTLYASWNRLTAVNVYPVPSL   500
 501  LTSLELSQNLLECVPDWACEAKKLEILDISHNLLTEVPMRILSSLSLRKL   550
 551  MVGHNHIHVLPALVEHIPLEVLDIQHNTLSRLPDTLFSKALNLRYLNASA   600
 601  NSLESLPSACAGEESLSVLQLLYLTSNLLTDQCIPVLVGHPHLRVLHLAN   650
 651  NQLQTFPASKLNKLEQLEELNLSGNKLTAIPTTIANCKRLHTLVAHANNI   700
 701  SIFPEILQLPQIQFVDLSCNDLTEILIPEALPATLQDLDLTGNTNLVLEH   750
 751  KTLDMFSHITALKIDQKPLPATDSAVTSTFWSHGLAEMAGQRNKLCVSAL   800
 801  AMDNFAEGVGAVYGMFDGDRNEELPRLLQCTMADVLLEEVQHSTNDTVFM   850
 851  TNTFLVSHRKLGMAGQKLGSSALLCYIRPDTADPTSSFSLTVANVGMCQA   900
 901  VLCRGGKPVPLSKVFSLEHDPEEAQRVKDQKAIITEDNKVNGVTCCTRLL   950
 951  GCTYLYPWILPKPHIASTPLTIQDELLILGNKALWEHLSYLEAVNAVRHV  1000
1001  QDPLAAAKKLCTLAQSYGCQDNVGAMVVYLNIGEEGCTCEMNGLTLPGPV  1050
1051  GFASTAALKDTPKPTTPSSSSGIASEFSSEMSTSEVSSEVGSTASDEHNT  1100
1101  VGLEASLLPRPERRCSLHPASSAGVFQRQPSCATFSSNQSDNGLDSDDDQ  1150
1151  PVEGVITNGSRVEVEVDIHCCRGREPESSPPLPKNSSNACSEERARGAGF  1200
1201  GIRRQNSVNSGILLPANRDKMELQKSPSTSCLYGKKLSNGSIVPLEDSLN  1250
1251  LIEVATEAPKRKTGYFAAPTQLEPEDQFVVPRDLEEEVKEQMKQHQEGRP  1300
1301  EPEPRGEERTEPLEEFDTAL                                1320

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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