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

NucPred

Fetching Q07890 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MQQAPQPYEFFSEENSPKWRGLLVSALRKVQEQVHPTLSANEESLYYIEE    50
51 LIFQLLNKLCMAQPRTVQDVEERVQKTFPHPIDKWAIADAQSAIEKRKRR 100
101 NPLLLPVDKIHPSLKEVLGYKVDYHVSLYIVAVLEYISADILKLAGNYVF 150
151 NIRHYEISQQDIKVSMCADKVLMDMFDQDDIGLVSLCEDEPSSSGELNYY 200
201 DLVRTEIAEERQYLRELNMIIKVFREAFLSDRKLFKPSDIEKIFSNISDI 250
251 HELTVKLLGLIEDTVEMTDESSPHPLAGSCFEDLAEEQAFDPYETLSQDI 300
301 LSPEFHEHFNKLMARPAVALHFQSIADGFKEAVRYVLPRLMLVPVYHCWH 350
351 YFELLKQLKACSEEQEDRECLNQAITALMNLQGSMDRIYKQYSPRRRPGD 400
401 PVCPFYSHQLRSKHLAIKKMNEIQKNIDGWEGKDIGQCCNEFIMEGPLTR 450
451 IGAKHERHIFLFDGLMISCKPNHGQTRLPGYSSAEYRLKEKFVMRKIQIC 500
501 DKEDTCEHKHAFELVSKDENSIIFAAKSAEEKNNWMAALISLHYRSTLDR 550
551 MLDSVLLKEENEQPLRLPSPEVYRFVVKDSEENIVFEDNLQSRSGIPIIK 600
601 GGTVVKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLLIERFEIPE 650
651 PEPTDADKLAIEKGEQPISADLKRFRKEYVQPVQLRILNVFRHWVEHHFY 700
701 DFERDLELLERLESFISSVRGKAMKKWVESIAKIIRRKKQAQANGVSHNI 750
751 TFESPPPPIEWHISKPGQFETFDLMTLHPIEIARQLTLLESDLYRKVQPS 800
801 ELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVEAENFEERVAVL 850
851 SRIIEILQVFQDLNNFNGVLEIVSAVNSVSVYRLDHTFEALQERKRKILD 900
901 EAVELSQDHFKKYLVKLKSINPPCVPFFGIYLTNILKTEEGNNDFLKKKG 950
951 KDLINFSKRRKVAEITGEIQQYQNQPYCLRIEPDMRRFFENLNPMGSASE 1000
1001 KEFTDYLFNKSLEIEPRNCKQPPRFPRKSTFSLKSPGIRPNTGRHGSTSG 1050
1051 TLRGHPTPLEREPCKISFSRIAETELESTVSAPTSPNTPSTPPVSASSDL 1100
1101 SVFLDVDLNSSCGSNSIFAPVLLPHSKSFFSSCGSLHKLSEEPLIPPPLP 1150
1151 PRKKFDHDASNSKGNMKSDDDPPAIPPRQPPPPKVKPRVPVPTGAFDGPL 1200
1201 HSPPPPPPRDPLPDTPPPVPLRPPEHFINCPFNLQPPPLGHLHRDSDWLR 1250
1251 DISTCPNSPSTPPSTPSPRVPRRCYVLSSSQNNLAHPPAPPVPPRQNSSP 1300
1301 HLPKLPPKTYKRELSHPPLYRLPLLENAETPQ 1332

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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