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

NucPred

Fetching Q8IX12 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MAQFGGQKNPPWATQFTATAVSQPAALGVQQPSLLGASPTIYTQQTALAA    50
51 AGLTTQTPANYQLTQTAALQQQAAAAAAALQQQYSQPQQALYSVQQQLQQ 100
101 PQQTLLTQPAVALPTSLSLSTPQPTAQITVSYPTPRSSQQQTQPQKQRVF 150
151 TGVVTKLHDTFGFVDEDVFFQLSAVKGKTPQVGDRVLVEATYNPNMPFKW 200
201 NAQRIQTLPNQNQSQTQPLLKTPPAVLQPIAPQTTFGVQTQPQPQSLLQA 250
251 QISAASITPLLQTQPQPLLQQPQQKAGLLQPPVRIVSQPQPARRLDPPSR 300
301 FSGRNDRGDQVPNRKDDRSRERERERRRSRERSPQRKRSRERSPRRERER 350
351 SPRRVRRVVPRYTVQFSKFSLDCPSCDMMELRRRYQNLYIPSDFFDAQFT 400
401 WVDAFPLSRPFQLGNYCNFYVMHREVESLEKNMAILDPPDADHLYSAKVM 450
451 LMASPSMEDLYHKSCALAEDPQELRDGFQHPARLVKFLVGMKGKDEAMAI 500
501 GGHWSPSLDGPDPEKDPSVLIKTAIRCCKALTGIDLSVCTQWYRFAEIRY 550
551 HRPEETHKGRTVPAHVETVVLFFPDVWHCLPTRSEWETLSRGYKQQLVEK 600
601 LQGERKEADGEQDEEEKDDGEAKEISTPTHWSKLDPKTMKVNDLRKELES 650
651 RALSSKGLKSQLIARLTKQLKVEEQKEEQKELEKSEKEEDEDDDRKSEDD 700
701 KEEEERKRQEEIERQRRERRYILPDEPAIIVHPNWAAKSGKFDCSIMSLS 750
751 VLLDYRLEDNKEHSFEVSLFAELFNEMLQRDFGVRIYKSLLSLPEKEDKK 800
801 EKDKKSKKDERKDKKEERDDETDEPKPKRRKSGDDKDKKEDRDERKKEDK 850
851 RKDDSKDDDETEEDNNQDEYDPMEAEEAEDEEDDRDEEEMTKRDDKRDIN 900
901 RYCKERPSKDKEKEKTQMITINRDLLMAFVYFDQSHCGYLLEKDLEEILY 950
951 TLGLHLSRAQVKKLLNKVVLRESCFYRKLTDTSKDEENHEESESLQEDML 1000
1001 GNRLLLPTPTVKQESKDVEENVGLIVYNGAMVDVGSLLQKLEKSEKVRAE 1050
1051 VEQKLQLLEEKTDEDEKTILNLENSNKSLSGELREVKKDLSQLQENLKIS 1100
1101 ENMNLQFENQMNKTIRNLSTVMDEIHTVLKKDNVKNEDKDQKSKENGASV 1150

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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