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

NucPred

Fetching O18964 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MAFSKGFRIYHKLDPPPFSLIVETRHKEECLMFESGAVAVLSSAEKEAIK    50
  51  GTYSKVLDAYGLLGVLRLNLGDIMLHYLVLVTGCMSVGKIQESEVFRVTS   100
 101  TEFISLRVDSSDEDRISEVRKVLNSGNFYFAWSASGVSLDLSLNAHRSLQ   150
 151  EHTTDNRFSWNQSLHLHLKHYGVNCADWLLRLMCGGVEIRTIYAAHKQAK   200
 201  ACLISRLSCERAGTRFNVRGTNDDGHVANFVETEQVVYLDDSVSSFIQIR   250
 251  GSVPLFWEQPGLQVGSHRVRMSRGFEANAPAFDRHFRTLKNLYGKQIIVN   300
 301  LLGSKEGEHMLSKAFQSHLKASEHAADIQMVNFDYHQMVKGGKAEKLHSV   350
 351  LKPQVQKFLDYGIFHFDGSEVQRCQSGTVRTNCLDCLDRTNSVQAFLGLE   400
 401  MLTKQLEALGLAEKPQLVTRFQEVFRSMWSVNGDSISKIYAGTGALEGKA   450
 451  KLKDGARSVSRTIQNNFFDSSKQEAIDVLLLGNTLNSDLADKARALLTTG   500
 501  SLRVSEQTLQSASSKVLKSMCENFYKYSKPKKIRVCVGTWNVNGGKQFRS   550
 551  IAFKNQTLTDWLLDAPKLAGIQEFQDKRSKPMDIFPIGFEEMVELNAGNI   600
 601  VNASTTNQKLWAAELQKTISRDNKYVLLASEQLVGVCLFVFIRPQHAPFI   650
 651  RDVAVDTVKTGMGGATGNKGAVAIRMLFHTTSLCFVCSHFAAGQSQVKER   700
 701  NDDFLEIARKLSFPMGRLLFSHDYVFWCGDFNYRIDLPNEEVKELIRQQN   750
 751  WDSLIAGDQLINQKNAGQIFRGFLEGKVTFAPTYKYDLFSDDYDTSEKCR   800
 801  TPAWTDRVLWRRRKWPFDRSAEDLDLLNASFQDESKILYTWTPGTLLHYG   850
 851  RAELKTSDHRPVVALIDIDIFEVEAEERQNIYKEVIAVQGPPDGTVLVSI   900
 901  KSSLPENNFFNDALIDELLQQFTNFGEVILIRFVEDKMWVTFLEGSSALN   950
 951  VLNLNGKELLGRTITITLKSPDWIKTLEEEMSLEKINVPLPSSTSSTLLG  1000
1001  EDAEVTADFDMEGDVDDYSAEVEEILPQHLQPSSSSALARPPVLHPGPVP  1050
1051  ASHLPYRRGPVPSLPVRPSRAPSRTPGPPASQSSPVDTLPATQLQQKDSS  1100
1101  QTLEPKRPPPPRPVAPPARPAPPQRPPPPSGARSPAPARERVWSTRKAQE  1150
1151  RPRRDNLGGSQLPPQGGLPGPGLAGHSAARPIIPPRAGVISAPESHGRVS  1200
1201  AGRLTPESQRKTXEVLKGPALLPEPLKPQAALPVPPSLAPPSQEMQEPLI  1250
1251  AVAAPLAQSALQPSLETPPQPPPRSRSSHSLPSDAPAAAAGATIRVTGEK  1300
1301  QTGVSAVRLDCPLKSDPFEDLSLN                            1324

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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