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

NucPred

Fetching Q9LK62 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MKQSYAMDNPIVFFLLESNYFPMFSIFFNLLLLLVMFGSCVYKKRLGWEN    50
  51  SDAFTNERFKDMSLTYNKLVVICCETLSALNSVLLLLSCFNLHKNGWDRS   100
 101  ELMILLDLLFTALSWGAISFYIRSQFTYSHDQKFPILLRVWWVLYFMFSC   150
 151  YRLLVDIALYKKQELVSVHLLLSDVLAVSVGLFLCYSCLQKQGQGERINL   200
 201  LLEEPLLNGAESSAATSVQLDKAEDDEVVTPFSNAGFLSHVSFSWMSPLI   250
 251  VLGNEKIIDSEDVPQVDNSDRAEKLFWIFRSKLEWDDGERRITTYKLIKA   300
 301  LFFSVWRDILLSTLFAFVYTVSCYVAPYLMDTFVQYLNGQRQYSNQGVVL   350
 351  VTTFFVAKLVECQARRNWYFRLQKAGIGMRSVLVSMIYEKGLTLPCYSKQ   400
 401  GHTSGEIINLMTVDAERISAFSWYMHDPWILVLQISLALLILYRSLGLGS   450
 451  IAAFAATFLVMLGNIPLAKLEEKFQGNLMESKDNRMKKTSEALLNMRILK   500
 501  LQGWEMKFLHKILDLRGIEAGWLKKFVYNSAAISSVLWAAPSFVSATAFG   550
 551  ACMLLKIPLESGKIIAALATFRILQTPIYKLPDTISMIVQTKVSLDRIAT   600
 601  FLCLDDLQQDGMERLPSGSSKMDVEVSNGAFSWDDSSPIPTLKDIRFKIP   650
 651  HGMNIAICGTVGSGKSSLLSSILGEVPKISGNLKVCGRKAYIAQSPWIQS   700
 701  GKVEENILFGKPMQREWYQRVLEACSLNKDLEVFPFRDQTVIGERGINLS   750
 751  GGQKQRIQIARALYQDADIYLFDDPFSAVDAHTGSHLFKEVLLGLLRNKT   800
 801  VIYVTHQLEFLPEADLILVMKDGRITQAGKYNEILESGTDFMELVGAHTD   850
 851  ALAAVDSYEKGSASAQSTTSKESKVSNDEEKQEEDLPSPKGQLVQEEERE   900
 901  KGKVGFTVYQKYMKLAYGGALVPIILVVQILFQVLNIGSNYWMAWVTPVS   950
 951  KDVKPLVSGSTLILVYVFLATASSFCILVRAMLSAMTGFKIATELFNQMH  1000
1001  FRIFRASMSFFDATPIGRILNRASTDQSAVDLRLPSQFSNLAIAAVNILG  1050
1051  IIGVMGQVAWQVLIVFIPVIAACTWYRQYYISAARELARLSGISRSPLVQ  1100
1101  HFSETLSGITTIRSFDQEPRFRTDIMRLNDCYSRLRFHAISAMEWLCFRL  1150
1151  DLLSTVAFALSLVILVSVPEGVINPSFAGLAVTYALNLNSLQATLIWTLC  1200
1201  DLENKMISVERMLQYIDIPSEPSLVIESTRPEKSWPCRGEITICNLQVRY  1250
1251  GPHLPMVLRGLTCTFRGGLKTGIVGRTGCGKSTLIQTLFRIVEPAAGEIR  1300
1301  IDGINILTIGLHDLRSRLSIIPQEPTMFEGTVRSNLDPLEEYADDQIWEA  1350
1351  LDKCQLGDEIRKKELKLDSPVSENGQNWSVGQRQLVCLGRVLLKRSKVLI  1400
1401  LDEATASVDTATDTLIQETLRQHFSGCTVITIAHRISSVIDSDMVLLLDQ  1450
1451  GLIEEHDSPARLLEDKSSSFSKLVAEYTASSDSRFKRSSMKTN         1493

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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