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

NucPred

Fetching Q8MT36 from www.uniprot.org...

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

   1  MKLSTDAHSEIEGDAAHGNVLCNSASDSLTATDEVAAGNDESVATEGDDV    50
  51  EIPRDTNNSTPVRLLDKPGQNPVQNGAQPAAEESELESQRQTPVQKQQQQ   100
 101  RVSMVNRKRDLINLQSALSPKYIGYANANSPTPLSDSDDTIRTTRRRVNQ   150
 151  AAALNNSSAGETLAHDNASPRTPGGGGGGGGDDSANQLLSKTYMSPIEKL   200
 201  LIKNGASSPNSTGFEAGSEDLGIRPIVRKHVKRKMKRVPKAKVTLELDEK   250
 251  NQQEVDEKSVKTEPIDEEVDRTDEAPTQEAQTTAISIKSETEAEHKAAVD   300
 301  VHIKQEDTIRLDIVNNPVESTSIVITEEPKDLEKSTEELAFALPLASSTE   350
 351  VDLKSPPDLSSTALATSIKSPSSVSIDSAKGLSIVTDPGWPTYQVGDLFW   400
 401  GKVFSYCFWPCMVCPDPLGQIVGNMPSHPQRSSLDNANVPIQVHVRFFAD   450
 451  NGRRNWIKPENLLTFAGLKAFDDMREELRIKHGPKSAKYRQMVPKRTKVV   500
 501  IWRQAIEEAQAMTQIPYSDRLEKFYQTYENVVTLNRQKRKRTKYMMQDTS   550
 551  DVGSSLYDSTDNLHNKQGTQLLAVKRERSESPFSPAFSPVKSKNEKRAKR   600
 601  RKLSNGTEADTGSNSMAVTPSQTETTVDSSAYENPEFRQLLSAVMEYVMM   650
 651  NRSDEKVEKVLLSVVSNIWSLKQIQLRELERDLASGEIEEPLGSSVVGRG   700
 701  SGVGTIKRLSNRLMTMMVRRSMTPVVTPSTTPAPSEPDRRLSEPPKTKKP   750
 751  VNRPIEEVIEDILQLDSKYLFRGLSREPICKYCYQAGSDLVRCSRTCSSW   800
 801  LHADCLERKVTGAPMPKIGSRKALVIPPTSKSPSPDEDHVTADAKEVVAV   850
 851  GTSLVCHECNVGEPEGCVICHQVESPAVPSTPRKEDSSSHTPIEDKLLTC   900
 901  SQPMCGKRFHTSCCKYWPQASSSKHSARCPRHVCHTCVSDDPSGKFQQLG   950
 951  SSKLAKCVRCPATYHQLSKCIPAGTQMLNTTNIICPRHNIAKADAHVNVL  1000
1001  WCYICVKGGELVCCETCPIAVHAHCRNIPIKTNESYICEECESGRLPLYG  1050
1051  EIVWAKFNNFRWWPAIILPPTEVPSNILKKAHGENDFVVRFFGTHDHGWI  1100
1101  SRRRVYLYIEGDTGDGHKTKSQLFRNYTTGVEEASRFLPIIKARRQEQDM  1150
1151  ERQSGNKLHPPPYVKIKTNKAVPPLRFSQNLEDLSTCNCLPVDEHPCGPE  1200
1201  AGCLNRMLFNECNPEYCKAGSLCENRMFEQRKSPRLEVVYMNERGFGLVN  1250
1251  REPIAVGDFVIEYVGEVINHAEFQRRMEQKQRDRDENYYFLGVEKDFIID  1300
1301  AGPKGNLARFMNHSCEPNCETQKWTVNCIHRVGIFAIKDIPVNSELTFNY  1350
1351  LWDDLMNNSKKACFCGAKRCSGEIGGKLKDDAVKAHAKLKQMRRAKASAV  1400
1401  RIHVKPKKTPKVKHISADDEPMDAKDE                         1427

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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