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

NucPred

Fetching Q95YM8 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MADCPYARCIQERRHIRRELLRWTKNMVFVVGLERVAEELMGRRRWKQYQ    50
  51  DTLYSGTRSSESLTAQAHHRLYPAFSSSCDPVPGNLEQIGSRPLHPPASS   100
 101  TSLPATITTTTTTTTTTTATAAATATTTATGLIKQETLQRHHHLQNHHHH   150
 151  LQSTAVQDHHRPYQQQQQQQQRQQQRQEERRLRPDEIKVEVGEDEFANGG   200
 201  AARDESKAGSTDASTPATVTTTGATTTLPAASATGTGPATPSAVVATSNA   250
 251  TAAMTTGTTTIPTRRLRKRRQNDGEGADDRDDDEENEEEEDGRGQSEAEK   300
 301  RLKLDEDADGAVSPLRREKDRGSREYPTSNATDTDGTKERTEEVALDRTP   350
 351  VTQGLLRVKKEEELQEAPSCGGGPTILTTPGLDSDGIRLPCREVEAAATA   400
 401  RNVVAPFLIGSRRTSPPPEDWKPLDKCYFCLDGKLPHDDQPPLSPQSDSS   450
 451  SSSRSAESPMSVQVDPMAASVVAAALTGTYPTLLPQWCLPPREAPLVGVQ   500
 501  PHQDSATPADQPLDLSAKPKNSQDNNISLLEQQKIPLRMTAGIDPKSIFN   550
 551  SGYRPKPRMSGPVAAVAAAAVAAAGVGGVPVVGAGGGRRAYTEEELQAAL   600
 601  RDIQSGKLGTRRAAVIYGIPRSTLRNKVYKLAMERERDASLSSTHSHPHE   650
 651  PGAPATTITTITTTTTTTTTTTTTTTTPNTTQNASATTPPPQVDEVDDKE   700
 701  LSGAEEEKEVEKALLKPLLSLEDLVRFSTLEGSGGDSLRTLLQRGQETGA   750
 751  EWPGLEHANIGPYIQKMIAAAAPFKGMETQDYRIPEVMRRLMSEDKRLSK   800
 801  SVNGDQSQPPHQQLHHHQSTHPQAQAQAQPQQQQQQQQQQPQQQQQQQQQ   850
 851  QQQQQRGPMTNDDFNPNIEEEASDSAQGRAILKIPSYKPASTPGCSSKNG   900
 901  EPTSAAFAQGFATAASSPGLLERASPAFSGTSSPTNSLVGKTVAVNFRDV   950
 951  IAKSISVKFQEGQTVSGGGMGGCQPGGVVQSQQPIMTDPSPFKRGRYTPP  1000
1001  QPANAQQGQAQAQAKPQSQEANKPKPATGGKGTRPKRGKYRNYDRDSLVE  1050
1051  AVRAVQRGEMSVHRAGSYYGVPHSTLEYKVKERHLMRPRKRDQKQSDDKT  1100
1101  KETSTVTAAAAATNIRPGTADNKPQLKPQKPFTSPGGIPGPNGIKMPSFM  1150
1151  EGMPHLPFTPFNFWNPPPFMPSPFMAGAPNVPTILPEQYFATSRIRGLQE  1200
1201  QQRNAAMVQQQQQQQQQQQQQQQQQQQQQQQQQHQAREREGVGAGIAETS  1250
1251  AGTSNSRGAAQMSKVPRDVSEGIYDGSGANGSFLDNLIRSSLETGIPRDQ  1300
1301  RAMTEARNQQQQASSQQQIPESMRSKALIDQLCRNSRRTPVPRLAQDSSE  1350
1351  DESYRGPSASGGRPVPERPERVPTVDLSPSPSDRGRNDDGSDRLTSPPTP  1400
1401  LSISRAGSRDEDSTRDSTKLDRSSREREVHNGGQQEDRDRKTLTSAPQQP  1450
1451  QQQQQQQQQQQQQQQQLNHYPDLHNLYAVPTDKKSACDSKLIVDHSSQKT  1500
1501  QQQQPQQQQQQQQQQQPQQQSQQPQQQQPQPQQQQQQQQQQQPQQQQKEY  1550
1551  GAVSGLVVQLQRGYNSGNNRSGEQANSQQQQQQQSGEPVIGMEDSVEQ    1598

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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