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

NucPred

Fetching P50996 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MGKAENYEMYSVELGPGPGGDMAAKMSKKKAGKGGGKKKEKLENMKKEME    50
  51  INDHQLSVAELEQKYQTSATKGLSASLAADLLLRDGPNALRPPRGTPEYV   100
 101  KFARQLAGGLQCLMWVAAAICLIAFAIQASEGDLTTDDNLYLALALIAVV   150
 151  VVTGCFGYYQEFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDL   200
 201  VEMKGGDRVPADIRILQAQGCKVDNSSLTGESEPQTRSPECTHESPLETR   250
 251  NIALFSTMCLEGTAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEH   300
 301  FVDIIAGLAILFGATFFVVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATV   350
 351  TVCLSLTAKRLASKNCVVKNLEAVETLGSKSVICSDKTGTLTQNSMTVSN   400
 401  LWFDNHIHTADTTEDQSGQKFDQSSETWRALCRVLTLCNRAAFKSGQDAV   450
 451  PVPKRIVIGDASETALLKFSELTLGNAMGYRERFPKVCEIPFNSTNKFQL   500
 501  SIHTLEDPRDPRHVLVMKGAPERVLERCSSILIKGQELPLDEQWREAFQT   550
 551  AYLSLGGLGERVLGFCQLYLSEKDYPPGYAFDVEAMNFPTSGLCFAGLVS   600
 601  MIDPPRATVPDAVLKCRTAGIRVIMVTGDHPITAKAIAASVGIISEGSET   650
 651  VEDIAARLRVPVDQVNRKDARACVINGMQLKDMDPSELVEALRTHPEMVF   700
 701  ARTSPQQKLVIVESCQRLGAIVAVTGDGVNDSPALKKADIGVAMGIAGSD   750
 751  AAKNAADMILLDDNFASIVTGVEQGRLIFDNLKKSIAYTLTKNIPELTPY   800
 801  LIYITVSVPLPLGCITILFIELCTDIFPSVSLAYEKAESDIMHLRPRNPK   850
 851  RDRLVNEPLAAYSYFQIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPYW   900
 901  ENHHLQDLQDSYGQEWTFGQRLYQQYTCYTVFFISIEMCQIADVLIRKTR   950
 951  RLSAFQQGFFRNRILVIAIVFQVCIGCFLCYCPGMPNIFNFMPIRYQWWL  1000
1001  VPMPFGLLIFVYDEIRKLGVRCCPGSWWDQELYY                  1034

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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