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

NucPred

Fetching Q9Z1A9 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MWLKPEEVLLKNALKLWVTQKSSCYFVLQRRRGHGEGGGRLTGRLVGALD    50
  51  AVLDSSARVAPFRILLQVPGSQVYSPIACGATLEEINRHWDWLEQNLLHT   100
 101  LSVFDNKDDIASFVKGKVKALIAEETSSRLAEQEEEPEKFREALVKFEAR   150
 151  FNFPEAEKLVTYYSCCCWKGRVPRQGWLYLSINHLCFYSFFLGKELKLVI   200
 201  PWVDIQKLERTSNVFLTDTIRITTQNKERDFSTFLNLDEVFKIMEQLADV   250
 251  TLRRLLDNEVFDLDPDLQEPSQITKRDLEARAQNEFFRAFFRLPREEKLH   300
 301  AVADCSLWTPFSRCHTAGRIFSSDSYICFASREDGCCNVVLPLREVVSIE   350
 351  KMEDTSLLPNPIIVSIRSKMAFQFIELKDRENLVEGLLLRLKQVHANHPV   400
 401  HYETSPSDDDMASPVFYSASICTDKFGDLEMVASQSSEEREEKRPLPHPE   450
 451  PLTAVFQQSGSQSPDSRLSREQIKISLWNDHFVEYGRTVCMFRTEKIRKL   500
 501  VAMGIPESLRGRLWLLFSDAVTDLASHPGYYGNLVEQSLGRCCLVTEEIE   550
 551  RDLHRSLPEHPAFQNETGIAALRRVLTAYAHRNPKIGYCQSMNILTSVLL   600
 601  LYAKEEEAFWLLVAVCERMLPDYFNHRVIGAQVDQSVFEELIKEQLPELA   650
 651  EHMSDLSALASISLSWFLTLFLSIMPLESAVHVVDCFFYDGIKAIFQLGL   700
 701  AVLEANAEELCSSKDDGQALMVLSRFLDHIKNEDSPGPPIGSHHAFFSDD   750
 751  QEPYPVTDIADLIRDSYEKFGNQSVEQIEHLRCKHRIRVLQGHEDTTKQN   800
 801  VLRVVIPEVSILPEDLEELYDLFKRAHMMSCYWEHHRPMALRHDPSRPYA   850
 851  EQYRIDARQFAHLFQLVSPWTCGVHTEILAERLFRLLDDNMDQLIEFKAF   900
 901  TSCLDIMYNGEMNEKIKLLYRLHIPPALTENDRDSQSPLKNPLLSTSRPL   950
 951  VLGKPNGDTIDYQKQLKQMIKDLAKEKDKMEKELPKMSQREFIQFCKTLY  1000
1001  SMFHEDPEENDLYQAIATVTTLLLQIGEVGQRGSSSGSCSQECEEPQASA  1050
1051  PPEQDSVFAEAGKSPQAFPETEGDWTVSLEHILASLLTEQSLVNFFEKPL  1100
1101  NIKSKLENAKLNQYSLKVLEMSHPPQAELKLNDL                  1134

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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