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

NucPred

Fetching O54824 from www.uniprot.org...

The NucPred score for your sequence is 0.75 (see score help below)

   1  MEPHGHSGKSRKSTKFRSISRSLILCNAKTSDDGSSPDEKYPDPFETSLC    50
  51  QGKEGFFHSSMQLADTFEAGLSNIPDLALASDSAQLAAAGSDRGKHCRKM   100
 101  FFMKESSSTSSKEKSGKPEAQSSSFLFPKACHQRTRSNSTSVNPYSAGEI   150
 151  DFPMTKKSAAPTDRQPYSLCSNRKSLSQQLDYPILGTARPTRSLSTAQLG   200
 201  QLSGGLQASVISNIVLMKGQAKGLGFSIVGGKDSIYGPIGIYVKSIFAGG   250
 251  AAAADGRLQEGDEILELNGESMAGLTHQDALQKFKQAKKGLLTLTVRTRL   300
 301  TTPPSLCSHLSPPLCRSLSSSTCGAQDSSPFSLESPASPASTAKPNYRIM   350
 351  VEVSLKKEAGVGLGIGLCSIPYFQCISGIFVHTLSPGSVAHLDGRLRCGD   400
 401  EIVEINDSPVHCLTLNEVYTILSHCDPGPVPIIVSRHPDPQVSEQQLKEA   450
 451  VAQAVEGVKFGKDRHQWSLEGVKRLESSWHGRPTLEKEREKHSAPPHRRA   500
 501  QKIMVRSSSDSSYMSGSPGGSPCSAGAEPQPSEREGSTHSPSLSPGEEQE   550
 551  PCPGVPSRPQQESPPLPESLERESHPPLRLKKSFEILVRKPTSSKPKPPP   600
 601  RKYFKNDSEPQKKLEEKEKVTDPSGHTLPTCSQETRELLPLLLQEDTAGR   650
 651  APCTAACCPGPAASTQTSSSTEGESRRSASPETPASPGKHPLLKRQARMD   700
 701  YSFDITAEDPWVRISDCIKNLFSPIMSENHSHTPLQPNTSLGEEDGTQGC   750
 751  PEGGLSKMDAANGAPRVYKSADGSTVKKGPPVAPKPAWFRQSLKGLRNRA   800
 801  PDPRRPPEVASAIQPTPVSRDPPGPQPQASSSIRQRISSFENFGSSQLPD   850
 851  RGVQRLSLQPSSGETTKFPGKQDGGRFSGLLGQGATVTAKHRQTEVESMS   900
 901  TTFPNSSEVRDPGLPESPPPGQRPSTKALSPDPLLRLLTTQSEDTQGPGL   950
 951  KMPSQRARSFPLTRTQSCETKLLDEKASKLYSISSQLSSAVMKSLLCLPS  1000
1001  SVSCGQITCIPKERVSPKSPCNNSSAAEGFGEAMASDTGFSLNLSELREY  1050
1051  SEGLTEPGETEDRNHCSSQAGQSVISLLSAEELEKLIEEVRVLDEATLKQ  1100
1101  LDSIHVTILHKEEGAGLGFSLAGGADLENKVITVHRVFPNGLASQEGTIQ  1150
1151  KGNEVLSINGKSLKGATHNDALAILRQARDPRQAVIVTRRTTVEATHDLN  1200
1201  SSTDSAASASAASDISVESKEATVCTVTLEKTSAGLGFSLEGGKGSLHGD  1250
1251  KPLTINRIFKGTEQGEMVQPGDEILQLAGTAVQGLTRFEAWNVIKALPDG  1300
1301  PVTIVIRRTSLQCKQTTASADS                              1322

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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