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

NucPred

Fetching Q6T3U3 from www.uniprot.org...

The NucPred score for your sequence is 0.24 (see score help below)

   1  MAAAWLGWLLWALLLSAAQGELYTPKHEAGVCTFYEECGKNPELSGGLTS    50
  51  LSNVSCLSNTPARHVTGEHLALLQRICPRLYNGPNTTFACCSTKQLLSLE   100
 101  SSMSITKALLTRCPACSDNFVSLHCHNTCSPDQSLFINVTRVVERGAGEP   150
 151  PAVVAYEAFYQRSFAEKAYESCSQVRIPAAASLAVGSMCGVYGSALCNAQ   200
 201  RWLNFQGDTGNGLAPLDITFHLLEPGQALPDGIQPLNGKIAPCNESQGDD   250
 251  SAVCSCQDCAASCPVIPPPEALRPSFYMGRMPGWLALIIIFTAVFVLLSA   300
 301  VLVRLRVVSNRNKNKAEGPQEAPKLPHKHKLSPHTILGRFFQNWGTRVAS   350
 351  WPLTVLALSFIVVIALAAGLTFIELTTDPVELWSAPKSQARKEKSFHDEH   400
 401  FGPFFRTNQIFVTARNRSSYKYDSLLLGSKNFSGILSLDFLLELLELQER   450
 451  LRHLQVWSPEAERNISLQDICYAPLNPYNTSLSDCCVNSLLQYFQNNRTL   500
 501  LMLTANQTLNGQTSLVDWKDHFLYCANAPLTFKDGTSLALSCMADYGAPV   550
 551  FPFLAVGGYQGTDYSEAEALIITFSLNNYPADDPRMAQAKLWEEAFLKEM   600
 601  ESFQRNTSDKFQVAFSAERSLEDEINRTTIQDLPVFAVSYIIVFLYISLA   650
 651  LGSYSRCSRVAVESKATLGLGGVIVVLGAVLAAMGFYSYLGVPSSLVIIQ   700
 701  VVPFLVLAVGADNIFIFVLEYQRLPRMPGEQREAHIGRTLGSVAPSMLLC   750
 751  SLSEAICFFLGALTPMPAVRTFALTSGLAIILDFLLQMTAFVALLSLDSK   800
 801  RQEASRPDVLCCFSTRKLPPPKEKEGLLLRFFRKIYAPFLLHRFIRPVVM   850
 851  LLFLTLFGANLYLMCNINVGLDQELALPKDSYLIDYFLFLNRYLEVGPPV   900
 901  YFVTTSGFNFSSEAGMNATCSSAGCKSFSLTQKIQYASEFPDQSYVAIAA   950
 951  SSWVDDFIDWLTPSSSCCRLYIRGPHKDEFCPSTDTSFNCLKNCMNRTLG  1000
1001  PVRPTAEQFHKYLPWFLNDPPNIRCPKGGLAAYRTSVNLSSDGQVIASQF  1050
1051  MAYHKPLRNSQDFTEALRASRLLAANITADLRKVPGTDPNFEVFPYTISN  1100
1101  VFYQQYLTVLPEGIFTLALCFVPTFVVCYLLLGLDMCSGILNLLSIIMIL  1150
1151  VDTIGLMAVWGISYNAVSLINLVTAVGMSVEFVSHITRSFAVSTKPTRLE  1200
1201  RAKDATVFMGSAVFAGVAMTNFPGILILGFAQAQLIQIFFFRLNLLITLL  1250
1251  GLLHGLVFLPVVLSYLGPDVNQALVQEEKLASEAAVAPEPSCPQYPSPAD  1300
1301  ADANVNYGFAPELAHGANAARSSLPKSDQKF                     1331

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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