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

NucPred

Fetching P38681 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MANTSLDMASSTSPSPSPESTTTPRKRIVVVGLGMVGIAFIEKLIKLDTQ    50
  51  RQYEIVVIGEEPHVAYNRVGLTSFFSHREVEQLYLNPLEWYKQHLQTSSL   100
 101  THHLSTAALSLSPATKSLTISPPPSTPSLTTLPYDHLILATGSSALLPTS   150
 151  TPGHDASGVFVYRNIADLQSLITWSSDTQIKGSTGVVVGGGLLGLEAAKA   200
 201  LMDLQVFGRVVVIERNGWVLSRQVDGEAGALVLEGVRGLGVEVLTRKRVK   250
 251  EVECDESKDEGEKEKKRVKGIRFEDGEYLACSTICFAIGIKARDELAREA   300
 301  GITCAERGGGGIVVDDSLQTSAPDVYAIGECASWKGQTFGLIGPGVEMAD   350
 351  VLAFNFTQAHLHTPRVFKRPDLSTKLKLLGVEVASFGDFFADRDGPKELP   400
 401  PKLRRELKKSGGKAEVKALTYKDPFLSVYKKYIFTSDGKYLLGGMMIGDT   450
 451  TDYVRLVPLVKTHKELDVPPSQLILGAKKSGDDNGDDDLPDDTQICSCHN   500
 501  VTKADLVAPLKSGECTSLGDLKSCTKAGTGCGGCMPLVTSIFNRTMASLG   550
 551  TEVKNNLCPHFPEYSRADLYNIISVKRLRTLPDVMREAGADADSLGCEAC   600
 601  KPAIASIFASLWNDHVMSPAHHGLQDTNDRFMGNIQRNGTFSVVPRVAAG   650
 651  EITPEKLIVIGEVAKEYNLYTKITGGQRIDMFGAKKQDLLKIWKKLVDAG   700
 701  MESGHAYAKSLRTVKSCVGTTWCRYGVGDSVGMAVRLEERYKGLRGPHKI   750
 751  KGGVSGCTRECAEAGNKDFGLIATEKGFNILICGNGGTTPKHSVLLAKDV   800
 801  PPTNVIPIIDRFLMFYIRTADKLQRTARWLEALPGGIDYLKEVILEDRLG   850
 851  ICASLEAQMQELVDSYFDEWAEALNNPAMQERFKQFANTDEGQPPMEVEI   900
 901  DRGQERPVMWPREDEGGSAKADFKGLRDKWSSTTWQPVLEASYFQGADDL   950
 951  PNGISASIKRGDTQLAVWRIKGKYYASQQMCPHKRTFALSDGFVGTDPSP  1000
1001  SSCSSSALPPSPPSTPPRSSSPVTSPPQSPTSSATPATTASSSCTTNPSG  1050
1051  PASPWISCPFHKRNFSLTSGSCKNDNELSIATFDVEERDDGMVYIKLPPV  1100
1101  DELDRELGTKKWMVKKGEAGEGQLRELDELNKSKGVEGKKGRRGRKPGAS  1150
1151  EAGKEVGKKLVEAVGGGGCGGPGLEW                          1176

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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