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

NucPred

Fetching P56941 from www.uniprot.org...

The NucPred score for your sequence is 0.10 (see score help below)

   1  MSARGPAFGLLLLLLCPVQVFSQSCVWYGECGIASGDKRYNCRYSGPPKP    50
  51  LPEDGYDLVQELCPGFFFGNVSLCCDVQQLRTLKDNLQLPLQFLSRCPSC   100
 101  FYNLMNLFCELTCSPRQSQFLNVTATEDYVDPVTNQTKTNVKELEYYVGE   150
 151  TFANAMYNACRDVEAPSSNEKALGLLCGREAQACNATNWIEYMFNKDNGQ   200
 201  APFTITPIFSDLPTHGMEPMNNATKGCDESVDEVTGPCSCQDCSIVCGPK   250
 251  PQPPPPPVPWRILGLDAMYVIMWSSYMAFLIVFFGAFFAVWCYRKRYFVS   300
 301  EYTPIDGNIAFSVNSSDKGQAFCCDPLGAAFERGLRRLFAQWGAFCVRHP   350
 351  GCVVFFSLAFIVACSSGLVFIRVTTDPVDLWSAPGSQARREKEYFDTHFG   400
 401  PFFRMEQLIIRATNNQSHIYHPYPAGADVPFGPPLSRDILHQVLDLQTAI   450
 451  ENITASYNNETVTLQDICLAPLSPYNKNCTILSVLNYFQNSHSVLDHQVG   500
 501  DFFFVYADYHTHFLYCVRAPASLNDASLLHDPCLGTFGGPVFPWLVLGGY   550
 551  DDQNYNNATALVITFPVNNYYNDTEKLQRAQAWESEFINFVKNYKNPNLT   600
 601  ISFMAERSIEDELNRESNSDLFTILISYAIMFLYISIALGHIKSCSRLLV   650
 651  DSKISLGIAGILIVLSSVACSLGIFSYIGVPLTLIVIEVIPFLVLAVGVD   700
 701  NIFILVQTYQRDERLQGETLDQQLGRVLGEVAPSMFLSSFSETVAFFLGG   750
 751  LSVVPAVHTFSLFAGMAVLIDFLLQITCFVSLLGLDIKRQEKNRLDVVCC   800
 801  VQGAEDGAGVQASESCLFRFFKNSYAPLLLKDWMRPIVIAVFVGVLSFSI   850
 851  AVLNKVEIGLDQSLSMPDDSYVMDYFQSLSRYLHAGPPVYFVVEEGHNYT   900
 901  SLKGQNMVCGGLGCNNDSLVQQIFTAAQLDNYTRIGFAPSSWIDDYFDWI   950
 951  KPQSSCCRVYNSTDQFCNASVVDPTCIRCRPLTSEGKQRPQGEDFMRFLP  1000
1001  MFLSDNPNPKCGKGGHAAYSSAVNILGNGSGVGATYFMTYHTVLQASADF  1050
1051  IDAMQKARLIASNITRTMGLEASSYRVFPYSVFYVFYEQYLTVIDDTIFN  1100
1101  LGVSLGAIFLVTVVLMGCELWATVIMCVTIAMILVNMFGVMWLWGISLNA  1150
1151  VSLVNLVMSCGISVEFCSHITRAFTLSTKGSRVDRAEEALAHMGSSVFSG  1200
1201  ITLTKFGGIVVLAFAKSQIFQIFYFRMYLAIVLLGATHGLIFLPVLLSYI  1250
1251  GPSINKAKSLATQERYKGTEREQLLNF                         1277

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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