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

NucPred

Fetching P08953 from www.uniprot.org...

The NucPred score for your sequence is 0.47 (see score help below)

   1  MSRLKAASELALLVIILQLLQWPGSEASFGRDACSEMSIDGLCQCAPIMS    50
  51  EYEIICPANAENPTFRLTIQPKDYVQIMCNLTDTTDYQQLPKKLRIGEVD   100
 101  RVQMRRCMLPGHTPIASILDYLGIVSPTTLIFESDNLGMNITRQHLDRLH   150
 151  GLKRFRFTTRRLTHIPANLLTDMRNLSHLELRANIEEMPSHLFDDLENLE   200
 201  SIEFGSNKLRQMPRGIFGKMPKLKQLNLWSNQLHNLTKHDFEGATSVLGI   250
 251  DIHDNGIEQLPHDVFAHLTNVTDINLSANLFRSLPQGLFDHNKHLNEVRL   300
 301  MNNRVPLATLPSRLFANQPELQILRLRAELQSLPGDLFEHSTQITNISLG   350
 351  DNLLKTLPATLLEHQVNLLSLDLSNNRLTHLPDSLFAHTTNLTDLRLEDN   400
 401  LLTGISGDIFSNLGNLVTLVMSRNRLRTIDSRAFVSTNGLRHLHLDHNDI   450
 451  DLQQPLLDIMLQTQINSPFGYMHGLLTLNLRNNSIIFVYNDWKNTMLQLR   500
 501  ELDLSYNNISSLGYEDLAFLSQNRLHVNMTHNKIRRIALPEDVHLGEGYN   550
 551  NNLVHVDLNDNPLVCDCTILWFIQLVRGVHKPQYSRQFKLRTDRLVCSQP   600
 601  NVLEGTPVRQIEPQTLICPLDFSDDPRERKCPRGCNCHVRTYDKALVINC   650
 651  HSGNLTHVPRLPNLHKNMQLMELHLENNTLLRLPSANTPGYESVTSLHLA   700
 701  GNNLTSIDVDQLPTNLTHLDISWNHLQMLNATVLGFLNRTMKWRSVKLSG   750
 751  NPWMCDCTAKPLLLFTQDNFERIGDRNEMMCVNAEMPTRMVELSTNDICP   800
 801  AEKGVFIALAVVIALTGLLAGFTAALYYKFQTEIKIWLYAHNLLLWFVTE   850
 851  EDLDKDKKFDAFISYSHKDQSFIEDYLVPQLEHGPQKFQLCVHERDWLVG   900
 901  GHIPENIMRSVADSRRTIIVLSQNFIKSEWARLEFRAAHRSALNEGRSRI   950
 951  IVIIYSDIGDVEKLDEELKAYLKMNTYLKWGDPWFWDKLRFALPHRRPVG  1000
1001  NIGNGALIKTALKGSTDDKLELIKPSPVTPPLTTPPAEATKNPLVAQLNG  1050
1051  VTPHQAIMIANGKNGLTNLYTPNGKSHGNGHINGAFIINTNAKQSDV     1097

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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