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

NucPred

Fetching Q22307 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MSRDVKEFLYAWLGKNKYGNPTYDTKSETRSGRQRFKCELRITGFGYTAF    50
  51  GNSTNKKDAATNAAQDFCQYLVREGKMQQSDIPTLTSSSLEASSTWQDSE   100
 101  TATMFCGGEDGNSFQESQQPIPQKRFPWSNNAYQRNEGTHEQYITQKAEE   150
 151  IAASETVDLKSEIHGGWTMENSKKALNEFLQKMRLPQVNYGTKIRESNTV   200
 201  KTMETTAQIFVPQINKNLVGKGTGSNKKVSEAACAMNIVRQMFHLNIMQS   250
 251  YSGPIKKSKVSTLPEIAISIPEDLSTRVTEYVRSCGLELPEINETSATPE   300
 301  APTSLLTDVKLAQFPVSEICSASNISWAPPLQNWNPWRASNIDEEPLAFM   350
 351  SMEQISQRIMEKEDFKRGEALDKITAQRGELPVAQYRENIVQTVAENRVT   400
 401  LIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERV   450
 451  ANERGEEVGETCGYNVRFDSATPRPYGSIMFCTVGVLLRMMENGLRGISH   500
 501  VIIDEIHERDVDTDFVLIVLREMISTYRDLRVVLMSATIDTDLFTNFFSS   550
 551  IPDVGPTPVITMHGRTFPVQSFYLEDILHNLQHMPEEPDQKKRKKGGPPP   600
 601  PDDDEGDEEVDDKGRNMNILTDPSINESLKTAMSRISEKDIPFGVIEAIL   650
 651  NDIASRGVDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQL   700
 701  TSQEQRKVFNHYPGKRKIIVSTNIAETSITIDDVVYVIDSCKAKERMYTS   750
 751  NNNMVHFATVWASKTNVIQRRGRAGRVRAGYAFHLCSKMRFEALDDHGTA   800
 801  EMLRIPLHQIALTIKLLRLGSVGEFLGKALQPPPYDMVVESEAVLQAMGA   850
 851  LDRNLELTSLGKMLARMPIEPVIAKVLILGTALGAGSVMCDVASAMSFPT   900
 901  PFVPREKHHSRLSGTQRKFAGNKFSDHVAIVSVIQGYREAVQMGASAAER   950
 951  EFCERYSLSNPVLKMTDGARRQLIDVLRNQCSFPEDILFDISVNVNGPDR  1000
1001  ELNLMRSLLVMALYPNVAYYVGKRKVLTIEQSSALINKYSMLVPMNNRQE  1050
1051  MDFPSPLLVFTEKVRTRCISCKQMSVISAIQLLVFGSRKVECVGEGLVRI  1100
1101  DETITIRMNVSTAAALIGLRPCIEALLVKSCENPESLAGLNPSDAELRQL  1150
1151  LRDISSEEFMSEAGPIKDSLLTDNALIQKGPAPNRLEYADWGPSNNNSSF  1200
1201  QNQDFPPAAGGKVHPYRGNRRGNHPYAQNRPYAPPNSGMGYQNFNNSGYG  1250
1251  ASGDWNAGRGNYGNVGSGYRGAGGGGGYRGGRGGRGGGRGGGGRGWNASN  1300
1301  W                                                   1301

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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