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

NucPred

Fetching Q8S628 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MAFAAGGIDHHVAVDVEGEEESRRRAVAEEADLLWAAFERLPSAKRRSHA    50
  51  VVLPDPDGLGGGDGGGRGEGQLVDVRKLDRPGLQRVLRHALATSELDNAN   100
 101  LLHGIKARFDAVGLEVPRVEVRFQNLTVSTDVHVGRRALPTLVNYVHDIA   150
 151  ERILISSHLLRPDKHKLVILDDVSGVIKPGRMTLLLGPPASGKSTLLLAL   200
 201  ADKLDSQLKKSGEVAYNGMALDQFCVQRTSAYISQTDNHIGELTVRETLD   250
 251  FAAKCQGASENWQECLKELVNLEKERGIRPSPEIDAFMKTASFRREKHNL   300
 301  VSDYVLRVLGLDICADTPVGSDMERGVSGGQKKRVTTGEMIIGPRKTLLM   350
 351  DEISTGLDSSTTFQIVNCMRNFVHEMEATVLMSLLQPAPETFELFDDLIL   400
 401  LSEGKIIYQGPIKHVVDYFKSLGFSLPPRKGIADFLQEVTSKKDQAQYWS   450
 451  DQSKQHIFVSASEMAAVFKESQYGTYLEANLSSSCGNKDSALVLPRSKFA   500
 501  VPKFSLVRACFARELILISRNRFLYTFRTCQVAFVGIITSTLFLRTRLHP   550
 551  VDEQNGNLYLACLFFGLVHMMFNGFTEMTMTISRLPVFYKQRDNFFHPAW   600
 601  AFSLPNWILRIPYSFIEAVVWSCVVYYTVGFAPTVDRFFRFMLLLFSIHQ   650
 651  MALGLFRMMGAIARDMTIASTFGSAVLLAIFLLGGFVVPKGFIKPWWDWA   700
 701  YWISPLMYAQRAVSVNEFSASRWSKVSVSGNMTVGTNILISHSLPTDDHW   750
 751  FWIGVGVLLAYSIFFNIMFTLALAFLNPLRKPQSMVPSDAGDGRDVHINT   800
 801  DSNKNTIGEIFENNDGFEGQTECKSKKGMILPFQPLTMTFHNVNYYVNMP   850
 851  KEMQAKGVPEKRLQLLSEVSGIFRPRVLTALVGASGSGKTTLMDVLAGRK   900
 901  TGGYIEGDIRISGHKKEQRTFARIAGYVEQNDIHSPQVTVEESLWFSSTL   950
 951  RLPNDISRETRHAFVEEVMALVELDQIRYALVGKQGLTGLSTEQRKRLTI  1000
1001  AVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTVVCTIHQPS  1050
1051  IDIFEAFDELLLMKRGGRVIYGGSLGVNSVDMINYFQGIPRVVPITEGYN  1100
1101  PATWMLEVTTQASEERLGIDFATVYKNSYQFRNVENLIVELSIPASGTEP  1150
1151  LKFSSEFSQNRLTQFMVCLRKQSLVYWRSPEYNVVRLFFTSVAAIIFGSI  1200
1201  FWNVGMKRESTEDILLLMGALYAACLFLGVNNASSVQPVVSVERTVYYRE  1250
1251  RAANMYSSFPYAAAQVYHGLVEIPYIAVQTLIFGLITYFMVNYERNIRKL  1300
1301  VLYLIYMFLTFTYFTFYGMVAVGLTPTQHMASVVSSAFYSLWNLLSGFLI  1350
1351  PQSRIPGWWIWFYYICPVAWTLRGVITSQLGDVDTRIVGPGFDGTVHEFL  1400
1401  QQNLGFEQGMTGATVAVLVAFSVFFFSIYAISIKMINFQRS           1441

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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