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

NucPred

Fetching O60312 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MEREPAGTEEPGPPGRRRRREGRTRTVRSNLLPPPGAEDPAAGAAKGERR    50
  51  RRRGCAQHLADNRLKTTKYTLLSFLPKNLFEQFHRPANVYFVFIALLNFV   100
 101  PAVNAFQPGLALAPVLFILAITAFRDLWEDYSRHRSDHKINHLGCLVFSR   150
 151  EEKKYVNRFWKEIHVGDFVRLRCNEIFPADILLLSSSDPDGLCHIETANL   200
 201  DGETNLKRRQVVRGFSELVSEFNPLTFTSVIECEKPNNDLSRFRGCIIHD   250
 251  NGKKAGLYKENLLLRGCTLRNTDAVVGIVIYAGHETKALLNNSGPRYKRS   300
 301  KLERQMNCDVLWCVLLLVCMSLFSAVGHGLWIWRYQEKKSLFYVPKSDGS   350
 351  SLSPVTAAVYSFLTMIIVLQVLIPISLYVSIEIVKACQVYFINQDMQLYD   400
 401  EETDSQLQCRALNITEDLGQIQYIFSDKTGTLTENKMVFRRCTVSGVEYS   450
 451  HDANAQRLARYQEADSEEEEVVPRGGSVSQRGSIGSHQSVRVVHRTQSTK   500
 501  SHRRTGSRAEAKRASMLSKHTAFSSPMEKDITPDPKLLEKVSECDKSLAV   550
 551  ARHQEHLLAHLSPELSDVFDFFIALTICNTVVVTSPDQPRTKVRVRFELK   600
 601  SPVKTIEDFLRRFTPSCLTSGCSSIGSLAANKSSHKLGSSFPSTPSSDGM   650
 651  LLRLEERLGQPTSAIASNGYSSQADNWASELAQEQESERELRYEAESPDE   700
 701  AALVYAARAYNCVLVERLHDQVSVELPHLGRLTFELLHTLGFDSVRKRMS   750
 751  VVIRHPLTDEINVYTKGADSVVMDLLQPCSSVDARGRHQKKIRSKTQNYL   800
 801  NVYAAEGLRTLCIAKRVLSKEEYACWLQSHLEAESSLENSEELLFQSAIR   850
 851  LETNLHLLGATGIEDRLQDGVPETISKLRQAGLQIWVLTGDKQETAVNIA   900
 901  YACKLLDHDEEVITLNATSQEACAALLDQCLCYVQSRGLQRAPEKTKGKV   950
 951  SMRFSSLCPPSTSTASGRRPSLVIDGRSLAYALEKNLEDKFLFLAKQCRS  1000
1001  VLCCRSTPLQKSMVVKLVRSKLKAMTLAIGDGANDVSMIQVADVGVGISG  1050
1051  QEGMQAVMASDFAVPKFRYLERLLILHGHWCYSRLANMVLYFFYKNTMFV  1100
1101  GLLFWFQFFCGFSASTMIDQWYLIFFNLLFSSLPPLVTGVLDRDVPANVL  1150
1151  LTNPQLYKSGQNMEEYRPRTFWFNMADAAFQSLVCFSIPYLAYYDSNVDL  1200
1201  FTWGTPIVTIALLTFLLHLGIETKTWTWLNWITCGFSVLLFFTVALIYNA  1250
1251  SCATCYPPSNPYWTMQALLGDPVFYLTCLMTPVAALLPRLFFRSLQGRVF  1300
1301  PTQLQLARQLTRKSPRRCSAPKETFAQGRLPKDSGTEHSSGRTVKTSVPL  1350
1351  SQPSWHTQQPVCSLEASGEPSTVDMSMPVREHTLLEGLSAPAPMSSAPGE  1400
1401  AVLRSPGGCPEESKVRAASTGRVTPLSSLFSLPTFSLLNWISSWSLVSRL  1450
1451  GSVLQFSRTEQLADGQAGRGLPVQPHSGRSGLQGPDHRLLIGASSRRSQ   1499

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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