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

NucPred

Fetching Q9PW73 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MELNMPTYNDQIEEPTDGLLLMGKLMQGEWSIEHEDEKRDHSSEHSLSRV    50
  51  PLGLTLEDLEQSCKSRENLLRSRNTVSQNAGNSLRAFKDKPTNSQSGSLI   100
 101  RNTEQQNRQLKEKLNFLQEQNASLVSQNHSLMNKIDCVQTELTKSRSRIR   150
 151  YVESAIGARAMRLPDLEERILTLEAKADAQENALRTTEDQLEHSRHILAE   200
 201  KERILQMFKDEMKALKEELFASCRLCKRTEKQRNEALFNAEELTKALQQY   250
 251  KNKMTEKMEKVQEEGELLKNKFSNCEKEQDALQQKCVMLDTELEKSRDAL   300
 301  RNLQSENIIRQERHQCVEAKNAELISLLTQSNQRILRLESELEHKEKALQ   350
 351  ENIDENKAMKDCFAKSKQSETISDQPKEQPADSASDGSGKLIADLRAKLL   400
 401  IREAENKELQAELVNGKLLTNRYRNSLEKNCLDALEAEPVKLNLQNTAEE   450
 451  KYLQLELLCKQIQMDKERLTDCVKELQGKLGKAQIELTNTKLSMEQRTSQ   500
 501  LQLIQQELLEKASKTTKLEQELVKKRMKISALQKLVEEKSQVYSAAEARN   550
 551  AGLEEKLKNYKDQIVNLEDNINKEHAEVLLALERSKDIHQDQQKELMKQI   600
 601  EHLQLQLEMKNLHAGEQKHTITILQQETLWHEQQLESVNHLLTQARKELE   650
 651  IQTKNTSAAMKSLQNQVEVESAKVSQLESALTVCKEELALYLHELEDNRE   700
 701  QFENQIKTKSEELWCLQNEIKLRTQSLQETSEENVRLQQTLQQQQHMLQQ   750
 751  GTGRIGELEDHHTELEKQVSKLEFELEKQRSMSEDMLQRTKDSLHAANKE   800
 801  LGLKTEEVQELCSTLNQVKLELKHTNVTLLQMEEELVSLKNKEEKNASML   850
 851  KLLQMDMQKTQVELDKKACAVLELEEKLHIAEKDSKRTEEMETQLSGMQK   900
 901  ELDGYTKQVEELQETLTKTHLSVEEKQVIIQGLTEKLRSYKQELEERDHE   950
 951  VLDMDQLLKDRNWELKQRAAQLTQLDMSIRGHKGEMEQKIIRLESALEKA  1000
1001  ELEARDHIKEISSLDERLQQARDQLCEKEFDLMQKDQIINQLKKDIERSH  1050
1051  QTVTDMEKTLKVQERRISEKHQDGVDLSKQVCLAQERMQLTHQELLETRQ  1100
1101  QLAEAQKESDRLAQKLEGMDLISKEKIQHLKQKLEETNDTVCNLKTELQA  1150
1151  RNEVIKATNEVLILKESELTRLKARISSYERTLGLKQLSDTTALPSISFT  1200
1201  DPHPLDSSKHPEASDFKMWHISPSISASNLSLTDMSSLELPKSMLEDLRN  1250
1251  LAPPDSPPMKDTSEGVSCVSSDSLNNSSFNPLTYALDENSDFTDCPDLTT  1300
1301  LTGMLKYIKKEMRLSEYPQEHSPSKAAGIDGGSLG                 1335

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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