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

NucPred

Fetching Q09847 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MNAENTFSILNTNEPNAGGSQVTESEIEEEDIEFLSFAALKIGATSSLSN    50
  51  SSLGLPEYSNLFAINNLKSLFVAGVPNYLIIGSTLDLQKSLIDADENVDA   100
 101  NVLKDSASIRHVSLPDAKFSMVSFSSNGEFVIAYDFVSFELSVYETDALL   150
 151  KNSATSIYKAVFPDLVQVLPNPEINNLVILRNLKLEVFLLSLSKFQVESP   200
 201  LAKDATCAAWSRRGKQCVIGFNNGTMSQYTPAGEIKLRIPRPPSLENYFV   250
 251  ECISWIENREFVVFYSPLTSLSNESDEPPHESECFVISVGMNGHFNFGKA   300
 301  GDPTPPFGAVNRRDHHYIASLHAWKPDLRSLVVVANTASADLGVLALSME   350
 351  KNQWSILNIVDETKRASLPYSNKKDSDSSPTALVMDFTATDRISKPLDPT   400
 401  EAPADCSPLPIVWVFNDEFQLVAYRIFYADAISKSIDYPEMNVIKDKNKD   450
 451  STVRASNNENIPTPDKQASPFVKNLSSTSSPFSQSSAFGNFKFGQATSFD   500
 501  KGLSTDASSGAKSNTPVFGQPSTFGQAPVFGQPSAFGQAPVFGQPSAFGQ   550
 551  SSFSFGTSNMNQKLDFGTFKSPLSGAATGEAKTNLEKAVTSASGKASFTG   600
 601  FAPSQSTTSGLNFDSIPKDNEAASIFGSSQVSTKNTSGFQFSNNTLLADN   650
 651  VDEDIESDHDTKIEELANSDVEPSTEQNIGGDVSWGASTFQSKPQPSFSF   700
 701  GLTLDDKSNTPGKNFSIFGKTAETQVEQKKPENNVLTKPFSFAPSDKSMF   750
 751  AANIPSAGEGLDQQKTSKALPSTGITKLSENDNEKAEESNETKGFNTTIA   800
 801  KQNDKSSKSEGKASVANMSALNKSTNNETSDSKPSLKSPLFNFSADAPTF   850
 851  TFNKPSETPPFSFNKPLVEKESKQDVSDTSDRSPFSFKAFGIDSKKSPTP   900
 901  EPTEMAESNISEESEGWKLIEQPNVESEIEDQDEESSDLNGKRRSTPPKI   950
 951  HEVGVNKMLDVVPKEKRDLNSFFPKQPLVVQSTDKNKKEPQESLEDEILS  1000
1001  AEGFSEVEAANKISRFEPFSSPKLKLATSDNAPEKYVFEESESSDLEEGP  1050
1051  VPLRNLESLADLPEAESNEKLPMVNTFERLYLQFKNELDLVWQNINIIAE  1100
1101  YIEGQTSTPSAVSEQATMAMLSQNTEELEDLLDTVTSFSAFCSDYSKQID  1150
1151  YLEACLVRINAKRIQVTRLLKALTNPAFEKQMELRQLGPEALRRQKELRL  1200
1201  KMEKVLKSLSTLEQQAVDARMSDTRRFKKPTLGSIEVAYSRIATLLGQRL  1250
1251  KQLYKLEKDIKRMATKKKMITKKSMSSDMMTQFRALGISQSSTKQVSAHY  1300
1301  LREFERQDAFRNGVFKRLTSLKKAD                           1325

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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