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

NucPred

Fetching P48634 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MSDRSGPTAKGKDGKKYSSLNLFDTYKGKSLEIQKPAVAPRHGLQSLGKV    50
  51  AIARRMPPPANLPSLKAENKGNDPNVSLVPKDGTGWASKQEQSDPKSSDA   100
 101  STAQPPESQPLPASQTPASNQPKRPPAAPENTPLVPSGVKSWAQASVTHG   150
 151  AHGDGGRASSLLSRFSREEFPTLQAAGDQDKAAKERESAEQSSGPGPSLR   200
 201  PQNSTTWRDGGGRGPDELEGPDSKLHHGHDPRGGLQPSGPPQFPPYRGMM   250
 251  PPFMYPPYLPFPPPYGPQGPYRYPTPDGPSRFPRVAGPRGSGPPMRLVEP   300
 301  VGRPSILKEDNLKEFDQLDQENDDGWAGAHEEVDYTEKLKFSDEEDGRDS   350
 351  DEEGAEGHRDSQSASGEERPPEADGKKGNSPNSEPPTPKTAWAETSRPPE   400
 401  TEPGPPAPKPPLPPPHRGPAGNWGPPGDYPDRGGPPCKPPAPEDEDEAWR   450
 451  QRRKQSSSEISLAVERARRRREEEERRMQEERRAACAEKLKRLDEKFGAP   500
 501  DKRLKAEPAAPPAAPSTPAPPPAVPKELPAPPAPPPASAPTPETEPEEPA   550
 551  QAPPAQSTPTPGVAAAPTLVSGGGSTSSTSSGSFEASPVEPQLPSKEGPE   600
 601  PPEEVPPPTTPPVPKVEPKGDGIGPTRQPPSQGLGYPKYQKSLPPRFQRQ   650
 651  QQEQLLKQQQQHQWQQHQQGSAPPTPVPPSPPQPVTLGAVPAPQAPPPPP   700
 701  KALYPGALGRPPPMPPMNFDPRWMMIPPYVDPRLLQGRPPLDFYPPGVHP   750
 751  SGLVPRERSDSGGSSSEPFDRHAPAMLRERGTPPVDPKLAWVGDVFTATP   800
 801  AEPRPLTSPLRQAADEDDKGMRSETPPVPPPPPYLASYPGFPENGAPGPP   850
 851  ISRFPLEEPGPRPLPWPPGSDEVAKIQTPPPKKEPPKEETAQLTGPEAGR   900
 901  KPARGVGSGGQGPPPPRRESRTETRWGPRPGSSRRGIPPEEPGAPPRRAG   950
 951  PIKKPPPPTKVEELPPKPLEQGDETPKPPKPDPLKITKGKLGGPKETPPN  1000
1001  GNLSPAPRLRRDYSYERVGPTSCRGRGRGEYFARGRGFRGTYGGRGRGAR  1050
1051  SREFRSYREFRGDDGRGGGTGGPNHPPAPRGRTASETRSEGSEYEEIPKR  1100
1101  RRQRGSETGSETHESDLAPSDKEAPTPKEGTLTQVPLAPPPPGAPPSPAP  1150
1151  ARFTARGGRVFTPRGVPSRRGRGGGRPPPQVCPGWSPPAKSLAPKKPPTG  1200
1201  PLPPSKEPLKEKLIPGPLSPVARGGSNGGSNVGMEDGERPRRRRHGRAQQ  1250
1251  QDKPPRFRRLKQERENAARGSEGKPSLTLPASAPGPEEALTTVTVAPAPR  1300
1301  RAAAKSPDLSNQNSDQANEEWETASESSDFTSERRGDKEAPPPVLLTPKA  1350
1351  VGTPGGGGGGAVPGISAMSRGDLSQRAKDLSKRSFSSQRPGMERQNRRPG  1400
1401  PGGKAGSSGSSSGGGGGGPGGRTGPGRGDKRSWPSPKNRSRPPEERPPGL  1450
1451  PLPPPPPSSSAVFRLDQVIHSNPAGIQQALAQLSSRQGSVTAPGGHPRHK  1500
1501  PGLPQAPQGPSPRPPTRYEPQRVNSGLSSDPHFEEPGPMVRGVGGTPRDS  1550
1551  AGVSPFPPKRRERPPRKPELLQEESLPPPHSSGFLGSKPEGPGPQAESRD  1600
1601  TGTEALTPHIWNRLHTATSRKSYRPSSMEPWMEPLSPFEDVAGTEMSQSD  1650
1651  SGVDLSGDSQVSSGPCSQRSSPDGGLKGAAEGPPKRPGGSSPLNAVPCEG  1700
1701  PPGSEPPRRPPPAPHDGDRKELPREQPLPPGPIGTERSQRTDRGTEPGPI  1750
1751  RPSHRPGPPVQFGTSDKDSDLRLVVGDSLKAEKELTASVTEAIPVSRDWE  1800
1801  LLPSAAASAEPQSKNLDSGHCVPEPSSSGQRLYPEVFYGSAGPSSSQISG  1850
1851  GAMDSQLHPNSGGFRPGTPSLHPYRSQPLYLPPGPAPPSALLSGLALKGQ  1900
1901  FLDFSTMQATELGKLPAGGVLYPPPSFLYSPAFCPSPLPDTSLLQVRQDL  1950
1951  PSPSDFYSTPLQPGGQSGFLPSGAPAQQMLLPMVDSQLPVVNFGSLPPAP  2000
2001  PPAPPPLSLLPVGPALQPPSLAVRPPPAPATRVLPSPARPFPASLGRAEL  2050
2051  HPVELKPFQDYQKLSSNLGGPGSSRTPPTGRSFSGLNSRLKATPSTYSGV  2100
2101  FRTQRVDLYQQASPPDALRWIPKPWERTGPPPREGPSRRAEEPGSRGDKE  2150
2151  PGLPPPR                                             2157

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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