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

NucPred

Fetching Q76LX8 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MHQRHPRARCPPLCVAGILACGFLLGCWGPSHFQQSCLQALEPQAVSSYL    50
  51  SPGAPLKGRPPSPGFQRQRQRQRRAAGGILHLELLVAVGPDVFQAHQEDT   100
 101  ERYVLTNLNIGAELLRDPSLGAQFRVHLVKMVILTEPEGAPNITANLTSS   150
 151  LLSVCGWSQTINPEDDTDPGHADLVLYITRFDLELPDGNRQVRGVTQLGG   200
 201  ACSPTWSCLITEDTGFDLGVTIAHEIGHSFGLEHDGAPGSGCGPSGHVMA   250
 251  SDGAAPRAGLAWSPCSRRQLLSLLSAGRARCVWDPPRPQPGSAGHPPDAQ   300
 301  PGLYYSANEQCRVAFGPKAVACTFAREHLDMCQALSCHTDPLDQSSCSRL   350
 351  LVPLLDGTECGVEKWCSKGRCRSLVELTPIAAVHGRWSSWGPRSPCSRSC   400
 401  GGGVVTRRRQCNNPRPAFGGRACVGADLQAEMCNTQACEKTQLEFMSQQC   450
 451  ARTDGQPLRSSPGGASFYHWGAAVPHSQGDALCRHMCRAIGESFIMKRGD   500
 501  SFLDGTRCMPSGPREDGTLSLCVSGSCRTFGCDGRMDSQQVWDRCQVCGG   550
 551  DNSTCSPRKGSFTAGRAREYVTFLTVTPNLTSVYIANHRPLFTHLAVRIG   600
 601  GRYVVAGKMSISPNTTYPSLLEDGRVEYRVALTEDRLPRLEEIRIWGPLQ   650
 651  EDADIQVYRRYGEEYGNLTRPDITFTYFQPKPRQAWVWAAVRGPCSVSCG   700
 701  AGLRWVNYSCLDQARKELVETVQCQGSQQPPAWPEACVLEPCPPYWAVGD   750
 751  FGPCSASCGGGLRERPVRCVEAQGSLLKTLPPARCRAGAQQPAVALETCN   800
 801  PQPCPARWEVSEPSSCTSAGGAGLALENETCVPGADGLEAPVTEGPGSVD   850
 851  EKLPAPEPCVGMSCPPGWGHLDATSAGEKAPSPWGSIRTGAQAAHVWTPA   900
 901  AGSCSVSCGRGLMELRFLCMDSALRVPVQEELCGLASKPGSRREVCQAVP   950
 951  CPARWQYKLAACSVSCGRGVVRRILYCARAHGEDDGEEILLDTQCQGLPR  1000
1001  PEPQEACSLEPCPPRWKVMSLGPCSASCGLGTARRSVACVQLDQGQDVEV  1050
1051  DEAACAALVRPEASVPCLIADCTYRWHVGTWMECSVSCGDGIQRRRDTCL  1100
1101  GPQAQAPVPADFCQHLPKPVTVRGCWAGPCVGQGTPSLVPHEEAAAPGRT  1150
1151  TATPAGASLEWSQARGLLFSPAPQPRRLLPGPQENSVQSSACGRQHLEPT  1200
1201  GTIDMRGPGQADCAVAIGRPLGEVVTLRVLESSLNCSAGDMLLLWGRLTW  1250
1251  RKMCRKLLDMTFSSKTNTLVVRQRCGRPGGGVLLRYGSQLAPETFYRECD  1300
1301  MQLFGPWGEIVSPSLSPATSNAGGCRLFINVAPHARIAIHALATNMGAGT  1350
1351  EGANASYILIRDTHSLRTTAFHGQQVLYWESESSQAEMEFSEGFLKAQAS  1400
1401  LRGQYWTLQSWVPEMQDPQSWKGKEGT                         1427

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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