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

NucPred

Fetching Q8IYW2 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MDLVITQELARAESQQDAASLKKAYELIKSANLGKSEFDPSESFSPDLFV    50
  51  LCAEQALKMRQPEVSEDCIQMYFKVKAPITQFLGRAHLCRAQMCAPKSAE   100
 101  NLEEFENCVTEYMKAINFAKGEPRYYFLVYNASVLYWQMVRPFLKPGYRH   150
 151  HLIPSLSQIINVLSQTEEEDKEWRAELMLELLECYLQAGRKEEAARFCST   200
 201  AAPFIKSHVPQKYRQIFSVMVRHELMDELQLKEEKKNSISLSVTFYINML   250
 251  KAKAEQNDLPGDISVILRKAYRHLGHYNHQRFPSISEEKMLLLFELARFS   300
 301  LTLKCMEISSACLSDLKKMESKDPGKLIEMECLECESEALRLESKMKVYN   350
 351  RAAVEAQLDIIQRLDVALQRAVRLGDPRVIHVVCATQWNTCLPLLQHNLR   400
 401  HHLRKPLAGVADVLEKLDSLMTLLRCQVHMEMAQIEEDEDRLEPATEHLR   450
 451  KAARLDSLGLYRDRIQMASTRLRLCTTLYQAPERAEDKAIMAVEQAKKAT   500
 501  PKDSVRKKRALLVNAGLALAPDAFQIVLDSENEAKVSTGKNRGRFTYLCA   550
 551  KAWHHTVSVDKAAGHLRRLGNENDKERIQIWAELAKVARKQGVWDVCRTA   600
 601  SRFCLLYDNVKVKKLRLRRGKKKRGRDGSVQDTWSQPEVVLQRQVCPDLL   650
 651  RKFAEVGFIHAEATVHLLRSEGVELNDRAIPPEDLSQHPAGYVPEPPEVN   700
 701  AEWITYRTWIESLSRCAMNNWLRSAEIGQEIQEAWIVQNAVVYVLNHNHH   750
 751  LILAGRQKELVDALYHLLSIVKATGHSGDPVMLVTLCNTLARGLIISWIP   800
 801  VQAAEKSRKFMRPNAFHSPLDAGATSEIKTAVEVCEFALNLTNGSAPEET   850
 851  VPTGTRQQLIATWVKAKQLLQQQIGPRLGTEEQGTNEDVSSVTRVLVALE   900
 901  MYSCNGLGLMDFTVPSLAQLVKMASECNWSDPLVELQTLTRLTHFAHAAR   950
 951  DHETTMACAHRALEMGIKYLKKFGPEESRLVAEMLCTATAIQGRSIMENL  1000
1001  KGRKQLRLVAAKAFTESARFGGIAGSSALVMLAARHYWNAWLPLLSSAVY  1050
1051  RKKAKGALKRLIGIINKTEARKQEKGKTLLLHQWPTADFQGGGTTEGYFL  1100
1101  PGAEDDLALRAALYGLLFHSHADQDDWEGGLKVLDEAVQVLPRTAHRLLI  1150
1151  FKHMVIVKAKLGQNFSMEIQKFKAESEDYLARMWHRLALNSPSVSGELAC  1200
1201  YNNAIQALQKPEMEWQKVEYLMEFGQWLHHRHFPLEDVVFHLRWAVEILL  1250
1251  AMKPPGDVPEPQPTPDGEYVAVEMPPRSPVSEAEEAVSLEQLRSVRQLEA  1300
1301  LARVHILLALVLSPGAEGYEDCCLAAYAFFRHIWQVSLMTAGKSVLENRP  1350
1351  LAATSSHLLLPKKEKENERSKEKEKERSKEKENERSKEKDKEKGKEEKVK  1400
1401  EPKQSQSPAPIKQLEDLPMSIEEWASYSCPEEVLSVLKQDRSDSTVNPSS  1450
1451  IQKPTYSLYFLDHLVKALQKMCLHELTVPVLQLGVLISDSVVGSKGLSDL  1500
1501  YHLRLAHACSELKLREAAARHEEAVGQVCVSELEQASCRKEIALKKEKNK  1550
1551  EPLLEESLPALNEQTLPVQPGEIKPLDAKDKILKMNGETGRDLDGTSFPH  1600
1601  LWMLKAEVLLEMNLYQPARLLLSEAYLAFQELDEPCAEAQCLLLLAQLAN  1650
1651  KEKNYGQAKKMIAQAQHLGGSEEFWYNSTLTLAEALLSMEHSGREATVCH  1700
1701  IFQKLINAFKILKKERPNRLPLLEFMITDLEARCLSLRVRVAQHSAVTEP  1750
1751  TECSLLLKEMDDGLLEIERKFIDCGCKENCVDVKLERAKIKRLRAQNEKD  1800
1801  EEQKTAYYLEAYGLAQGAVAEEEGRLHSIQGLYGLAQGAMAEEEGRLHSV  1850
1851  QGLLSLQDLQNVNTPLMRKLARLKLGLVEMALDMLQFIWEEAHGQQSEQG  1900
1901  SLEKLLADYLQNTSDYTSVGLQWFTLKRTLAHGALAQLGSLQPLSVGCVE  1950
1951  IRARLLGLAGRALHLLAMQADPVHPTCYWEAGPSVGAKLSGLKSLELEVE  2000
2001  EEGATKSSRDPPASRAAPEEHCRRGEDLKRRMVLAQQYLAQASEVLLQCL  2050
2051  QVALGSGLLDVAAAASLEMVECVGTLDPATTCQFLALSQSCSASETMRDV  2100
2101  LLAATANTSSSQLAALLQLQHQLRCQDRTTTSLGARVEQRLAAVSKAWQN  2150
2151  LCVTEQHFNLLNEMPPTFWILFLHLSGDRSRLYGAAYEKPKFITAAKGKV  2200
2201  QAVGGSCKVMRLAISPTAFSHLLACAQQFRKQTQAQVYSEDMALNIGSEP  2250
2251  EGLQVEEKERPVQRLSSVLGPLEELLQPLFPLLSLSKARVQTPAVVADSG  2300
2301  KSKGKDKERKTSTGQHSTVQPEVADKIVLVADRHLLELPLEGLSVFDEGT  2350
2351  ISSVSREFSLQMLWNRLHKEETEGGVKKEGRSRDPKKRSLAKKGRKGSIP  2400
2401  RTIPPDCIIVDSDNFKFVVDPYEEAQGPEMLTPVSITQDILERFQDTFTS  2450
2451  RWAGHLGSKHFPSQAQWEQALGSCSGFFFYGMESFLSHILVERLVAMNLQ  2500
2501  ECQVAVLLDLARSYQSLKRHMESVEHRRSVGRWEANWRNSASPSEDEWRR  2550
2551  GGEPRRGFSDLEGQAAAAPKLRAPSHHAQLGPVWAAAPSHRVVQAWTCLP  2600
2601  SAAGAPALASALGSAPLPTHPHLPAPIPSSQLALPFLGLSPALGAASARD  2650
2651  PPPATSRKAAAWTSSSACLCAPWGLRRGWSCVSSRGQDKGGLPLAALVLS  2700
2701  CLDQKTIQTVSLFLI                                     2715

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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