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

NucPred

Fetching Q3L8U1 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MTDPMMDFFDDANLFGETLEGLSDDAFVQPGPVSLVDELNLGAEFEPLHI    50
51 DSLNHVQGTPTHQKMTDFEQLNQFDSIKFHHVNQSFGSPAEHVLSPHSQF 100
101 NCSPIHPQNQPNGLFPDVSDGSPMWGHQTATTISNQNGSPFHQQGHSHSM 150
151 HQNKSFVAHHDFALFQANEQQTQCTSLRSQQNRNNLNPGQNSLSQSKNFM 200
201 NVSGPHRVNVNHPPQMTNASNSQQSISMQQFSQTSNPSAHFHKCSSHQEG 250
251 NFNGPSPNMTSCSVSNSQQFSSHYSFSSNHISPNSLLQSSAVLASNHTNQ 300
301 TLSDFTGSNSFSPHRGIKQESTQHILNPNTSLNSNNFQILHSSHPQGNYS 350
351 NSKLSPVHMNFPDPVDSGTQMGHFNDHVETNGFSSLEENLLHQVESQTEP 400
401 FTGLDPEDLLQEGLLPHFDESTFGQDNSSHILDHDLDRQFTSHLVTRPSD 450
451 MAQTQLQSQARSWHSSFSNHQHLHDRNHLCLQRQPPSSKKSDGSGTYTKL 500
501 QNTQVRVMSEKKQRKKVESESKQEKANRIISEAIAKAKERGERNIPRVMS 550
551 PENFPTASVEGKEEKKGRRMKSKPKDKDSKKTKTCSKLKEKTKIGKLIIT 600
601 LGKKQKRKNESSDEISDAEQMPQHTLKDQDSQKRRSNRQIKRKKYAEDIE 650
651 GKQSEEEVKGSMKIKKNSAPLPGEQPLQLFVENPSEEDAAIVDKILSSRT 700
701 VKKEISPGVMIDTEEFFVKYKNYSYLHCEWATEEQLLKDKRIQQKIKRFK 750
751 LRQAQRAHFFADMEEEPFNPDYVEVDRVLEVSFCEDKDTGEPVIYYLVKW 800
801 CSLPYEDSTWELKEDVDLAKIEEFEQLQASRPDTRRLDRPPSNIWKKIDQ 850
851 SRDYKNGNQLREYQLEGLNWLLFNWYNRRNCILADEMGLGKTIQSITFLY 900
901 EILLTGIRGPFLIIAPLSTIANWEREFRTWTDINVVVYHGSLISRQMIQQ 950
951 YEMYFRDSQGRIIRGAYRFQAIITTFEMILGGCGELNAIEWRCVIIDEAH 1000
1001 RLKNKNCKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPS 1050
1051 ESTFMQEFGDLKTEEQVQKLQAILKPMMLRRLKEDVEKKLAPKEETIIEV 1100
1101 ELTNIQKKYYRAILEKNFSFLSKGAGQTNVPNLVNTMMELRKCCNHPYLI 1150
1151 KGAEEKILGEFRDTYNPAASDFHLQAMIQSAGKLVLIDKLLPKMKAGGHK 1200
1201 VLIFSQMVRCLDILEDYLIHKRYLYERIDGRVRGNLRQAAIDRFSKPDSD 1250
1251 RFVFLLCTRAGGLGINLTAADTCIIFDSDWNPQNDLQAQARCHRIGQNKA 1300
1301 VKVYRLVTRNSYEREMFDRASLKLGLDKAVLQSMSGRESNVGGIQQLSKK 1350
1351 EIEDLLRRGAYGAIMEEEDEGSKFCEEDIDQILLRRTKTITIESEGRGST 1400
1401 FAKASFVASGNRTDISLDDPNFWQKWAKKAEIDIEAISGRNSLVIDTPRI 1450
1451 RKQTRPFSATKDELAELSEAESEGDEKPKLRRPCDRSNGYGRTECFRVEK 1500
1501 NLLVYGWGRWREILSHGRFKRQLNEHDVEIICRALLAYCLVHYRGDEKIK 1550
1551 GFIWDLITPTEDGQTRELQNHLGLSAPVPRGRKGKKVKTQTSSFDIQKAE 1600
1601 WLRKYNPEQLLQDEGYKKHIKHHCNKVLLRVRMLYYLKQEVIGNECQKVF 1650
1651 DGVDASDIDVWVPEPDHSEVPAEWWDFDADKSLLIGVFKHGYEKYNTIRA 1700
1701 DPALCFLERVGKPDEKAVAAEQRANDYMDGDVEDPEYKPAPAIFKDDIED 1750
1751 DVSSPGDLVIADGDGQLMEGDKVYWPTQSALTTRLRRLITAYQRTNKNRQ 1800
1801 IQQIQPTFSVPTSVMQPIYEEATLNPKMAAKIERQQRWTRREEADFYRVV 1850
1851 STFGVVFDPDRGQFDWTKFRAMARLHKKTDDSLEKYLYAFMSMCRRVCRL 1900
1901 PSKEELVDPNIFIQPITEERASRTLYRIELLRKVREQALRHPQLFERLKL 1950
1951 CHPNPDLPVWWECGPHDRDLLIGAAKHGVSRTDYHILRDPELSFMAAQRN 2000
2001 YSQSKMAHSRTSTPLLQQYQVALSASPLTSLPRLLDAKGIILEEMKVKSE 2050
2051 NLKEEPQSSEEESMSSVETRTLIKSEPVSPKNGVLPQATGDQKSGGKCET 2100
2101 DRRMVAARTEPLTPNPASKKPRVHKRGSESSSDSDSDSERSSCSSRSSSS 2150
2151 SSSSSCSHSRSGSSSSSSSSCSSASSSSSSSTSSSSSSSSSSSEESDSDE 2200
2201 EEAQKRESTTHMKAYDEESVASLSTTQDETQDSFQMNNGTPESAYILQGG 2250
2251 YMLAASYWPKDRVMINRLDSICQTVLKGKWPSARRSYDANTVASFYTTKL 2300
2301 LDSPGAATEYSDPSVPTPPGAGVKEEHDQSTQMSKVKKHVREKEFTVKIK 2350
2351 DEGGLKLTFQKQGLAQKRPFDGEDGALGQQQYLTRLRELQSASETSLVNF 2400
2401 PKSIPVSGTSIQPTLGANGVILDNQPIVKKRRGRRKNVEGVDIFFFNRNK 2450
2451 PPNHVSLGLTSSQISTGINPALSYTQPQGIPDTESPVPVINLKDGTRLAG 2500
2501 DDAPKRKDLEKWLKEHPGYVEDLGAFIPRMQLHEGRPKQKRHRCRNPNKL 2550
2551 DVNSLTGEERVQLINRRNARKVGGAFAPPLKDLCRFLKENSEYGVAPEWG 2600
2601 DVVKQSGFLPESMYERILTGPVVREEVSRRGRRPKSGIAKATAAAAAASA 2650
2651 TSVSGNPLLANGLLPGVDLTTLQALQQNLQNLQSLQVTAGLMGMPTGLPS 2700
2701 GGEAKNMAAMFPMLLSGMAGLPNLLGMGGLLTKPTESGTEDKKGSDSKES 2750
2751 EGKTERTESQSSENGGENSVSSSPSTSSTAALNTAAAANPLALNPLLLSN 2800
2801 ILYPGMLLTPGLNLHIPTLSQSNTFDVQNKNSDLGSSKSVEVKEEDSRIK 2850
2851 DQEDKGGTEPSPLNENSTDEGSEKADASSGSDSTSSSSEDSDSSNED 2897

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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