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

NucPred

Fetching P61407 from www.uniprot.org...

The NucPred score for your sequence is 0.68 (see score help below)

   1  MSSTPGLPTPGASLALRVSFVDVHPEVIPVQLWGLVGQRREEYVRLSREI    50
  51  QEAAATRGPWALGGASASPGELCLVQVGLMWHRCRVVSRQAQDSRVFLLD   100
 101  EGRTITAGAGSLAPGRSEFFHLPSEVLGCVLAGLVPAGGGGTGGGEPQQW   150
 151  SPRAVDFLSNLQGKEVHGRVLDVLLLHRLVLLEVPVVSQQMEELGLARQV   200
 201  PDSLFCSLLKRYLTAAGQGSSGAPVLPRAAPKQEHPGLDYFYPQLQLGVT   250
 251  EPVVVTQVCHPHRIHCQLRSLSQEIHRLSESMAQVYRAPVGTDDEDSGSA   300
 301  TWEEREESPDKPGSPCASCGLDGQWYRALLLETFRPQRCAQVLHVDYGRK   350
 351  ELVSCSSLRYLLPEYFRMPVVTYPCALYGLWDCGRGWSRSQVGDLKALIL   400
 401  GQAVNAKIEFYCSFEHMYYVTLYGEDGINLNSAFGVQSCCLADWFLQSQG   450
 451  IEEEEEEDEDEVEAAFQSQSPAEEMEAEVSLPSLRSIRLKMNTFYDAQVE   500
 501  FVKSPSEFWIRLRKHKNTFSKLTKRMCSFYSSASKLDGVILRPEPDDLCC   550
 551  VKWKENGYYRATVTRLDSKSVDVFLVDRGNSENVDWCDVRMLLPQFRQLP   600
 601  ILALKCTLADIWPLGKTWSQEATSFFKKTVLHKELVVHVLDKQDHQYVIE   650
 651  ILDESRMGEENISKVIAQAGFAKFQEFETKENIRLSAHSPGHVSGHFMAE   700
 701  PSKITSAKKAEGDQRAKKDNKTLSVSEALADTVSLSNLSTAQDTEKVTSD   750
 751  PSLLMLNFLKTKPDCCGKGELEVGSTVEVKVSHIENPGSFWCQLMRNAQG   800
 801  FRTLMCDIEDYCKSSEPSPYEGDTRVCLAKRTASGRWSRALISGAHSLEH   850
 851  VRVVFVDYGDRDVVSTKDILSVSDVFFQVRAQAFRCSLYNLIQPMGENPF   900
 901  VWDEKAVQAFSGFIDSARQNNLELKCTVFALASRHEEEWFNVVDLLTPFQ   950
 951  SACRFLVEKRLARPVKHQKPLEPSVQLHSYYYSTHDLKIGSEELVYVTHA  1000
1001  DDPWTFYCQLARNINVLEQLSYNIMQLSKALLNLKASTLAPGTLCLARYT  1050
1051  DGNWYRGIIIEKEPSKVFFVDFGNTYIAVDHLLPIPRDAHDVLLLPMQAL  1100
1101  KCSLSDIPHHIPEEVTAWFQETVLDKSLKALVVAKDPDGRLIIELYDDSV  1150
1151  QINASINEKLGLLGYKNRTRRKEKENEIILHETKALEDKKESVKPSLADY  1200
1201  LGKPGESKAHSIEIMGESCKPKMGPACKELRYLQGSAKANLVPPYQDSVG  1250
1251  NKNDGGFPLTREKKEDIFASSPMSGTKLDSALPERRMGEPSGRDLPPKFC  1300
1301  EFPQKTIAPGFKTSVYVSHINDLSDFYIQLIEDEAEINNLSERLNDVRTR  1350
1351  PQYHTGPQWQSGDVICAVFPEDNLWYRALVMEQQPNGLLSVQFIDYGNMS  1400
1401  VVHTNRTGRLGPVDAVLPALCLHCSLWGLSVPVCKEMVSYFSQRTDEAQI  1450
1451  RCEFVKFQGTWEVILADEHGVIAEDMISRFPCNGNSQAGLTTQTMKGDCL  1500
1501  KIANKPNTDTSVLLNWYNPKAKLIKAYATVIDGPEYFWCQFADSEKLQYL  1550
1551  ETEVQSAGKQLSDRRSCTQCPQIGDPCIVRYREDGHYYRALITNICDGEL  1600
1601  ASVRLVDFGNAEDCVDAKELWSIPSELLLVPMQAFPCCLAGFSVSGGVCP  1650
1651  QEGNDYFYDIVTEDVLDITILEIKRDVCNIPLAIVELRSKGENINEKMKK  1700
1701  YAKTGVPKNDLSSEKRGPERKGSLASPDLGLKKPSHKIAQDKTFYGEARA  1750
1751  SELSERLEKDLNIETKTSKFYERSTRSIFNAFENSCKGKMGSERLEGSMD  1800
1801  YHFVDRAKFDNNYLITGFNPILAHASEPKELLELSSLEVPLSADNDDECK  1850
1851  EFLELESIELQHSPAGEEEKEELGLGSPMAPLSPGCQAGATLESFMMQLP  1900
1901  LDCEAEKQLELKLPTPQLSLEDSISPLSAAVSQDIQGSRCSEDERKAGYM  1950
1951  GSSDDDHSRSPLLQHGKGGNSPAHDGRNLSEEEFPQFESRDSAALLAPLF  2000
2001  SEEEAREGRKCGSMVPAQLQSTYTLKGFSVGSKCVVWSSLRNTWSKCEIL  2050
2051  ELAEEGTRVLNLSNGVEETVSPENVWNGIPKVDKRPSEAVFQTVGKDLPF  2100
2101  MPSDDATTKGFSSVSEEEACGGDADSLSTAKLNI                  2134

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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