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

NucPred

Fetching Q9BV73 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  METRSPGLNNMKPQSLQLVLEEQVLALQQQMAENQAASWRKLKNSQEAQQ    50
  51  RQATLVRKLQAKVLQYRSWCQELEKRLEATGGPIPQRWENVEEPNLDELL   100
 101  VRLEEEQQRCESLAEVNTQLRLHMEKADVVNKALREDVEKLTVDWSRARD   150
 151  ELMRKESQWQMEQEFFKGYLKGEHGRLLSLWREVVTFRRHFLEMKSATDR   200
 201  DLMELKAEHVRLSGSLLTCCLRLTVGAQSREPNGSGRMDGREPAQLLLLL   250
 251  AKTQELEKEAHERSQELIQLKSQGDLEKAELQDRVTELSALLTQSQKQNE   300
 301  DYEKMIKALRETVEILETNHTELMEHEASLSRNAQEEKLSLQQVIKDITQ   350
 351  VMVEEGDNIAQGSGHENSLELDSSIFSQFDYQDADKALTLVRSVLTRRRQ   400
 401  AVQDLRQQLAGCQEAVNLLQQQHDQWEEEGKALRQRLQKLTGERDTLAGQ   450
 451  TVDLQGEVDSLSKERELLQKAREELRQQLEVLEQEAWRLRRVNVELQLQG   500
 501  DSAQGQKEEQQEELHLAVRERERLQEMLMGLEAKQSESLSELITLREALE   550
 551  SSHLEGELLRQEQTEVTAALARAEQSIAELSSSENTLKTEVADLRAAAVK   600
 601  LSALNEALALDKVGLNQQLLQLEEENQSVCSRMEAAEQARNALQVDLAEA   650
 651  EKRREALWEKNTHLEAQLQKAEEAGAELQADLRDIQEEKEEIQKKLSESR   700
 701  HQQEAATTQLEQLHQEAKRQEEVLARAVQEKEALVREKAALEVRLQAVER   750
 751  DRQDLAEQLQGLSSAKELLESSLFEAQQQNSVIEVTKGQLEVQIQTVTQA   800
 801  KEVIQGEVRCLKLELDTERSQAEQERDAAARQLAQAEQEGKTALEQQKAA   850
 851  HEKEVNQLREKWEKERSWHQQELAKALESLEREKMELEMRLKEQQTEMEA   900
 901  IQAQREEERTQAESALCQMQLETEKERVSLLETLLQTQKELADASQQLER   950
 951  LRQDMKVQKLKEQETTGILQTQLQEAQRELKEAARQHRDDLAALQEESSS  1000
1001  LLQDKMDLQKQVEDLKSQLVAQDDSQRLVEQEVQEKLRETQEYNRIQKEL  1050
1051  EREKASLTLSLMEKEQRLLVLQEADSIRQQELSALRQDMQEAQGEQKELS  1100
1101  AQMELLRQEVKEKEADFLAQEAQLLEELEASHITEQQLRASLWAQEAKAA  1150
1151  QLQLRLRSTESQLEALAAEQQPGNQAQAQAQLASLYSALQQALGSVCESR  1200
1201  PELSGGGDSAPSVWGLEPDQNGARSLFKRGPLLTALSAEAVASALHKLHQ  1250
1251  DLWKTQQTRDVLRDQVQKLEERLTDTEAEKSQVHTELQDLQRQLSQNQEE  1300
1301  KSKWEGKQNSLESELMELHETMASLQSRLRRAELQRMEAQGERELLQAAK  1350
1351  ENLTAQVEHLQAAVVEARAQASAAGILEEDLRTARSALKLKNEEVESERE  1400
1401  RAQALQEQGELKVAQGKALQENLALLTQTLAEREEEVETLRGQIQELEKQ  1450
1451  REMQKAALELLSLDLKKRNQEVDLQQEQIQELEKCRSVLEHLPMAVQERE  1500
1501  QKLTVQREQIRELEKDRETQRNVLEHQLLELEKKDQMIESQRGQVQDLKK  1550
1551  QLVTLECLALELEENHHKMECQQKLIKELEGQRETQRVALTHLTLDLEER  1600
1601  SQELQAQSSQIHDLESHSTVLARELQERDQEVKSQREQIEELQRQKEHLT  1650
1651  QDLERRDQELMLQKERIQVLEDQRTRQTKILEEDLEQIKLSLRERGRELT  1700
1701  TQRQLMQERAEEGKGPSKAQRGSLEHMKLILRDKEKEVECQQEHIHELQE  1750
1751  LKDQLEQQLQGLHRKVGETSLLLSQREQEIVVLQQQLQEAREQGELKEQS  1800
1801  LQSQLDEAQRALAQRDQELEALQQEQQQAQGQEERVKEKADALQGALEQA  1850
1851  HMTLKERHGELQDHKEQARRLEEELAVEGRRVQALEEVLGDLRAESREQE  1900
1901  KALLALQQQCAEQAQEHEVETRALQDSWLQAQAVLKERDQELEALRAESQ  1950
1951  SSRHQEEAARARAEALQEALGKAHAALQGKEQHLLEQAELSRSLEASTAT  2000
2001  LQASLDACQAHSRQLEEALRIQEGEIQDQDLRYQEDVQQLQQALAQRDEE  2050
2051  LRHQQEREQLLEKSLAQRVQENMIQEKQNLGQEREEEEIRGLHQSVRELQ  2100
2101  LTLAQKEQEILELRETQQRNNLEALPHSHKTSPMEEQSLKLDSLEPRLQR  2150
2151  ELERLQAALRQTEAREIEWREKAQDLALSLAQTKASVSSLQEVAMFLQAS  2200
2201  VLERDSEQQRLQDELELTRRALEKERLHSPGATSTAELGSRGEQGVQLGE  2250
2251  VSGVEAEPSPDGMEKQSWRQRLEHLQQAVARLEIDRSRLQRHNVQLRSTL  2300
2301  EQVERERRKLKREAMRAAQAGSLEISKATASSPTQQDGRGQKNSDAKCVA  2350
2351  ELQKEVVLLQAQLTLERKQKQDYITRSAQTSRELAGLHHSLSHSLLAVAQ  2400
2401  APEATVLEAETRRLDESLTQSLTSPGPVLLHPSPSTTQAASR          2442

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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