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

NucPred

Fetching P98159 from www.uniprot.org...

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

   1  MNYNMDEMEATRLLRHPRRWWSIGFGKRIVAISILVIIVLLFSLVYHGLV    50
  51  VEKIDQVQQIAALNARHQVLFNQPFEEDQSALIVSPQTLHFKLLDEDMNK   100
 101  DMEDSKNRRRKHMRQMLVKFRLNKKHRMRRDLHGLDLLDPVRMEANMQHL   150
 151  YTKLRSKRAREALSQLEHEFVRCKKHTPQDCMSAFLRMYKMAKEVTEKME   200
 201  KMKAIMREQQPKLESSSMESHEQKGTFSPADLIQVTTAEATTVAVHATEK   250
 251  PARTKIKPSRISWIIDGHDHDESPVYTDGAPKKETTKAPWNTTQLVEITT   300
 301  TKIDATATERTTVESTTEKISWILDHFDKPQEILRTTEGPGQRIIRNVTT   350
 351  TSASSEPIVDTENTNSDHVPTTENGLVFNITTDGPVETTKSTAQRKLSFD   400
 401  WILDGEENVEPEVKSTNTTTTTAATTTTGATSETIIVTTELPKITFDWII   450
 451  DGREVVEPQETTTEVTGTTERLRKMPFDWIIDGEEVVEPQENVTTTTIAT   500
 501  TVAVSTTEINERIHNSTAYPTKPKPVKFDWIIDGGESSGEVSTSSTSQPK   550
 551  LTTREAISNPESPRSSHPLDNPTSIENMLESFEQHEEQKPILRVLNANES   600
 601  SSETVTDGYERQLWLKKFEDQARPNQNELIDTFGTALDAKALDKMGPKIN   650
 651  PLNGHTWNAADAQILSLCERVALRMRNKVATMSDGETKEKGETFTASPSV   700
 701  QFTSRAPGGFPVSGETMKASAQFMFNPNFGMPSIPVCFYMTPANFRMPMW   750
 751  SNTPTFMGMQGAHFGGSSNPGAGIFFVPQQFGPSGNFFGGSGGSGAGGQG   800
 801  ANIFSKNASPQKPTNGQQQVYCSYMQNQSGQGAGQSQTSSQQQQGGQSAF   850
 851  SNANFKMRHANQTNTANQQGQIIYASYAGLPQQPIQERSRCPEPDQFSCF   900
 901  GQQECIPAARWCDNVVDCSDGSDESACTCADRVDEERLCDGYEDCPMGED   950
 951  ELGCFGCESLAYSCYENPQDFAKRNRSTISMCYSRLERCDGFMNCLNGRD  1000
1001  EEQCSMLVTDVADHMSHGASASEGYLYHNYRGDWHPVCNNGEKWAALACQ  1050
1051  MDENSRMDHSASLNVSFQTLTLPGPFIEPSLHAGVHFAQACHGRNSHDSL  1100
1101  VDHVAYVKCPPMQCGLPSKSSMLEHSKRVRRAVSDSKEIVGDGRIVGGSY  1150
1151  TSALQWPFVVAIYRNGKFHCGGTIYSDRWIISAAHCVINYGKYFYEVRAG  1200
1201  LLRRSSYSPATQIQPVSHVVVHQAYERRSMRNDLSLLRLLNPLQFNRWVK  1250
1251  PICLPDKGRTTVGDDWIWGPVEHTLCTVVGWGAIREKGPSSDPMRQVIVP  1300
1301  IRKKCTDPEDQASEDICAGDPDGGRDACQGDSGGPLFCRSVSNPDEFYLA  1350
1351  GVVSHGNGCARPQEFGVYTRVTLYLDWLEMATTPRLLPKLQPLQLCPGFI  1400
1401  CVWGGKRCIAKRQRCDRNVDCLGGEDEVGCTYNFLPDMVGGVRQNISTTT  1450
1451  ESDYHPVKESEEKSKMREVIPIDDEDLKAEQDEEDLLKSTTSLGQTETTQ  1500
1501  GPMDLSFAEQITSTTSDDLSITDETTSTDFTVSDSATSPSTLLPTTTNPS  1550
1551  TWLPSTNIETSTFSFTTTESEASTKQETLPTTVAQTTTIPTSTEDLKKLT  1600
1601  DLVTEFIESTTFETTMEVETTTLSLTSTDAPKLVTTEGVKETTTTEDTTT  1650
1651  ISSIVTLTTTPLATISTTILTTEKHVAVTTLAPTTTTESAKTTTTHSSST  1700
1701  HSEKDQIQIPNKFVCKKMSQIVDIMMRCDRKVDCEDGTDELDCTCKDYLK  1750
1751  GSLKGLICDGKADCEDLTDEQNCVECQSNEFRCPLSKTCLPLSSRCDNKV  1800
1801  DCKFKEDEKDCFALTNGHDVHFDVHQQPKFSSTGIFSRNGHGVWRVVCAH  1850
1851  ETGYHEHQAKTADAVCALLGFNGAHYFNSSEFVTQHEMQPITPELKGGRN  1900
1901  RMSAQIHSMVGDNVQFTENEVIIPELGHPSASRPEKDRLLPRKCVGIYVE  1950
1951  CNPYSNKTTPLKTFSAGQVVKEKPIEQVPVLSPTIETHNTPNVHFKPQIP  2000
2001  AMVVNKKDEILDRLDKLIKSKKNKTILVNEQLHEAIEELHWPWLADVYMN  2050
2051  GDLWCIGVLIDKHWVMVHESCLSGIDLETHYVSVLLGGGKTKRSAHRSNH  2100
2101  EQIRRVDCFEGVPKSNVLLLHLERPVRFTHHVLPTFLPDSSHQNQSHARQ  2150
2151  CISVLHDDATGRIKTVAITRIHNATNCDSCYKLQEKQPPANLMRLLNVSA  2200
2201  EDMASISEEVELINGVAPTELPAITKFTTCNQFGLKNVSDAHHNPSDQGV  2250
2251  LVCRDSHTGWFPTALFNYNNSDCQSFKQPFGIRTLELVYKSLQDIIDKPS  2300
2301  CKMLLPAPDCSTHRCPLGTCLPQAAMCNGRSDCHDGSDEEETKCRQQKQQ  2350
2351  CAPGEMKCRTSFKCVPKSKFCDHVPDCEDMTDEPTICSCFTYLQATDPSK  2400
2401  ICDGKRNCWDKSDESSVLCNCTADHFQCSSSPEDCIPRDFVCDKEKDCPN  2450
2451  GEDERYCFGIEHPLHLQKKDFWTNSQHTQPEIAPQYGQVIEQTYGIWHTK  2500
2501  CFPKSKPPQVDEVREICKKLGYNPYRQPSYRLIDDEENKPVHTYELADRQ  2550
2551  GRSFSNESLMGKYRDSTKALIISKFSPLQLNERLTLFLKSSRPIAELVRW  2600
2601  NATDSSMCYRLEIRCA                                    2616

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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