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

NucPred

Fetching Q9H2D6 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MEEVPGDALCEHFEANILTQNRCQNCFHPEEAHGARYQELRSPSGAEVPY    50
  51  CDLPRCPPAPEDPLSASTSGCQSVVDPGLRPGPKRGPSPSAGLPEEGPTA   100
 101  APRSRSRELEAVPYLEGLTTSLCGSCNEDPGSDPTSSPDSATPDDTSNSS   150
 151  SVDWDTVERQEEEAPSWDELAVMIPRRPREGPRADSSQRAPSLLTRSPVG   200
 201  GDAAGQKKEDTGGGGRSAGQHWARLRGESGLSLERHRSTLTQASSMTPHS   250
 251  GPRSTTSQASPAQRDTAQAASTREIPRASSPHRITQRDTSRASSTQQEIS   300
 301  RASSTQQETSRASSTQEDTPRASSTQEDTPRASSTQWNTPRASSPSRSTQ   350
 351  LDNPRTSSTQQDNPQTSFPTCTPQRENPRTPCVQQDDPRASSPNRTTQRE   400
 401  NSRTSCAQRDNPKASRTSSPNRATRDNPRTSCAQRDNPRASSPSRATRDN   450
 451  PTTSCAQRDNPRASRTSSPNRATRDNPRTSCAQRDNPRASSPSRATRDNP   500
 501  TTSCAQRDNPRASRTSSPNRATRDNPRTSCAQRDNPRASSPNRAARDNPT   550
 551  TSCAQRDNPRASRTSSPNRATRDNPRTSCAQRDNPRASSPNRATRDNPTT   600
 601  SCAQRDNPRASRTSSPNRATRDNPRTSCAQRDNPRASSPNRTTQQDSPRT   650
 651  SCARRDDPRASSPNRTIQQENPRTSCALRDNPRASSPSRTIQQENPRTSC   700
 701  AQRDDPRASSPNRTTQQENPRTSCARRDNPRASSRNRTIQRDNPRTSCAQ   750
 751  RDNPRASSPNRTIQQENLRTSCTRQDNPRTSSPNRATRDNPRTSCAQRDN   800
 801  LRASSPIRATQQDNPRTCIQQNIPRSSSTQQDNPKTSCTKRDNLRPTCTQ   850
 851  RDRTQSFSFQRDNPGTSSSQCCTQKENLRPSSPHRSTQWNNPRNSSPHRT   900
 901  NKDIPWASFPLRPTQSDGPRTSSPSRSKQSEVPWASIALRPTQGDRPQTS   950
 951  SPSRPAQHDPPQSSFGPTQYNLPSRATSSSHNPGHQSTSRTSSPVYPAAY  1000
1001  GAPLTSPEPSQPPCAVCIGHRDAPRASSPPRYLQHDPFPFFPEPRAPESE  1050
1051  PPHHEPPYIPPAVCIGHRDAPRASSPPRHTQFDPFPFLPDTSDAEHQCQS  1100
1101  PQHEPLQLPAPVCIGYRDAPRASSPPRQAPEPSLLFQDLPRASTESLVPS  1150
1151  MDSLHECPHIPTPVCIGHRDAPSFSSPPRQAPEPSLFFQDPPGTSMESLA  1200
1201  PSTDSLHGSPVLIPQVCIGHRDAPRASSPPRHPPSDLAFLAPSPSPGSSG  1250
1251  GSRGSAPPGETRHNLEREEYTVLADLPPPRRLAQRQPGPQAQCSSGGRTH  1300
1301  SPGRAEVERLFGQERRKSEAAGAFQAQDEGRSQQPSQGQSQLLRRQSSPA  1350
1351  PSRQVTMLPAKQAELTRRSQAEPPHPWSPEKRPEGDRQLQGSPLPPRTSA  1400
1401  RTPERELRTQRPLESGQAGPRQPLGVWQSQEEPPGSQGPHRHLERSWSSQ  1450
1451  EGGLGPGGWWGCGEPSLGAAKAPEGAWGGTSREYKESWGQPEAWEEKPTH  1500
1501  ELPRELGKRSPLTSPPENWGGPAESSQSWHSGTPTAVGWGAEGACPYPRG  1550
1551  SERRPELDWRDLLGLLRAPGEGVWARVPSLDWEGLLELLQARLPRKDPAG  1600
1601  HRDDLARALGPELGPPGTNDVPEQESHSQPEGWAEATPVNGHSPALQSQS  1650
1651  PVQLPSPACTSTQWPKIKVTRGPATATLAGLEQTGPLGSRSTAKGPSLPE  1700
1701  LQFQPEEPEESEPSRGQDPLTDQKQADSADKRPAEGKAGSPLKGRLVTSW  1750
1751  RMPGDRPTLFNPFLLSLGVLRWRRPDLLNFKKGWMSILDEPGEPPSPSLT  1800
1801  TTSTSQWKKHWFVLTDSSLKYYRDSTAEEADELDGEIDLRSCTDVTEYAV  1850
1851  QRNYGFQIHTKDAVYTLSAMTSGIRRNWIEALRKTVRPTSAPDVTKLSDS  1900
1901  NKENALHSYSTQKGPLKAGEQRAGSEVISRGGPRKADGQRQALDYVELSP  1950
1951  LTQASPQRARTPARTPDRLAKQEELERDLAQRSEERRKWFEATDSRTPEV  2000
2001  PAGEGPRRGLGAPLTEDQQNRLSEEIEKKWQELEKLPLRENKRVPLTALL  2050
2051  NQSRGERRGPPSDGHEALEKEVQALRAQLEAWRLQGEAPQSALRSQEDGH  2100
2101  IPPGYISQEACERSLAEMESSHQQVMEELQRHHERELQRLQQEKEWLLAE  2150
2151  ETAATASAIEAMKKAYQEELSRELSKTRSLQQGPDGLRKQHQSDVEALKR  2200
2201  ELQVLSEQYSQKCLEIGALMRQAEEREHTLRRCQQEGQELLRHNQELHGR  2250
2251  LSEEIDQLRGFIASQGMGNGCGRSNERSSCELEVLLRVKENELQYLKKEV  2300
2301  QCLRDELQMMQKDKRFTSGKYQDVYVELSHIKTRSEREIEQLKEHLRLAM  2350
2351  AALQEKESMRNSLAE                                     2365

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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