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

NucPred

Fetching Q01705 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MPRLLTPLLCLTLLPALAARGLRCSQPSGTCLNGGRCEVANGTEACVCSG    50
  51  AFVGQRCQDSNPCLSTPCKNAGTCHVVDHGGTVDYACSCPLGFSGPLCLT   100
 101  PLDNACLANPCRNGGTCDLLTLTEYKCRCPPGWSGKSCQQADPCASNPCA   150
 151  NGGQCLPFESSYICRCPPGFHGPTCRQDVNECSQNPGLCRHGGTCHNEIG   200
 201  SYRCACRATHTGPHCELPYVPCSPSPCQNGGTCRPTGDTTHECACLPGFA   250
 251  GQNCEENVDDCPGNNCKNGGACVDGVNTYNCRCPPEWTGQYCTEDVDECQ   300
 301  LMPNACQNGGTCHNTHGGYNCVCVNGWTGEDCSENIDDCASAACFQGATC   350
 351  HDRVASFYCECPHGRTGLLCHLNDACISNPCNEGSNCDTNPVNGKAICTC   400
 401  PSGYTGPACSQDVDECALGANPCEHAGKCLNTLGSFECQCLQGYTGPRCE   450
 451  IDVNECISNPCQNDATCLDQIGEFQCICMPGYEGVYCEINTDECASSPCL   500
 501  HNGHCMDKINEFQCQCPKGFNGHLCQYDVDECASTPCKNGAKCLDGPNTY   550
 551  TCVCTEGYTGTHCEVDIDECDPDPCHYGSCKDGVATFTCLCQPGYTGHHC   600
 601  ETNINECHSQPCRHGGTCQDRDNSYLCLCLKGTTGPNCEINLDDCASNPC   650
 651  DSGTCLDKIDGYECACEPGYTGSMCNVNIDECAGSPCHNGGTCEDGIAGF   700
 701  TCRCPEGYHDPTCLSEVNECNSNPCIHGACRDGLNGYKCDCAPGWSGTNC   750
 751  DINNNECESNPCVNGGTCKDMTSGYVCTCREGFSGPNCQTNINECASNPC   800
 801  LNQGTCIDDVAGYKCNCPLPYTGATCEVVLAPCATSPCKNSGVCKESEDY   850
 851  ESFSCVCPTGWQGQTCEVDINECVKSPCRHGASCQNTNGSYRCLCQAGYT   900
 901  GRNCESDIDDCRPNPCHNGGSCTDGINTAFCDCLPGFQGAFCEEDINECA   950
 951  SNPCQNGANCTDCVDSYTCTCPVGFNGIHCENNTPDCTESSCFNGGTCVD  1000
1001  GINSFTCLCPPGFTGSYCQYDVNECDSRPCLHGGTCQDSYGTYKCTCPQG  1050
1051  YTGLNCQNLVRWCDSAPCKNGGRCWQTNTQYHCECRSGWTGVNCDVLSVS  1100
1101  CEVAAQKRGIDVTLLCQHGGLCVDEGDKHYCHCQAGYTGSYCEDEVDECS  1150
1151  PNPCQNGATCTDYLGGFSCKCVAGYHGSNCSEEINECLSQPCQNGGTCID  1200
1201  LTNSYKCSCPRGTQGVHCEINVDDCHPPLDPASRSPKCFNNGTCVDQVGG  1250
1251  YTCTCPPGFVGERCEGDVNECLSNPCDPRGTQNCVQRVNDFHCECRAGHT  1300
1301  GRRCESVINGCRGKPCKNGGVCAVASNTARGFICRCPAGFEGATCENDAR  1350
1351  TCGSLRCLNGGTCISGPRSPTCLCLGSFTGPECQFPASSPCVGSNPCYNQ  1400
1401  GTCEPTSENPFYRCLCPAKFNGLLCHILDYSFTGGAGRDIPPPQIEEACE  1450
1451  LPECQVDAGNKVCNLQCNNHACGWDGGDCSLNFNDPWKNCTQSLQCWKYF  1500
1501  SDGHCDSQCNSAGCLFDGFDCQLTEGQCNPLYDQYCKDHFSDGHCDQGCN  1550
1551  SAECEWDGLDCAEHVPERLAAGTLVLVVLLPPDQLRNNSFHFLRELSHVL  1600
1601  HTNVVFKRDAQGQQMIFPYYGHEEELRKHPIKRSTVGWATSSLLPGTSGG  1650
1651  RQRRELDPMDIRGSIVYLEIDNRQCVQSSSQCFQSATDVAAFLGALASLG  1700
1701  SLNIPYKIEAVKSEPVEPPLPSQLHLMYVAAAAFVLLFFVGCGVLLSRKR  1750
1751  RRQHGQLWFPEGFKVSEASKKKRREPLGEDSVGLKPLKNASDGALMDDNQ  1800
1801  NEWGDEDLETKKFRFEEPVVLPDLSDQTDHRQWTQQHLDAADLRMSAMAP  1850
1851  TPPQGEVDADCMDVNVRGPDGFTPLMIASCSGGGLETGNSEEEEDAPAVI  1900
1901  SDFIYQGASLHNQTDRTGETALHLAARYSRSDAAKRLLEASADANIQDNM  1950
1951  GRTPLHAAVSADAQGVFQILLRNRATDLDARMHDGTTPLILAARLAVEGM  2000
2001  LEDLINSHADVNAVDDLGKSALHWAAAVNNVDAAVVLLKNGANKDMQNNK  2050
2051  EETPLFLAAREGSYETAKVLLDHFANRDITDHMDRLPRDIAQERMHHDIV  2100
2101  RLLDEYNLVRSPQLHGTALGGTPTLSPTLCSPNGYLGNLKSATQGKKARK  2150
2151  PSTKGLACGSKEAKDLKARRKKSQDGKGCLLDSSSMLSPVDSLESPHGYL  2200
2201  SDVASPPLLPSPFQQSPSMPLSHLPGMPDTHLGISHLNVAAKPEMAALAG  2250
2251  GSRLAFEPPPPRLSHLPVASSASTVLSTNGTGAMNFTVGAPASLNGQCEW  2300
2301  LPRLQNGMVPSQYNPLRPGVTPGTLSTQAAGLQHSMMGPLHSSLSTNTLS  2350
2351  PIIYQGLPNTRLATQPHLVQTQQVQPQNLQLQPQNLQPPSQPHLSVSSAA  2400
2401  NGHLGRSFLSGEPSQADVQPLGPSSLPVHTILPQESQALPTSLPSSMVPP  2450
2451  MTTTQFLTPPSQHSYSSSPVDNTPSHQLQVPEHPFLTPSPESPDQWSSSS  2500
2501  PHSNISDWSEGISSPPTTMPSQITHIPEAFK                     2531

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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