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

NucPred

Fetching P51827 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MDSFDLALLQEWDLESLWGEDILSQRNDSLVLEVQASASRCRSVYEPDRN    50
  51  ALRRKERERRSQETQQDSGSFNSGYSLFSEPYKTNKGDELSNRIQNTLGN   100
 101  YDEMKDFLTDRSNQSHLVGVPKPGVPQTPVNKIDEHFGAESRAQPQPSTV   150
 151  CSTASSTPAAVPVQQGKRGAMGWQKAGHPPSDGQQRAAQQGSLRTLLGDG   200
 201  VGRQQTRAKQVCNMETGLQTQERPPAMAAKHGGSGHCVQNFPPSLASKPS   250
 251  LVQQKPTAYVRPMDGQDQAPDESPKLKSSTETAVHCTAYRGVPANKPESA   300
 301  RAKAKLAKFSIPKQAEESRSGENNSCVEEIIREMTWLPPLSAIQAPAKVE   350
 351  PSKFPFPNKDSQLVSSGHSNPKKADAEPGSPDNGASNTSTLEDDLKLSSD   400
 401  DEEGEQQAAQRTALRALADSSVVQQTNCRGSAPSSKGGGSSSSSGGSSSS   450
 451  SDSESTSGSDSETESSSSSSESEGSKPPHCSSPEAEPASSNKWQLDKWLN   500
 501  KVNPHKPPILIQNESHGPERNQYYTPPVKDEGQDCGKLPEICQASLRDKE   550
 551  LKTTCKEEQRPRTANKAPGSKSVKQKSPPAAVAVTAAALPPAVPSAPTES   600
 601  APAPTRRSAGKKPTRRTERTSAGDGANCHRPEEPVAPDTLGASVVGPLEP   650
 651  PKTRPCGNNRTGHRKELRSSVTCEKRRTRGLSRIVPKSKEFIETESSSSS   700
 701  SSSDSDLESEQEEYVLSKAPTTTGSEQRLKEAASSNNNSNSNSSTSRASV   750
 751  GSINARTTSDIAKELEEQFYTLVPFGRNELLSPLKDSDEVRSLWVKIDLT   800
 801  LLSRIPEHLSQEPGVLSAPSAKDTDSAPASHALDAPAEKTLPKSKRKRKC   850
 851  DNEDDYREIKKVQGRKESASRLAASTNNTLSGNHCNVNVNSLAIPINKNE   900
 901  KMLRSPTSPLSDTCKHKYASEDLTSSSRPHGNGLLTSASSNKEPKAESQL   950
 951  QTIAGDLTKASHNSSENGTLHSKSRPQTEPWSPGSNGHRDCKRQKLIFDD  1000
1001  MPRSADYFMREAKRMKHKADAMVEKFGKALNYAEAALSFIECGNAMEQGP  1050
1051  MESKSPYTMYSETVELIRYAMRLKTHSGPNATPEDKQLAALCYRCLALLY  1100
1101  WRMFRLKRDHAVKYSKALIDYFKNSSKAAQAPSPWGSSGKSTGSPSPMSP  1150
1151  NPSPASSVGSQGSLSSSSGLSPSTIVSIPQRIHQMAANHVSITNSILHSY  1200
1201  DYWEMADNLAKENREFFNDLDLLMGPVTLHSSMEHLVQYSQQGLHWLRSS  1250
1251  VHLS                                                1254

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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