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

NucPred

Fetching Q9R0I7 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MYPNWGRYGGSSHYPPPPVPPPPPPVALPEASPGPGYSSSTAPAAPSSSG    50
  51  FMSFREQHLAQLQQLQQMHQKQMQCVLQPHHLPPPPLPPPPVMPGGGYGD   100
 101  WQPPPPPMPPPPGPALSYQKQQQYKHQMIHHQRDGPPGLVPMELESPPES   150
 151  PPVPPGSYMPPSQSYMPPPQPPPSYYPPSSAQPYLPPAQPGPSKPQLPPP   200
 201  PSIPSGNKTAIQQEPLESGAKNKTAEQKQAAPEPDPSTMTPQEQQQYWYR   250
 251  QHLLSLQQRTKVHLPGHKKGLVTAKDVPEPIKEEAPGPAASQVAEPLAAE   300
 301  KPPLPPPNEEAPPPLSPEEPQSEDSEDSEDSEEDARFKQLKAIAAHWQAA   350
 351  AAHWQQQQQQRVGFQYQGIMQRHTQLQQILQQYQQVIQHSPHIQTMSLDV   400
 401  QLRHYEMQQQQFQHLFQDWEREFQLWEEQLHSYPHKDQLQEYEKQWKTWQ   450
 451  GHMKATQTYLQEKVNSFQTVKSQYLGNMAMPPPFVPYSQMPPPLPTMPPP   500
 501  VLPPSLPPPVMPPALPTSIPPPGMPPPVMPPSLPTSVPPPGMPPSLSSGP   550
 551  PPVLPPPALSSAGSPPVLPPPALPGGPPILPLPPLSSATPPPGIPPPGAP   600
 601  QGMPPQLTAPLPPASGSQNSQIPEKPRQALLPTPVSFGSTPPSPYHPPPQ   650
 651  SEQVNSKPLNKVFSSEQGLGESSALSQSIIAAKDTPVKSGGLLADPPKGS   700
 701  FLEGPRGPREQKEQLQKLKDFGSEPQMADHLPPPDSRLQNPSRPGMYPPP   750
 751  GSYRPPPPMGKPPGSIVRPSAPPARSSIPMTRPPVPIPPPPPPPPPPPPP   800
 801  PPVIKSKTSSVKQERWDEDSFFGLWDTNDDQGLNSEFKRDTATIPSAPVL   850
 851  PPPPVHSSIPPPGPMPMGMPPMSKPPPVQHTVDYGHGRDMPTNKVEQIPY   900
 901  GERITLRPDPLPERSTFDADHAGQRDRYDRDRDREPYFDRPSNITDHRDF   950
 951  KRDRETHRDRDRDRVLDYERDRFDRERRPRDDRNQSYRDKKDHSSSRRGG  1000
1001  FDRPSYDRKSDRPPYEGPPMFGGERRTYPEERMPLPAPALGHQPPPVPRV  1050
1051  EKKPESKNVDDILKPPGRESRPERIVVIMRGLPGSGKTHVAKLIRDKEVE  1100
1101  FGGPAPRVLSLDDYFIAEVEKEEKDPDSGKKVKKKVMEYEYEADMEETYR  1150
1151  TSMFKTFKKTLDDGFFPFIILDAINDRVRHFDQFWSAAKTKGFEVYLAEM  1200
1201  SADNQTCGKRNIHGRKLKEINKMAEHWEVAPRHMMRLDIRSLLQDAAIEE  1250
1251  VEMEDFDANIEDQKEEKKDAEEEESELGYIPKSKWEMDTSEAKLDKLDGL  1300
1301  RTGTKRKRDWEAIASRMEDYLQLPDDYETRASEPGKKRVRWADLEEKKDA  1350
1351  DRKRAIGFVVGQTDWEKITDESGHLAERALNRTKYI                1386

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.)

Go back to the NucPred Home Page.