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

NucPred

Fetching Q811B3 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MPCARGSWLAKLSIVAQLINFGAFCHGRQTQPWPVRFPDPRQEHFIKSLP    50
  51  EYHIVSPVQVDAGGHVLSYGLHHPVTSSRKKRAAGGSGDQLYYRISHEEK   100
 101  DLFFNLTVNWEFLSNGYVVEKRYGNLSHVKMVASSGQPCHLRGTVLQQGT   150
 151  TVGIGTAALSACQGLTGFFHLPHGDFFIEPVKKHPLTEEGSYPHVVYRRQ   200
 201  SIRAPETKEPICGLKDSLDNSVKQELQREKWERKTLRSRSLSRRSISKER   250
 251  WVETLVVADTKTVEYHGSENVESYILTIMNMVTGLFHSPSIGNLVHIVVV   300
 301  RLILLEEEEQGLKIVHHAEKTLSSFCKWQKSINPKSDLNPVHHDVAVLIT   350
 351  RKDICAGVNRPCETLGLSQLSGMCQPHRSCNINEDSGLPLAFTIAHELGH   400
 401  SFGIQHDGKENDCEPVGRHPYIMSQQIQYDPTPLTWSKCSKEYITRFLDR   450
 451  GRGFCLDDIPSKKGLKSNVIAPGVIYDVHHQCQLQYGPNATFCQEVENVC   500
 501  QTLWCSVKGFCRSKLDAAADGTRCGEKKWCMAGKCITVGKKPESIPGGWG   550
 551  RWSPWSHCSRTCGAGAQSAERLCNNPEPKFGGKYCTGERKRYRLCNVHPC   600
 601  RSDTPTFRQMQCSEFDTVPYKNQFYRWFPVFNAAHPCELYCRPIDEQFSE   650
 651  RMLEAVIDGTPCFEGGNSRNVCINGICKRVGCDYEIDSNATEDRCGVCLG   700
 701  DGSACQTVKKLFRQKEGSGYVDIGLIPKGARDIRVMEIKAAGNFLAIRSE   750
 751  DPEKYYLNGGFIIQWNGNYKLAGTVFQYDRKGDLEKLIAPGPTNESVWLQ   800
 801  LLFQVTNPGIKYEYTVRKDGLDNDVEKLLYFWQFGRWTECSVTCGTGIRR   850
 851  QAAHCVKKGHGIVKTTFCNPETQPSVRQKKCHEKDCPPRWWAGEWEACST   900
 901  TCGPYGEKKRTVLCIQTMGSDEQALPATDCQHLLKPKALVSCNRDILCPS   950
 951  DWTVGNWSECSVSCGGGVRIRSVTCAKNLNEPCDKTRKPNSRALCGLQQC  1000
1001  PFSRRVLKPNKDIAPSGKNQSTAEHDPFKPIPAPTSRPTPLSTPTVPESM  1050
1051  STSTPTINSLGSTIASQEDANGMGWQNNSTQAEEGSHFPTSSGSTSQVPV  1100
1101  TSWSLSIQPDDENVSSSAIGPTSEGDFWATTTSDSGLSSSDAMTWQVTPF  1150
1151  YSTMTTDPEVEIHSGSGEDSDQPLNKDKSNSVIWNKIGVPEHDAPMETDA  1200
1201  ELPLGPPPTSYMGEEPSWPPFSTKMEGSLPAWSFKNETPRDDGMIAEKSR  1250
1251  KIPLPLAGDHHPATSEKLENHDKLALPNTTNPTQGFGPVLTEEDASNLIA  1300
1301  EGFLLNASDYKHLMKDHSPAYWIVGNWSKCSTTCGLGAYWRSVECSSGVD  1350
1351  ADCTTIQRPDPAKKCHLRPCAGWRVGNWSKCSRNCSGGFKIREVQCMDSL  1400
1401  DHHRSLRPFHCQFLAGAPPPLSMSCNLEPCGEWQVEPWSQCSRSCGGGVQ  1450
1451  ERGVSCPGGLCDWTKRPATTVPCNRHLCCHWATGNWELCNTSCGGGSQKR  1500
1501  TIHCIPSENSTTEDQDQCLCDHQVKPPEFQTCNQQACRKSADLTCLKDRL  1550
1551  SISFCQTLKSMRKCSVPSVRAQCCLSCPQAPSIHTQRQRKQQLLQNHDML  1600

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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