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

NucPred

Fetching Q9H9J4 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MTIVDKASESSDPSAYQNQPGSSEAVSPGDMDAGSASWGAVSSLNDVSNH    50
  51  TLSLGPVPGAVVYSSSSVPDKSKPSPQKDQALGDGIAPPQKVLFPSEKIC   100
 101  LKWQQTHRVGAGLQNLGNTCFANAALQCLTYTPPLANYMLSHEHSKTCHA   150
 151  EGFCMMCTMQAHITQALSNPGDVIKPMFVINEMRRIARHFRFGNQEDAHE   200
 201  FLQYTVDAMQKACLNGSNKLDRHTQATTLVCQIFGGYLRSRVKCLNCKGV   250
 251  SDTFDPYLDITLEIKAAQSVNKALEQFVKPEQLDGENSYKCSKCKKMVPA   300
 301  SKRFTIHRSSNVLTLSLKRFANFTGGKIAKDVKYPEYLDIRPYMSQPNGE   350
 351  PIVYVLYAVLVHTGFNCHAGHYFCYIKASNGLWYQMNDSIVSTSDIRSVL   400
 401  SQQAYVLFYIRSHDVKNGGELTHPTHSPGQSSPRPVISQRVVTNKQAAPG   450
 451  FIGPQLPSHMIKNPPHLNGTGPLKDTPSSSMSSPNGNSSVNRASPVNASA   500
 501  SVQNWSVNRSSVIPEHPKKQKITISIHNKLPVRQCQSQPNLHSNSLENPT   550
 551  KPVPSSTITNSAVQSTSNASTMSVSSKVTKPIPRSESCSQPVMNGKSKLN   600
 601  SSVLVPYGAESSEDSDEESKGLGKENGIGTIVSSHSPGQDAEDEEATPHE   650
 651  LQEPMTLNGANSADSDSDPKENGLAPDGASCQGQPALHSENPFAKANGLP   700
 701  GKLMPAPLLSLPEDKILETFRLSNKLKGSTDEMSAPGAERGPPEDRDAEP   750
 751  QPGSPAAESLEEPDAAAGLSSTKKAPPPRDPGTPATKEGAWEAMAVAPEE   800
 801  PPPSAGEDIVGDTAPPDLCDPGSLTGDASPLSQDAKGMIAEGPRDSALAE   850
 851  APEGLSPAPPARSEEPCEQPLLVHPSGDHARDAQDPSQSLGAPEAAERPP   900
 901  APVLDMAPAGHPEGDAEPSPGERVEDAAAPKAPGPSPAKEKIGSLRKVDR   950
 951  GHYRSRRERSSSGEPARESRSKTEGHRHRRRRTCPRERDRQDRHAPEHHP  1000
1001  GHGDRLSPGERRSLGRCSHHHSRHRSGVELDWVRHHYTEGERGWGREKFY  1050
1051  PDRPRWDRCRYYHDRYALYAARDWKPFHGGREHERAGLHERPHKDHNRGR  1100
1101  RGCEPARERERHRPSSPRAGAPHALAPHPDRFSHDRTALVAGDNCNLSDR  1150
1151  FHEHENGKSRKRRHDSVENSDSHVEKKARRSEQKDPLEEPKAKKHKKSKK  1200
1201  KKKSKDKHRDRDSRHQQDSDLSAACSDADLHRHKKKKKKKKRHSRKSEDF  1250
1251  VKDSELHLPRVTSLETVAQFRRAQGGFPLSGGPPLEGVGPFREKTKHLRM  1300
1301  ESRDDRCRLFEYGQGKRRYLELGR                            1324

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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