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

NucPred

Fetching Q4WXX4 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MAEEDAEKAFFQAQTMNAESVDYKAVEEHGADSSDSDDYDPSKTLQDQYS    50
  51  SSMTDLKQSENVSSSASPEPNPTEQNSVQPDHDPSQPDGASYPSQTPPRD   100
 101  ESRTSTMVPTSGTSVQPKTRTIGGFVVEDEDEDDAGDADYEPPAVLGVED   150
 151  MNTVATNVPQQSVSGNENEASSTPDVSLDDAAQQSASLNNVSHNSYSPAP   200
 201  AVAPKSDVAVAAGQSLYNSHALQSGNVQDSATATPTPDSPSTSKGRLPHD   250
 251  RVGILEDRIQEDPRGDIPAWLELINEHRSRNRFDSARDVFERFLKVFPFA   300
 301  AEQWVAYAKMESELNDLYRLEQIFNRTLLTIPDVQLWSVYLDYVRRRNPL   350
 351  TTDTTGQARRIISSAYELAFQHIGVDKDSGSIWSDYVQFIKSGPGNVGGS   400
 401  GWQDQQKMDLLRKAYQKAICVPTQAVNTLWKEYDQFEMGLNKLTGRKFLQ   450
 451  EQSPAYMTARSSYTELQNITRDLIRTTLPRLPPVPGSDGDIEFTQQVDIW   500
 501  KRWIKWEKGDPLVLKEEDPAAFKGRVVYVYKQALMALRFLPEMWFDAAEF   550
 551  CFLNDLESEGNEFLKQGMEANPESCLLAFKRADRLEITSESEQDPIKRGA   600
 601  KVREPYDKLLDALYDLIAKARTREAQDVARLEETFAKMNADNPPAKTDDD   650
 651  DDDQSESKARESVKNAQIDAVRKAHAIQIGILSKTISFAWIALMRAMRRI   700
 701  QGKGKPGETPGSRQVFADARKRGRITSDVYIASALIEYHCYKDPAATKIF   750
 751  ERGAKLFPDDENFALEYLKHLIDINDIINARAVFEMTVRKLASNPDNVHK   800
 801  TKPIFAFLHEYESRYGDLVQVINLENRMRELFPEDPTLEQFAHRYSAPTF   850
 851  DPTAVRPIISPSQMRPKAVFPTSEQPMSRHGTPTPRYPGSVTDSPKRPLE   900
 901  DFDDDYNRPRKFVRAESPLKTSQRRQLDQQKRSQLSNVQTGSQFRSQGSP   950
 951  APLPRDIVHLLSIIPPASAYTAGRFSPEKLVDLIRRIEMPSSISQIPLPQ  1000
1001  SARGLGTTQTPMQPFSGKASPSLSVRAVY                       1029

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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