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

NucPred

Fetching Q9EQZ7 from www.uniprot.org...

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

   1  MSAPLGPRGRPAPTPAASQPPPQPEMPDLSHLTEEERKIILAVMDRQKKE    50
  51  EEKEQSVLKIKEEHKAQPTQWFPFSGITELVNNVLQPQQKQPNEKEPQTK   100
 101  LHQQFEMYKEQVKKMGEESQQQQEQKGDAPTCGICHKTKFADGCGHNCSY   150
 151  CQTKFCARCGGRVSLRSNKVMWVCNLCRKQQEILTKSGAWFYNSGSNTLQ   200
 201  QPDQKVPRGLRNEEAPQEKKAKLHEQPQFQGAPGDLSVPAVEKGRAHGLT   250
 251  RQDTIKNGSGVKHQIASDMPSDRKRSPSVSRDQNRRYEQSEEREDYSQYV   300
 301  PSDGTMPRSPSDYADRRSQREPQFYEEPGHLNYRDSNRRGHRHSKEYIVD   350
 351  DEDVESRDEYERQRREEEYQARYRSDPNLARYPVKPQPYEEQMRIHAEVS   400
 401  RARHERRHSDVSLANAELEDSRISLLRMDRPSRQRSVSERRAAMENQRSY   450
 451  SMERTREAQGQSSYPQRTSNHSPPTPRRSPIPLDRPDMRRADSLRKQHHL   500
 501  DPSSAVRKTKREKMETMLRNDSLSSDQSESVRPPPPRPHKSKKGGKMRQV   550
 551  SLSSSEEELASTPEYTSCDDVELESESVSEKGDSQKGKRKTSEQGVLSDS   600
 601  NTRSERQKKRMYYGGHSLEEDLEWSEPQIKDSGVDTCSSTTLNEEHSHSD   650
 651  KHPVTWQPSKDGDRLIGRILLNKRLKDGSVPRDSGAMLGLKVVGGKMTES   700
 701  GRLCAFITKVKKGSLADTVGHLRPGDEVLEWNGRLLQGATFEEVYNIILE   750
 751  SKPEPQVELVVSRPIGDIPRIPDSTHAQLESSSSSFESQKMDRPSISVTS   800
 801  PMSPGMLRDVPQFLSGQLSIKLWFDKVGHQLIVTILGAKDLPSREDGRPR   850
 851  NPYVKIYFLPDRSDKNKRRTKTVKKTLEPKWNQTFIYSPVHRREFRERML   900
 901  EITLWDQARVREEESEFLGEILIELETALLDDEPHWYKLQTHDVSSLPLP   950
 951  RPSPYLPRRQLHGESPTRRLQRSKRISDSEVSDYDCEDGVGVVSDYRHNG  1000
1001  RDLQSSTLSVPEQVMSSNHCSPSGSPHRVDVIGRTRSWSPSAPPPQRNVE  1050
1051  QGHRGTRATGHYNTISRMDRHRVMDDHYSSDRDRSHPRTGSVQTSPSSTP  1100
1101  GTGRRGRQLPQLPPKGTLERSAMDIEERNRQMKLNKYKQVAGSDPRLEQD  1150
1151  YHSKYRSGWDPHRGADTVSTKSSDSDVSDVSAVSRTSSASRFSSTSYMSV  1200
1201  QSERPRGNRKISVFTSKMQNRQMGVSGKNLTKSTSISGDMCSLEKNDGSQ  1250
1251  SDTAVGALGTSGKKRRSSIGAKMVAIVGLSRKSRSASQLSQTEGGGKKLR  1300
1301  STVQRSTETGLAVEMRNWMTRQASRESTDGSMNSYSSEGNLIFPGVRLAS  1350
1351  DSQFSDFLDGLGPAQLVGRQTLATPAMGDIQVGMMDKKGQLEVEIIRARG  1400
1401  LVVKPGSKTLPAPYVKVYLLDNGVCIAKKKTKVARKTLEPLYQQLLSFEE  1450
1451  SPQGRVLQIIVWGDYGRMDHKSFMGVAQILLDELELSNMVIGWFKLFPPS  1500
1501  SLVDPTLAPLTRRASQSSLESSTGPSYSRS                      1530

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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