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

NucPred

Fetching Q8VE73 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MVGELRYREFRVPLGPGLHAYPDELIRQRVGHNGHPEYQIRWLILRRGDD    50
  51  GDRDSTVDCKAEHILLWMSDDEIYANCHKMLGENGQVIAPSRESTEAGAL   100
 101  DKSVLGEMETDVKSLIQRALRQLEECVGTVPPAPLLHTVHVLSAYASIEP   150
 151  LTGIFKDRRVVNLLMHMLSSPDYQIRWSAGRMIQALSSHDAGTRTQILLS   200
 201  LSQQEAIEKHLDFDSRCALLALFAQATLTEHPMSFEGVQLPQVPGRLLFS   250
 251  LVKRYLHVTFLLDRLNGDAGDQGAQNNFIPEELNVGRGRLELEFSMAMGT   300
 301  LISELVQAMRWDGASSRPESSSSSTFQPRPAQFRPYTQRFRRSRRFRPRA   350
 351  SFASFNTYALYVRDTLRPGMRVRMLENYEEIAAGDEGQFRQSNDGVPPAQ   400
 401  VLWDSTGHTYWVHWHMLEILGFEEDIEDVIDIEELQELGANGALSIVPPS   450
 451  QRWKPITQLFAEPYVVPEEEDREESENLTQAEWWELLFFIRQLSEAERLH   500
 501  IVDLLQDHLEEERVLDYDMLPELTVPVDLAQDLLLSLPQQLEDSALRDLF   550
 551  SCSVYRKYGPEVLVGHLSYPFVPGAQPNLFGANEESEAKDPPLQSASPAL   600
 601  QRLVESLGPEGEVLVELEQALGSEAPQETEVKSCLLQLQEQPQPFLALMR   650
 651  SLDTSASNKTLHLTVLRILMQLVNFPEALLLPWHEAMDACVTCLRSPNTD   700
 701  REVLQELIFFLHRLTTTSRDYAVILNQLGARDAISKVLEKHRGKLELAQE   750
 751  LRDMVSKCEKHAHLYRKLTTNILGGCIQMVLGQIEDHRRTHRPIQIPFFD   800
 801  VFLRYLCQGSSEEMKKNRYWEKVEVSSNPQRASRLTDRNPKTYWESSGRA   850
 851  GSHFITLHMRPGVIIRQLTLLVAGEDSSYMPAWVVVCGGNSIKSVNKELN   900
 901  TVNVMPSASRVTLLENLTRFWPIIQIRIKRCQQGGINTRIRGLEVLGPKP   950
 951  TFWPVFREQLCRHTRLFYMVRAQAWSQDIAEDRRSLLHLSSRLNGALRHE  1000
1001  QNFAERFLPDMEAAQALSKTCWEALVSPLVQNITSPDEDSTSSLGWLLDQ  1050
1051  YLGCREAAYNPQSRAAAFSSRVRRLTHLLVHVEPREAAPPVVAIPRSKGR  1100
1101  NRIHDWSYLITRGLPSSIMKNLTRCWRSVVEEQMNKFLTASWKDDDFVPR  1150
1151  YCERYYVLQKSSSELFGPRAAFLLAMRNGCADAVLRLPFLRAAHVSEQFA  1200
1201  RHIDQRIQGSRMGGARGMEMLAQLQRCLESVLIFSPLEIATTFEHYYQHY  1250
1251  MADRLLSVGSSWLEGAVLEQIGPCFPSRLPQQMLQSLNVSEELQRQFHVY  1300
1301  QLQQLDQELLKLEDTEKKIQVAHEDSGREDKSKKEEAIGEAAAVAMAEEE  1350
1351  DQGKKEEGEEEGEGEDEEEERYYKGTMPEVCVLVVTPRFWPVASVCQMLN  1400
1401  PATCLPAYLRGTINHYTNFYSKSQSRSSLEKEPQRRLQWTWQGRAEVQFG  1450
1451  GQILHVSTVQMWLLLHLNNQKEVSVESLQAISELPPDVLHRAIGPLTSSR  1500
1501  GPLDLQEQKNVPGGVLKIRDDSEEPRPRRGNVWLIPPQTYLQAEAEEGRN  1550
1551  MEKRRNLLNCLVVRILKAHGDEGLHVDRLVYLVLEAWEKGPCPARGLVSS  1600
1601  LGRGATCRSSDVLSCILHLLVKGTLRRHDDRPQVLYYAVPVTVMEPHMES  1650
1651  LNPGSAGPNPPLTFHTLQIRSRGVPYASCTDNHTFSTFR             1689

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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