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

NucPred

Fetching Q60677 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MKWLFHTLLCMASLKPQGAFNLDVDWAWVTALQPGAPAVLSSLLHQDPSN    50
  51  NQTCLLVARRSSNRNTAALYRCAISISPDEIACQPVEHICMPKGRYQGVT   100
 101  LVGNHNGVLVCIQVQARKFRSLNSELTGACSLLTPNLDLQAQAYFSDLEG   150
 151  FLDPGAHVDSGDYCRSKGGSTGEEKKSARRRRTVEEEDEEEDGTEIAIVL   200
 201  DGSGSIEPSDFQKAKNFISTMMRNFYEKCFECNFALVQYGAVIQTEFDLQ   250
 251  ESRDINASLAKVQSIVQVKEVTKTASAMQHVLDNIFIPSRGSRKKALKVM   300
 301  VVLTDGDIFGDPLNLTTVINSPKMQGVVRFAIGVGDAFKNNNTYRELKLI   350
 351  ASDPKEAHTFKVTNYSALDGLLSKLQQHIVHMEGTVGDALQYQLAQTGFS   400
 401  AQILDKGQVLLGTVGAFNWSGGALLYSTQNGRGCFLNQTAKEDSRTVQYS   450
 451  YLGYSLAVLHKAHGVSYVAGAPRHKLRGAVFELRKEDREEDAFVRRIEGE   500
 501  QMGSYFGSVLCPVDIDMDGTTDFLLVAAPFYHIRGEEGRVYVYQVPEQDA   550
 551  SFSLAHTLSGHPGLTNSRFGFAMAAVGDINQDKFTDVAIGAPLEGFGAGD   600
 601  GASYGSVYIYNGHSGGLYDSPSQQIRASSVASGLHYFGMSVSGGLDFNGD   650
 651  GLADITVGSRDSAVVLRSRPVVDLTVSMTFTPDALPMVFIGKMDVKLCFE   700
 701  VDSSGVASEPGLREMFLNFTVDVDVTKQRQRLQCEDSSGCQSCLRKWNGG   750
 751  SFLCEHFWLISTEELCEEDCFSNITIKVTYEFQTSGGRRDYPNPTLDHYK   800
 801  EPSAIFQLPYEKDCKNKVFCIAEIQLTTNISQQELVVGVTKEVTMNISLT   850
 851  NSGEDSYMTNMALNYPRNLQFKKIQKPVSPDVQCDDPKPVASVLVMNCKI   900
 901  GHPILKRSSVNVSVTWQLEESVFPNRTADITVTISNSNEKSLARETRSLQ   950
 951  FRHAFIAVLSRPSVMYMNTSQSPSDHKEFFFNVHGENLFGAVFQLQICVP  1000
1001  IKLQDFQIVRVKNLTKTQDHTECTQSQEPACGSDPVQHVKEWHSVVCAIT  1050
1051  SNKENVTVAAEISVGHTKQLLRDVSELPILGEISFNKSLYEGLNAENHRT  1100
1101  KITVIFLKEEETRSLPLIIGSSIGGLLVLVVIIAILFKCGFFKRKYQQLN  1150
1151  LESTRRAQLKADSLLQD                                   1167

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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