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

NucPred

Fetching Q61738 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MARIPRCDFLRPPGIYYLITSLLAGLFLPPAIAFNLDVMGAIRKEGEPGS    50
  51  LFGFSVALHRQLQPRPQSWLLVGAPQALALPGQQANRTGGLFACPLSLEE   100
 101  TDCYRVDIDRGANVQKESKENQWLGVSVRSQGAGGKIVTCAHRYESRQRV   150
 151  DQALETRDVIGRCFVLSQDLAIRDELDGGEWKFCEGRPQGHEQFGFCQQG   200
 201  TAATFSPDSHYLVFGAPGTYNWKGTARVELCAQGSPDLAHLDDGPYEAGG   250
 251  EKEQDPRLIPVPANSYLGLLFVTNIDSSDPDQLVYKTLDPADRLTGPAGD   300
 301  LTLNSYLGFSIDSGKGLMRSEELSFVAGAPRANHKGAVVILRKDSATRLI   350
 351  PEVVLSGERLTSGFGYSLAVTDLNNDGWADLIVGAPYFFERQEELGGAVY   400
 401  VYMNQGGHWADISPLRICGSPDSMFGISLAVLGDLNQDGFPDIAVGAPFD   450
 451  GDGKVFIYHGSSLGVVVKPSQVLEGEAVGIKSFGYSLSGGLDVDGNHYPD   500
 501  LLVGSLADTAALFRARPVLHVSQEIFIDPRAIDLEQPNCADGRLVCVDIK   550
 551  ICFSYVAVPSSYSPSVALDYMLDGDTDRRLRGQVPRVTFLSRGLDDLRHQ   600
 601  SSGTVWLKHQHDRVCGDTVFQLQENVKDKLRAIVVTLSYGLRTPPLGRQA   650
 651  PGQELPTVAPILNAHQPSTQRTEIHFLKQGCGQDKICQSNLQLERYQFCS   700
 701  RISDTEFQALPMDLDGRTALFALSGQPFIGLELTVTNLPSDPSRPQADGD   750
 751  DAHEAQLLVTLPASLRYSGVRALDSVEKPLCLSNDSASHVECELGNPMKR   800
 801  GAQVTFYLILSTSGITIETTELEVKLLLATISEQELDPVSVRAHVFIELP   850
 851  LSISGVATPQQLFFSGEVKGESAMRSERELGRKVKYEVTVSNQGQSLNTL   900
 901  GSANLNIMWPHEIANGKWLLYPMRVELEGGQGPGKRGICSPRPNILQLDV   950
 951  DSRDRRRRELGQPEPQEPPEKVEPSTSWWPVSSAEKRNMTLDCPRTAKCV  1000
1001  VFSCPLYSFDRAAVLHVWGRLWNSTFLEEYMAVKSLEVIVRANITVKSSI  1050
1051  KNLLLRDASTVIPVMVYLDPMAVVVEGVPWWVILLGVLAGLLVLALLVLL  1100
1101  LWKLGFFKRAKHPEATVPQYHAVKIPREDRQQFKEEKTGTIQRSNWGNSQ  1150
1151  WEGSDAHPILAADWHPELGPDGHPVPATA                       1179

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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