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

NucPred

Fetching Q09259 from www.uniprot.org...

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

   1  MESGDHLGNLFDDMVEEDNDEDSFEEPACEDSFDSQEASSKANEPQNDSF    50
  51  DEPIQSSVSKQSDDANGEDEINEEVIQEQKELDLNEEDFNLLTIEEVPLD   100
 101  VLTARIRRVFTEVTYRAEPAAIALFDVAHKIIFKSTMLDCKRNTVIDSII   150
 151  EGLISIIVDERERDQGAEEAEHVLMIFIAKLAIKNKSMKCSDLLYKLILL   200
 201  VDRLYLHADSFVRCRIYRLIACLMEEANRYADVMREHGDDAFLSDEDPTE   250
 251  SEVMIPSGVKNRWMGKLAKSLLDKSPEVRCKAVIALSLWDHDIECKTTCC   300
 301  DEVTVNDLLWKSVHDVDESVRVNAARRVHIANENDIDKCIDYVETSKDNR   350
 351  VKQAIIVRLASDVSLLSFSEKQRFRLVNLLNNSDSARVQDVIHQLLVESW   400
 401  MKVAGDEIISPSIFPFPDSDNNNIPKEFPSIILEYLDPLVDPTAVYVFMK   450
 451  FATVRFIQKSTVQQACGSLDVEKFMKDLLSMTIPDCERVGLMRRTTFRLI   500
 501  PKDNNDGNEDIRKIFSRIFISRCFVDVIFNFAKGRLDATHLRSRALTFFL   550
 551  PDVTTFVEHLEKFCDAYFHRNMSTDYTCKDLVLYNLLHLMNVATKYGDLH   600
 601  DDKMLYKHALKKILGNSSFVFSSETILTIVMICFDLCKIGDDVKQLCDWM   650
 651  CDTAKQLMLSHEEVLNLEEAMKNDKVLEQMYLRSATMLLATCKHEEVESP   700
 701  TASMSSLFKTIIPALLGNKNEELQQLGLELIGFATSIDFENCEPYLKLTT   750
 751  LLIQRGDEVLTSTGVNTLIKVIKSQGFPKTANAIFQGEEQTEDDCQDALA   800
 801  KVFEKALVSLQGMALVQSVQDCLSMLSYGRYAWSKLMCAIIMLVFQKSNE   850
 851  CLPLVKIFASYCKKSIRSDFNKMNLLLGFCRAVGIISKTGEDDSNIKLLE   900
 901  MTELVCECISSVHTIDGDEVIPQKKRKTDNEEELYPEIVLANRMVGRANS   950
 951  HPSSWIIRHVFTAMATSLRLECVPMKIVDTLHELLVDTYTVVRFNSNKTT  1000
1001  QIAFKRFLTHCEKVITLHERMNALKLGVDFKKVKKEVICADEDPKSVSSS  1050
1051  SSLGRKRGRKRENSEEEEKIDADDSFELFQYVPKSTRTRIRPTVNVEEDQ  1100
1101  NIKTEIEDSDDLEDSFEL                                  1118

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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