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

NucPred

Fetching P12866 from www.uniprot.org...

The NucPred score for your sequence is 0.58 (see score help below)

   1  MNFLSFKTTKHYHIFRYVNIRNDYRLLMIMIIGTVATGLVPAITSILTGR    50
  51  VFDLLSVFVANGSHQGLYSQLVQRSMAVMALGAASVPVMWLSLTSWMHIG   100
 101  ERQGFRIRSQILEAYLEEKPMEWYDNNEKLLGDFTQINRCVEELRSSSAE   150
 151  ASAITFQNLVAICALLGTSFYYSWSLTLIILCSSPIITFFAVVFSRMIHV   200
 201  YSEKENSETSKAAQLLTWSMNAAQLVRLYCTQRLERKKFKEIILNCNTFF   250
 251  IKSCFFVAANAGILRFLTLTMFVQGFWFGSAMIKKGKLNINDVITCFHSC   300
 301  IMLGSTLNNTLHQIVVLQKGGVAMEKIMTLLKDGSKRNPLNKTVAHQFPL   350
 351  DYATSDLTFANVSFSYPSRPSEAVLKNVSLNFSAGQFTFIVGKSGSGKST   400
 401  LSNLLLRFYDGYNGSISINGHNIQTIDQKLLIENITVVEQRCTLFNDTLR   450
 451  KNILLGSTDSVRNADCSTNENRHLIKDACQMALLDRFILDLPDGLETLIG   500
 501  TGGVTLSGGQQQRVAIARAFIRDTPILFLDEAVSALDIVHRNLLMKAIRH   550
 551  WRKGKTTIILTHELSQIESDDYLYLMKEGEVVESGTQSELLADPTTTFST   600
 601  WYHLQNDYSDAKTIVDTETEEKSIHTVESFNSQLETPKLGSCLSNLGYDE   650
 651  TDQLSFYEAIYQKRSNVRTRRVKVEEENIGYALKQQKNTESSTGPQLLSI   700
 701  IQIIKRMIKSIRYKKILILGLLCSLIAGATNPVFSYTFSFLLEGIVPSTD   750
 751  GKTGSSHYLAKWSLLVLGVAAADGIFNFAKGFLLDCCSEYWVMDLRNEVM   800
 801  EKLTRKNMDWFSGENNKASEISALVLNDLRDLRSLVSEFLSAMTSFVTVS   850
 851  TIGLIWALVSGWKLSLVCISMFPLIIIFSAIYGGILQKCETDYKTSVAQL   900
 901  ENCLYQIVTNIKTIKCLQAEFHFQLTYHDLKIKMQQIASKRAIATGFGIS   950
 951  MTNMIVMCIQAIIYYYGLKLVMIHEYTSKEMFTTFTLLLFTIMSCTSLVS  1000
1001  QIPDISRGQRAASWIYRILDEKHNTLEVENNNARTVGIAGHTYHGKEKKP  1050
1051  IVSIQNLTFAYPSAPTAFVYKNMNFDMFCGQTLGIIGESGTGKSTLVLLL  1100
1101  TKLYNCEVGKIKIDGTDVNDWNLTSLRKEISVVEQKPLLFNGTIRDNLTY  1150
1151  GLQDEILEIEMYDALKYVGIHDFVISSPQGLDTRIDTTLLSGGQAQRLCI  1200
1201  ARALLRKSKILILDECTSALDSVSSSIINEIVKKGPPALLTMVITHSEQM  1250
1251  MRSCNSIAVLKDGKVVERGNFDTLYNNRGELFQIVSNQSS            1290

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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