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

NucPred

Fetching Q9JIX8 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MWGRKRPNSSGETRGILSGNRGVDYGSGRGQSGPFEGRWRKLPKMPEAVG    50
  51  TDPSTSRKMAELEEVTLDGKPLQALRVTDLKAALEQRGLAKSGQKSALVK   100
 101  RLKGALMLENLQKHSTPHAAFQPNSQIGEEMSQNSFIKQYLEKQQELLRQ   150
 151  RLEREAREAAELEEASAESEDEMTHPEGVASLLPPDFQSSLNRPELELST   200
 201  HSPRKSSSFSEEKGESDDEKPRKGERRSSRVRQAKSKLPEYSQTAEEEED   250
 251  QETPSRNLRVRADRNLKIEEEEEEEEEEEDDDDEEEEEVDEAQKSREAEA   300
 301  PTLKQFEDEEGEERTRAKPEKVVDEKPLNIRSQEKGELEKGGRVTRSQEE   350
 351  ARRSHLARQQQEKETQIVSLPQEENEVKSSQSLEEKSQSPSPPPLPEDLE   400
 401  KAPVVLQPEQIVSEEETPPPLLTKEASSPPTHIQLQEEMEPVEGPAPPVL   450
 451  IQLSPPNTDAGAREPLASPHPAQLLRSLSPLSGTTDTKAESPAGRVSDES   500
 501  VLPLAQKSSLPECSTQKGVESEREKSAPLPLTVEEFAPAKGITEEPMKKQ   550
 551  SLEQKEGRRASHALFPEHSGKQSADSSSSRSSSPSSSSSPSRSPSPDSVA   600
 601  SRPQSSPGSKQRDGAQARVHANPHERPKMGSRSTSESRSRSRSRSRSASS   650
 651  SSRKSLSPGVSRDSNTSYTETKDPSCGQEAAAPSGPQLQVLEPKEKAPTF   700
 701  SASVRGRHLSHPEPEQQHVIQRLQPEQGSPKKCEAEEAEPPAATQPQTSE   750
 751  TQISHLLESERTHHTVEEKEEVTMDTSENRPENEVPEPPLPVADQVSNDE   800
 801  RPEGGAEEEEKKESSMPKSFKRKISVVSATKGVQAGNSDTEGGQPGRKRR   850
 851  WGASTAATQKKPSISITTESLKSLIPDIKPLAGQEAVVDLHADDSRISED   900
 901  ETERNGDDGTHDKGLKICRTVTQVVPAEGQENGQREEEEEKEPEAELPAP   950
 951  PQVSVEVALPPPVEHEVKKVTLGDTLTRRSISQQKSGVSITIDDPVRTAQ  1000
1001  VPSPPRGKISNIVHISNLVRPFTLGQLKELLGRTGTLVEEAFWIDKIKSH  1050
1051  CFVTYSTVEEAVATRTALHGVKWPQSNPKFLCADYAEQDELDYHRGLLVD  1100
1101  RPSETKAEEQGAPRPLHPPPPPPVQPPPHPRAEQREQERAVREQWAERER  1150
1151  EMERRERTRSEREWDRDKVREGPRSRSRSRDRRRKERAKSKEKKSEKKEK  1200
1201  AQEEPPAKLLDDLFRKTKAAPCIYWLPLTESQIVQKEAEQAERAKEREKR  1250
1251  RKEREEEEQKEREKEAERERNRQLEREKRREHSRERERDRERERDRGDRE  1300
1301  RERERDRDRGRERDRRDTKRHSRSRSRSTPVRDRGGRR              1338

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.)

Go back to the NucPred Home Page.