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

NucPred

Fetching Q9VPQ6 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MLSSNTRGDCSDTAEEMTVDSRDSKDLSAQDIGEQKQQQMEDQLEDQLND    50
  51  SRDPQNNNNNIDDDADEDAEFEEPEKANPQQDQDLGETEMEQEHDLQQED   100
 101  LQQELPANSPSTPPRSPSSPQLIPKLEQPATPPSEPEASPCPSPSPCPTP   150
 151  KYPKVRLNALLASDPALKPDAKELTLPDSRLLAPPPLVKPDTQAQPEVAE   200
 201  PLLKPARFMCLPCGIAFSSPSTLEAHQAYYCSHRIKDTDEAGSDKSGAGG   250
 251  SGATAGDAAGLTGGSTEPPAKMARTGKQYGCTQCSYSADKKVSLNRHMRM   300
 301  HQTSPAAPTLAGLPSLLQNGIAPPGVTPNPMEDSSSQQTDRYCSHCDIRF   350
 351  NNIKTYRAHKQHYCSSRRPEGQLTPKPDASPGAGSGPGSAGGSIGVSAQA   400
 401  ATPGKLSPQARNKTPTPAMVAVAAAAAAAAASLQATPHSHPPFLALPTHP   450
 451  IIIVPCSLIRAASFIPGPLPTPNSGIVNPETTCFTVDNGTIKPLATALVG   500
 501  ATLEPERPSAPSSAAEATEAKSSPPEPKRKEAGLTRESAPLDLSLRRSPI   550
 551  TLNSLSLRQRQLRNALLDVEEVLLAGVGTGKENVETPRGGGSVTPEQIVC   600
 601  APSLPSSPSMSPSPKRRAISPRSSGAGSASSMSPPGLNVAVPHLLDMRSM   650
 651  LPADFGLSESLLAKTNPELALKLAAAAAAAAVAGSSGAAAFPPASLPAQT   700
 701  SSGNPGSGGSAGGAQQPQIYVKKGVSKCMECNIVFCKYENYLAHKQHYCS   750
 751  ARSQEGASEVDVKSAVSPSIAGAGGLGAGAAEAASSVETTPVAYQQLICA   800
 801  ACGIKYTSLDNLRAHQNYYCPKGGAVAAPAATPTDPGQLGMPKEKCGKCK   850
 851  TLHEIGLPCPPPVANPLAAPTVNPQPATNSLNKCPVCGVVSPTAALAKKH   900
 901  MEMHGTVKAYRCSICQYKGNTLRGMRTHIRTHFDKKTSDVNEELYMTCIF   950
 951  EEDASALSQELVTPTGASTTTGHDSMDHPSQMFNCDYCNYVSTYKGNVLR  1000
1001  HMKLMHPHVAINSPSISPDTRDQDVTSNPTTNQHSNSDVSNGEAPSFHIK  1050
1051  SEPLDPPPTVNLVHENNNSPIATPHIKAEPIEVGADAAPGGLVPPMTSPL  1100
1101  GNSSSVAAAAAAAAEVMKKYCSTCDISFNYVKTYLAHKQFYCKNKPIRPE  1150
1151  ASDSPSPNHLGGGVAVGLGIGGLVGGHGQQKNKENLQEAAI           1191

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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