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

NucPred

Fetching Q6L400 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MNFNNELSDLEKSFLFWTLRVQEYSYDTMHRIDFFLWELQVLNCFLHLQS    50
  51  FTFASECGMLDISQKMLEICKRFNTPPPHNAFAYWKELICKRLCAISIRP   100
 101  DDGFAYWKKVIWKTKQEFRAKYSFPKTLLADNKVDDDDTNPEFVMEFIDA   150
 151  VVGNLNVLVKINDPSSLLFVPGPKEQIEQVLKELKLLRFFVCFVSNKCIE   200
 201  PQYQHTTFYTHALIEASHIAMVVWLNLPIYGNRNQDLASSEVSCLLSNFM   250
 251  EMKIKSIQPGISRNNIYIDVLQALKSTIPQAQKKHAAESGIVEIPTHSLM   300
 301  VGLSDQMANLQEMLCLLKDNLIHLPILDLEFQPQDMDSVIIDAGLLIYSF   350
 351  YDMKGEKEDTTLEDINRELGFDLSRNIEPIKVMIYLVMQKAFQCNLPRIH   400
 401  GLGYVDFLLKNLKDFQGRYSDSFALHKTQIQVIQKEFESLQPFLKVVVEE   450
 451  PHNTFKRLSEDCAIQIIRKAHEVEYVVDACINKGIPHWRLKGWLQIIIED   500
 501  ITCIKEKIQEKNTVDDTMKTVIARTSSKLARTPRMNEEIVGFKDVIENLR   550
 551  NQLLNGTKGQDAISIHGMPGLGKTTLANTLYSDRSVVSQFDICAQCCVSQ   600
 601  VYSYKDLLLALLCDAVGEDSDRRELPDNELADMLRKTLLPRRYLILVDDV   650
 651  WDNSAWDDLRGCFPDVNNRSRIILTTRHHEVAKYASVHSDPLHLRMFDKD   700
 701  ESWKLLEKKVFGEQSCSPLLKDVGLRIAKMCGQLPLSIVLVAGILSEMEK   750
 751  EVECWEQVANNLGTHIHNDSRAIVNQSYHVLPCHLKSCFLYFGAFLEDEV   800
 801  IDISRLIRLWISESFIKSSEGRRLEDIAEGYLENLIGRNLVMVTQRADSD   850
 851  GKVKACRLHDVLLDFCKERAAEENFLLWINRDQSTNAVYSHKRHAHLAFT   900
 901  EMDSLVEWSASCSLVGSVLLKNYARRPLSSPAFSISHILLNFKFLKVLDL   950
 951  EHQVVIDSIPTELFYLRYLSARIEQNSIPSSISNLWNLETLILKHVSRCT  1000
1001  VLLPSTVWDMVKLRHLHIPNFRPENEEALLENSAKLYDLETLSTPYFSRV  1050
1051  EDAELMLRKTPNLRKLVCEVECLEYPPQYHVLNFPIRLEILKLYRSKAFN  1100
1101  TIPFCISAPNLKYLKLSRSYMDSQYLSETADHLKNLEVLKLYFVKFADHR  1150
1151  EWKVSNGMFPQLKILKLEYLALMKWIVADDAFPNLEQLVLHECRHLMEIP  1200
1201  SCFMDIPSLKYIEVENCNESVVKSAMNIQETQVEDYQNTNFKLVLIGIES  1250
1251  ISTDTKEKKLTVTRDVDADEVQLVVEKQRKRGML                  1284

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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