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

NucPred

Fetching Q96QU1 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MFRQFYLWTCLASGIILGSLFEICLGQYDDDCKLARGGPPATIVAIDEES    50
  51  RNGTILVDNMLIKGTAGGPDPTIELSLKDNVDYWVLMDPVKQMLFLNSTG   100
 101  RVLDRDPPMNIHSIVVQVQCINKKVGTIIYHEVRIVVRDRNDNSPTFKHE   150
 151  SYYATVNELTPVGTTIFTGFSGDNGATDIDDGPNGQIEYVIQYNPDDPTS   200
 201  NDTFEIPLMLTGNIVLRKRLNYEDKTRYFVIIQANDRAQNLNERRTTTTT   250
 251  LTVDVLDGDDLGPMFLPCVLVPNTRDCRPLTYQAAIPELRTPEELNPIIV   300
 301  TPPIQAIDQDRNIQPPSDRPGILYSILVGTPEDYPRFFHMHPRTAELSLL   350
 351  EPVNRDFHQKFDLVIKAEQDNGHPLPAFAGLHIEILDENNQSPYFTMPSY   400
 401  QGYILESAPVGATISDSLNLTSPLRIVALDKDIEDTKDPELHLFLNDYTS   450
 451  VFTVTQTGITRYLTLLQPVDREEQQTYTFSITAFDGVQESEPVIVNIQVM   500
 501  DANDNTPTFPEISYDVYVYTDMRPGDSVIQLTAVDADEGSNGEITYEILV   550
 551  GAQGDFIINKTTGLITIAPGVEMIVGRTYALTVQAADNAPPAERRNSICT   600
 601  VYIEVLPPNNQSPPRFPQLMYSLEISEAMRVGAVLLNLQATDREGDSITY   650
 651  AIENGDPQRVFNLSETTGILTLGKALDRESTDRYILIITASDGRPDGTST   700
 701  ATVNIVVTDVNDNAPVFDPYLPRNLSVVEEEANAFVGQVKATDPDAGING   750
 751  QVHYSLGNFNNLFRITSNGSIYTAVKLNREVRDYYELVVVATDGAVHPRH   800
 801  STLTLAIKVLDIDDNSPVFTNSTYTVLVEENLPAGTTILQIEAKDVDLGA   850
 851  NVSYRIRSPEVKHFFALHPFTGELSLLRSLDYEAFPDQEASITFLVEAFD   900
 901  IYGTMPPGIATVTVIVKDMNDYPPVFSKRIYKGMVAPDAVKGTPITTVYA   950
 951  EDADPPGLPASRVRYRVDDVQFPYPASIFEVEEDSGRVITRVNLNEEPTT  1000
1001  IFKLVVVAFDDGEPVMSSSATVKILVLHPGEIPRFTQEEYRPPPVSELAT  1050
1051  KGTMVGVISAAAINQSIVYSIVSGNEEDTFGINNITGVIYVNGPLDYETR  1100
1101  TSYVLRVQADSLEVVLANLRVPSKSNTAKVYIEIQDENNHPPVFQKKFYI  1150
1151  GGVSEDARMFTSVLRVKATDKDTGNYSVMAYRLIIPPIKEGKEGFVVETY  1200
1201  TGLIKTAMLFHNMRRSYFKFQVIATDDYGKGLSGKADVLVSVVNQLDMQV  1250
1251  IVSNVPPTLVEKKIEDLTEILDRYVQEQIPGAKVVVESIGARRHGDAFSL  1300
1301  EDYTKCDLTVYAIDPQTNRAIDRNELFKFLDGKLLDINKDFQPYYGEGGR  1350
1351  ILEIRTPEAVTSIKKRGESLGYTEGALLALAFIIILCCIPAILVVLVSYR  1400
1401  QFKVRQAECTKTARIQAALPAAKPAVPAPAPVAAPPPPPPPPPGAHLYEE  1450
1451  LGDSSILFLLYHFQQSRGNNSVSEDRKHQQVVMPFSSNTIEAHKSAHVDG  1500
1501  SLKSNKLKSARKFTFLSDEDDLSAHNPLYKENISQVSTNSDISQRTDFVD  1550
1551  PFSPKIQAKSKSLRGPREKIQRLWSQSVSLPRRLMRKVPNRPEIIDLQQW  1600
1601  QGTRQKAENENTGICTNKRGSSNPLLTTEEANLTEKEEIRQGETLMIEGT  1650
1651  EQLKSLSSDSSFCFPRPHFSFSTLPTVSRTVELKSEPNVISSPAECSLEL  1700
1701  SPSRPCVLHSSLSRRETPICMLPIETERNIFENFAHPPNISPSACPLPPP  1750
1751  PPISPPSPPPAPAPLAPPPDISPFSLFCPPPSPPSIPLPLPPPTFFPLSV  1800
1801  STSGPPTPPLLPPFPTPLPPPPPSIPCPPPPSASFLSTECVCITGVKCTT  1850
1851  NLMPAEKIKSSMTQLSTTTVCKTDPQREPKGILRHVKNLAELEKSVANMY  1900
1901  SQIEKNYLRTNVSELQTMCPSEVTNMEITSEQNKGSLNNIVEGTEKQSHS  1950
1951  QSTSL                                               1955

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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