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

NucPred

Fetching Q6P1G2 from www.uniprot.org...

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

   1  MEAEKDSGRRLRAIDRQRYDENEDLSDVEEIVSVRGFSLEEKLRSQLYQG    50
  51  DFVHAMEGKDFNYEYVQREALRVPLVFRDKDGLGIKMPDPDFTVRDVKLL   100
 101  VGSRRLVDVMDVNTQKGTEMSMSQFVRYYETPEAQRDKLYNVISLEFSHT   150
 151  KLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNALAEMKYPKVKKYCL   200
 201  MSVKGCFTDFHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSG   250
 251  KQSDIFLGDRVERCQRIELKQGYTFFIPSGWIHAVYTPVDSLVFGGNILH   300
 301  SFNVPMQLRIYEIEDRTRVQPKFRYPFYYEMCWYVLERYVYCVTQRSYLT   350
 351  QEYQRELMLIDAPRKTSVDGFSSDSWLDMEEESCEQQPQEEEEEEEDKEE   400
 401  EGDGADKTPKPPTDDPTSPTSTPPEDQDSTGKKPKAPAIRFLKRTLSNES   450
 451  EESVKSTSMPTDDPKTPTGSPATEVSTKWTHLTEFELKGLKALVEKLESL   500
 501  PENKKCVPEGIEDPQALLEGVKNVLKEHVDDDPTLAITGVPVVSWPKKTA   550
 551  KNRVVGRPKGKLGPASAVKLAANRTTAGARRRRTRCRKCEACLRTECGEC   600
 601  HFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDTVEEE   650
 651  EGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCNHAGK   700
 701  TGKQKRGPGFKYASNLPGSLLKEQKMNRDNKEGQEPAKRRSECEEAPRRR   750
 751  SDEHPKKVPADGILRRKSDDVHLRRKRKYEKPQELSGRKRASSLQTSPGS   800
 801  SSHLSPRPPLGSSLSPWWRSSLTYFQQQLKPGKEDKLFRKKRRSWKNAED   850
 851  RLSLANKPLRRFKQEPEDDLPEAPPKTRESDQSRSSSPTAGPSTEGAEGP   900
 901  EEKKKVKMRRKRRLVNKELSKELSKELNHEIQKTESTLAHESQQPIKSEP   950
 951  ESENDEPKRPLSHCERPHRFSKGLNGTPRELRHSLGPGLRSPPRVMSRPP  1000
1001  PSASPPKCIQMERHVIRPPPISPPPDSLPLDDGAAHVMHREVWMAVFSYL  1050
1051  SHRDLCVCMRVCRTWNRWCCDKRLWTRIDLNRCKSITPLMLSGIIRRQPV  1100
1101  SLDLSWTNISKKQLSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRT  1150
1151  LDVQWVEGLKDAQMRDLLSPPTDNRPGQMDNRSKLRNIVELRLAGLDITD  1200
1201  VSLRLIIRHMPLLSKLQLSYCNHINDQSINLLTAVGTTTRDSLTEVNLSD  1250
1251  CNKVTDLCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSVSVQFGQV  1300
1301  EEKLLQKLS                                           1309

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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