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

NucPred

Fetching Q7ZUV7 from www.uniprot.org...

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

   1  MPVVWPTLLDLSRDECKRILRKLELEAYAGVISALRAQGDLTKDKKELLG    50
  51  ELTRVLSISTERHRAEVRRAVNDERLTTIAHHMSGPNSSSEWSIEGRRLV   100
 101  PLMPRLVPQTAFTVMANAVANATAHQNASLPLPAETANKEVVVCYSYTST   150
 151  TSTPPSASAPSSSSAAVKSPRPASPASNVVVLPSGSTVYVKSVSCSDEDE   200
 201  KPRKRRRTSSSSSSPVLLKEVPKVAVTAPGPKTITLPVSGGPKISNLMQS   250
 251  IANSLPPHMSPVKITFTKPSTQTTNTTTQKVIIVTTSPSSNFVPNILSKS   300
 301  HNYAAVSKLVSSAALTASSQKQTMVISAGGSSVAPGPGPVAVTTVVSSTP   350
 351  SVVMSTVAQAGSAAVKVASTRLPSPKALIGSPSQILQIPKAQQAVLQSAA   400
 401  PKALQGSISTAQSTALAAAGPGAKPTIQIKQESGVKIITQQMQPSKILPK   450
 451  PSSAALPSSSSAPIMVVSSNGAIMTTKLVSTPTGSASTYTRPTVSPMGTR   500
 501  VATSPAGATYVKTTSGSIITVVPKALATLGGKIITTSMVSGTTTKITTIP   550
 551  MTSKPNVIVVQKTTGKGTTIQGLPGKNVVTTLLNAGGEKTLQAIPGAKPA   600
 601  IITASRPITKMIVTQPKSLGAGVQPSTTTKIIPTKIVYGQQGKTQVLIKP   650
 651  KPMAFQTAVVSEQTRQLVSETLQQVNRSAENNTTSTHTSAAAAGLENRDD   700
 701  THTYTEGSPVPSDSTHDAPPVVHLISSRGQEWAEQEVSVESSPALIYQEL   750
 751  TAESQSATSTIKALLELQQTSVKEKSEAKPRQHTIDLSQMAVPIPVSAEQ   800
 801  RESPEPSGQSAAESDAHTEFIPIGKVSKAAEVSASSTPGQSASAVSAAPH   850
 851  VVKISTAAVTTQQVEAQVKPQQEQVLVEECELEGDTLDPQTGLFYRSSPQ   900
 901  QQLSRVCEAASSSSSSSSSSSRRAEPPLTVKILTHRSSSSAPATAASANT   950
 951  PHTPQLPRLQQAPTTHNRPNTHTQLSQPPPLQAHHPVGSSKTSSGAQVQQ  1000
1001  PIITQGATVTKITFGAPHVPRAPVSSSSSSEAALKLQAESSSEKPSVPDI  1050
1051  LKISMMEAEIDPGAEPMLVDSSSDCGPLTKAPAGPSLISSSKQTLAHGPF  1100
1101  SRKSKELDIIQVIPQYSIMPDSSQSNVVVEPSGFLEISDYTSQRLDEEQA  1150
1151  MEQEVDSSNDEGAAASPSADQSQ                             1173

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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