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

NucPred

Fetching P70475 from www.uniprot.org...

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

   1  MDVDAEEKRHRTRSKGVRVPVEPAIQELFSCPTPGCDGSGHVSGKYARHR    50
  51  SVYGCPLAKKRKTQDKQPQEPAPKRKPFAVKADSSSVDECYESDGTEDMD   100
 101  DKEEDDDEEFSEDNDEQGDDDDEDEVDREDEEEIEEEDDEDDEDDDDGDD   150
 151  VEEEEDDDDEEEEEEEEEEENEDHQMSCTRIMQDPEKDDNNNDEYDNYDE   200
 201  LVAKSLLNLGKIAEDAAYRARTESEMNSNTSNSLEDDSDKNENLGRKSEL   250
 251  SLDLDSDVVRETVDSLKLLAQGHGVVLSENISDRSYAEGMSQQDSRNMNY   300
 301  VMLGKPMNNGLMEKMVEESDEEVCLSSLECLRNQCFDLARKLSETNPQDR   350
 351  SQPPNMSVRQHVRQEDDFPGRTPDRSYSDMMNLMRLEEQLSPRSRTFSSC   400
 401  AKEDGCHERDDDTTSVNSDRSEEVFDMTKGNLTLLEKAIALETERAKAMR   450
 451  EKMAMDAGRRDNLRSYEDQSPRQLAGEDRKSKSSDSHVKKPYYDPSRTEK   500
 501  RESKCPTPGCDGTGHVTGLYPHHRSLSGCPHKDRVPPEILAMHENVLKCP   550
 551  TPGCTGRGHVNSNRNSHRSLSGCPIAAAEKLAKAQEKHQSCDVSKSNQAS   600
 601  DRVLRPMCFVKQLEIPQYGYRNNVPTTTPRSNLAKELEKYSKTSFEYNSY   650
 651  DNHTYGKRAIAPKVQTRDISPKGYDDAKRYCKNASPSSSTTSSYAPSSSS   700
 701  NLSCGGGSSASSTCSKSSFDYTHDMEAAHMAATAILNLSTRCREMPQNLS   750
 751  TKPQDLCTARNPDMEVDENGTLDLSMNKQRPRDSCCPVLTPLEPMSPQQQ   800
 801  AVMSSRCFQLSEGDCWDLPVDYTKMKPRRVDEEDPKEITPEDLDPFQEAL   850
 851  EERRYPGEVTIPSPKPKYPQCKESKKDLITLSGCPLADKSIRSMLATSSQ   900
 901  ELKCPTPGCDGSGHITGNYASHRSLSGCPRAKKSGIRIAQSKEDKEDQEP   950
 951  IRCPVPGCDGQGHITGKYASHRSASGCPLAAKRQKDGYLNGSQFSWKSVK  1000
1001  TEGMSCPTPGCDGSGHVSGSFLTHRSLSGCPRATSAMKKAKLSGEQMLTI  1050
1051  KQRASNGIENDEEIKQLDEEIKELNESNSQMEADMIKLRTQVTITTMESN  1100
1101  LKTIEEENKVIEQQNESLLHELANLSQSLIHSLANIQLPHMDPINEQNFD  1150
1151  AYVTTLTEMYTNQDRYQSPENKALLENIKQAVRGIQV               1187

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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