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

NucPred

Fetching Q8HYY4 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MMSCWFSCAPKNRQAADWNKYDDRLMRAAERGDVEKVSSILAKKGVNPGK    50
  51  LDVEGRSAFHVVASKGNLECLNAILIHGVDITTSDTAGRNALHLAAKYGH   100
 101  ALCLQKLLQYNCPTEHVDLQGRTALHDAAMADCPSSIQLLCDHGASVNAK   150
 151  DVDGRTPLVLATQMCRPTICQLLIDRGADINSRDKQNRTALMLGCEYGCK   200
 201  DAVEVLIKNGADVTLLDALGHDSSYYARIGDNLDILTLLKTASENSNKGR   250
 251  ELWKKGPSLQQRNLSQMLDEVNTKSNQREHQNIQDLEIENEDLKERLRKI   300
 301  QQEQRILLDKVNGLQLQLNEEVMVADDLESEKEKLKSLLAAKEKQHEESL   350
 351  RTIEALKSRFKYFESDHLGSGSHFRKEDMLLKQGQMYMTDSQCTSTGMPV   400
 401  HMQSRSMLRPLELALPNQASYSENEILKKELEAMRTFCDSAKQDRLKLQN   450
 451  ELAHKVAECKALALECERVKEDSDEQIKQLEDALKDVQKRMYESEGKVKQ   500
 501  MQTHFLALKEHLTSDAATGNHRLMEELKDQLKDMKVKYEGASAEVGKLRN   550
 551  QIKQNEMLVEEFKRDEGKLMEENKRLQKELSMCELEREKRGRKLTEMEGQ   600
 601  LKDLSAKLALSIPAEKFENMKSLLSNELNEKAKKLIDVEREYERSLNETR   650
 651  PLKRELENLKAKLAQHVKPEEHEQLKSRLEQKSGELGKRITELTSKNQTL   700
 701  QKEIEKVCLDNKLLTQQVNNLTTEMKNHYVPLKVSEEMKKSHDVIVDDLN   750
 751  KKLSDVTHKYTEKKLEMEKLLMENASLSKNVSRLETVFIPPERHEKEMMA   800
 801  LKSNITELKKQLSELNKKCGEDQEKIYSLMSENNDLKKTMSHQYVPVKTH   850
 851  EEIKTALSSTLDKTNRELVDVKKKCEDINQEFVKIKDENEILKRNLENTQ   900
 901  NQVKAEYISLREHEEKMSGLRKSMKKVQDNSAEILAKYKKSQEEIVTLHE   950
 951  EIAAQKRELDTIQECIKLKYAPIISLEECERKFKATEKELKEQLSQQTQK  1000
1001  YNTSEEEAKKCKQENDKLKKEILTLQKDLKDKNVHIENSYETERALSRKT  1050
1051  EELNRQLKDLLQKYTEAKKEKEKLVEENAKQTSEILAAQTLLQKQHVPLE  1100
1101  QVESLKKSLSGTIETLKEELKTKQRCYEKEQQTVTQLRQMLENQKNSSVP  1150
1151  LAEHLQVKEAFEKEVGIIKASLREKEEESQNKTEEVSKLQSEIQNTKQAL  1200
1201  KKLETREVVDLSKYKATKSDLETQISDLNEKLANLNRKYEEVCEEVLHAK  1250
1251  KKELSAKDEKELLHFSIEQEIKDQQERCDKSLTTITELQRRIQESAKQIE  1300
1301  AKDNKITELLNDVERLKQALNGLSQLTYGSGSPSKRQSQLIDSLQQQVRS  1350
1351  LQQQLADADRQHQEVIAIYRTHLLSAAQGHMDEDVQAALLQIIQMRQGLV  1400
1401  C                                                   1401

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.)

Go back to the NucPred Home Page.