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

NucPred

Fetching Q7PC88 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MAAASNGSEYFEFDVETGRESFARPSNAETVEQDEEDLRWAAIGRLPSQR    50
  51  QGTHNAILRRSQTQTQTSGYADGNVVQTIDVKKLDRADREMLVRQALATS   100
 101  DQDNFKLLSAIKERLDRVGMEVPKIEVRFENLNIEADVQAGTRALPTLVN   150
 151  VSRDFFERCLSSLRIIKPRKHKLNILKDISGIIKPGRMTLLLGPPGSGKS   200
 201  TLLLALAGKLDKSLKKTGNITYNGENLNKFHVKRTSAYISQTDNHIAELT   250
 251  VRETLDFAARCQGASEGFAGYMKDLTRLEKERGIRPSSEIDAFMKAASVK   300
 301  GEKHSVSTDYVLKVLGLDVCSDTMVGNDMMRGVSGGQRKRVTTGEMTVGP   350
 351  RKTLFMDEISTGLDSSTTFQIVKCIRNFVHLMDATVLMALLQPAPETFDL   400
 401  FDDLILLSEGYMVYQGPREDVIAFFESLGFRLPPRKGVADFLQEVTSKKD   450
 451  QAQYWADPSKPYQFIPVSDIAAAFRNSKYGHAADSKLAAPFDKKSADPSA   500
 501  LCRTKFAISGWENLKVCFVRELLLIKRHKFLYTFRTCQVGFVGLVTATVF   550
 551  LKTRLHPTSEQFGNEYLSCLFFGLVHMMFNGFSELPLMISRLPVFYKQRD   600
 601  NSFHPAWSWSIASWLLRVPYSVLEAVVWSGVVYFTVGLAPSAGRFFRYML   650
 651  LLFSVHQMALGLFRMMASLARDMVIANTFGSAAILIVFLLGGFVIPKADI   700
 701  KPWWVWGFWVSPLSYGQRAIAVNEFTATRWMTPSAISDTTIGLNLLKLRS   750
 751  FPTNDYWYWIGIAVLIGYAILFNNVVTLALAYLNPLRKARAVVLDDPNEE   800
 801  TALVADANQVISEKKGMILPFKPLTMTFHNVNYYVDMPKEMRSQGVPETR   850
 851  LQLLSNVSGVFSPGVLTALVGSSGAGKTTLMDVLAGRKTGGYTEGDIRIS   900
 901  GHPKEQQTFARISGYVEQNDIHSPQVTVEESLWFSASLRLPKEITKEQKK   950
 951  EFVEQVMRLVELDTLRYALVGLPGTTGLSTEQRKRLTIAVELVANPSIIF  1000
1001  MDEPTSGLDARAAAIVMRTVRNTVDTGRTVVCTIHQPSIDIFEAFDELLL  1050
1051  MKRGGQVIYGGKLGTHSQVLVDYFQGINGVPPISSGYNPATWMLEVTTPA  1100
1101  LEEKYNMEFADLYKKSDQFREVEANIKQLSVPPEGSEPISFTSRYSQNQL  1150
1151  SQFLLCLWKQNLVYWRSPEYNLVRLVFTTIAAFILGTVFWDIGSKRTSSQ  1200
1201  DLITVMGALYSACLFLGVSNASSVQPIVSIERTVFYREKAAGMYAPIPYA  1250
1251  AAQGLVEIPYILTQTILYGVITYFTIGFERTFSKFVLYLVFMFLTFTYFT  1300
1301  FYGMMAVGLTPNQHLAAVISSAFYSLWNLLSGFLVQKPLIPVWWIWFYYI  1350
1351  CPVAWTLQGVILSQLGDVESMINEPLFHGTVKEFIEYYFGYKPNMIGVSA  1400
1401  AVLVGFCALFFSAFALSVKYLNFQRR                          1426

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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