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

NucPred

Fetching Q92878 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MSRIEKMSILGVRSFGIEDKDKQIITFFSPLTILVGPNGAGKTTIIECLK    50
  51  YICTGDFPPGTKGNTFVHDPKVAQETDVRAQIRLQFRDVNGELIAVQRSM   100
 101  VCTQKSKKTEFKTLEGVITRTKHGEKVSLSSKCAEIDREMISSLGVSKAV   150
 151  LNNVIFCHQEDSNWPLSEGKALKQKFDEIFSATRYIKALETLRQVRQTQG   200
 201  QKVKEYQMELKYLKQYKEKACEIRDQITSKEAQLTSSKEIVKSYENELDP   250
 251  LKNRLKEIEHNLSKIMKLDNEIKALDSRKKQMEKDNSELEEKMEKVFQGT   300
 301  DEQLNDLYHNHQRTVREKERKLVDCHRELEKLNKESRLLNQEKSELLVEQ   350
 351  GRLQLQADRHQEHIRARDSLIQSLATQLELDGFERGPFSERQIKNFHKLV   400
 401  RERQEGEAKTANQLMNDFAEKETLKQKQIDEIRDKKTGLGRIIELKSEIL   450
 451  SKKQNELKNVKYELQQLEGSSDRILELDQELIKAERELSKAEKNSNVETL   500
 501  KMEVISLQNEKADLDRTLRKLDQEMEQLNHHTTTRTQMEMLTKDKADKDE   550
 551  QIRKIKSRHSDELTSLLGYFPNKKQLEDWLHSKSKEINQTRDRLAKLNKE   600
 601  LASSEQNKNHINNELKRKEEQLSSYEDKLFDVCGSQDFESDLDRLKEEIE   650
 651  KSSKQRAMLAGATAVYSQFITQLTDENQSCCPVCQRVFQTEAELQEVISD   700
 701  LQSKLRLAPDKLKSTESELKKKEKRRDEMLGLVPMRQSIIDLKEKEIPEL   750
 751  RNKLQNVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQM   800
 801  ELKDVERKIAQQAAKLQGIDLDRTVQQVNQEKQEKQHKLDTVSSKIELNR   850
 851  KLIQDQQEQIQHLKSTTNELKSEKLQISTNLQRRQQLEEQTVELSTEVQS   900
 901  LYREIKDAKEQVSPLETTLEKFQQEKEELINKKNTSNKIAQDKLNDIKEK   950
 951  VKNIHGYMKDIENYIQDGKDDYKKQKETELNKVIAQLSECEKHKEKINED  1000
1001  MRLMRQDIDTQKIQERWLQDNLTLRKRNEELKEVEEERKQHLKEMGQMQV  1050
1051  LQMKSEHQKLEENIDNIKRNHNLALGRQKGYEEEIIHFKKELREPQFRDA  1100
1101  EEKYREMMIVMRTTELVNKDLDIYYKTLDQAIMKFHSMKMEEINKIIRDL  1150
1151  WRSTYRGQDIEYIEIRSDADENVSASDKRRNYNYRVVMLKGDTALDMRGR  1200
1201  CSAGQKVLASLIIRLALAETFCLNCGIIALDEPTTNLDRENIESLAHALV  1250
1251  EIIKSRSQQRNFQLLVITHDEDFVELLGRSEYVEKFYRIKKNIDQCSEIV  1300
1301  KCSVSSLGFNVH                                        1312

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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