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

NucPred

Fetching Q5Z9S8 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MEKVWESGRRMSRSIGRGMGMEAWGVDEAFMPQNSGGGGGSRGRRRSGRG    50
  51  GTADDDEEALRWAAIERLPTYSRMRTAILSSAEEEAAAAAAGAGKQQYKE   100
 101  VDVRRLGVGERQEFIERVFRVAEEDNQRFLQKLRNRIDRVGIELPTVEVR   150
 151  FEELMVQARCHVGSRALPTLLNTARNIAEAALGLVGVRPGRQATLTILRG   200
 201  VSGAVRPSRMTLLLGPPSSGKTTLLLALAGKLDPSLRRGGEVTYNGFELE   250
 251  EFVAQKTAAYISQTDVHVGEMTVKETLDFSARCQGVGTKYDLLTELARRE   300
 301  KEAGIRPEPEVDLFMKATSMEGVESSLQTDYTLRILGLDICADTIVGDQM   350
 351  QRGISGGQKKRVTTGEMIVGPTKVLFMDEISTGLDSSTTFQIVKCLQQIV   400
 401  HLGEATILMSLLQPAPETFELFDDIILLSEGQIVYQGPREYVLEFFESCG   450
 451  FRCPERKGTADFLQEVTSKKDQEQYWADKHRPYRYISVSEFAQRFKRFHV   500
 501  GLQLENHLSVPFDKTRSHQAALVFSKQSVSTTELLKASFAKEWLLIKRNS   550
 551  FVYIFKTIQLIIVALVASTVFLRTQMHTRNLDDGFVYIGALLFSLIVNMF   600
 601  NGFAELSLTITRLPVFFKHRDLLFYPAWIFTLPNVILRIPFSIIESIVWV   650
 651  IVTYYTIGFAPEADRFFKQLLLVFLIQQMAGGLFRATAGLCRSMIIAQTG   700
 701  GALALLIFFVLGGFLLPKAFIPKWWIWGYWVSPLMYGYNALAVNEFYSPR   750
 751  WMNKFVLDNNGVPKRLGIALMEGANIFTDKNWFWIGAAGLLGFTMFFNVL   800
 801  FTLSLVYLNPLGKPQAVISEETAKEAEGNGDARHTVRNGSTKSNGGNHKE   850
 851  MREMRLSARLSNSSSNGVSRLMSIGSNEAGPRRGMVLPFTPLSMSFDDVN   900
 901  YYVDMPAEMKQQGVVDDRLQLLRDVTGSFRPAVLTALMGVSGAGKTTLMD   950
 951  VLAGRKTGGYIEGDMRISGYPKNQETFARISGYCEQNDIHSPQVTVRESL  1000
1001  IYSAFLRLPEKIGDQEITDDIKIQFVDEVMELVELDNLKDALVGLPGITG  1050
1051  LSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTG  1100
1101  RTVVCTIHQPSIDIFEAFDELLLLKRGGQVIYSGQLGRNSQKMIEYFEAI  1150
1151  PGVPKIKDKYNPATWMLEVSSVAAEVRLNMDFAEYYKTSDLYKQNKVLVN  1200
1201  QLSQPEPGTSDLHFPTKYSQSTIGQFRACLWKQWLTYWRSPDYNLVRFSF  1250
1251  TLFTALLLGTIFWKIGTKMGNANSLRMVIGAMYTAVMFIGINNCATVQPI  1300
1301  VSIERTVFYRERAAGMYSAMPYAIAQVVMEIPYVFVQTAYYTLIVYAMMS  1350
1351  FQWTAAKFFWFFFVSYFSFLYFTYYGMMTVAISPNHEVAAIFAAAFYSLF  1400
1401  NLFSGFFIPRPRIPKWWIWYYWLCPLAWTVYGLIVTQYGDLEQIISVPGQ  1450
1451  SNQTISYYVTHHFGYHRKFMPVVAPVLVLFAVFFAFMYAICIKKLNFQHR  1500

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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