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

NucPred

Fetching Q7FMW4 from www.uniprot.org...

The NucPred score for your sequence is 0.31 (see score help below)

   1  MADPQHVQEEAAGAEAVHAHAARHDGAVVMEILSRSLQSMPASPDVSAYF    50
  51  SGASSRRPSAADEVDDEEALRWAALERLPSFDRLRTGLMRADADSSGVGV   100
 101  GAVGRGRRWYAHREVDVRTLELAQRQAFVERVFHVAEEDNERFLKKLRAR   150
 151  IDRAGIQMPTVEVRFRNVNVQAECHVGTRALPTLANVSRDVGESLLGLVG   200
 201  LNFAKRKALHILKDVSGIVRPSRMTLLLGPPSSGKTTLLLALAGKLDPTL   250
 251  ETSGEVTYNGYGLDEFVPQKTAAYISQHDVHAGEMTVKETLDFSAKCQGV   300
 301  GQRYELLKELAKKERQLGIYPDPEVDLFMKATSVEGSTLQTDYILRILGL   350
 351  DMCADVIVGDELRRGISGGQKKRLTTAEMLVGPTKVLFMDEISTGLDSST   400
 401  TFQIIRCIQQIVHMGEATVLVSLLQPAPEIFELFDDVMLLSEGQIVYQGP   450
 451  REHVLEFFERCGFRCPERKGVADFLQEVTSKKDQEQYWIQSEKPYRYVSV   500
 501  PEFVAKFKKFHMGKSLKKQLSVPFNKGKIHKSALVFSKQSVSTLELLKTS   550
 551  CSKEWLLMKRNSFVYIFKTVQGILVALIASTVFLRTQLNTRDEDDGQIYI   600
 601  GALIFVMITNMFSGFADLSLTLARLPVFYKHRDFLFYRPWTFALPNVLVR   650
 651  IPSSLFESIIWVAITYYTMGFAPEASRFFKHLLVVFMLQQMAAGLFRVTA   700
 701  GLCRTVVVTNTAGSLAVLIMFVLGGFILPKDAIPKWWVWAYWCSPLTYAY   750
 751  IAFSSNEMHSPRWMDKFVPDGKRLGVAVLENSGVFTNKEWYWIATGALLG   800
 801  FTILFNVLFSLSLMYLNPVGKPQSILPEETDSQENIQEGKNKAHIKQIIT   850
 851  VETPEPVSPNSIITLDKVIQQLRGYSANTSDRSHSYINAAGRTAPGRGMV   900
 901  LPFEPLYMSFNEINYYVDMPLEMKSQGVTADKLQLLSGISGAFRPGVLTA   950
 951  LMGVSGAGKTTLMDVLSGRKTGGYIEGEIYISGYPKNQATFARISGYCEQ  1000
1001  NDIHSPQITVRESLLFSAFLRLPKEVNDQEKKIFVDEVMELVELTGLKDA  1050
1051  IVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMR  1100
1101  TVRNTVNTGRTVVCTIHQPSIDIFEAFDELLLLKRGGQVIYSGPLGTNSH  1150
1151  KVVEYFEAIPGVPKIEENRNPATWMLDVSSAASEVRLEIDFAEYYRSSTM  1200
1201  HQRTKALVKELSNPPPGSDDLYFPSQYSQSTFNQFKLCLWKQWWTYWRSP  1250
1251  DYNLVRIFFALFTALMLGTIFWRVGHKMESSKDLLVIIGSMYAAVLFVGF  1300
1301  ENSVTVQPVVAVERTVFYRERAAGMYSAIPYALAQVVVEIPYVFVETVIY  1350
1351  TLIVYPMMSFQWTPAKFFWFFYVSFFTFLYFTYYGMMNVSVSPNLQVASI  1400
1401  LGAAFYTLFNLFSGFFIPRPKIPKWWVWYYWLCPVAWTVYGLIVSQYGDV  1450
1451  EDFITVPGQSDQQVRPFIKDYFGYDPDFMGVVAAVLAGFTVFFAFTYAYS  1500
1501  IRTLNFQQR                                           1509

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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