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

NucPred

Fetching Q7Z4S6 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MLGAPDESSVRVAVRIRPQLAKEKIEGCHICTSVTPGEPQVFLGKDKAFT    50
51 FDYVFDIDSQQEQIYIQCIEKLIEGCFEGYNATVFAYGQTGAGKTYTMGT 100
101 GFDVNIVEEELGIISRAVKHLFKSIEEKKHIAIKNGLPAPDFKVNAQFLE 150
151 LYNEEVLDLFDTTRDIDAKSKKSNIRIHEDSTGGIYTVGVTTRTVNTESE 200
201 MMQCLKLGALSRTTASTQMNVQSSRSHAIFTIHVCQTRVCPQIDADNATD 250
251 NKIISESAQMNEFETLTAKFHFVDLAGSERLKRTGATGERAKEGISINCG 300
301 LLALGNVISALGDKSKRATHVPYRDSKLTRLLQDSLGGNSQTIMIACVSP 350
351 SDRDFMETLNTLKYANRARNIKNKVMVNQDRASQQINALRSEITRLQMEL 400
401 MEYKTGKRIIDEEGVESINDMFHENAMLQTENNNLRVRIKAMQETVDALR 450
451 SRITQLVSDQANHVLARAGEGNEEISNMIHSYIKEIEDLRAKLLESEAVN 500
501 ENLRKNLTRATARAPYFSGSSTFSPTILSSDKETIEIIDLAKKDLEKLKR 550
551 KEKRKKKRLQKLEESNREERSVAGKEDNTDTDQEKKEEKGVSERENNELE 600
601 VEESQEVSDHEDEEEEEEEEEDDIDGGESSDESDSESDEKANYQADLANI 650
651 TCEIAIKQKLIDELENSQKRLQTLKKQYEEKLMMLQHKIRDTQLERDQVL 700
701 QNLGSVESYSEEKAKKVRSEYEKKLQAMNKELQRLQAAQKEHARLLKNQS 750
751 QYEKQLKKLQQDVMEMKKTKVRLMKQMKEEQEKARLTESRRNREIAQLKK 800
801 DQRKRDHQLRLLEAQKRNQEVVLRRKTEEVTALRRQVRPMSDKVAGKVTR 850
851 KLSSSDAPAQDTGSSAAAVETDASRTGAQQKMRIPVARVQALPTPATNGN 900
901 RKKYQRKGLTGRVFISKTARMKWQLLERRVTDIIMQKMTISNMEADMNRL 950
951 LKQREELTKRREKLSKRREKIVKENGEGDKNVANINEEMESLTANIDYIN 1000
1001 DSISDCQANIMQMEEAKEEGETLDVTAVINACTLTEARYLLDHFLSMGIN 1050
1051 KGLQAAQKEAQIKVLEGRLKQTEITSATQNQLLFHMLKEKAELNPELDAL 1100
1101 LGHALQDLDSVPLENVEDSTDEDAPLNSPGSEGSTLSSDLMKLCGEVKPK 1150
1151 NKARRRTTTQMELLYADSSELASDTSTGDASLPGPLTPVAEGQEIGMNTE 1200
1201 TSGTSAREKELSPPPGLPSKIGSISRQSSLSEKKIPEPSPVTRRKAYEKA 1250
1251 EKSKAKEQKHSDSGTSEASLSPPSSPPSRPRNELNVFNRLTVSQGNTSVQ 1300
1301 QDKSDESDSSLSEVHRSSRRGIINPFPASKGIRAFPLQCIHIAEGHTKAV 1350
1351 LCVDSTDDLLFTGSKDRTCKVWNLVTGQEIMSLGGHPNNVVSVKYCNYTS 1400
1401 LVFTVSTSYIKVWDIRDSAKCIRTLTSSGQVTLGDACSASTSRTVAIPSG 1450
1451 ENQINQIALNPTGTFLYAASGNAVRMWDLKRFQSTGKLTGHLGPVMCLTV 1500
1501 DQISSGQDLIITGSKDHYIKMFDVTEGALGTVSPTHNFEPPHYDGIEALT 1550
1551 IQGDNLFSGSRDNGIKKWDLTQKDLLQQVPNAHKDWVCALGVVPDHPVLL 1600
1601 SGCRGGILKVWNMDTFMPVGEMKGHDSPINAICVNSTHIFTAADDRTVRI 1650
1651 WKARNLQDGQISDTGDLGEDIASN 1674

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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