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

NucPred

Fetching Q7YR40 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MEDTQAIDWDVEEEEETEQSSESLRCNVEPVGRLHIFSGAHGPEKDFPLH    50
  51  LGKNVVGRMPDCSVALPFPSISKQHAEIEILAWDKAPILRDCGSLNGTQI   100
 101  LRPPKVLSPGVSHRLRDQELILFADLLCQYHRLDVSLPFVSRGPLTVEET   150
 151  PRVQGGTQPQRLLLAEDSEEEVDFLSERRMVKKSRTTSSSVIVPESDEEG   200
 201  HSPVLGGLGPPFAFNLNSDTDVEEGQQPATEEASSAARRGATVEAKQSEA   250
 251  EVVTEIQLEKDQPLVKERDDDTKVKRGAENGVVPAGVILERSQPPGEDSD   300
 301  TDVDDDSRPPGRPAEVHLERAQPFGFINSDTDAEEERIPATPVVIPMKKR   350
 351  KIFHGVGTRGPGAPGLAHLQESQAGSDTDVEEGKAPQAVPLEKSQASMVI   400
 401  NSDTDDEEEVSAALTLAHLKESQPAIWNRDAEEDMPQRVVLLQRSQTTTE   450
 451  RDSDTDVEEEELPVENREAVLKDHTKIRALVRAHSEKDQPPFGDSDDSVE   500
 501  ADKSSPGIHLERSQASTTVDINTQVEKEVPPGSAIIHIKKHQVSVEGTNQ   550
 551  TDVKAVGGPAKLLVVSLEEAWPLHGDCETDAEEDTSLAASAVADVRKSQL   600
 601  PAEGDAGAEWAAAVLKQERAHEVGAQGGPPVAQVEQDLPISRENLTDLVV   650
 651  DTDTLGESTQPQREGAQVPTGREREQHVGGTKDSEDNYGDSEDLDLQATQ   700
 701  CFLENQGLEAVQSMEDEPTQAFMLTPPQELGPSHCSFQTTGTLDEPWEVL   750
 751  ATQPFCLRESEDSETQPFDTHLEAYGPCLSPPRAIPGDQHPESPVHTEPM   800
 801  GIQGRGRQTVDKVMGIPKETAERVGPERGPLERETEKLLPERQTDVTGEE   850
 851  ELTKGKQDREQKQLLARDTQRQESDKNGESASPERDRESLKVEIETSEEI   900
 901  QEKQVQKQTLPSKAFEREVERPVANRECDPAELEEKVPKVILERDTQRGE   950
 951  PEGGSQDQKGQASSPIPEPGVEAGDLPGPTSAPVTSGSQSGGRGSPVSPR  1000
1001  RHQKGLLNCKMPPAEKASRIRAAEKVSRGDQESPDACLPPTVPEAPAPPQ  1050
1051  KPLNSQSQKHLAPPPLLSPLLPSIKPTVRKTRQDGSQEAPEAPLSSELEP  1100
1101  FHPKPKIRTRKSSRMTTFPATSAAPEPHPSTSTAQPVTPKPTSQATRSRT  1150
1151  NRSSVKTPEQGVPTAPELQPCTSTDQPVTSEPTSQVTRGRKSRSSVKTPE  1200
1201  TVVPTALELQPSTSTDRPVTSEPTSHATRGRKNRSSVKTPEPVVPTAPEL  1250
1251  QPSTSTDQPVTSEPTYQATRGRKNRSSVKTPEPVVPTAPELQPSTSTDQP  1300
1301  VTPKPTSRTTRSRTNMSSVKNPESTVPIAPELPPSTSTEQPVTPEPTSRA  1350
1351  TRGRKNRSSGKTPETLVPTAPKLEPSTSTDQPVTPEPTSQATRGRTNRSS  1400
1401  VKTPETVVPTAPELQLSTSTDQAVTPKPTSRTTRSRTNMSSVKNPESTVP  1450
1451  IAPELPPSTSTEQPVTPEPTSRATRGRKNRSSGKTPETLVPTAPKLEPST  1500
1501  STDQPVTPEPTSQATRGRTNRSSVKTPETVVPTAPELQPSTSTDQPVTPE  1550
1551  PTSQVTRGRTDRSSVKTPETVVPTAPELQASASTDQPVTSEPTSRTTRGR  1600
1601  KNRSSVKTPETVVPTAPELQPSTSTDQPVTPEPTSQATRGRTNRSSVKTP  1650
1651  ESIVPIAPELQPSTSRNQLVTPEPTSRATRCRTNRSSVKTPEPVVPTAPE  1700
1701  PHPTTSTDQPVTPKLTSRATRRKTNRSSVKTPKPVEPAASDLEPFTPTDQ  1750
1751  SVTPEAIAQGGQSKTLRSSTVRAMPVPTTPEFQSPVTTDQPISPEPITQP  1800
1801  SCIKRQRAAGNPGSLAAPIDHKPCSAPLEPKSQASRNQRWGAVRAAESLT  1850
1851  AIPEPASPQLLETPIHASQIQKVEPAGRSRFTPELQPKASQSRKRSLATM  1900
1901  DSPPHQKQPQRGEVSQKTVIIKEEEEDTAEKPGKEEDVVTPKPGKRKRDQ  1950
1951  AEEEPNRIPSRSLRRTKLNQESTAPKVLFTGVVDARGERAVLALGGSLAG  2000
2001  SAAEASHLVTDRIRRTVKFLCALGRGIPILSLDWLHQSHKAGFFLPPDEY  2050
2051  VVTDPEQEKNFGFSLQDALSRARERRLLEGYEIYVTPGVQPPPPQMGEII  2100
2101  SCCGGTYLPSMPRSYKPQRVVITCPQDFPHCSIPLRVGLPLLSPEFLLTG  2150
2151  VLKQEAKPEAFVLSPLEMSST                               2171

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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