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

NucPred

Fetching Q03610 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MMFHSLGLLYLFLYVTLAEDCIDRPCVECRHYIKQDDPCLHHGTKPMLFC    50
  51  DPQTNLIQESSTNFLECVQNRWVLRECVTGTIYESGRGCVDPTIQPFMQG   100
 101  FSVSGSGRVGDVCQYNTDCLSGMYCATGLCSCLSTYILRESYCYEKVNPN   150
 151  QPGCTYDVQCEAVWPGSKCRMDSSIGTCRCPEETHVARETRDGWVCISLR   200
 201  DLSSGGTAPLYFVCALPEGAGFKISLNDPSPSMGAFPVGCTVGSSATIEP   250
 251  VQGLHGGGACMWPSDGEYIGDVYDCIHTSPHINLAEKFPQSNYAPTADGV   300
 301  CCPSRALACIQPQLTGPNPSEPRWWYNSVTGTCQQFMWDSGATEAKYHSP   350
 351  NNFKTIQHCESYCRDTCQRGSPQYSTESAVHSERPITSCAASVSCANDFQ   400
 401  CTAIGSQHLCCPTPGSVCSAKGGRPYDIQPRTSIHHPGFMVYTGKESIRF   450
 451  YYDPGTGRCQDFVYKGAGGNYNNFLSKHECEMYCARLQCERGSPLRIGEE   500
 501  AQRCQNNAQCPSSHECKADQGVCCPRKQTICAQPLRIGDCTENVKRYWYN   550
 551  ARTRQCQMFEYTGCQGNDNNFDSIMDCQNFCKNAIPEPKCIQGQAYKDMF   600
 601  GNFVTCSNGMGCPANYECYFDGSQWGCCPTKAFTCSLNTDSGIQCGAGST   650
 651  FKYYYNPQTQNCESFQYNGCDGNSNNFANRDACESYCSVGGCPNGGTPLR   700
 701  DHSGMVMVCGAQQTSCPDSHECIPVLVGNSLINRCCPTRAYMCGLPPQQG   750
 751  TQCGANYVQRYYFNIVTSQCTSFQFGGCDGNANNFLNIQQCRNFCMSNAC   800
 801  PAGNVAYVDPNSQMPINCNEALSNSCPSGYACTFNPLINNHVCCGATDSG   850
 851  VCPEAEKAFIDTIDMSPRECLINIEQSCPANYLCRFNMQKNKYYCCSSIT   900
 901  GKTCPVGKFLYKDLRTSQPIRCTIGRNDQCPDGFTCQSYLANAFQGFCCT   950
 951  ANSVCPDNADYLIDDQSQQPRACTQGTFVSCPNGYACRSLTSSADGFCCK  1000
1001  SGTGALPPSVTDGCPPNEYVYLVQGEIAQCDPFNPPNAPCPSEFTCQWSL  1050
1051  SNQRYQCCGSNPAPTPQRPSDGCPNAQIAFRDADAVRVCSAGAANCPAGY  1100
1101  FCQFSSSNNQFQCCGVSGGCPEESVAFVGMSGEPEKCVVGQSNCPRGFAC  1150
1151  QKSLAGHHVCCTVRKVACESNEVIIEGECHAQVGPGSECLANEQCTGGSV  1200
1201  CEDAKCECRPPLKAVGGFCQEEIQCSSNQVLHNGLCHNKAKLGEACLTVR  1250
1251  QCQENSGCIEGSCECKKGFIEKAGKCMTPVEKKSAVSSKSINNGVTCSKP  1300
1301  GWNPLIDEEHERPKHCSPIGKACPNGYECQINNRRTQYLCCAPDMSMSST  1350
1351  VSIPSLPPPSTTTTERIMTTKKANLKVCPTGRTPYLLNGAPQKCTISRCP  1400
1401  AGYECTYRNNGYHCCSMANKPGLTVAGTTGSVVSKSTPSPDQEKCPRGNP  1450
1451  LIYPSTSSPVLCQPGKRGCPVGFGCVQSSTSNNHICCPSRHSDRPGYQSE  1500
1501  SFGLGAYYSRGPPAAINPCEGYLVLVTRGVNGRIEKRCERSCPFPQIPIG  1550
1551  GVCYELKNKAT                                         1561

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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