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

NucPred

Fetching Q8CGI1 from www.uniprot.org...

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

   1  MSPADAKRGAKRRKNKRGGGGGSGGGGSGGKAGSAAALRGPQAPGPGAAG    50
  51  LLGGAAAHGPLGAGAGGAAGGYFETPFSFGMNHRTPPYPAGDYCLLCRSE   100
 101  RKDSSFLESGVKTASKLALSMAPKGNSVLHLPLWVCPDCRRTVEKEERHS   150
 151  GLDQPGQDFLLHSSLGGSQPETSGAGRLALGTQTMTSSGLGTTPSDACSC   200
 201  EACSERRDISAETEREPQQLQNYWSEVRYMVRCIYRQAGTPLAEDQDQSL   250
 251  VPDKEGVKELVDRLCERDPYQLYQRLEQQAREYVLEMKVRLLRQLSAAAK   300
 301  AKAPSGLQGPPQAHHFVSLLLEEYAALCQAARSISTFLGTLENEHLKKFQ   350
 351  VTWELHNKHLFENLVFSEPLLQSNLPALVSQIRLGTTTHDTCTEDMYSTL   400
 401  LQRYQRSEEELRKVAEEWLECQKRIDAYVDEQMTMKTKQRMLTEDWEIFK   450
 451  QRRLIEEQLTNKKVVTGENNFTDTRRHMLSSRLSMPDCPNCNYRRRCACD   500
 501  DCSLSHILTCGIMDTPVTDDIHIHQLPLQVDSAPDYLSEMRPPSVSSASS   550
 551  GSGSSSPITIQQHPRLILTDNGSAPTFCSDDEDVAPLSAKFADIYPLTNY   600
 601  DDTNVVANMNGIHSELNGGGENMALKDESPQVSSTSRSSSEADDEDADGE   650
 651  SSGEPPGAPKQEEAIGNGNPKTEESNVNTPPPSYPAQQAEQTPNTCECHV   700
 701  CKQEASGLPASAMTAGALPPGHQFLSPEKPTHPALHLYPHIHGHVPLHTV   750
 751  PHLPRPLIHPTLYPAPPFTHSKALPPAPVQSHTNKPQAFNASLQDHIYPS   800
 801  CFGNTPDWNSSKFISLWESEMMNDKNWNPGTFLPDTISGNDILGPVLSET   850
 851  RPEALPPPPSNEAPAVSDIKEKKNAAKKKCLYNFQDAFMEANEVAMANTV   900
 901  AMATSSATSSVSCTATTVQSSSSQFKVSSRRPPSIGDVFHGLNKEDHRHS   950
 951  APAAPRNSPTGLAPLPALSPSALSPASTPHLPNLAAPSFPKTATTAPGFV  1000
1001  DTRKSFCPTPVAPPPSTTDGSISAPPSVCSDPDCEGHRCENGVYDPQQDD  1050
1051  GDESADEDSCSEHSSSTSTSTNQKEGKYCDCCYCEFFGHGGPPAAPTSRN  1100
1101  YAEMREKLRLRLTKRKEEQPKKMEQISEREGVVDHRRVEDLLQFINSSEA  1150
1151  KPVSSSRAAKRARHKQRKLEEKARLEAEARAREHLHHQEEQKQREEEEDE  1200
1201  EEEDEEQHFKEEFQRLQELQKLRAAKKKKKDRPSKDCSKLDMLARNFQAA  1250
1251  TESISNSENIHNGSLEQTEEPETSSHSPSRHMNHSEPRPGPGANGDATDP  1300
1301  VDPRDPSKLLLPKEVNGKQHEPLAFLLDMMHHHKEGNSKQKLKQTSKTSN  1350
1351  EPARKPTEPPKTTEVQLKPRAQPELKPKVVDLALLTEQKREERKTNSNNN  1400
1401  NKKQLSHIKEEKLSTVTPEPPSPSQLLQNGRLILASSPQPKGKNKKNKKK  1450
1451  KGDRTSSSLDDVFLPKDIDLDSVDMDETEREVEYFKRFCLDSARQNRQRL  1500
1501  SINWSNFSLKKATFAAH                                   1517

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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