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

NucPred

Fetching Q9WV30 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MPSDFISLLSADLDLESPKSLYSRESVYDLLPKELQLPPPRETSVASMSQ    50
  51  TSGGEAGSPPPAVVAADASSAPSSSSMGGACSSFTTSSSPTIYSTSVTDS   100
 101  KAMQVESCSSAVGVSNRGVSEKQLTGNTVQQHPSTPKRHTVLYISPPPED   150
 151  LLDNSRMSCQDEGCGLESEQSCSMWMEDSPSNFSNMSTSSYNDNTEVPRK   200
 201  SRKRNPKQRPGVKRRDCEESNMDIFDADSAKAPHYVLSQLTTDNKGNSKA   250
 251  GNGTLDSQKGTGVKKSPMLCGQYPVKSEGKELKIVVQPETQHRARYLTEG   300
 301  SRGSVKDRTQQGFPTVKLEGHNEPVVLQVFVGNDSGRVKPHGFYQACRVT   350
 351  GRNTTPCKEVDIEGTTVIEVGLDPSNNMTLAVDCVGILKLRNADVEARIG   400
 401  IAGSKKKSTRARLVFRVNITRKDGSTLTLQTPSSPILCTQPAGVPEILKK   450
 451  SLHSCSVKGEEEVFLIGKNFLKGTKVIFQENVSDENSWKSEAEIDMELFH   500
 501  QNHLIVKVPPYHDQHITLPVSVGIYVVTNAGRSHDVQPFTYTPDPAAGAL   550
 551  NVNVKKEISSPARPCSFEEAMKAMKTTGCNVDKVTILPNALITPLISSSM   600
 601  IKTEDVTPMEVTSEKRSSPIFQTTKSIGSTQQTLETISNIAGGAPFSSPS   650
 651  SSSHLTPESENQQQLQPKAYNPETLTTIQTQDISQPGTFPAVSAASQLPS   700
 701  SDALLQQATQFQTREAQSRDTIQSDTVVNLSQLTEASQQQQSPLQEQAQT   750
 751  LQQQIPSNIFPSPSSVSQLQSTIQQLQAGSFTGSAAGGRSGSVDLVQQVL   800
 801  EAQQQLSSVLFSTPDGNENVQEQLNADIFQVSQIQNSVSPGMFSSAESAV   850
 851  HTRPDNLLPGRADSVHQQTENTLSNQQQQQQQQQQVMESSAAMVMEMQQS   900
 901  ICQAAAQIQSELFPSAASASGSLQQSPVYQQPSHMMSALPTNEDMQMQCE   950
 951  LFSSPPAASGNETSTTTTPQVATPGSTMFQTPSSGDGEETGAQAKQIQNS  1000
1001  VFQTMVQMQRSGDSQPQVNLFSSTKNIMSVQNNGTQQQGNSLFQQGSEMM  1050
1051  SLQSGNFLQQSSHSQAQLFHPQNPIADAQNLSQETQGSIFHSPNPIVHSQ  1100
1101  TSTASSEQLQPSMFHSQNTIAVLQGSSVPQDQQSPNIFLSQSSINNLQTN  1150
1151  TVAQEEQISFFAAQNSISPLQSTSNTEQQAAFQQQPPISHIQTPILSQEQ  1200
1201  AQPSQQGLFQPQVALGSLPPNPMPQNQQGPIFQTQRPIVGMQSNSPSQEQ  1250
1251  QQQQQQQQQQQQQQQQQQQSILFSNQNAMATMASQKQPPPNMMFSPNQNP  1300
1301  MASQEQQNQSIFHQQSNMAPMNQEQQPMQFQNQPTVSSLQNPGPTQSESP  1350
1351  QTSLFHSSPQIQLVQGSPSSQDQQVTLFLSPASMSALQTSINQPDMQQSP  1400
1401  LYSPQNNIPGIQGSTSSPQPQATLFHNTTGGTINQIQNSPGSSQQTSGMF  1450
1451  LFGIQNNCSQLLTSGPATLPDQLMAINQQGQPQNEGQSSVTTLLSQQMPE  1500
1501  TSPLASSVNSSQNMEKIDLLVSLQSQGNNLTGSF                  1534

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.)

Go back to the NucPred Home Page.