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

NucPred

Fetching O94916 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MPSDFISLLSADLDLESPKSLYSRESVYDLLPKELQLPPSRETSVASMSQ    50
  51  TSGGEAGSPPPAVVAADASSAPSSSSMGGACSSFTTSSSPTIYSTSVTDS   100
 101  KAMQVESCSSAVGVSNRGVSEKQLTSNTVQQHPSTPKRHTVLYISPPPED   150
 151  LLDNSRMSCQDEGCGLESEQSCSMWMEDSPSNFSNMSTSSYNDNTEVPRK   200
 201  SRKRNPKQRPGVKRRDCEESNMDIFDADSAKAPHYVLSQLTTDNKGNSKA   250
 251  GNGTLENQKGTGVKKSPMLCGQYPVKSEGKELKIVVQPETQHRARYLTEG   300
 301  SRGSVKDRTQQGFPTVKLEGHNEPVVLQVFVGNDSGRVKPHGFYQACRVT   350
 351  GRNTTPCKEVDIEGTTVIEVGLDPSNNMTLAVDCVGILKLRNADVEARIG   400
 401  IAGSKKKSTRARLVFRVNIMRKDGSTLTLQTPSSPILCTQPAGVPEILKK   450
 451  SLHSCSVKGEEEVFLIGKNFLKGTKVIFQENVSDENSWKSEAEIDMELFH   500
 501  QNHLIVKVPPYHDQHITLPVSVGIYVVTNAGRSHDVQPFTYTPDPAAAGA   550
 551  LNVNVKKEISSPARPCSFEEAMKAMKTTGCNLDKVNIIPNALMTPLIPSS   600
 601  MIKSEDVTPMEVTAEKRSSTIFKTTKSVGSTQQTLENISNIAGNGSFSSP   650
 651  SSSHLPSENEKQQQIQPKAYNPETLTTIQTQDISQPGTFPAVSASSQLPN   700
 701  SDALLQQATQFQTRETQSREILQSDGTVVNLSQLTEASQQQQQSPLQEQA   750
 751  QTLQQQISSNIFPSPNSVSQLQNTIQQLQAGSFTGSTASGSSGSVDLVQQ   800
 801  VLEAQQQLSSVLFSAPDGNENVQEQLSADIFQQVSQIQSGVSPGMFSSTE   850
 851  PTVHTRPDNLLPGRAESVHPQSENTLSNQQQQQQQQQQVMESSAAMVMEM   900
 901  QQSICQAAAQIQSELFPSTASANGNLQQSPVYQQTSHMMSALSTNEDMQM   950
 951  QCELFSSPPAVSGNETSTTTTQQVATPGTTMFQTSSSGDGEETGTQAKQI  1000
1001  QNSVFQTMVQMQHSGDNQPQVNLFSSTKSMMSVQNSGTQQQGNGLFQQGN  1050
1051  EMMSLQSGNFLQQSSHSQAQLFHPQNPIADAQNLSQETQGSLFHSPNPIV  1100
1101  HSQTSTTSSEQMQPPMFHSQSTIAVLQGSSVPQDQQSTNIFLSQSPMNNL  1150
1151  QTNTVAQEAFFAAPNSISPLQSTSNSEQQAAFQQQAPISHIQTPMLSQEQ  1200
1201  AQPPQQGLFQPQVALGSLPPNPMPQSQQGTMFQSQHSIVAMQSNSPSQEQ  1250
1251  QQQQQQQQQQQQQQQQSILFSNQNTMATMASPKQPPPNMIFNPNQNPMAN  1300
1301  QEQQNQSIFHQQSNMAPMNQEQQPMQFQSQSTVSSLQNPGPTQSESSQTP  1350
1351  LFHSSPQIQLVQGSPSSQEQQVTLFLSPASMSALQTSINQQDMQQSPLYS  1400
1401  PQNNMPGIQGATSSPQPQATLFHNTAGGTMNQLQNSPGSSQQTSGMFLFG  1450
1451  IQNNCSQLLTSGPATLPDQLMAISQPGQPQNEGQPPVTTLLSQQMPENSP  1500
1501  LASSINTNQNIEKIDLLVSLQNQGNNLTGSF                     1531

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.