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

NucPred

Fetching O61366 from www.uniprot.org...

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

   1  MPEALILPGMADAEPDLSTFENKTGLAEDMKFLASMPELCDVTFLVGDTR    50
  51  EPVCAVKAVLASRSRVFAKMLYAAPSPQRKRETSTKENKLRLFLKRSSEP   100
 101  LLNLQNAAQQRTGYTQQLAPIPEPSGQQHQTLIIEEFEPDVFRQLIEYIH   150
 151  TGCVTLQPRTLLGVMNAADYYGLEELRRACAGFVQCCINVDTVCALLASA   200
 201  ERYIQYKCTKTLVQKVLEFVDEHGTEVLNLGSFTLLPQHVVRLILAREEL   250
 251  RADEFTKFQAALMWSKKYYDNNPNIDIKEILGTFCEYIQFHKIPANVLMR   300
 301  EIHPLNLVPYAIIMNALAYQADPESIDPGKLSPNSSRQHHRHRHHHQSLP   350
 351  KIRKAKSQSFRTRRSPSERRSPNNAPNLTLNTSLTSGNGEKKRSPLTPKS   400
 401  PVMPVPESKSPGSSSQKTPTSLSRQGTLRASNRRKNSGQLSISLGTQGRR   450
 451  SPVGLNDRSPQGRRSPLFPSSGLRSPNDPMTSPTVRSPTGEPRRSSPTFS   500
 501  VHTQERRSPLGAVAPTDFGCQFGVPGTRRSPTSTVHVQDMATEPEEAGFV   550
 551  GLKRPSISLFTPIYFASEKRSPMGPIPPITVSNPAETYKSAEREREAAEA   600
 601  AAREKEKEKEKEAAQPQEKKSVMREILAFVRKPSKHLSSRTNRFANAFTR   650
 651  AESGSSGGPLIRQSTFSASPAASSTAAKSAVQKQMSEVGFEPKISQKFTH   700
 701  YAKMSLRLRRSTKRDDEEKEKQKQSSASGSKRPSADLSQTNADQQVGGSS   750
 751  DELPFELANVHFEKVGESYIKHERLRELQEPEVVKEEDTEKDAEAEVEVE   800
 801  QTDAAMAQFVEEVTNSLKVVALNGEGGTAAVHHFTRRSESREPIEPRISE   850
 851  ERESDSNDLMIPDDMRAELVEILKAYPPEPVYVNLQALRRETEDADLAIA   900
 901  QAEAAALAAAEPAKKPLQCPTIEFEPPSRRSSFDPPRSPFLEQLRSPGVD   950
 951  TETDLINLQRLDSGGDSFELVESKWSKSSRGESSFDCPYSSRDTSFDVSI  1000
1001  SRYQSTSYEDQTSSFEIVDTDEKGQGRRAVDLRKSSIELVDAETFQRSGS  1050
1051  SCGGRKSSLETHFDYTPTEGGGRSPSLPFPAMSKKQRTENFRQLHVSQFS  1100
1101  AFSRARSPLSQQTSSNYSSRDSYDSSGSYPHGYGYPPEPQRSPYGDPSRK  1150
1151  HFPLTVRQKGEEEREVRTFLCTDQRCASIFEPRPSSVLTQQLSTGSMSTP  1200
1201  SGYTNGTPRIPGAAPVGPVPLPHPSAPLSSCGFSSGSEFEPPSPRRAASA  1250
1251  SPKHTFTFRIVMKKVDSSPEALCPERHRSRIIDRYRRRDSRRKRIHDAGK  1300
1301  SF                                                  1302

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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