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

NucPred

Fetching Q92448 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MPEPSISALSFTSFVTNDDKLFEETFNFYTKLGFHATRSYVKDNRSDFEL    50
  51  TGISTDSIKEIWLESFPLSEVVETSAGRELRKPLQESVGYQSEALLGYSP   100
 101  YQSDGVVIKLRLSNHDLQKNKDLPGEVTFFTASIDKLRAKLIEIGAEIIP   150
 151  SEIDLVEFSTKDPMGDVISFSSYPSLSSKKITSPDFFLHPKKEVRSQESI   200
 201  VEQVKSEEGKKKIAIITSGGDAPGMNAAVRAVTRAGIFYGCKVYACYEGY   250
 251  TGLVKGGDMLKELQWQDVRGLLSIGGTIIGTARSKEFRERWGRLQACYNM   300
 301  VSNGIDALVVCGGDGSLTGADLFRNEWPELIKELLGEGKITKEQYETHRN   350
 351  LTIVGLVGSIDNDMCGTDSTIGAYSSLERIIELVDYIDATAASHSRAFVV   400
 401  EVMGRHCGWLGLMSGIATGADYIFIPERPPSETNWKDDLKKVCLRHREKG   450
 451  RRKTTVIVAEGAIDDQLNPITSEEVKDVLVEIGLDTRITRLGHVQRGGAP   500
 501  CAFDRFLATVQGVDAVRAVLESTPAIPSPVISILENKIVRQPLVESVAQT   550
 551  KTVSDAIEAKDFDKALKLRDQEFATSYESFLSVSKYDDGSYLVPESSRLN   600
 601  IAIIHVGAPTSALNPATRVATLNSLAKGHRVFAIRNGFAGLIRHGAVREL   650
 651  NWIDVEDWHNTGGSEIGTNRSLPSDDMGTVAYYFQQYKFDGLIIIGGFEA   700
 701  FTALYQLDAARAQYPIFNIPMCCLPATVSNNVPGTEYSLGSDTCLNTLSG   750
 751  YCDAVKQSASASRRRTFVVEVQGGYSGYLASYAGLITGALAVYTPENPIN   800
 801  LQTVQEDIELLTRTYEEDDGKNRSGKIFIHNEKASKVYTTDLIAAIIGEA   850
 851  GKGRFESRTAVPGHVQQGKSPSSIDRVNACRLAIKCCNFIEDANFQVKHN   900
 901  ANLSADERHLRFFYDDGVKTSAVSGKSSVIDDNTSVVIGIQGSEVTFTPV   950
 951  KQLWEKETHHKWRKGKNVHWEQLNIVSDLLSGRLSIRTT              989

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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