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

NucPred

Fetching Q91289 from www.uniprot.org...

The NucPred score for your sequence is 0.47 (see score help below)

   1  HESEAPITRTVVTPISPPTDLHLEPSPDFATLTVSWSRSPSPGITGYRIN    50
  51  TALLLGIRLHSGYTLEEEVTESQSRVCIFDNLSPGVEYNVSVVSVKDDQE   100
 101  SEPIWKTITQEVPSLTDLNFVDVTDTSIDLRWTPLKGPTIIGYRVTVVAA   150
 151  GESVPIYEDKVGPTQGYYKVSGLEPGIDYDISVITLVTDGESAPTTLTTA   200
 201  DCCPTATDLRFTNVGPDSMLVTWSAPPSMVLSSFLVRYVPSKNEEDAAEL   250
 251  TISPSDNMVVLTNLLPGTEYIVSVFAVYEERESTPLTGVQRTGLDSPTGL   300
 301  DFSDTTSSSFTVYWMAPRATVTGYKIQYHPETGGAGQKEERCVPPSRNSL   350
 351  TLTNLTPGTEYVVSIFAVNGRQESVPLVGQQATVSDTPTNLEVTSSTPTS   400
 401  MSISWDAPPVGVRYYRITYTETGGETPVQEFTVPGDRSDAPIRGLKPGAE   450
 451  YIITVYAVTGRGDSPASSKPVTVTHKTVVDKPTQLQVTDVQDHSIQVRWM   500
 501  PSSTPVTGYRVTSVPKSGVGPTVSHVVPPDQTEMTIEGLEPTVEYVVSVY   550
 551  AQGKNGETEPLVETAVTNIDRPKGLAFTEVDVDSLKLVWESPKGQVTTYK   600
 601  VTYSNPEDGIHELVPAPNGDEDTAQLHGLRPGAEYTVSVVALHDDMESQP   650
 651  LIGTQVTAIPPPTNLLFSQITPTSVTVSWRPPNVQLTGYRVRVHPKEKAG   700
 701  PMKEINLSPDSTSAVVTGLMVATKYEVSVYALKDSLTSRPAQGIVTTQEN   750
 751  VSPPRRRRITDVTETTVTITWRTKTETITGFHIDAIPAGGQNPIQRTISP   800
 801  DLRTYVITGLQPGTDYKIHIYTLNDNARSSPVTIDATTAVDSPSNLRFLT   850
 851  TTSNSLLFSWQPPRSKLTGYIIKYEKPGGPVREVVPRPHPGATESQQSQN   900
 901  LEPGTEYTIYIIAVRSNYKSGPLVGKKRTDELPRLVTLAQPGQQGRILDV   950
 951  PSLVENTPFISQTSFDNGNGIQLPGTSGQQNIGHQGQQVFLEEHGFRSPV  1000
1001  LPTTATPVKPGYQAPEQHTLDKYTPGQHVPTIREDIELARFPPRQIDMDR  1050
1051  PTSHDSGPQQVDRTGQEAQTTISWRPLLETTEYIITCHPVGNEETPQQFT  1100
1101  VPGTSSSATLNGLTRGATYNIIVEALKGKNKHKSRELVTVTSAAHGSGVL  1150
1151  HGLEDTCYDITTGSSYSIGQEWERMSESGFKLWCRCLGLGSGHFKCDSSK  1200
1201  WCHDSGLNYRVGEKWDRSGENGQMMSCTCLGMEWKGEFKCEPHEATCYDD  1250
1251  GKMYVGEQWQKEYLGAICSCTCYGGQQGWRCDNCRRPGAGVTPSADGVVG  1300
1301  QTLSHFSQRYQQNANFNLKCPIECYLPL                        1328

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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