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

NucPred

Fetching Q9UR07 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MSYANYRYMKARAKRWRPENLDGIQTSDEHLINLFAKILSKHVPEIGKFD    50
  51  PNKDVESYISKLDQHFTEYPSLFPNEHTKRQYTLNHLEELEQQFAERMFS   100
 101  ENGSLTWQELLRQPGKVQGSNKGDRLTKTFEGFRNQLDKVQFIRKLMSKA   150
 151  NVDDFHTRLFILWMLPYSLRKLKERNYWKSEISEIYDFLEDKRTASYGKT   200
 201  HKRFQPQNKNLGKEFLPKKNNTTNSRNLRKTNISRIEYSSNKFLNHTRKR   250
 251  YEMVLQAELPDFKCSIPCLIDTGTQANIITEETVRAHKLPTRPWSKSVIY   300
 301  GGVYPNKINRKTIKLNISLNGISIKTEFLVVKKFSHPAAISFTTLYDNNI   350
 351  EISSSKHTLSQMNKVSNIVKEPELPDIYKEFKDITAETNTEKLPKPIKGL   400
 401  EFEVELTQENYRLPIRNYPLPPGKMQAMNDEINQGLKSGIIRESKAINAC   450
 451  PVMFVPKKEGTLRMVVDYKPLNKYVKPNIYPLPLIEQLLAKIQGSTIFTK   500
 501  LDLKSAYHLIRVRKGDEHKLAFRCPRGVFEYLVMPYGISIAPAHFQYFIN   550
 551  TILGEVKESHVVCYMDNILIHSKSESEHVKHVKDVLQKLKNANLIINQAK   600
 601  CEFHQSQVKFIGYHISEKGFTPCQENIDKVLQWKQPKNRKELRQFLGSVN   650
 651  YLRKFIPKTSQLTHPLNNLLKKDVRWKWTPTQTQAIENIKQCLVSPPVLR   700
 701  HFDFSKKILLETDASDVAVGAVLSQKHDDDKYYPVGYYSAKMSKAQLNYS   750
 751  VSDKEMLAIIKSLKHWRHYLESTIEPFKILTDHRNLIGRITNESEPENKR   800
 801  LARWQLFLQDFNFEINYRPGSANHIADALSRIVDETEPIPKDSEDNSINF   850
 851  VNQISITDDFKNQVVTEYTNDTKLLNLLNNEDKRVEENIQLKDGLLINSK   900
 901  DQILLPNDTQLTRTIIKKYHEEGKLIHPGIELLTNIILRRFTWKGIRKQI   950
 951  QEYVQNCHTCQINKSRNHKPYGPLQPIPPSERPWESLSMDFITALPESSG  1000
1001  YNALFVVVDRFSKMAILVPCTKSITAEQTARMFDQRVIAYFGNPKEIIAD  1050
1051  NDHIFTSQTWKDFAHKYNFVMKFSLPYRPQTDGQTERTNQTVEKLLRCVC  1100
1101  STHPNTWVDHISLVQQSYNNAIHSATQMTPFEIVHRYSPALSPLELPSFS  1150
1151  DKTDENSQETIQVFQTVKEHLNTNNIKMKKYFDMKIQEIEEFQPGDLVMV  1200
1201  KRTKTGFLHKSNKLAPSFAGPFYVLQKSGPNNYELDLPDSIKHMFSSTFH  1250
1251  VSHLEKYRHNSELNYATIDESDIGTILHILEHKNREQVLYLNVKYISNLN  1300
1301  PSTIMSGWTTLATALQADKAIVNDYIKNNNLNI                   1333

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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