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

NucPred

Fetching Q9XPS9 from www.uniprot.org...

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

   1  MAERANLVFHNKEIDGTGMKRLISRLIDHFGMGYTSHILDQLKTLGFHQA    50
  51  TTTSISLGIEDLLTIPSKGWLVQDAEQQSFLLEKHYYYGAVHAVEKLRQS   100
 101  VEIWYATSEYLKQEMNSNFRITDPSNPVYLMSFSGARGNASQVHQLVGMR   150
 151  GLMSDPQGQMIDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTADAG   200
 201  YLTRRLVEVVQHIIVRRRDCGTIRGISVSPQNGMTEKLFVQTLIGRVLAD   250
 251  DIYIGSRCIAARNQDIGIGLVNRFITAFRAQPFRAQPIYIRTPFTCRSTS   300
 301  WICQLCYGRSPTHSDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFT   350
 351  GGTADLVRSPSNGKIKFNENLVHPTRTRHGQPAFLCYIDLHVTIQSQDIL   400
 401  YSVNIPSKSLILVQNDQYVKSEQVIAEIRAGTSTLHFKERVQKHIYSESD   450
 451  GEMHWSTDVYHAPEYQYGNLRRLPKTSHLWILSVSMCRSSIASFSLHKDQ   500
 501  DQMNTYGKKDREILDYSTSDRIMSNGHWNFIYPSIFQDNSDLLAKKRRNR   550
 551  FVIPLQYHQEQEKELISCFGISIEIPLMGVLRRNTIFAYFDDPRYRKDKK   600
 601  GSGIVKFRYRTLEEEYRTRAEDSEEEYETLEDEYRTREDEYEYETLEESK   650
 651  YGILEDEYEYETLEDEYGSPENEYGNPENEYRTLEKDSEEEYGSPESKYR   700
 701  TQEDEYGTIEEDSEDEYGSPGESAEEKYGTLEEDSEEDSEDEYESPEEDS   750
 751  ILKKEGLIEHRGTKEFSLKYQKEVDRFFFILQELHILPRSSSLKILDNSI   800
 801  IGVDTQLTKNTRSRLGGLVRVKRKKSHTELKIFSGDIHFPEEADKILGGC   850
 851  LIPPERQKKDSKESKKRKNWVYVQRKKILKSKEKYFVSVRPTVAYEMDEG   900
 901  RNLATLFPQDLLQEENNLQIRLVNFISHENSKLTQRIYHTNSQFVRTCLV   950
 951  VNWEQEEKEKAGASLVEVRANDLIRDFLRIELVKSTISYTRKRYDRTSAG  1000
1001  PIPHNRLDRANINSFYSKAKIESLSQHPEAIGTLLNRNKEYHSLMILSAS  1050
1051  NCSRIGLFKNSKHPNAIKEWNPRIPIREIFGPLGAIVASISHFSSSYYLL  1100
1101  THNKILLKKYLFVDNLKQTFQVLQELKYSLIDENKRISNFDSNIMLDPFL  1150
1151  LNCHFVHHDSWEETLAIIHLGQFICENVCLFKSHIKKSGQIFIVNMNSFV  1200
1201  IRAAKPYLATTGATVNGHYGEILYKGDRLVTFIYEKSRSSDITQGLPKVE  1250
1251  QIFEARSIDSLSPNLERRIEDWNERIPRILGVPWGFLIGAELTIAQSRIS  1300
1301  LVNKIQKVYRSQGVQIHNRHIEIIIRQVTSKVRVSEDGMSNVFSPGELIG  1350
1351  LLRAERAGRALDESIYYRAILLGITRASLNTQSFISEASFQETARVLAKA  1400
1401  ALRGRIDWLKGLKENVVLGGIIPVGTGFQKFVHRSPQDKNLYFEIKKKNL  1450
1451  FASEMRDFLFLHTELVSSDSDVTNNFYET                       1479

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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