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

NucPred

Fetching Q01923 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MAERANLVFHNKEIDGTAMKRLISRLIDHFGMGYTSHILDQIKTLGFHQA    50
  51  TTTSISLGIEDLLTIPSKGWLVQDAEQQSFLLEKHYYYGAVHAVEKLRQS   100
 101  VEIWYATSEYLKQEMNSNFRITDPSNPVYLMSFSGARGNASQVHQLVGMR   150
 151  GLMADPQGQMIDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTADAG   200
 201  YLTRRLVEVVQHIIVRRRDCGTIQGISVSPQNGMTEKLFVQTLIGRVLAD   250
 251  DIYIGSRCIASRNQDIGIGLVNRFITAFRAQPFRAQPIYIRTPFTCRSTS   300
 301  WICQLCYGRSPTHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFT   350
 351  GGTADLIRSPSNGKIQFNEDLVHPTRTRHGQPAFLCYIDLHVTIQSQDIL   400
 401  HSVNIPLKSLILVQNDQYVESEQVIAEIRAGTSTLHFKEKVQKHIYSESD   450
 451  GEMHWSTDVYHAPEYQYGNLRRLPKTSHLWILSVSMCRSSIASFSLHKDQ   500
 501  DQMNTYSFSVDGRYIFDFSMANDQVSHRLLDTFGKKDREILDYLTPDRIV   550
 551  SNGHWNCFYPSILQDNSDLLAKKRRNRFAVPLQYHQEQEKERISCLGISM   600
 601  EIPFMGVLRRNTIFAYFDDPRYRKDKRGSGIVKFRYRTLEEEYRTREEEY   650
 651  RTREEDSEDEYESPENKYRTREGEGEYEILEDEYRTLEDEYETLEDEYGI   700
 701  LEDEYRTLEKDSEEEYGSLENKYRTREGEGEYEILEEDSEEEYGSSEDGS   750
 751  EKEYGTLEEDSEEDSEEDSEDEYGSPEEDSILKKEGFIEHRGTKEFSLKY   800
 801  QKEVDRFFFILQELHILPRSSSLKVLDNSIIGVDTQLTKNTRSRLGGLVR   850
 851  VKRKKSHTELKIFSGDIHFPEEADKILGGSLIPPEREKKDSKESKKRKNW   900
 901  VYVQRKKILKSKEKYFVSVRPAVSYEMDEGRNLATLFPQDLLQEEDNLQL   950
 951  RLVNFISHENSKLTQRIYHTNSQFVRTCLVVNWEQEVKEGARASLVEVRT  1000
1001  NDLIRDFLRIELVKSTISYTRRRYDRTSVGLIPNNRLDRNNTNSFYSKAK  1050
1051  IQSLSQHQEVIGTLLNRNKEYPSLMILLASNCSRIGLFKNSKYPNAVKES  1100
1101  NPRIPIRDVFGLLGVIVPSISNFSSSYYLLTHNQILLKKYLFLDNLKQTF  1150
1151  QVLQGLKYSLIDENQRISNFGSNIMLEPFHLNWHFLHHDSWEETLAIIHL  1200
1201  GQFICENLCLFKSHIKKSGQIFIVNMDSFVLRAAKPYLATIGATVHGHYG  1250
1251  KILYKGDRLVTFIYEKSRSSDITQGLPKVEQIFEARSIDSLSPNLERRIE  1300
1301  DWNERIPRILGVPWGFLIGAELTIAQSRISLVNKIQKVYRSQGVQIHNRH  1350
1351  IEIIIRQVTSKVRVSEDGMSNVFLPGELIGLLRAERAGRALDESIYYRAI  1400
1401  LLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGG  1450
1451  IIPVGTGFQKFVHRSPQDKNLYFEIKKKNLFASEMRDILFLHTELVSSDS  1500
1501  DVTNNFYETSETPFTPIYTI                                1520

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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