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

NucPred

Fetching Q10309 from www.uniprot.org...

The NucPred score for your sequence is 0.59 (see score help below)

   1  MDSRLNRIQSKMKLWIKDKNLSNPSIPLKVLNKSFRSSRQSSVSNGHGLY    50
  51  SLDRDETESLMSSHEASNAGISLDSSFRVIQVGQPEPQYGNNAVTNTKYD   100
 101  LFTFLPKCLYEQFRYFYNMYFLLVSLSQLIPPLKIGYLSTYIAPLIFVLL   150
 151  ITLTKEAVDDLKRRRRDSYANNEIYTVNDSPCAAQNIQAGDVVYIAKDQR   200
 201  IPADMILLETTVGNEAFIRTDQLDGETDWKLRIPCSNQHTEGIVHADAPI   250
 251  KSVHHFYGTFTLNNQKRPISVDHTLWANTVLASDGVYGVVVYTGKDTRQS   300
 301  MNSSKAKTKVGLLEKEINFYSKILCTFVLVLSIGLTFSHGIKTDWYISVF   350
 351  RYLILFSSIIPINLRVNLDLAKIVHSKNTESDPNLPGVVVRSSNIPEELG   400
 401  RIEYVLTDKTGTLTQNEMEMKKLHVGTMGFSAESMDVVQACIQNYSTPIP   450
 451  LSEDSKTLVRNLVLALSLCHNVTPSKGHDGVVSYQAASPDEVAIVKWTST   500
 501  LGLVLTNRTRDAITLNNNVYKILNIFPFKSETKRMGIIVQSPDEKITFYL   550
 551  KGADSIMQNFVKPSFWLEEECGNLAREGLRTLVVAKKDLSAEEYSAFSLA   600
 601  HSDASLSFSNSRDKKMEEIVSRYLENDMDLLGLTGVEDKLQKDVKITLEL   650
 651  LRNAGIHVWMLTGDKVETARCIAISSRLVSRGQYIHTINQLSSREEAHNH   700
 701  LLTLRNKPDSCLIIDGESMEFCIGYLQNEFIDIVSDLSSVVICRCTPTQK   750
 751  ANMTRLIQEKKQASVCCIGDGGNDVGMIQVANVGIGIVGKEGQQASLAAD   800
 801  YSVKEFSHVSRLLLWHGRISYKQTSKLAMFVIHRGLLISVCQVVYSVISA   850
 851  FEPIALFQGLLLVGYSTMYTMLPVFSIVYDRDVSEKLVFLFPELYKEMRE   900
 901  QKCFSYKNFISCVLISVYQGLIIQLFTFYLIGFEEEGKMLAVCFSCLIFN   950
 951  ELIMVALQINTWEQTIVMSELLTLMMYILSVPFLTNYFELKFLLGLKFYW  1000
1001  VSALILFISLLPVWCGKALKRKLKPSSYAKLQR                   1033

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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