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

NucPred

Fetching O13936 from www.uniprot.org...

The NucPred score for your sequence is 0.52 (see score help below)

   1  MDTNSPKSIDKDANSTEVDAAEQDAASVKINSTRASPNGSDLLNDDSEAA    50
  51  KITTNEKQSSPVDSHNESPNDTTINKGEDGNENEVDNVNNNDKKEDEDNV   100
 101  EENEEEADANEEEEEDEEDDEEDEEDEDESGGGRRKRARHDRRNQFLDIE   150
 151  AEVDEDEEELEDEEDEIGREDGFIEEEVGADYVGDDRRHRELDRQRQELQ   200
 201  SVDAERLAEEYREKYGRSQTVVGDTSNVPQRLLLPSVNDPNIWAVRCKIG   250
 251  KEKDIVFTIMRKAMDLQYTSSPLEIISAFQRDSLVGYIYVEARKQSHVLD   300
 301  ALNGVLNVYTNNMILVPIKEMPDLLKVQKQVVELLPGAYVRIRRGKYAGD   350
 351  LAQVDNLSENGLTARVRIVPRIDYSDGLKRKNSATRPQARLFNESEAFKS   400
 401  NPSKFSKRGPRLFLFNNEEFEDGFLVKDIRISSLITEGVNPTLDEVSKFN   450
 451  PNNEDLDLSSLALSVKGGHAEFQPGDHVEVYVGEQTGVSGVVENVRGSVI   500
 501  TMVSSDGLRLDVPSRGLRKRFRHGDYVKVIAGKYKDDTGMVVRISKDEVT   550
 551  FLSDTLMTELTVFSRDLGEASSAQAVNSAYELHDLVQLDVNTVACIFSVD   600
 601  RDTYKVIDQNGGVRTVLASQITMRHSNRRGVATDRNGAEIRIGDKVKEVG   650
 651  GEGKQGTILHIYRAFVFLHNRDIAENNGVFSARSRNVATIAAKGARISAD   700
 701  LTKMNPALSNGPALPPVANLKRTIGRDKAIGATVRIRRGPMKGLLGVIKD   750
 751  TTDANARVELHTGNKMVTIPKENLLYTTKTGELISYTEFIERSRGIRPGS   800
 801  ISTADGPNVPNWAQGARTPAVANGSRTPAWNTGSRTPAWNSGSKTPAWNS   850
 851  GSRTPAWNSGNKTPAWNAGSRTPAWNSGNKTPAWNVGNKTPAWNSGAKTP   900
 901  AWNAGNKTPSWNNGTKTPAWNANQTPMVANGTNTSWGQTPAYGGFSETNW   950
 951  DTEDNSKPYTAPTPGAWAAPTPGGWDDEEGDSPKYVPPSP             990

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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