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

NucPred

Fetching Q8CHG7 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MKPLAAPANHGVLGQQEKQSLPADFTKLHLTDSLHPQVTHVSSSHSGCSI    50
  51  TSDSGSSSLSDIYQATESEAGDMDLSGLPETAVDSEDDDDEEDIERASDP   100
 101  LMSRDIVRDCLEKDPIDRTDDDIEQLLEFMHQLPAFANMTMSVRRELCAV   150
 151  MVFAVVERAGTIVLNDGEELDSWSVILNGSVEVTYPDGKAEILCMGNSFG   200
 201  VSPTMDKEYMKGVMRTKVDDCQFVCIAQQDYCRILNQVEKNMQKVEEEGE   250
 251  IVMVKEHRELDRTGTRKGHIVIKGTSERLTMHLVEEHSVVDPTFIEDFLL   300
 301  TYRTFLSSPMEVGKKLLEWFNDPSLRDKVTRVVLLWVNNHFNDFEGDPAM   350
 351  TRFLEEFENNLEREKMGGHLRLLNIACAAKAKRRLMTLTKPSREAPLPFI   400
 401  LLGGSEKGFGIFVDSVDSCSKATEAGLKRGDQILEVNGQNFENIQLSKAM   450
 451  EILRNNTHLSITVKTNLFVFKELLTRLSEEKRNGAPHLPKIGDIKKASRY   500
 501  SIPDLAVDVEQVIGLEKVNKKSKANTVGGRNKLKKILDKTRISILPQKPY   550
 551  NDIGIGQSQDDSIVGLRQTKHIPAALPVSGTLSSSNPDLLQSHHRILDFS   600
 601  TTPDLPDQVLRVFKADQQSRYIMISKDTTAKEVVIQAIREFAVTATPEQY   650
 651  SLCEVSVTPEGVIKQRRLPDQLSKLADRIQLSGRYYLKNNMETETLCSDE   700
 701  DAQELLRESQISLLQLSTVEVATQLSMRNFELFRNIEPTEYIDDLFKLKS   750
 751  KTSCANLKKFEEVINQETFWVASEILRETNQLKRMKIIKHFIKIALHCRE   800
 801  CKNFNSMFAIISGLNLAPVARLRTTWEKLPNKYEKLFQDLQDLFDPSRNM   850
 851  AKYRNVLSGQNLQPPVIPLFPVIKKDLTFLHEGNDSKVDGLVNFEKLRMI   900
 901  AKEIRHVGRMASVNMDPALMFRTRKKKWRSLGSLSQGSANATVLDVAQTG   950
 951  GHKKRVRRSSFLNAKKLYEDAQMARKVKQYLSNLELEMDEESLQTLSLQC  1000
1001  EPATSTLPKNPGDKKPVKSETSPVAPRAGPQQKVQPQQPLAQPQPPHKVS  1050
1051  QGLQVPAVSLYPSRKKVPVKDLPPFGINSPQALKKILSLSEEGSLERHRK  1100
1101  QAEDTISNASSQLSSPPTSPQSSPRKGYALALSGTVDNFSDSGHSEISSR  1150
1151  SSIVSNSSFDSVPVSLHDERRQRHSVSIVESNLGVGRMERRTLMEPDQYS  1200
1201  LGSYAPVSESRGLYAAATVISSPSTEELSHDQGDRASLDAADSGRGSWTS  1250
1251  CSSGSHDNIQTIQHQRSWETLPFGHTHFDYSGDAASIWASGGHMDQMMFS  1300
1301  DHSTKYNRQNQSRESLEQAQSRASWASSTGYWGEDSEGDTGTIKRRGGKD  1350
1351  VSAEAESSSMVPVTTEEAKPVPMPAHIAVTPSTTKGLIARKEGRYREPPP  1400
1401  TPPGYVGIPIADFPEGPCHPARKPPDYNVALQRSRMVARPTEAPAPGQTP  1450
1451  PAAAASRPGSKPQWHKPSDADPRLAPFQPQGFAGAEEDEDEQVSAV      1496

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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