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

NucPred

Fetching Q8LPT9 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MSNSIGRNVLHQSLLCSTVFEHQSNRHSSGIPANSLFQAVSINQPAGASA    50
  51  ARKSPLSTKFYGTSLNARPKMAMGRHRPVLITPRAVLAVDSASELAGKFN   100
 101  LEGNVELQITVGAPTPGSLTQVNIEISYSSNSLLLHWGAIRDKKEKWVLP   150
 151  SRPPDGTKILKNRALRTPFVSSGSKSLVKLEIDDPAIEAVEFLILDEAQN   200
 201  KWFKNNGANFHVKLPSERSLIQNVSVPEDLVQTQAYLRWERKGKQIYTPE   250
 251  QEKEEYEAARTELLEEIVRGTSVEDLRAKLTNKNDRQEIKESSSHGTKNA   300
 301  IPDDLVQIQSYIRWERAGKPNYSADQQLREFEEARKELQSELEKGISLDE   350
 351  IWKKITKGEIQTKVSDQLKTKKYFRTERIQRKQRDFMQILNKHVAEPTEK   400
 401  KNISVEPKALTPVELFVGATEEQEGDSILNKKIYKLAGKELLVLVHKPGG   450
 451  KTKIHLATDGKEPLILHWALSKKAGEWLAPPPSVLPAGSVLLSGSVETTF   500
 501  TTSSLADLPYQVQSIEIEIEEEGYVGMPSVLQSGGNWIKNKGSDFYVDFS   550
 551  YESKQVQQDFGDGKGTAKALLEKIAGLEIEAQKSFMHRFNIAADLIQEAK   600
 601  EAGELGFAGILVWMRFMATRQLIWNKNYNVKPREISKAQDRLTDLLQNVY   650
 651  ISNPEYREIVRMILSTVGRGGEGDVGQRIRDEILVIQRNNNCKGGMMEEW   700
 701  HQKLHNNTSPDDVIICQALIDYIKSDFDISAYWKTLNDNGITKERLLSYD   750
 751  RAIHSEPNFRRDQKDGLLRDLGNYMRTLKAVHSGADLESAITNCLGYRSE   800
 801  GQGFMVGVQINPIPNLPSGFPELLQFVSEHVEDRNVEALLEGLLEARQEI   850
 851  RPLLCKHNDRLKDLLFLDIALESSVRTAIEKGYEELNEAGPEKIMYFVSL   900
 901  ILENLALSLDDNEDLIYCLKGWSNALSMSKSKSDNWALFAKSVLDRTRLA   950
 951  LAGKADWYQKVLQPSAEYLGTLLSVDKWAVDIFTEEMIRAGSAAALSLLL  1000
1001  NRLDPVLRKTASLGSWQVISPVEVFGYVAVVDELLAVQDKSYDQPTILLA  1050
1051  RRVKGEEEIPHGTVAVLTADMPDVLSHVSVRARNCKVCFATCFDPNILAD  1100
1101  LQSNEGKMLHLKPTSADIAYSVVEGSELQDSSSANLKEEDGPSSSVALVK  1150
1151  KQFAGRYAITSDEFTGELVGAKSRNIAYLKGKVPSWIGIPTSVALPFGVF  1200
1201  EKVLSDDINQAVAEKLQILKQKLGEEDHSALREIRETVLQMKAPNQLVQE  1250
1251  LKTEMKSSGMPWPGDEGEQRWEQAWMAIKKVWASKWNERAFFSTRRVKLD  1300
1301  HEYLCMAVLVQEIINADYAFVIHTTNPSSGDSSEIYAEVVKGLGETLVGA  1350
1351  YPGRALSFVCKKNDLKSPRVLGYPSKPIGLFIRRSIIFRSDSNGEDLEGY  1400
1401  AGAGLYDSVPMDEAEKVVLDYSSDHLITDGHFQQSILSSIARAGCEIEEL  1450
1451  FGSAQDIEGVVRDGKIYVVQTRPQM                           1475

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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