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

NucPred

Fetching Q9DGG6 from www.uniprot.org...

The NucPred score for your sequence is 0.53 (see score help below)

   1  MASPPHQQLLHHHSTEVSCDSSGDSNSVTVRINPRQQQALSAKRCKYSIS    50
  51  SSCSSGESGGVGRGGGGGLRRQKKLPQLFERASSRWWDPKFDSTNLEEAS   100
 101  MERCFPQTQRRFRYALFYIGSACLLWGIYFGVHMREKQMVFMVPALCFLL   150
 151  VCVAFFAFTFTKAYARRYVWTSGYTLLVFALTLAPQFQPWTLGERQRVQP   200
 201  RPAAPVDTCLSQVGSFSMCVEVLLLLYTVMHLPLYLSLFLGLSYSVLFET   250
 251  SAFRDESCTLLGGGAVYWELLSKAFLHVCIHAIGIHLFIMSEVRSRSTFL   300
 301  KVGQSIMHGKDLEVEKALKERMIHSVMPRIIADDLMKQGDDESENSVKRH   350
 351  STSSPKNRKKKPSIQKTPIIFRPFKMQQIEQVSILFADIVGFTKMSANKS   400
 401  AHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYC   450
 451  CIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWS   500
 501  NDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVAD   550
 551  QLKGLKTYLISGQKVKEPHCSCSQALLQLGGWGWSQMQAAPSAENTADST   600
 601  KALKHVEKPKPCPSCSTTLVPPCDVSIDEGAIQNGCQDEHKNSTKAPGGH   650
 651  SPKTQNGLLSPPQEEKLSNSQTSLYEMLQEKGRWGGVSLDQSALLPLRFK   700
 701  NIREKTDAHFVDVIKEDSLMKDYFFKPPISKLSLNFLDQDLEMAYRTSYQ   750
 751  EEVMRNAPVKTFASATFSSLLDVFLSTTVFLILSVTCFLKHGMVASPPPP   800
 801  AAVVVFVIAILLEVLSLVISVRMVFFLEEVMACTKRLLELISGWLPRHFL   850
 851  GAILVSLPALAVFSHFTSDFETNIHYTMFMCCAILIAIVQYCNFCQLSSW   900
 901  MRSLLATVVGAVLLILLYVSLCPDSSVETLHLDLAQNLSSRKSPCNSSMP   950
 951  ADVKRPADLIGQEVILAVFLLLLLVWFLNRSFEVSYRLHYHGDVEADLHR  1000
1001  TKIQSMRDQPDSCVRNIIPYHVADELKVSQSYSKNHDSGGVIFASIVNFS  1050
1051  EFYEENYEGGKECYRVLNELIGDFDELLSKPHYSSIEKIKTIGATYMAAS  1100
1101  GLNTSQCQDSNHPHGHLQTLFEFAKEMMRVVDDFNNNMLWFNFKLRIGFN  1150
1151  HGPLTAGVIGTTKLLYDIWGDTVNIASRMDTIGVECRIQVSEETYRILSK  1200
1201  MGYDFDYRGTVNVKGKGQMKTYLYPKCMDNGIVPHHQLSISPDIRVQVDG  1250
1251  SIGRSPTDEIANLVPSVQNSDKTAHATDNSETKDALPSSKKLQKEPTKAE  1300
1301  ERCRFGKAVEKTDCEEAGTEEVNELTKLNVSKSV                  1334

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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