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

NucPred

Fetching O93309 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MYIKQVIIQGFRSYRDQTIVDPFSSKHNVIVGRNGSGKSNFFYAIQFVLS    50
  51  DEFSHLRPEQRLALLHEGTGPRVISAFVEIIFDNSDNRLPIDKEEVSLRR   100
 101  VIGAKKDQYFLDKKMVTKNDVMNLLESAGFSRSNPYYIVKQGKINQMATA   150
 151  PDSQRLKLLREVAGTRVYDERKEESISLMKETEGKRDKINELLKYIEERL   200
 201  HTLEEEKEELAQYQKWDKMRRALEYTIYNQELNETRAKLDELSSKRETSG   250
 251  EKSRQLRDAQQDARDKMEEIERQVRELKSKISAMKEEKEQLSSERQEQIK   300
 301  QRTKLELKTKDLQDELAGNSEQRKRLLKERQKLLEKIEEKQKELAETEPK   350
 351  FSSVKQKEESGIARLAQATQERTDLYAKQGRGSQFTSKEERDKWIKKELK   400
 401  SLDQAINDKKRQIAAINKDLEETEVNKEKNLEQYTKLDQDLNEVKTRVEE   450
 451  LDKKYYEVKNKKDELQSERNYLWREENAEQQSLAAKREDLEKKQQLLRAA   500
 501  TGKAILNGIDSINKVLEHFRRKGINQHVINGYHGIVMNNFDCEPAFYTCV   550
 551  EVTAGNRLFYHIVESDEVSTKILMEFNKMNLPGEVTFLPLNKLDVRDTAY   600
 601  PETNDAIPMISKLRYNLRFDKAFKHVFGKTLICRSMEVSTQLARAFTMDC   650
 651  ITLEGDQVSHRGALTGGYYDTRKSRLELQKDVRKVEDELHALEAKLNENL   700
 701  RRNIERINNEIDQLMNQMQQIETQQRKFKASRDSILSEMKMLKEKRQQSE   750
 751  KTFMPKQRSLQSLEASLHAMESTRESLKAELGTDLLSQLSLEDQKRVDAL   800
 801  NDEIRQLQQENRQLLNERIKLEGTITRVETYLNENLRKRLDQVEQELNEL   850
 851  RETEGGTVLTATTSELEAINKRVKDTLARSEGLDITIDKTEVESKDLVKS   900
 901  MDRWKNMEKDHMDAINHDTKELEKMTNRQGMLLKKKEECMKKIRELGSLP   950
 951  QEAFEKYQTLSLKQLFRKLEQCNTELKKYSHVNKKALDQFVNFSEQKEKL  1000
1001  IKRQEELDRGHKSIMELMNVLELRKYEAIQLTFKQVSKNFSEVFQKLVPG  1050
1051  GKATLVMKKGDVEGSQSQDEGEGSTQSSVPSVDQFTGVGIRVSFTGKQAE  1100
1101  MREMQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDQALDAQHRKAVS  1150
1151  DMIMELASHAQFITTTFRPELLESADKFYGVKFRNKVSHIDVITAEQAKD  1200
1201  FVEDDTTHG                                           1209

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.)

Go back to the NucPred Home Page.