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

NucPred

Fetching Q8IRG6 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MSSFVLDKEAFVRRVKRLYTEWRAPSIGHDDALRNLDCIMSIVGVEEDVM    50
  51  YSKSMALQLWLLGYELTDTISVFCSDAVYFLTSKKKIEFLKQTQNITEEG   100
 101  FPEINLLVRDRTDKDQGNFEKLIKALQNSKKGKRLGVFAKDAYPGEFSEA   150
 151  WKKSLTASKFEHVDISTIIAYLMCPKDESEINNIRKASLVSMDIFNKYLK   200
 201  DEIMDIIDSDRKVKHNKLSDGCEAAIGEKKYTSGLDPRLLDMAYPPIIQS   250
 251  GGAYSLKFSAVADKNPLHFGVIVCSLGARYKSYCSNISRTFLVNPTEAMQ   300
 301  ENYTFLVSVQEEILKLLVPGTKLCDVYEKTLDFVKKEKPSMVDNLPKSFG   350
 351  FAMGLEFRENSIVIGPKCQALLKKNMVFNLHVGISNLTNPEATDKEGKNY   400
 401  ALFIGDTVLVGEQSPASVMTPSKKKIKNVGIFIKDDSDEEDVDDKKTAKE   450
 451  DQGTEILGRSKRNAVLESKLRNEINTEEKRKEHQRELAQQLNERAKDRLA   500
 501  RQGNSKEVEKVRKNTVSYKSISQMPREPEVKELKLYVDKKYETVIMPVFG   550
 551  IQVPFHISTIKNISQSVEGEYTYLRINFFHPGATMGRNEGGLYPQPEATF   600
 601  VKEVTYRSSNVKEHGEVGAPSANLNNAFRLIKEVQKRFKTREAEEREKED   650
 651  LVKQDTLILSQNKGNPKLKDLYIRPNIVTKRMTGSLEAHSNGFRYISVRG   700
 701  DKVDILYNNIKSAFFQPCDGEMIILLHFHLKYAIMFGKKKHVDVQFYTEV   750
 751  GEITTDLGKHQHMHDRDDLAAEQAERELRHKLKTAFKSFCEKVETMTKSV   800
 801  VEFDTPFRELGFPGAPFRSTVTLQPTSGSLVNLTEWPPFVITLDDVELVH   850
 851  FERVQFHLRNFDMIFVFKEYNKKVAMVNAIPMNMLDHVKEWLNSCDIRYS   900
 901  EGVQSLNWQKIMKTITDDPEGFFEQGGWTFLDPESGSEGENETAESEEDE   950
 951  AYNPTDAESDEESDEDSEYSEASEDSEESDEDLGSDEESGKDWSDLEREA  1000
1001  AEEDRNHDYAADDKPRNGKFDSKKHGKSSKHSPSKSSKDKYNSRDKHHSS  1050
1051  SSSGNKSSSKDKDRKRSRDDSRDNGHKSKKSRH                   1083

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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