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

NucPred

Fetching Q62635 from www.uniprot.org...

The NucPred score for your sequence is 0.32 (see score help below)

   1  MGLPLARLVAVCLVLALAKGLELQKEARSRNHVCSTWGDFHYKTFDGDVF    50
  51  RFPGLCDYNFASDCRDSYKEFAVHLKRGLDKAGGHSSIESVLITIKDDTI   100
 101  YLTHKLAVVNGAMVSTPHYSSGLLIEKNDAYTKVYSRAGLSLMWNREDAL   150
 151  MVELDGRFQNHTCGLCGDFNGMQANNEFLSDGIRFSAIEFGNMQKINKPE   200
 201  VVCEDPEEVQEPESCSEHRAECERLLTSTAFEDCQARVPVELYVLACMHD   250
 251  RCQCPQGGACECSTLAEFSRQCSHAGGRPENWRTASLCPKKCPGNMVYLE   300
 301  SGSPWLDTCSHLEVSSLCEEHYMDGCFCPEGTVYDDITGSGCIPVSQCHC   350
 351  KLHGHLYMPGQEITNDCEQCVCNAGRWMCKDLPCPETCALEGGSHITTFD   400
 401  GKKFTFHGDCYYVLTKTKYNDSYALLGELASCGSTDKQTCLKTVVLLTDN   450
 451  KKNVVAFKSGGSVLLNEMEVSLPHVAASFSIFKPSSYHIVVNTMFGLRLQ   500
 501  IQLVPVMQLFVTLDQSAQGQVQGLCGNFNGLESDDFMTSGGMVEATGAGF   550
 551  ANTWKAQSSCHDKLDWLDDPCPLNIESANYAEHWCSLLKRSETPFARCHL   600
 601  AVDPTEYYKRCKYDTCNCQNNEDCMCAALSSYARACAAKGVMLWGWRESV   650
 651  CNKDVHACPSSQIFMYNLTTCQQTCRSISEGDTHCLKGFAPVEGCGCPDH   700
 701  TFMDEKGRCVPLSKCSCYHHGLYLEAGDVILRQEERCICRNGRLQCTQVK   750
 751  LIGHTCLSPQILVDCNNLTALAIREPRPTSCQTLVARYYHTECISGCVCP   800
 801  DGLLDNGRGGCVVEDECPCIHNKQFYDSGKSIKLDCNNTCTCQKGRWECT   850
 851  RYACHSTCSIYGSGHYITFDGKHYDFDGHCSYVAVQDYCGQNSTGSFSII   900
 901  TENVPCGTTGVTCSKAIKIFIGGTELKLVDKHRVVKQLEEGHHVPFITRE   950
 951  VGLYLVVEVSSGIIVIWDKKTTIFIKLDPSYKGNVCGLCGNFDDQTKNDF  1000
1001  TTRDHMVVASELDFGNSWKEASTCPDVSHNPDPCSLNPHRRSWAEKQCSI  1050
1051  IKSDVFLACHGKVDPTVFYDACVHDSCSCDTGGDCECFCSAVASYAQECT  1100
1101  KAEACVFWRTPDLCPVFCDYYNPPDECEWHYEPCGNRSFETCRTLNGIHS  1150
1151  NISVSYLEGCYPRCPEDRPIYDEDLKKCVSGDKCGCYIEDTRYPPGGSVP  1200
1201  TDEICMSCTCTNTSEIICRPDEGKIINQTQDGIFCYWETCGSNGTVEKHF  1250
1251  EICVSSTLSPTSMTSFTTTSTPISTTPISTTITTTSATATTTVPCCFWSD  1300
1301  WINNNHPTSGNGGDRENFEHVCSAPENIECRAATDPKLDWTELGQKVQCN  1350
1351  VSEGLICNNEDQYGTGQFELCYDYEIRVNCCFPMEYCLSTVSPTTSTPIS  1400
1401  STPQPTSSPTTLPTTSPLTSSATSPTTSHITSTVSPTTSPTTSTTSPTTS  1450
1451  PTTSTTSPTTSTTSPTPSPTTSTTSPTPSPTTSTTSPTPSPTTSTTSPTT  1500
1501  SPITSPTTSTTSP                                       1513

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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