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

NucPred

Fetching Q03921 from www.uniprot.org...

The NucPred score for your sequence is 0.74 (see score help below)

   1  MSLPLKPLTIDSNNKQLDSKQKKFRANVERALERFDSVTEWADYIASLGT    50
  51  LLKALQSWSPKFQNVRYYVPSPYQVSRRLTSSLSPALPAGVHQKTLEVYT   100
 101  YIFEHIGLETLATECNIWIPGILPLMTYASMSVRSHLIELYDNYILLLPQ   150
 151  TTLRLLIRPLISSLLPGIDDESNDFLPLTLKLIETLQENLDDDSLFWQTL   200
 201  FLVMTANKGRRLGGLTWLTRKFPSLNAVPHLVNKIKMEAEENPSETETND   250
 251  SHLDRKKRKEEAFKVLLPAAKDLVTPEPGLLIRCLVGCLEDENDILIKRS   300
 301  VLDLLLQRLRLDSPVLNVLITSEDKKLLIMSCCRTTLSKDMSLNRRIWNW   350
 351  LLGPTAGGMLNNNGGNSMEYTTSVKSANEESNVYFTKYGLSALLEGLSDL   400
 401  LSEEESVLTAFRISMAVMDRWEIGSLVIPELFIPLLYSSEKFKQNEQIMK   450
 451  TARTFFDNTETNIIWGKLFQELEDIKNLKILDFVLTNFNIGNDEEIIVRH   500
 501  LPLILLTLLALPSNDKDFDNIYKLQKFSLYNKLLNYIPERALLPLSHSKL   550
 551  KHDDEVSCEELLAKIRGFYTNVSNPSSILEKENIAERLPPFTTEDLTFLI   600
 601  ADLIQKKLLSSLWDLENINESSKLFIAIFEKIPESEELKGRSHISWSDKK   650
 651  ITQSIFEAIPRLCESNNDAKSEEIVGIVEIFGNYLYSRMEFIESMKLLKV   700
 701  VMMAVWKSLKDPRHQILGVKNLKTLNRFIPSKFIESALVYTFVEEEDISE   750
 751  RLSVLDLLWTQLDSDSNLIRRPLELILGELFDDQNPFYLTVSKWILSILN   800
 801  SGSASRLFYILTDNILKVNRLEKERLDERDDLDMLTYEFQMLAYVLKTNN   850
 851  GRTRKVFSTELTSIKSSTIWKNEDVSTYKSLLLVTLMRFLNIKSNTHAKS   900
 901  IRSALILLDILLDGTEQNFKDIVIFLLQMSSKYIAEEGIEPELIAVSLLD   950
 951  IVSKVLRLSHDNGIKLDIFDDNAAHLKYIDFLVTSVSNMKSPLIVTAYVK  1000
1001  LLSESIVYFENSIFRMILPLSASLVQCVQRLFLLEKREGGYYQPIALLLG  1050
1051  GLEELLEISHGYLVTEEREGYFSGSNLKGDFIQSVVSNVFSSDSSNEESK  1100
1101  IQGERDVILQSFRQVISCCLDIWYWAHNISCKSNDDSSLDATNHNSYKFK  1150
1151  FRSKKLLETLFLLEPLELLENLISIRSDNTTVTLVHVLDGNKPAITIPHL  1200
1201  LYGVIIRYNRTASVKFSNRDGSRSSTTKLTKGEPSMLKRLSGESIIAFLF  1250
1251  NYVDSVENSAMEEFYGDFLLFFREVATNYNLYSDVSLSILKLVALISGKV  1300
1301  SKTQFGEQKRVRREISDVFFKYLPNAFINFTNLYRGHPDSFKDLEFVVWR  1350
1351  VQYIVNDQIGGDKFNTTLATIVNQCLTPYIKPKSEKTIPGYVLELAAVVS  1400
1401  HLGSKVKSWRLLIAELFQNDKKLSVIGSDQTWEKIIYEWSIYPENKSKIL  1450
1451  NDLLLEIGSKRSSVTPTLITFNLGSDSEVEYKCQNLLKISYLLMVSPNDA  1500
1501  YLLHFSSLISCIFHYLVSKDIKLKGSCWILLRVLLLRFSESHFNDYWSMI  1550
1551  SYCLQTNLQEFYESLQIQSEVDPQTILQVCKTLDLLLLLNMEGFTSTNEW  1600
1601  IFVIDTINCVYKTNSFVALVDEIAEFKDYEITKTDDLELPTTLKDGLPLL  1650
1651  RGIHKIERHTQLRSFFQNLSYLHYEKVYGLGSVDLYGCGEDLKKDILS    1698

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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