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

NucPred

Fetching Q01833 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MEGMALYLVAALLIGFPGSSHGALYTLITPAVLRTDTEEQILVEAHGDST    50
  51  PKSLDIFVHDFPRKQKTLFQSRVDMNQAGSMFVTPTIKVPAKELNKDSKQ   100
 101  NQYVVVKVTGPQVALEKVVLLSYQSGFVFIQTDKGIYTPGSPVRYRVFSV   150
 151  DHNMHRMDKTVIVEFQTPEGIVVSSKPVNPSGSIRPYNLPELVSFGTWKA   200
 201  VAKYEHSPEESYTAYFDVREYVLPSFEVRLQPSDKFLYIDGNKNFHVSIT   250
 251  ARYLYGKKVEGVAFVVFGVKIDDAKKSIPDSLTRIPIIDGDGEATLKRDT   300
 301  LRSRFQDLNQLVGHTLYVSVTVITESGSDMVVTEQGGIHIVTSPYQIYFT   350
 351  KTPKYFKPGMPYELTVYVTNPDGSPAAHVPVVSEAIHSEGTTLSDGTAKL   400
 401  ILNTPLNIQSLPITVRTNHGDLPRERQAIKSMTATAYQTQGGSENYLHVA   450
 451  ITSTEIKPGDNLPVNFNVRGNANSLNQIKYFTYLILNKGKIFKVGRQPRR   500
 501  DGQNLVTMNLHITPDLIPSFRFVAYYQVGNNEIVADSVWVDVKDTCMGTL   550
 551  VVKGASSRDDRIQKPGAAMKIKLEGDPGARVGLVAVDKAVYVLNDKYKIS   600
 601  QAKIWDTIEKSDFGCTAGSGQNNLGVFEDAGLALTTSTNLNTKQRSAAKC   650
 651  PQPANRRRRSSVLLLDSKASKAAQFQDQGLRKCCEDGMHENPMGYTCEKR   700
 701  AKYIQEGDACKAAFLECCHYIKGIRDENQRESELFLARSDFEDELFGDDN   750
 751  IISRSDFPESWLWLTEELTGEPNNQGISSKTVPFYLRDSITTWELLAVGL   800
 801  SPTKGICVAEPYEITVMKDFFIDLRLPYSVVKNEQVEIRAILYNYADEDI   850
 851  YVRVELIYNPAFCSASTEGQRYRQQFPIKALSSRAVPFVIVPLEQGLHDV   900
 901  EVIASVRGELASDGVRKKLKVVPEGERKNIVTIIELDPSVKGVGGTQELT   950
 951  VIANKLDDKVPDTEVETRISVLGDPVAQIIENSIDGSKLNHLIITPSGCG  1000
1001  EQNMITMTPSVIATYYLDATGQWENLGVDRRTEAIKQIMTGYAQQMVYKK  1050
1051  ADHSYAAFTNRASSSWLTAYVVKVLAMASNMVKDISHEIICGGVKWLILN  1100
1101  RQQPDGVFKENAPVIHGEMLGGTKGAEPEASLTAFIVTALLESRSVCKEQ  1150
1151  INILDSSINKATDYLLKKYEKLQRPYTTALTAYALAAADRLNDDRVLMAA  1200
1201  STGRNRWEEYNARTHNIEGTSYALLALLKMKKFAEVGPVVRWLIDQKYYG  1250
1251  GTYGQTQATVMVFQALAEYEIQMPTHQDLNLDISIKLPEREVPERYSIND  1300
1301  RNAVQARTVETKLNEDFTVSASGDGKATMTILTVYNAQLREDANVCNKFH  1350
1351  LDVSVENVELNLKQAKGGKAALRLKICTRYLGEVDSTMTIIDISMLTGFF  1400
1401  PDAEDLKRLSNGVDRYISKFEIDNNMAQKGTVVIYLDKVSHSEDECLHFK  1450
1451  IHKHFEVGFIQPGSVKVYSYYNLDEQCTKFYHPDKETGLLNKICHGNICR  1500
1501  CAEETCSLLNQQKKIDLQLRIQKACAQNVDYVYKTKLLRIEEKDGNDIYF  1550
1551  MDVLEVIKGGTDRNAQAKARQYVSQRKCQEALNLKLDNDYLIWGLSSDLW  1600
1601  PMKDDISYLITKNTWIERWPNEDECQDEEFQNLCDDFAQLSNTLTIFGCP  1650
1651  T                                                   1651

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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