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

NucPred

Fetching Q13459 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MSVKEAGSSGRREQAAYHLHIYPQLSTTESQASCRVTATKDSTTSDVIKD    50
  51  AIASLRLDGTKCYVLVEVKESGGEEWVLDANDSPVHRVLLWPRRAQDEHP   100
 101  QEDGYYFLLQERNADGTIKYVHMQLVAQATATRRLVERGLLPRQQADFDD   150
 151  LCNLPELTEGNLLKNLKHRFLQQKIYTYAGSILVAINPFKFLPIYNPKYV   200
 201  KMYENQQLGKLEPHVFALADVAYYTMLRKRVNQCIVISGESGSGKTQSTN   250
 251  FLIHCLTALSQKGYASGVERTILGAGPVLEAFGNAKTAHNNNSSRFGKFI   300
 301  QVSYLESGIVRGAVVEKYLLEKSRLVSQEKDERNYHVFYYLLLGVSEEER   350
 351  QEFQLKQPEDYFYLNQHNLKIEDGEDLKHDFERLKQAMEMVGFLPATKKQ   400
 401  IFAVLSAILYLGNVTYKKRATGREEGLEVGPPEVLDTLSQLLKVKREILV   450
 451  EVLTKRKTVTVNDKLILPYSLSEAITARDSMAKSLYSALFDWIVLRINHA   500
 501  LLNKKDVEEAVSCLSIGVLDIFGFEDFERNSFEQFCINYANEQLQYYFNQ   550
 551  HIFKLEQEEYQGEGITWHNIGYTDNVGCIHLISKKPTGLFYLLDEESNFP   600
 601  HATSQTLLAKFKQQHEDNKYFLGTPVMEPAFIIQHFAGKVKYQIKDFREK   650
 651  NMDYMRPDIVALLRGSDSSYVRELIGMDPVAVFRWAVLRAAIRAMAVLRE   700
 701  AGRLRAERAEKAAGMSSPGAQSHPEELPRGASTPSEKLYRDLHNQMIKSI   750
 751  KGLPWQGEDPRSLLQSLSRLQKPRAFILKSKGIKQKQIIPKNLLDSKSLK   800
 801  LIISMTLHDRTTKSLLHLHKKKKPPSISAQFQTSLNKLLEALGKAEPFFI   850
 851  RCIRSNAEKKELCFDDELVLQQLRYTGMLETVRIRRSGYSAKYTFQDFTE   900
 901  QFQVLLPKDAQPCREVISTLLEKMKIDKRNYQIGKTKVFLKETERQALQE   950
 951  TLHREVVRKILLLQSWFRMVLERRHFLQMKRAAVTIQACWRSYRVRRALE  1000
1001  RTQAAVYLQASWRGYWQRKLYRHQKQSIIRLQSLCRGHLQRKSFSQMISE  1050
1051  KQKAEEKEREALEAARAGAEEGGQGQAAGGQQVAEQGPEPAEDGGHLASE  1100
1101  PEVQPSDRSPLEHSSPEKEAPSPEKTLPPQKTVAAESHEKVPSSREKRES  1150
1151  RRQRGLEHVKFQNKHIQSCKEESALREPSRRVTQEQGVSLLEDKKESRED  1200
1201  ETLLVVETEAENTSQKQPTEQPQAMAVGKVSEETEKTLPSGSPRPGQLER  1250
1251  PTSLALDSRVSPPAPGSAPETPEDKSKPCGSPRVQEKPDSPGGSTQIQRY  1300
1301  LDAERLASAVELWRGKKLVAAASPSAMLSQSLDLSDRHRATGAALTPTEE  1350
1351  RRTSFSTSDVSKLLPSLAKAQPAAETTDGERSAKKPAVQKKKPGDASSLP  1400
1401  DAGLSPGSQVDSKSTFKRLFLHKTKDKKYSLEGAEELENAVSGHVVLEAT  1450
1451  TMKKGLEAPSGQQHRHAAGEKRTKEPGGKGKKNRNVKIGKITVSEKWRES  1500
1501  VFRQITNANELKYLDEFLLNKINDLRSQKTPIESLFIEATEKFRSNIKTM  1550
1551  YSVPNGKIHVGYKDLMENYQIVVSNLATERGQKDTNLVLNLFQSLLDEFT  1600
1601  RGYTKNDFEPVKQSKAQKKKRKQERAVQEHNGHVFASYQVSIPQSCEQCL  1650
1651  SYIWLMDKALLCSVCKMTCHKKCVHKIQSHCSYTYGRKGEPGVEPGHFGV  1700
1701  CVDSLTSDKASVPIVLEKLLEHVEMHGLYTEGLYRKSGAANRTRELRQAL  1750
1751  QTDPAAVKLENFPIHAITGVLKQWLRELPEPLMTFAQYGDFLRAVELPEK  1800
1801  QEQLAAIYAVLEHLPEANHNSLERLIFHLVKVALLEDVNRMSPGALAIIF  1850
1851  APCLLRCPDNSDPLTSMKDVLKITTCVEMLIKEQMRKYKVKMEEISQLEA  1900
1901  AESIAFRRLSLLRQNAPWPLKLGFSSPYEGVLNKSPKTRDIQEEELEVLL  1950
1951  EEEAAGGDEDREKEILIERIQSIKEEKEDITYRLPELDPRGSDEENLDSE  2000
2001  TSASTESLLEERAGRGASEGPPAPALPCPGAPTPSPLPTVAAPPRRRPSS  2050
2051  FVTVRVKTPRRTPIMPTANIKLPPGLPSHLPRWAPGAREAAAPVRRREPP  2100
2101  ARRPDQIHSVYITPGADLPVQGALEPLEEDGQPPGAKRRYSDPPTYCLPP  2150
2151  ASGQTNG                                             2157

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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