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

NucPred

Fetching P08922 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MKNIYCLIPKLVNFATLGCLWISVVQCTVLNSCLKSCVTNLGQQLDLGTP    50
  51  HNLSEPCIQGCHFWNSVDQKNCALKCRESCEVGCSSAEGAYEEEVLENAD   100
 101  LPTAPFASSIGSHNMTLRWKSANFSGVKYIIQWKYAQLLGSWTYTKTVSR   150
 151  PSYVVKPLHPFTEYIFRVVWIFTAQLQLYSPPSPSYRTHPHGVPETAPLI   200
 201  RNIESSSPDTVEVSWDPPQFPGGPILGYNLRLISKNQKLDAGTQRTSFQF   250
 251  YSTLPNTIYRFSIAAVNEVGEGPEAESSITTSSSAVQQEEQWLFLSRKTS   300
 301  LRKRSLKHLVDEAHCLRLDAIYHNITGISVDVHQQIVYFSEGTLIWAKKA   350
 351  ANMSDVSDLRIFYRGSGLISSISIDWLYQRMYFIMDELVCVCDLENCSNI   400
 401  EEITPPSISAPQKIVADSYNGYVFYLLRDGIYRADLPVPSGRCAEAVRIV   450
 451  ESCTLKDFAIKPQAKRIIYFNDTAQVFMSTFLDGSASHLILPRIPFADVK   500
 501  SFACENNDFLVTDGKVIFQQDALSFNEFIVGCDLSHIEEFGFGNLVIFGS   550
 551  SSQLHPLPGRPQELSVLFGSHQALVQWKPPALAIGANVILISDIIELFEL   600
 601  GPSAWQNWTYEVKVSTQDPPEVTHIFLNISGTMLNVPELQSAMKYKVSVR   650
 651  ASSPKRPGPWSEPSVGTTLVPASEPPFIMAVKEDGLWSKPLNSFGPGEFL   700
 701  SSDIGNVSDMDWYNNSLYYSDTKGDVFVWLLNGTDISENYHLPSIAGAGA   750
 751  LAFEWLGHFLYWAGKTYVIQRQSVLTGHTDIVTHVKLLVNDMVVDSVGGY   800
 801  LYWTTLYSVESTRLNGESSLVLQTQPWFSGKKVIALTLDLSDGLLYWLVQ   850
 851  DSQCIHLYTAVLRGQSTGDTTITEFAAWSTSEISQNALMYYSGRLFWING   900
 901  FRIITTQEIGQKTSVSVLEPARFNQFTIIQTSLKPLPGNFSFTPKVIPDS   950
 951  VQESSFRIEGNASSFQILWNGPPAVDWGVVFYSVEFSAHSKFLASEQHSL  1000
1001  PVFTVEGLEPYALFNLSVTPYTYWGKGPKTSLSLRAPETVPSAPENPRIF  1050
1051  ILPSGKCCNKNEVVVEFRWNKPKHENGVLTKFEIFYNISNQSITNKTCED  1100
1101  WIAVNVTPSVMSFQLEGMSPRCFIAFQVRAFTSKGPGPYADVVKSTTSEI  1150
1151  NPFPHLITLLGNKIVFLDMDQNQVVWTFSAERVISAVCYTADNEMGYYAE  1200
1201  GDSLFLLHLHNRSSSELFQDSLVFDITVITIDWISRHLYFALKESQNGMQ  1250
1251  VFDVDLEHKVKYPREVKIHNRNSTIISFSVYPLLSRLYWTEVSNFGYQMF  1300
1301  YYSIISHTLHRILQPTATNQQNKRNQCSCNVTEFELSGAMAIDTSNLEKP  1350
1351  LIYFAKAQEIWAMDLEGCQCWRVITVPAMLAGKTLVSLTVDGDLIYWIIT  1400
1401  AKDSTQIYQAKKGNGAIVSQVKALRSRHILAYSSVMQPFPDKAFLSLASD  1450
1451  TVEPTILNATNTSLTIRLPLAKTNLTWYGITSPTPTYLVYYAEVNDRKNS  1500
1501  SDLKYRILEFQDSIALIEDLQPFSTYMIQIAVKNYYSDPLEHLPPGKEIW  1550
1551  GKTKNGVPEAVQLINTTVRSDTSLIISWRESHKPNGPKESVRYQLAISHL  1600
1601  ALIPETPLRQSEFPNGRLTLLVTRLSGGNIYVLKVLACHSEEMWCTESHP  1650
1651  VTVEMFNTPEKPYSLVPENTSLQFNWKAPLNVNLIRFWVELQKWKYNEFY  1700
1701  HVKTSCSQGPAYVCNITNLQPYTSYNVRVVVVYKTGENSTSLPESFKTKA  1750
1751  GVPNKPGIPKLLEGSKNSIQWEKAEDNGCRITYYILEIRKSTSNNLQNQN  1800
1801  LRWKMTFNGSCSSVCTWKSKNLKGIFQFRVVAANNLGFGEYSGISENIIL  1850
1851  VGDDFWIPETSFILTIIVGIFLVVTIPLTFVWHRRLKNQKSAKEGVTVLI  1900
1901  NEDKELAELRGLAAGVGLANACYAIHTLPTQEEIENLPAFPREKLTLRLL  1950
1951  LGSGAFGEVYEGTAVDILGVGSGEIKVAVKTLKKGSTDQEKIEFLKEAHL  2000
2001  MSKFNHPNILKQLGVCLLNEPQYIILELMEGGDLLTYLRKARMATFYGPL  2050
2051  LTLVDLVDLCVDISKGCVYLERMHFIHRDLAARNCLVSVKDYTSPRIVKI  2100
2101  GDFGLARDIYKNDYYRKRGEGLLPVRWMAPESLMDGIFTTQSDVWSFGIL  2150
2151  IWEILTLGHQPYPAHSNLDVLNYVQTGGRLEPPRNCPDDLWNLMTQCWAQ  2200
2201  EPDQRPTFHRIQDQLQLFRNFFLNSIYKSRDEANNSGVINESFEGEDGDV  2250
2251  ICLNSDDIMPVALMETKNREGLNYMVLATECGQGEEKSEGPLGSQESESC  2300
2301  GLRKEEKEPHADKDFCQEKQVAYCPSGKPEGLNYACLTHSGYGDGSD     2347

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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