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

NucPred

Fetching P07898 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MTTLLLVFVCLQAITTAASAELSDSSDGLEVKIPEQSPLRVVLGSSLNIP    50
  51  CYFNIPEEEDTNALLTPRIKWSKLSNGTEIVLLVATGGKIRLNAEYREVI   100
 101  SLPNYPAIPTDATLEIKALRSNHTGIYRCEVMYGIEDRQDTIEVLVKGVV   150
 151  FHYRAISTRYTLNFERAKQACIQNSAVIATPEQLQAAYEDGYEQCDAGWL   200
 201  ADQTVRYPIHLPRERCYGDKDEFPGVRTYGVRETDETYDVYCYAEQMQGK   250
 251  VFYATSPEKFTFQEAFDKCHSLGARLATTGELYLAWKDGMDMCSAGWLAD   300
 301  RSVRYPISRARPNCGGNLVGVRTVYLNPANQTGYPHPSSRYDAICYSGDD   350
 351  FEALVPGLFTDEVGTELGSAFTIQTVTQTEVELPLPRNVTEEEARGSIAT   400
 401  LEPMEITATATELYEAFTVLPDLFATSVTVETASPREENVTREEITGIWA   450
 451  VPEEVTTSVSGTAFTTGMAEVSSVEEAIAVTATPGLESASPFTIEDHLVQ   500
 501  VTAAPDVALLPRQPISPTGVVFHYRAATSRYAFSFIQAQQACLENNAVIA   550
 551  TPEQLQAAYEAGFDQCDAGWLRDQTVRYPIVNPRSNCVGDKESSPGVRSY   600
 601  GMRPASETYDVYCYIDRLKGEVFFATQPEQFTFQEAQLYCESQNATLASA   650
 651  GQLHAAWKQGLDRCYPGWLADGSLRYPIVSPRPACGGDAPGVRTIYQHHN   700
 701  QTGFPDPLSRHHAFCFRALPSVVEEGVTSLFEEEVMVTQLIPGVEGIPSG   750
 751  EETTVETELSSEPENQTAQGTEVFPTDVSLLSARPSAFPPATVIPEETST   800
 801  NASIPEVSGEFPESGEHPTSGEPSASGAPDTSGEPTSVGFELSGEQSGIG   850
 851  ESGLPSVDLQSSGFVPGESGLPSGDVSGLPSGIVDISGLPSAEEEVTVSV   900
 901  SRIPEVSGMPSGAESSGLHSGFSGEISGTELISGLPSGEESGLASGFPTI   950
 951  SLVDSTLVEVVTAAPGRQEEGKGSIGVSGEEELSGFPSAEWDSSGARGLP  1000
1001  SGAETSGEQSGVPELSGEHSGVPGLSGEAFEVPELSGEHSGVTELSGEHS  1050
1051  GLPELSGEPFGVPELSGFPSGLDISGEPSGAPEVSGPVDVSGLTSGVDGS  1100
1101  GEVSGVTFISTSLQEVTTPSVAEAEAKEILEISGLPSGETSGMVSGSLDV  1150
1151  SGQPSGHIGFGGSASGVLEMSGFPGGAVESSGEASGVEVTSGLASGEESG  1200
1201  LTSGFPTVSLVDTTLVEVVTQTSVAQEVGEGPSGMIEISGFLSGDRGVSG  1250
1251  EGSGAVQSSGLPSGTGDFSGEPSGIPYFSGDISGATDLSGQPSAVTDISG  1300
1301  EDSGLPEVTLVTSDLVEVVTRPTVSQELGGETAVTFPYVFGPSGEGSASG  1350
1351  DLSGGASAEGGIETSTAYEISGESSAFPETSIETSTDQEISGEASAYPEI  1400
1401  SVETSTHLETSGETSAYPEISTETSTIQEVSGETSAFPEISTETSTIQEI  1450
1451  SGETSAFPEIRIETSTFQEISGETSAFPEIRIETSTSQEARGETSAFPEI  1500
1501  TIEASTVHETSGETSAFPEISIETSTVHETSGETSAFPEISIETSTVHEI  1550
1551  SGESSAFPEIRIETSTSQEARGETSAFPEITIEASTIQEISGETSAFPEI  1600
1601  SIETSTVREISGETSAFPEIRIETSTSQEARGETSALPEITIETSTVHET  1650
1651  SGEASAFPEISIETSTRQEARSEASAYPEVSIEASTTQEVSGESSAFPEI  1700
1701  SVETSTSQEARGETSAFPEIGIETSTAHEGSGETPGLPAVSTDTAATSLA  1750
1751  SGEPSGAPEKETPDTTSHLITGVSGETSVPDAVISTSAPDVELAQEPRNT  1800
1801  EETQLEIEPSTPAASGQETETAAVLDNPHLPATATAALHPASQEAVDALG  1850
1851  PTTEDTDECHSSPCLNGATCVDGIDSFKCLCLPSYGGDLCEIDLANCEEG  1900
1901  WIKFQGHCYRHFEERETWMDAESRCREHQAHLSSIITPEEQEFVNSHAQD  1950
1951  YQWIGLSDRAVENDFRWSDGHSLQFENWRPNQPDNFFFAGEDCVVMIWHE  2000
2001  QGEWNDVPCNYHLPFTCKKGTVACGDPPVVENARTFGRKKDRYEINSLVR  2050
2051  YQCDHGYIQRHVPTIRCQPNGHWEEPRISCTNPSSYQRRLYKRSPRSRLR  2100
2101  PGVVHRPTH                                           2109

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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