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

NucPred

Fetching Q92508 from www.uniprot.org...

The NucPred score for your sequence is 0.63 (see score help below)

   1  MEPHVLGAVLYWLLLPCALLAACLLRFSGLSLVYLLFLLLLPWFPGPTRC    50
  51  GLQGHTGRLLRALLGLSLLFLVAHLALQICLHIVPRLDQLLGPSCSRWET   100
 101  LSRHIGVTRLDLKDIPNAIRLVAPDLGILVVSSVCLGICGRLARNTRQSP   150
 151  HPRELDDDERDVDASPTAGLQEAATLAPTRRSRLAARFRVTAHWLLVAAG   200
 201  RVLAVTLLALAGIAHPSALSSVYLLLFLALCTWWACHFPISTRGFSRLCV   250
 251  AVGCFGAGHLICLYCYQMPLAQALLPPAGIWARVLGLKDFVGPTNCSSPH   300
 301  ALVLNTGLDWPVYASPGVLLLLCYATASLRKLRAYRPSGQRKEAAKGYEA   350
 351  RELELAELDQWPQERESDQHVVPTAPDTEADNCIVHELTGQSSVLRRPVR   400
 401  PKRAEPREASPLHSLGHLIMDQSYVCALIAMMVWSITYHSWLTFVLLLWA   450
 451  CLIWTVRSRHQLAMLCSPCILLYGMTLCCLRYVWAMDLRPELPTTLGPVS   500
 501  LRQLGLEHTRYPCLDLGAMLLYTLTFWLLLRQFVKEKLLKWAESPAALTE   550
 551  VTVADTEPTRTQTLLQSLGELVKGVYAKYWIYVCAGMFIVVSFAGRLVVY   600
 601  KIVYMFLFLLCLTLFQVYYSLWRKLLKAFWWLVVAYTMLVLIAVYTFQFQ   650
 651  DFPAYWRNLTGFTDEQLGDLGLEQFSVSELFSSILVPGFFLLACILQLHY   700
 701  FHRPFMQLTDMEHVSLPGTRLPRWAHRQDAVSGTPLLREEQQEHQQQQQE   750
 751  EEEEEEDSRDEGLGVATPHQATQVPEGAAKWGLVAERLLELAAGFSDVLS   800
 801  RVQVFLRRLLELHVFKLVALYTVWVALKEVSVMNLLLVVLWAFALPYPRF   850
 851  RPMASCLSTVWTCVIIVCKMLYQLKVVNPQEYSSNCTEPFPNSTNLLPTE   900
 901  ISQSLLYRGPVDPANWFGVRKGFPNLGYIQNHLQVLLLLVFEAIVYRRQE   950
 951  HYRRQHQLAPLPAQAVFASGTRQQLDQDLLGCLKYFINFFFYKFGLEICF  1000
1001  LMAVNVIGQRMNFLVTLHGCWLVAILTRRHRQAIARLWPNYCLFLALFLL  1050
1051  YQYLLCLGMPPALCIDYPWRWSRAVPMNSALIKWLYLPDFFRAPNSTNLI  1100
1101  SDFLLLLCASQQWQVFSAERTEEWQRMAGVNTDRLEPLRGEPNPVPNFIH  1150
1151  CRSYLDMLKVAVFRYLFWLVLVVVFVTGATRISIFGLGYLLACFYLLLFG  1200
1201  TALLQRDTRARLVLWDCLILYNVTVIISKNMLSLLACVFVEQMQTGFCWV  1250
1251  IQLFSLVCTVKGYYDPKEMMDRDQDCLLPVEEAGIIWDSVCFFFLLLQRR  1300
1301  VFLSHYYLHVRADLQATALLASRGFALYNAANLKSIDFHRRIEEKSLAQL  1350
1351  KRQMERIRAKQEKHRQGRVDRSRPQDTLGPKDPGLEPGPDSPGGSSPPRR  1400
1401  QWWRPWLDHATVIHSGDYFLFESDSEEEEEAVPEDPRPSAQSAFQLAYQA  1450
1451  WVTNAQAVLRRRQQEQEQARQEQAGQLPTGGGPSQEVEPAEGPEEAAAGR  1500
1501  SHVVQRVLSTAQFLWMLGQALVDELTRWLQEFTRHHGTMSDVLRAERYLL  1550
1551  TQELLQGGEVHRGVLDQLYTSQAEATLPGPTEAPNAPSTVSSGLGAEEPL  1600
1601  SSMTDDMGSPLSTGYHTRSGSEEAVTDPGEREAGASLYQGLMRTASELLL  1650
1651  DRRLRIPELEEAELFAEGQGRALRLLRAVYQCVAAHSELLCYFIIILNHM  1700
1701  VTASAGSLVLPVLVFLWAMLSIPRPSKRFWMTAIVFTEIAVVVKYLFQFG  1750
1751  FFPWNSHVVLRRYENKPYFPPRILGLEKTDGYIKYDLVQLMALFFHRSQL  1800
1801  LCYGLWDHEEDSPSKEHDKSGEEEQGAEEGPGVPAATTEDHIQVEARVGP  1850
1851  TDGTPEPQVELRPRDTRRISLRFRRRKKEGPARKGAAAIEAEDREEEEGE  1900
1901  EEKEAPTGREKRPSRSGGRVRAAGRRLQGFCLSLAQGTYRPLRRFFHDIL  1950
1951  HTKYRAATDVYALMFLADVVDFIIIIFGFWAFGKHSAATDITSSLSDDQV  2000
2001  PEAFLVMLLIQFSTMVVDRALYLRKTVLGKLAFQVALVLAIHLWMFFILP  2050
2051  AVTERMFNQNVVAQLWYFVKCIYFALSAYQIRCGYPTRILGNFLTKKYNH  2100
2101  LNLFLFQGFRLVPFLVELRAVMDWVWTDTTLSLSSWMCVEDIYANIFIIK  2150
2151  CSRETEKKYPQPKGQKKKKIVKYGMGGLIILFLIAIIWFPLLFMSLVRSV  2200
2201  VGVVNQPIDVTVTLKLGGYEPLFTMSAQQPSIIPFTAQAYEELSRQFDPQ  2250
2251  PLAMQFISQYSPEDIVTAQIEGSSGALWRISPPSRAQMKRELYNGTADIT  2300
2301  LRFTWNFQRDLAKGGTVEYANEKHMLALAPNSTARRQLASLLEGTSDQSV  2350
2351  VIPNLFPKYIRAPNGPEANPVKQLQPNEEADYLGVRIQLRREQGAGATGF  2400
2401  LEWWVIELQECRTDCNLLPMVIFSDKVSPPSLGFLAGYGIMGLYVSIVLV  2450
2451  IGKFVRGFFSEISHSIMFEELPCVDRILKLCQDIFLVRETRELELEEELY  2500
2501  AKLIFLYRSPETMIKWTREKE                               2521

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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