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

NucPred

Fetching P27625 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MMKKKNIDIEELKRLIEESSMKKRFVKDIKRNCEIKSIRFGIMSKEDIIK    50
  51  YSEVKIMNREMYKNNSGIPYPYGVLDLKLGAHKSNSVCETCNKKLINCSG   100
 101  HFGYIELNYPVFHIGYYKYIIHILYCICKYCSSLLLSKEKIDFYCNLKKK   150
 151  STDDSFYKKHLFKRILNNCKKVNKCYICGNPQGVIKKIIKPSLDQFMKLK   200
 201  HILKVKENGKMIIKEEDLNSLYVLKLFKNINPYHVKLLNIENPEKLIITA   250
 251  LLVPPNTIRPSVIIDEHGTAEDDLTCILSEITQLNNTIYNQCTNGYQTNQ   300
 301  FLGNVEFLQLQITRFINSDSPAVSQLLATQNISKPGRGICQRLKGKEGRF   350
 351  RCNLSGKRVDFSSRTVISPDPNISIDEVVIPKIIAMRLTYPETVNKYNID   400
 401  KLKMLIKNGCNKWPGANYIIKKSKKGTDPYSDISTSYNNNSNNISSIGCS   450
 451  NIFNVVNNYINNNCKNVRYNIKDVNNNVLLKDMCDINNMNNDINNNINNI   500
 501  YKNTSETNLCNVNNHNNNNNIYCNNQTQDNEEERKNSQFNKISLKYANKN   550
 551  HVIQNLNIGDVVERHICDGDIVLFNRQPSLHRMSIMCHKAKIMDFKTFRF   600
 601  NECVCSPYNADFDGDEMNLDVPQTEEARAEALYLMNVKHNLITPKNGEVI   650
 651  IALTQDFLSASYIITNKDTFLDRDTFCLLCSYFSDASLYIELPIPAILKP   700
 701  KELWTGKQLISVLIKPNKKENTIINFEIQEREYSNKFGDLKHLCLNDSYV   750
 751  CFYKSELICGSLGKKVLGSSKYGLFYYLIHHNSSHIALKIMNRLSKLTSR   800
 801  YFSNKGMTIGIDDVRPSQTLTEKKKDLLLKGYEKVNNEIILYNEKKMQIQ   850
 851  PGCTLEETLEIKVKSILDDLRNDAGKTCNQYLHYLNKPLIMFNSGAKGAL   900
 901  INIAQMIACVGQQNVAGQRIQNGFINRTLPHFHFHCKDSESRGFVQNSFY   950
 951  TGLSPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSIHYDYS  1000
1001  VRSCDKQIVQFIYGDDALNPSYIDNNNTYLDQFDKVFDHIVSISSSHLLL  1050
1051  SYKNKIPYLPHVQHQNKTSNMNNIYNNMNNINNNDSNRSIIYNNDSNMNN  1100
1101  INNNDSNMNSIHNNNSNMNNIHNNDSNRSIIHNNDSNMNSIHNNDSNMNS  1150
1151  IHNNNSNMNNIHNNDSNRSIIHNNDSNMNSIHNNDSNNNNNYKDCTHNPY  1200
1201  ICNESLIIRNIMNRLIYQNIAQEDLFIPLEHDEFLVNKIMESYTDQECNY  1250
1251  EDIIRSLDLNKNVSYIHNDQGKHLSLQMCAEEHITINNTNNDNTYVEQIE  1300
1301  MKELSKNKTKEKQSFKGTIRDMHEDSEEQMNKFITKKAKFFIEKKKGKMH  1350
1351  ECNDDIEYNNTQYDNIQYNNISCNYIKSQNLENTHHQVNNDLSFIKNNVI  1400
1401  LPPKEYHSIFHFVNDYRNVVEIKNLMDKKKIFLNNSEKNVVQSKYNRMSK  1450
1451  NLKKKIEIINNIYRNEKKKLNRWKTKMDNDDNYWSSDDDSIIAKKIIKIK  1500
1501  NKEKRKYHPKEEKENFDRNNYKMITDNNNNDNNNNNNDNNNNDNNNNNNN  1550
1551  SNNNNYYYNLHDDVNNLGVTNYNTNIYPNDCNGIYEKETNNNELTTNSNM  1600
1601  CDKNNDFSDEFFNNINENDLLYDNKYYRQIFKNVIGFVSVFEYVESYKQH  1650
1651  YILFPYEIIKWTSFLLEYLTEIIPTNIFLHTKLSKKEKPTHQKNTGKMKI  1700
1701  YIEEIKKWLFIKAINIYKYFSFKKSIELIKKKDYFNYIIKNYDISHRYII  1750
1751  HDYSFINLKQLYLFIFFNIYKYFKYISTPGDAVGSISAQSIGEPGTQMTL  1800
1801  KTFHFAGVASMNVTLGVPRIKEIINASNSIQTPILNIPLEVNDNYNFALM  1850
1851  MKSKLEKTTIRDICMYIKEDYTSRGVFLSVKFNEELIQKLFLNINAYNIK  1900
1901  DIILKQSHINKIKINKIHINVINKYKLHISLKNDEFIFFQMESLKKGLLD  1950
1951  LLIYGDKDIKRCIIKKEDIEVTDNEDEICDDMDEYYNVSQGTELYERKCN  2000
2001  SKEENKNAIRVKKEEIDDNLEKEENIIYVSEKDSVNQLKSEKKKDINDDN  2050
2051  NNNDDNNNNNDDDNKINDTIFNDDIDSDRNNLKENGSKLENVGEHIIERL  2100
2101  SYKMKEKNVKKEHIKKEPNLINLDTINLDTLNFDEINVHNINNEKIEFYD  2150
2151  EHLNICQGNKKHIQKKKKKKTVYSILVEGNSLNYVLGLEGVDFKHIISNH  2200
2201  VINVFQVLGIEAARITIINEIKKCVEAYSIDIDIRHIMLLADIMAFTGDI  2250
2251  LGINRFGIQKARQSTLMLASFEETNEHLFVSSFFKNVDEINNISESIIVG  2300
2301  KNIPIGTGAFQLLYDYKLEKETKNLTLLEKAERETAMNY             2339

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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