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

NucPred

Fetching P08169 from www.uniprot.org...

The NucPred score for your sequence is 0.54 (see score help below)

   1  MEAAAGRSSHLGPAPAGRPPRCPLLLQLQLLLLLLLLPPGWVPGAAGTQG    50
  51  AEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDS   100
 101  FHSVGDSLLKTASRSLLEFNTTVNCKQQNHKIQSSITFLCGKTLGTPEFV   150
 151  TATDCVHYFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSG   200
 201  AYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFD   250
 251  VGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGHSPAVTITFVCPSERRE   300
 301  GTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPL   350
 351  SRVEASDSLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQ   400
 401  VKVAGRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNN   450
 451  GRGAPVFTGEVDCTYFFTWDTKYACVHEKEALLCGVSDGKQRFDLSALAR   500
 501  HSELEQNWEAVDGSQREAEKKHFFINICHRVLQTGQARGCPEDAAVCAVD   550
 551  KNGSKNLGRFISSPTREKGNIQLSYSDGDECGGGQKIITNITLMCKPGDL   600
 601  ESAPVLTTSRADGCFYEFEWRTAAACVLSRTEGDNCTVFDSQAGFSFDLT   650
 651  PLTKKDAYKVETDKYEFHINVCGPVSVGACPPDSGACQVSRSDRKSWNLG   700
 701  RSNAKLSYYDGMIQLTYRDGTPYNNEKRTPRATLITFLCDRDAGVGFPEY   750
 751  QEEDNSTYNFRWYTSYACPEEPLECIVTDPVTLDQYDLSRLAKSEGGPGG   800
 801  NWYSLDNGGARSTWRKYYINVCRPLNPVPGCDRYASACQMKYQGEQGSYS   850
 851  ETVSISNLGVAKTGPMVEDSGSLLLEYVNGSACTTSDQRRTTYTTRIHLV   900
 901  CSTGSLYTHPIFSLNWECVVSFLWNTAAACPIRITTDIDQVCSIKDPNSG   950
 951  YVFDLNPLNNSRGYVVLGIGKTFLFNVCGDMPACGTLDGKPASGCEAEVQ  1000
1001  MDDMKTLKPGRLVGLEKSLQLSTEGFITLNYTGLPSHPNGRADAFIIRFV  1050
1051  CNDDVYPGTPKFLHQDIDSSLGIRDTFFEFETALACVPSPVDCQVTDPAG  1100
1101  NEYDLSGLSKARKPWTAVDTFDEGKKRTFYLSVCTPLPYIPGCHGTAVGC  1150
1151  CLVTEDSKLNLGVVQISPQVGANGSLSLVYVNGDKCKNQRFSTRINLECA  1200
1201  HTTGSPTFQLQNDCEYVFLWRTVEACPVVRAEGDYCEVRDPRHGNLYNLI  1250
1251  PLGLNDTVVRAGEYTYYFRVCGELTSGVCPTSDKSKVISSCQEKRGPQGF  1300
1301  QKVAGLFNQKLTYENGVLKMNYTGGDTCHKVYQRSTTIFFYCDRSTQAPV  1350
1351  FLQETSDCSYLFEWRTQYACPPYDLTECSFKNEAGETYDLSSLSRYSDNW  1400
1401  EAVTGTGSTEHYLINVCKSLSPQAGSDPCPPEAAVCLLGGPKPVNLGRVR  1450
1451  DSPQWSQGLTLLKYVDGDLCPDQIRKKSTTIRFTCSESHVNSRPMFISAV  1500
1501  EDCEYTFSWPTAAACAVKSNVHDDCQVTNPATGHLFDLSSLSGRAGFTAA  1550
1551  YSEKGLVYLSVCGDNENCANGVGACFGQTRISVGKASKRLTYVDQVLQLV  1600
1601  YEGGSPCPSKTGLSYKSVISFVCRPEVGPTNRPMLISLDKRTCTLFFSWH  1650
1651  TPLACEQTTECSVRNGSSLIDLSPLIHRTGGYEAYDESEDDGSDTSPDFY  1700
1701  INICQPLNPMHGLACPAGTAVCKVPVDGPPIDIGRVAGPPILNPIANEVY  1750
1751  LNFESSTPCLADRHFNYTSLITFHCKRGVSMGTPKLLRTSVCDFVFEWET  1800
1801  PLVCPDEVKTDGCSLTDEQLYYSFNLSSLSKSTFKVTRGPHTYSVGVCTA  1850
1851  AAGLDEGGCKDGAVCLLSGSKGASFGRLASMKLDYRHQDEAVILSYANGD  1900
1901  TCPPETEDGEPCVFPFVFNGKSYEECVVESRARLWCATTANYDRDHEWGF  1950
1951  CKHSTSHRTSVIIFKCDEDADVGRPQVFSEVRGCEVTFEWKTKVVCPPKK  2000
2001  MECKFVQKHRTYDLRLLSSLTGSWSFVHNGASYYINLCQKIYKGPQDCSE  2050
2051  RASVCKKSTSGEVQVLGLVHTQKLDVVDDRVIVTYSKGHYCGDNKTASAV  2100
2101  IELTCAKTVGRPSFTRFDVDSCTYHFSWDSRAACAVKPQEVQMVNGTITN  2150
2151  PANGRSFSLGDIYFKRFSASGDVRTNGDRYIYEIQLSSITGSSSPACSGA  2200
2201  SICQRKANDQHFSRKVGTSNQTRYYVQDGDLDVVFTSSSKCGKDKTKSVS  2250
2251  STIFFHCDPLVKDGIPEFSHETADCQYLFSWHTSAVCPLGAGFDEEIAGD  2300
2301  DAQEHKGLSERSQAVGAVLSLLLVALTACLLTLLLYKKERREMVMSRLTN  2350
2351  CCRRSANVSYKYSKVNKEEEADENETEWLMEEIQPPAPRPGKEGQENGHV  2400
2401  AAKSVRAADTLSALHGDEQDSEDEVLTLPEVKVRPPGRAPGAEGGPPLRP  2450
2451  LPRKAPPPLRADDRVGLVRGEPARRGRPRAAATPISTFHDDSDEDLLHV   2499

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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