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

NucPred

Fetching Q6TXD4 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MEPGSMVRAIFDFCPSVSEELPLFVGDVIEVLAVVDEFWLLGKKEDVTGQ    50
  51  FPSSFVEIVTIPSLKEGERLFVCICEFVSRELNSLSLHRGDLVILDDSAP   100
 101  TAGWLQGRSCWGAWGFFPSSCVQELCLSSRSRRWHAQSALLQAPEYSLGQ   150
 151  ARALMGLSAQLDEELDFREGDLITIIGVPEPGWFEGELEGRRGIFPEGFV   200
 201  ELLGPLRTVDESVNSRSGDDSAVNGEVDVPPEEAESGGDEDDQQSGTYGI   250
 251  ALYRFQALETNELDFEVGDRIQILGTLEDGWLEGCLKGKTGVFPHRFVKL   300
 301  CPSNRTEETTAQPQESSFPKDSESSVGKSGDSVVEEARQEPWECEEERPD   350
 351  YDLPGQASVPQDHVAPEWTGDTISGQDKDASGSSPDVDLERPLAKDLSTP   400
 401  DPSEEVNGVSSQPQVPIHPKVQKSQHYLTAGGSHQTSDPFSELVPLEART   450
 451  RDYSSLPPRRTYAQGWSFQKPASHLQRASSLTASRLDRPSHFCHPAMASY   500
 501  AQKHQTSTENTASLHDPPERPERRPGLQDRGPATDITTASQGDSLDLDSK   550
 551  LTQQLIEFEKSLSGPSTEPETIVRRFSIMDFYSEKDIVRGSSNSLPSQAF   600
 601  PERRKTLRPPPPRPRTPTPISSHLLVDQSPKPVPTLVVRPSRPAPLPPPA   650
 651  QQRMNTASPKPTSCAHPGWEAPEKEDSEHMEKSPAQTFPCPSMLARIRDV   700
 701  EQDLDTCTRAQEELNLLLEEKQDDPSRAETLETLRSYESTIQSLTLELQQ   750
 751  LRDMTLLSSQSSSLAAPFGSVSTENPEQRMLEKRAKVVAELLQTERDYIR   800
 801  DLEMCIERVMVPLQQAQVPNVDFEGLFGNMQTVIKVSKQLLAALEISDAV   850
 851  GMSSCDCLVPGPVFLDHRDELEGTYRVYCQNHDEAISLLEMYEKDEKTQK   900
 901  HLQDYLADLKGCTNYINLGSFLIKPVQRIMRYPLLLMELLNSTPESHPDK   950
 951  VPLTNAVLAVKEINVNINEYKRRKDLVLKYRKGDEDSLMEKISKLNIHSI  1000
1001  IKKSSRVSSHLKHLTGFAPQLKDEVFEETEKNFRMQERLIKSFIRDLSLY  1050
1051  LQHIRESACVKVVAAMSIWDLCMERGHHDLEQFEKVHRYISDQLFTRFKE  1100
1101  RTERLVINPLNQLLNMFTGPYKLVQKRFDKLLDFYNCTERAEKLKDKKTL  1150
1151  EELQSARNNYEALNSQLLDELPKFQQYAQSLFTNCIHGYAEAHCDFVQQA  1200
1201  LEQLQPLLSLLKATDREGNLIAIFLEEHSRVLQQLQVFTFFPESLPAPRK  1250
1251  PFERKTTDRQSSRKTLLGMPSYMLQSEELRSSLLARYPPEKLFHVQRNFN  1300
1301  AAQDLDVSLLEGDLVGVIKKKDPMGSQNRWLVDNGVTKGFVYSSFLKPYN  1350
1351  PRCSHSDASVASHSSTESEHSGSSPGCHRQNSHSALTFNSNNMTVSFTSG  1400
1401  LALTQPQDASPLKDCAHETLAVSWNTGHPETGPSTCSSDPGFSCQRRLGN  1450
1451  PADGARDISQPASTLRGCQRSSPHSEVVGYSVPGRNDQGSDSIKGSARVC  1500
1501  QAPEDRDRGVGSSETEGNQVYFAIYTFKARNPNELSVLANQRLRIHEFKD  1550
1551  VTGNTEWWLAEVNGRKGYVPSNYIRKTEYT                      1580

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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