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

NucPred

Fetching Q80Z71 from www.uniprot.org...

The NucPred score for your sequence is 0.31 (see score help below)

   1  MGLWGMLAFPLGFLLASVLLVASAPATPESPGCSNKEQQVTVSHTYKIDV    50
  51  PKSALVQVETDPQSLSDDGTSLLAPGEDGEEQNIIFRHNIRLQTPQKNCD   100
 101  LADSVQDLLARMKKLEEEMAELKEQCNTNRCCQGAADLSRHCSGHGTFLP   150
 151  ETCSCHCDQGWEGADCDQPTCPGACNGHGRCVDGQCVCDAPYVGVDCAYA   200
 201  ACPQDCSGHGVCVQGVCQCHEDFTAEDCSEQRCPGDCSGNGFCDTGECYC   250
 251  EMGFTGPDCSQVVAPQGLQLLKSTENSLLVSWEPSSEVDYYLLSYYPLGK   300
 301  EQATKQVRVPKEQHTYDITGLLPGTKYIVTLRNVKKDISSSPQHLLATTD   350
 351  LAVVGTAWVNEETETSLDVEWENPLTEVDYYKLRYGPLTGQEVTEVTVPK   400
 401  SRDPKSRYDITGLQPGTEYKITVVPIRGDLEGKPILLNGRTEIDGPTNVV   450
 451  TNQVTEDTASVSWDPVRADIDKYVVRYIAPDGETKEKAVPKDQSSTVLTG   500
 501  LKPGEAYKVFVWAERGNQGSKKADTKALTEIDSPENLVTDRVTENSLSVS   550
 551  WDPVEADIDRYVVSYTSVDGETKQVPVKKDQRSTVLTGLSPGVEYKVYVW   600
 601  AEKGDRESKKANTKAPTDIDSPKNLVTDQVTENTLSVSWDPVQANIDRYM   650
 651  VSYTSADGETREVPVPKEKSSTVLTGLRPGVEYKVHVWAQKGTQESRKAN   700
 701  TKAPTDIDGPKNLVTDQVTETTLSVSWDPVEADIDRYMVRYTSPDGETKE   750
 751  VPVSKDKSSTVLRGLRPGVEYKVDVWAQKGAQDSRKANTKAPTDIDSPKN   800
 801  LVTEQVTESTATVSWDPVEADIDRYVVRYTSVDGETREFLVGKDQTSTVL   850
 851  TGMRPGVEYQVDVWAQKGTQESRKTSTKAPTDIDGPKNLVTDQVTETTLS   900
 901  VSWDPVEADIDRYMVRYTSPDGETKEVPVSKDKSSTVLRGLRPGVEYKVD   950
 951  VWAQKGAQDSRKANTKAPTDIDSPKNLAIDQVTETTLSVSWDPVQADIDR  1000
1001  YVVRYTSADGESKEFLIGKEQRSTVLTGLRPGVEYKVEVWAQKGARESKK  1050
1051  ANTEGHTDIDSPKNLVTNQVTENTATISWDPVQADIDRYMVRYTSADGET  1100
1101  REIPVRKEKSSTVLTGLRPGVEYTVQVWAQKGARESKKAKTKAPTEIDSP  1150
1151  KNLVTNRVTENTATISWDPVRANIDRYMVRYTSADGETKEIPVSKDQSST  1200
1201  ILTGLKPGMEYTIHVWAQKGARESKKADTKALTEIDPPRNLRPFGVTHSG  1250
1251  GVLTWLPPSAQIDGYILTYQFPNGTVKEVELPRGQQRFELQDLEQGVTYP  1300
1301  VSLVAFKGNQRSRTVSTTLSTVDARFPHPSDCSQVQQNTNAASGLYTIYL  1350
1351  NGDASRPMQVYCDMDTDGGGWIVFQRRNTGQLDFFKRWRSYVEGFGDPMK  1400
1401  EFWLGLDKLHNLTTGTTTRYEVRADLQTFNESAYAVYDFFQVASSKERYK  1450
1451  LSVGKYRGTAGDALTYHNGWKFTTFDRDNDIALSNCALTHHGGWWYKNCH  1500
1501  LANPNGKYGETKHSEGVNWEPWKGHEFSIPYVELKIRPFGYSRDRFSGRK  1550
1551  KRSIGKARMF                                          1560

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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