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

NucPred

Fetching Q8K3H5 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MLPLIGKTIIFDNFPDPSDTWEIIETIGKGTYGKVFKVLNKKSGQKAAVK    50
  51  ILDPIHDIDEEIEAEYNILRTLSDHPNVVRFYGIYFKKDKINGDKLWLVL   100
 101  ELCNGGSVTDLVKGFLKRGERMSEPVIAYILHEALMGLQHLHSNKTIHRD   150
 151  VKGNNILLTTEGGVKLVDFGVSAQLSSTRHRLNTSVGTPFWMAPEVIACE   200
 201  QQLDTTYDARCDTWSLGITAIELGDGDPPLAELHPMRALFKIPRNPPPKL   250
 251  RQPELWSAEFNDFISKCLTKDYEKRPTVSDLLKHKFITQIEGKDVILQKQ   300
 301  LMEFIDIHQCLGSTEKARHERIHTKKGNLNRSLISSLKDVDDLATLDVLD   350
 351  EPTASPHLHPCHSRDQIHIHVADILIALNPFQSLGIYSPKLSRLYIGAKR   400
 401  TANPPHIFAMADLGYQSMVTYNADQCIVISGESGAGKTESAHLLVQQLTV   450
 451  LGKANNRTLQEKILQMNNLVEAFGNACTIINDNSSRFGKYLEMKFTSSGA   500
 501  VVGAQISEYLLEKSRVIHQAMGEKNFHIFYYIYGGLAEKKKLALYKSPEH   550
 551  KPPRYLQNDNLRTVQDMMNNSFYKSQYELIEQCFKVIGFTMEQLASVYSV   600
 601  LAAILNVGNIEFSSVATEYQMDKSYICNHTALENCASLLCIQADELQEAL   650
 651  TSHCVVTRGETIIRPNTVEKAADVRDAMAKTLYGRLFSCIVNCINSLLKH   700
 701  DTSPSGDEELNIGILDIFGFENFKRNSFEQLCINIANEQIQYYFNQHVFA   750
 751  WEQNEYLNEDVDARVIEYEDNRPLLDMFLQKPMGLLSLLDEESRFPKATD   800
 801  QTLIEKFEDNLKSQYFWRPKRMELSFGIHHYAGKVLYSASGFLAKNRDTF   850
 851  PTDIVLPLRSSENSVIRQLVNHPLTKTGNLPLSKTKNIVNYQMWNSEKST   900
 901  NLTKGETRDVTCHACETTNVKTQTVSSYFRYSLMDLLSKMVVGQPHFVRC   950
 951  IKPNNERQARKYDKEKVLLQLRCTGILETARIRRLGYSHRILFANFIKRY  1000
1001  YILCYKSSEEPPVSPDTCAAILEKAGLDNWALGKTKVFLKYYHVEQLNLM  1050
1051  RKEATNKLVLIQASVRAFLGARRYQELQQKRKSSAVIIQSAARGHLVRKQ  1100
1101  RKEIVDMKNTAVTTIQTSDQEFDYKKNFENTRESFVKKQTENAVPTNESN  1150
1151  TSTPNNKESPSAGKTAPFIAESKATNVESNNRRYHTQKKMSNVYAEGQNQ  1200
1201  ELYIVEDTWAEVSPRQKYVQDLEESRKMRKEEKGDAVIQSYCQWYTEGSN  1250
1251  FEESKATCLEGRETWERTSCPGLWLTEEIYLRKTLDPTLSQKSVYQNADG  1300
1301  KEKEHKVSVVTQNAPLGNLERDYHLLGFLGEEDTGPVPQAQEEHKAVSIH  1350
1351  SKYQSSKKKQQLGKDRLAPPFKNQKILSSSTEVAKTTHNVYPCPTKQEGV  1400
1401  HHSKMVDERDSKMASKKEAWDLAMFSRQISKLSEEYFILQKNLNEIILAQ  1450
1451  QLKPFYLGIYRHKPINRHVSTHQYLSGVSKGEEPKILRPPRRPRKPKTLN  1500
1501  NPEDSTYYYLLHKSTQEEKRRPGKDSQGKLLGLEDFYYKEFLPTHYGPKA  1550
1551  HSSNAREWKALKEPQAQPIESNERCWTTSENESLEEERISANPYDYRRLL  1600
1601  RKTSQRQRLVQQL                                       1613

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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