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.)

Go back to the NucPred Home Page.