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

NucPred

Fetching Q9VCU9 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MAFHWCDNNLHTTVFTPRDFQVELLATAYERNTIICLGHRSSKEFIALKL    50
  51  LQELSRRARRHGRVSVYLSCEVGTSTEPCSIYTMLTHLTDLRVWQEQPDM   100
 101  QIPFDHCWTDYHVSILRPEGFLYLLETRELLLSSVELIVLEDCHDSAVYQ   150
 151  RIRPLFENHIMPAPPADRPRILGLAGPLHSAGCELQQLSAMLATLEQSVL   200
 201  CQIETASDIVTVLRYCSRPHEYIVQCAPFEMDELSLVLADVLNTHKSFLL   250
 251  DHRYDPYEIYGTDQFMDELKDIPDPKVDPLNVINSLLVVLHEMGPWCTQR   300
 301  AAHHFYQCNEKLKVKTPHERHYLLYCLVSTALIQLYSLCEHAFHRHLGSG   350
 351  SDSRQTIERYSSPKVRRLLQTLRCFKPEEVHTQADGLRRMRHQVDQADFN   400
 401  RLSHTLESKCRMVDQMDQPPTETRALVATLEQILHTTEDRQTNRSAARVT   450
 451  PTPTPAHAKPKPSSGANTAQPRTRRRVYTRRHHRDHNDGSDTLCALIYCN   500
 501  QNHTARVLFELLAEISRRDPDLKFLRCQYTTDRVADPTTEPKEAELEHRR   550
 551  QEEVLKRFRMHDCNVLIGTSVLEEGIDVPKCNLVVRWDPPTTYRSYVQCK   600
 601  GRARAAPAYHVILVAPSYKSPTVGSVQLTDRSHRYICATGDTTEADSDSD   650
 651  DSAMPNSSGSDPYTFGTARGTVKILNPEVFSKQPPTACDIKLQEIQDELP   700
 701  AAAQLDTSNSSDEAVSMSNTSPSESSTEQKSRRFQCELSSLTEPEDTSDT   750
 751  TAEIDTAHSLASTTKDLVHQMAQYREIEQMLLSKCANTEPPEQEQSEAER   800
 801  FSACLAAYRPKPHLLTGASVDLGSAIALVNKYCARLPSDTFTKLTALWRC   850
 851  TRNERAGVTLFQYTLRLPINSPLKHDIVGLPMPTQTLARRLAALQACVEL   900
 901  HRIGELDDQLQPIGKEGFRALEPDWECFELEPEDEQIVQLSDEPRPGTTK   950
 951  RRQYYYKRIASEFCDCRPVAGAPCYLYFIQLTLQCPIPEEQNTRGRKIYP  1000
1001  PEDAQQGFGILTTKRIPKLSAFSIFTRSGEVKVSLELAKERVILTSEQIV  1050
1051  CINGFLNYTFTNVLRLQKFLMLFDPDSTENCVFIVPTVKAPAGGKHIDWQ  1100
1101  FLELIQANGNTMPRAVPDEERQAQPFDPQRFQDAVVMPWYRNQDQPQYFY  1150
1151  VAEICPHLSPLSCFPGDNYRTFKHYYLVKYGLTIQNTSQPLLDVDHTSAR  1200
1201  LNFLTPRYVNRKGVALPTSSEETKRAKRENLEQKQILVPELCTVHPFPAS  1250
1251  LWRTAVCLPCILYRINGLLLADDIRKQVSADLGLGRQQIEDEDFEWPMLD  1300
1301  FGWSLSEVLKKSRESKQKESLKDDTINGKDLADVEKKPTSEETQLDKDSK  1350
1351  DDKVEKSAIELIIEGEEKLQEADDFIEIGTWSNDMADDIASFNQEDDDED  1400
1401  DAFHLPVLPANVKFCDQQTRYGSPTFWDVSNGESGFKGPKSSQNKQGGKG  1450
1451  KAKGPAKPTFNYYDSDNSLGSSYDDDDNAGPLNYMHHNYSSDDDDVADDI  1500
1501  DAGRIAFTSKNEAETIETAQEVEKRQKQLSIIQATNANERQYQQTKNLLI  1550
1551  GFNFKHEDQKEPATIRYEESIAKLKTEIESGGMLVPHDQQLVLKRSDAAE  1600
1601  AQVAKVSMMELLKQLLPYVNEDVLAKKLGDRRELLLSDLVELNADWVARH  1650
1651  EQETYNVMGCGDSFDNYNDHHRLNLDEKQLKLQYERIEIEPPTSTKAITS  1700
1701  AILPAGFSFDRQPDLVGHPGPSPSIILQALTMSNANDGINLERLETIGDS  1750
1751  FLKYAITTYLYITYENVHEGKLSHLRSKQVANLNLYRLGRRKRLGEYMIA  1800
1801  TKFEPHDNWLPPCYYVPKELEKALIEAKIPTHHWKLADLLDIKNLSSVQI  1850
1851  CEMVREKADALGLEQNGGAQNGQLDDSNDSCNDFSCFIPYNLVSQHSIPD  1900
1901  KSIADCVEALIGAYLIECGPRGALLFMAWLGVRVLPITRQLDGGNQEQRI  1950
1951  PGSTKPNAENVVTVYGAWPTPRSPLLHFAPNATEELDQLLSGFEEFEESL  2000
2001  GYKFRDRSYLLQAMTHASYTPNRLTDCYQRLEFLGDAVLDYLITRHLYED  2050
2051  PRQHSPGALTDLRSALVNNTIFASLAVRHGFHKFFRHLSPGLNDVIDRFV  2100
2101  RIQQENGHCISEEYYLLSEEECDDAEDVEVPKALGDVFESIAGAIFLDSN  2150
2151  MSLDVVWHVYSNMMSPEIEQFSNSVPKSPIRELLELEPETAKFGKPEKLA  2200
2201  DGRRVRVTVDVFCKGTFRGIGRNYRIAKCTAAKCALRQLKKQGLIAKKD   2249

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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