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

NucPred

Fetching Q85B60 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MVKKVIEKGRGVRGRDYSSKVWDFLEIDALNYFSESLKNHYLEELVVSPA    50
  51  STAEPFIRLSDLRFLSLLFLRNLRHSIMRGSGVTLEMLMLLAIPIFMHCL   100
 101  SYKNSIDRGFVLAKVIDGGEGIRKKQTENYGNFSYDCFLQFKRFLSVGRD   150
 151  GKREILEPYYLGLNKDISISASSSKEEREIRYDVTTPLPSGRWKARIMRR   200
 201  DSLLFGGDRFKGKTEGIQVVRGGRYLQDLVRFFKFYKNLVVSKNGSDCHQ   250
 251  NNFDSLLLREICDKQDLGRLQAIRLGNNSLSSVVLYPFESESADSADPRR   300
 301  DGSAFPSEQEVFSNLYSFTSREKTILFRNSISGLDYGEDEGGFPVLHAYS   350
 351  QVRNQLINRLTNFLSIIRKSNLPLGGKIVIDVSNRIKSERVFFPSGMKKN   400
 401  MPFTKISGKKLRLASGGYFDFVEIFPTYFKASLEIPRETTNQNGNTNFLD   450
 451  ELEGGGNLDSIYSLVRLYGRNRIIPLYSTYIFLLHDYFCALSTEYFFRIK   500
 501  YWLDGWTGGRVYISFTGIATEETVFKWKDDVERLSNEYVTSHIGQCRNVQ   550
 551  SNLYRRLDATRNLYVSPVKKFLGEAMKYNLAELICRVSLVGNELLNKTGV   600
 601  SLRSTNRHTKKYFHRFLDVLFLSKMIVAEATRQKILIDTVDYCIEKLDDI   650
 651  DFEKLNKMDRIELDFFSSLSDGYIDEEILLFKTILEERKSFLVESRLLTS   700
 701  EKSVGSSTALKPASNFTSLGLSCIEAIRAGFSGEALSIMGRQNWNLFVCD   750
 751  LSRGGNSIRNIGESLPKNISDQMDEINNSPIRSRAGNNFIQRIKRGFFVG   800
 801  NCSNSYLDVLENFYLSSDEKAISSSDILSLIHLQLSDSLSSNFSKQTAGE   850
 851  VADHLLTPIQLISPNLHESATIVTHLDGLPNSISDLNGLLASLSSSPREA   900
 901  TDSFLFSCSNDGVSLEEASRNSDSWSDHQRTQPRRNLLVLDRVNSEKFFK   950
 951  DGLDSRNGSPTSQVYRNGLSIEYFWEPKKLDTPYWSLRFSLFNGVTSRFI  1000
1001  AGSIGEDVTRQDAGFADSSAREEATCPSHFINFNELSEDLNRYKISWIFW  1050
1051  RDSIGENWSLLGDYIPLFFTPTWWRYFCDLITKAYPEIVLKISYDSNHDL  1100
1101  RRISEGIARGLVGSAKGYLLRSLQRLGLIFGNNSINTISSETDLLILEKI  1150
1151  PDKAEILHPGEWSVSQFSNRPISYCCILSILLVLLSLKHPLSAVSGSNFF  1200
1201  HLWKRFATIDYLTDPMRGSYLRKVMYSPPTSQMLTRDLLIHSLNRFLNCV  1250
1251  SNILFFLFVKNEIDSWIFRRESSDILDSNKELLTQHLVTTKILYRYASKS  1300
1301  KFNYDLSSNKIFHEPYPQDRSNVLAYLLQFWQNDLLGHKIRKLDPAEKWA  1350
1351  FSALGRDILFSATTRRRDSLLNMPCRDIPISLQSGLLPSKGILLVGPVET  1400
1401  GRSSLIRDVASNSYFPVVKLPLKKFIYNRSFFNNVRGNFISKESVHRLNI  1450
1451  VFEIAKEMSPCTLWIQDIHELNICRSYNKLEADPKFLLCQILKSIGHKLG  1500
1501  NSDIRENVVIATTHVPARIDPALVAPNRLNQLINFRRSNGRQRQKELSIL  1550
1551  LRIKGFEVGANPTLLESTVSGTAGYSKRDLLLLANEALLIGTSKGRKFVC  1600
1601  SNTIGLALHRQHSTVSDMGNEMESNSEWEISSYKMAEVKNSLTDISLTTF  1650
1651  PFIGRDELKMRFYYLSNWYVEPSTTESTIDEFTMFLHLPELIAKLVARDS  1700
1701  FQMDRGKEDNFIVIDKLVENDLNLACGVLENLSNNFPRPEICRGESRRSN  1750
1751  SFPPPLPIGKPKYCSGVTSLSRSSKSLKRGRISSLTDFEMQQSPELRNSA  1800
1801  AEISREITWSRKAWRLRFLRSGTYELMGVLSEPNHLYNLILLYYNQNYIP  1850
1851  QQDFEFSKIRGKRSKWREKSGYLFSFEKSVTNGTDNSIKRLENRLDNMLL  1900
1901  REQFLELGISGDSSNEYETHCDRLNEMTRLFGGRFIWDPMLLFQPDPNIP  1950
1951  SLRRNLLSTKELARRLHTIYGMRRQRLQKMSNNKIKDFFLYSEENPKLKP  2000
2001  DSSLNRRNNLPLEEEERDSEYVRETSSVDIHLQYPQIFTPVRLGCYAVAE  2050
2051  DFPERFLRFRLLVHRNKWLRRNRSPFRDFLIYNMLLETYEYLSNPFRFGK  2100
2101  ASLD                                                2104

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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