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

NucPred

Fetching P42173 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MATTRAATFSAKIRTLSEFQIRLSTNQQPPSNAEIITTLRYFQQTLIGFL    50
  51  KDFPSTQTNYCERFSSDAARWNLYPNLNYSALYYAIVNLLDVFPLITSQP   100
 101  QAIGEAILDTIKALMIFLERESLEQLPLLLASQLGIFPRELDKQIVHLLA   150
 151  DCVFPFAINDETYVKYSVPGVLMLVLQQTHDPSLHTWIVESAMNCSQGVY   200
 201  QDLLQVIAKGTCESRVAAANLLFHYWPFPNPQILHRKTIQYRVHAWRTVQ   250
 251  CQSTGCSDKTASVKRCYDPVICADVADTSPPIFLCRKCAEQVTGERKVIT   300
 301  QHIAQPMPASNATCQRQECQSQSRLAVTICCSHECTRGHNHVPMRLCMDC   350
 351  STLVHEEGTIKHLQHQGSGVVWSTDDQWPTVESIVKLLRETTMFEGNEGE   400
 401  GKKPKWLRQLDGGTSMGKEIDKMADERRMLSRFGVWLMAGLCPPNESADP   450
 451  RAIGYIMQNVFEWFSTTALLPNDSMGASLEQLKTDFVSDWINIGMRVHNA   500
 501  VFISSLCGECEEQDGRPVIDRIKEGLGRLLALMPYDVISLETWSRVMPRW   550
 551  LEAIVNDCTEDNQPELKILLCKIFEPDLCPLPFETKEVYGFMTGRIGGDD   600
 601  YDEMFNALQWIHQLSRLDITIPLNMILEHFNRCLQKLRTIEIPPLSENDL   650
 651  EEEEMSVHVVLVDTLVLQMKLNDSDRSMTPALTDKLFECMQLLVSIPIRA   700
 701  VPHSCHDPELDGFADCQQCQQTAFVHQMVMNITQKVCPKREVAIITTVDE   750
 751  DPNYDEQTTDTPTGPGSTLLSPLTESGSKGTSPGTSAPSRPFPEHLQAQT   800
 801  MCVAQACEAEEEVEECEFVGILPCEEMEVAMAEAVTHDNVLETGQVVTST   850
 851  TVHPSIKGQIIQTPQTPVQKQPPSDFWVTSVGRFRFSFEQLPSQLKMIHS   900
 901  LLSCLDEAVEPDVEFFVMSSMKYLCLHCEALSNARREHRGFLIWTQENQM   950
 951  VPKLWERLRSDYIQVGELATHLLLHAMTLPCGEEMFWKMVHRDFTSPQWN  1000
1001  VRFDAVGKAYVMAQMIKTAPVKANKVVQTCLAAVFYHFIASLHDPNPSVA  1050
1051  QRAIIALRAMPRHTLKLMCMCFESQFDHCIVDRPLIIHAITMMSILLPDQ  1100
1101  TTLTFDFFIQRFETLVLESQLSSQTEENIFVQDLMHTDPMSELYQRKVSK  1150
1151  ARSAIENASTARSIVRHLKQYDGMKHQLAHLPSDPANVAVNDDVSSPNSS  1200
1201  VTANYGHGGYGRLREFTDEESNMCLLFNRVVDMENPERHTVYLVVSLFVT  1250
1251  FLSNKNSTPTDEKANAKKQSLVFRHFNTLLGYSSTEKCFTIPPARLRKAA  1300
1301  VCNAFISGLPEILDMNLHTGNQLLPTVAQLLIHLPSPQKLASDQNVTNYS  1350
1351  LALLTQHTRHLWLQSLILILYKYRFDQLPVSEYIVRLIGIVVKTLQNQVH  1400
1401  ECSDAADQSAEIDTWDEIEDDDVARAELIRPESLTVTTIQEATPAAEGMV  1450
1451  HIGAVCVMQPTIVEPEGLAPEPLIARKRSTAVQEVRRKKSAIEVVKKSCT  1500
1501  LRCGHCNEAIEMFDEETISLCLIALETFLHREPSMAAPILFKILYTVTRL  1550
1551  IDTPMYPWHSTEMFVPANSRSVAKQMLRVSLHHLSTSAICLQLFDTKIPR  1600
1601  PDAFWSVVALSLADFPELSPVYFIQILMEDLEESWPGSVKLIMKNLAFYI  1650
1651  VEIPTDMYNNPWKDLVGHLETFFKRYHSAISADNGITPTRAEIENVIIVM  1700
1701  THVFKVQTFSSSKSPVTLVEAFARWLSESLHSADVSLESLLGVCTACNRA  1750
1751  LIRERDKQCITRALVTELMQAIKFKVKLHESNYVTIANMILQDAGEDIEV  1800
1801  PLLDDQFNTAASEAIRPFLFEVLDFIADLHVIAKLKKESNSDALGGDLKV  1850
1851  KLAEAIAVEMSRSNARDCRTVIRFIPWLMSPPSVTQAAPSAFADSVTNVR  1900
1901  VLSWLLLGALHANHSCLPVPIECSQHMADYIHFVLAGFADQSKQSVVHMS  1950
1951  ALFHAFHLCQLWTVYCERAATYSSTTAFAHLVDFWARVTPAILQLLSHSK  2000
2001  VLADMVNLHFLNTIQALQQVNSALLCQLYSMWAPILTAYHSQIPNQLRMK  2050
2051  LDSCQNQPSLEAPLVTEWLKKVRYKISQVELQTSAASPYYTV          2092

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.