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

NucPred

Fetching P41234 from www.uniprot.org...

The NucPred score for your sequence is 0.53 (see score help below)

   1  MGFLHQLQLLLWKNVTLKRRSPWVLAFEIFIPLVLFFILLGLRQKKPTIS    50
  51  VKEAFYTAAPLTSAGILPVMQSLCPDGQRDEFGFLQYANSTVTQLLERLH   100
 101  RVVEEGNLFDPVRPSLGSELEALRQRLEALSSGPGTWESHSARPAVSSFS   150
 151  LDSVARDQRELWRFLMQNLSLPNSTAQALLAARVDPSEVYRLLFGPLPDL   200
 201  DGKLGFLRKQEPWSRLGSNPLLQMEELLLAPALLEQLTCAPGSGELGRIL   250
 251  TMPEGHQVDLQGYRDAVCSGQATARAQRFSDLAAELRNQLDTAKIAQQLG   300
 301  FDVPNGSDPQPQAPSPQSLPALLGDLLDAQKLLQDVDVLSALALLLPQGA   350
 351  CAGQASAPQASSLNGLANSTGIGANSGSNTTVEEGTQSPVSPASPDTLQG   400
 401  QCSAFVQLWAGLQPILCGNNRTIEPEALRRGNMSSLGFTSKEQRNLGLLV   450
 451  HLMTSNPKILYAPVGSEADRVILKANETFAFVGNVTHYAQVWLNISTEIR   500
 501  SFLEQGRLQQHLQWLQQYVADLQLHPEAMNLSLEELPPALRQDFSLPNGT   550
 551  ALLQQLDTIDNAACGWIQFMSKVSVDIFKGFPDEESIVNYTLNQAYQDNV   600
 601  TVFASVIFQTRKDGSLPPHVHYKIRQNSSFTEKTNEIRRAYWRPGPNTGG   650
 651  RFYFLYGLRLDQDMMERAIINTFVGHDVVEPGNYVQMFPYPCYTRDDFLF   700
 701  VIEHMMPLCMVISWVYSVAMTIQHIVAEKEHRLKEVMKTMGLNNAVHWVA   750
 751  WFITGFVQLSISVTALTAILKYCQVLMHSHVLIIWLFLAVYAVATIMFCF   800
 801  LVSVLYSKAKLASACGGIIYFLSYVPYMYVAIREEVAHDKITAFEKCIAS   850
 851  RCPQQPLAWVPSTLHCMKWQEWASIQWHTFSQSPVEGDDFNLLLAVTMLM   900
 901  VDTVVYGVLTWYIEAVHPGMYGLPRPWYSRYRSPIGWAVGGQKPGSGAGH   950
 951  GHTHRASALWRRIQACAMESRHFEETRGMEEEPTHLPLVVCVDKLTKVYK  1000
1001  NDKKLALNKLSLNLYENQVVSFLGHNGAGKTTTMSILTGLFPPTSGSATI  1050
1051  YGHDIRTEMDEIRKNLGMCPQHNVLFDRLTVEEHLWFYSRLKSMAQEEIR  1100
1101  KETDKMIEDLELSNKRHSLVQTLSGGMKRKLSVAIAFVGGSRAIILDEPT  1150
1151  AGVDPYARRAIWDLILKYKPGRTILLSTHHMDEADLLGDRIAIISHGKLK  1200
1201  CCGSPLFLKGAYGDGYRLTLVKQPAEPGTSQEPGLASSPSGCPRLSSCSE  1250
1251  PQVSQFIRKHVASSLLVSDTSTELSYILPSEAVKKGAFERLFQQLEHSLD  1300
1301  ALHLSSFGLMDTTLEEVFLKVSEEDQSLENSEADVKESRKDVLPGAEGLT  1350
1351  AVGGQAGNLARCSELAQSQASLQSASSVGSARGEEGTGYSDGYGDYRPLF  1400
1401  DNLQDPDNVSLQEAEMEALAQVGQGSRKLEGWWLKMRQFHGLLVKRFHCA  1450
1451  RRNSKALCSQILLPAFFVCVAMTVALSVPEIGDLPPLVLSPSQYHNYTQP  1500
1501  RGNFIPYANEERQEYRLRLSPDASPQQLVSTFRLPSGVGATCVLKSPANG  1550
1551  SLGPMLNLSSGESRLLAARFFDSMCLESFTQGLPLSNFVPPPPSPAPSDS  1600
1601  PVSPDEDSLQAWNMSLPPTAGPETWTSAPSLPRLVHEPVRCTCSAQGTGF  1650
1651  SCPSSVGGHPPQMRVVTGDILTDITGHNVSEYLLFTSDRFRLHRYGAITF  1700
1701  GNVQKSIPASFGARVPPMVRKIAVRRVAQVLYNNKGYHSMPTYLNSLNNA  1750
1751  ILRANLPKSKGNPAAYGITVTNHPMNKTSASLSLDYLLQGTDVVIAIFII  1800
1801  VAMSFVPASFVVFLVAEKSTKAKHLQFVSGCNPVIYWLANYVWDMLNYLV  1850
1851  PATCCVIILFVFDLPAYTSPTNFPAVLSLFLLYGWSITPIMYPASFWFEV  1900
1901  PSSAYVFLIVINLFIGITATVATFLLQLFEHDKDLKVVNSYLKSCFLIFP  1950
1951  NYNLGHGLMEMAYNEYINEYYAKIGQFDKMKSPFEWDIVTRGLVAMTVEG  2000
2001  FVGFFLTIMCQYNFLRQPQRLPVSTKPVEDDVDVASERQRVLRGDADNDM  2050
2051  VKIENLTKVYKSRKIGRILAVDRLCLGVRPGECFGLLGVNGAGKTSTFKM  2100
2101  LTGDESTTGGEAFVNGHSVLKDLLQVQQSLGYCPQFDALFDELTAREHLQ  2150
2151  LYTRLRGIPWKDEAQVVKWALEKLELTKYADKPAGTYSGGNKRKLSTAIA  2200
2201  LIGYPAFIFLDEPTTGMDPKARRFLWNLILDLIKTGRSVVLTSHSMEECE  2250
2251  ALCTRLAIMVNGRLRCLGSIQHLKNRFGDGYMITVRTKSSQNVKDVVRFF  2300
2301  NRNFPEAMLKERHHTKVQYQLKSEHISLAQVFSKMEQVVGVLGIEDYSVS  2350
2351  QTTLDNVFVNFAKKQSDNVEQQEAEPSSLPSPLGLLSLLRPRPAPTELRA  2400
2401  LVADEPEDLDTEDEGLISFEEERAQLSFNTDTLC                  2434

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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