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

NucPred

Fetching Q9ESR9 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MGFLHQLQLLLWKNVTLKRRSPWVLAFEIFIPLVLFFILLGLRQKKPTIS    50
  51  VKEAFYTAAPLTSAGILPVMQSLCPDGQRDEFGFLQYANSTVTQLLERLN   100
 101  RVVEESNLFDPERPSLGSELEALHQRLEALSSGPGTWESHSARPAVSSFS   150
 151  LDSVARDKRELWRFLMQNLSLPNSTAQALLAARVDPSEVYRLLFGPLPDL   200
 201  DGKLGFLRKQEPWSHLGSNPLFQMEELLLAPALLEQLTCAPGSGELGRIL   250
 251  TMPEGHQVDLQGYRDAVCSGQATARAQHFSDLATELRNQLDIAKIAQQLG   300
 301  FNVPNGSDPQPQAPSPQSLQALLGDLLDVQKVLQDVDVLSALALLLPQGA   350
 351  CAGRAPAPQAGSPSGPANSTGVGANTGPNTTVEEGTQSPVTPASPDTLQG   400
 401  QCSAFVQLWAGLQPILCGNNRTIEPEALRRGNMSSLGFTSKEQRNLGLLV   450
 451  HLMTSNPKILYAPAGSEADHVILKANETFAFVGNVTHYAQVWLNISAEIR   500
 501  SFLEQGRLQQHLHWLQQYVADLRLHPEAMNLSLDELPPALRLDYFSLPNG   550
 551  TALLQQLDTIDNAACGWIQFMSKVSVDIFKGFPDEESIVNYTLNQAYQDN   600
 601  VTVFASVIFQTRKDGSLPPHVHYKIRQNSSFTEKTNEIRRAYWRPGPNTG   650
 651  GRFYFLYGFVWIQDMIERAIINTFVGHDVVEPGNYVQMFPYPCYTRDDFL   700
 701  FVIEHMMPLCMVISWVYSVAMTIQHIVAEKEHRLKEVMKTMGLNNAVHWV   750
 751  AWFITGFVQLSISVTALTAILKYGQVLMHSHVLIIWLFLAVYAVATIMFC   800
 801  FLVSVLYSKAKLASACGGIIYFLSYVPYMYVAIREEVAHDKITAFEKCIA   850
 851  SLMSTTAFGLGSKYFALYEVAGVGIQWHTFSQSPVEGDDFNLLLAVTMLM   900
 901  VDTVVYGVLTWYIEAVHPGMYGLPRPWYFPLQKSYWLGSGRTETWEWSWP   950
 951  WAHAPRLSVMEEDQACAMESRHFEETRGMEEEPTHLPLVVCVDKLTKVYK  1000
1001  NDKKLALNKLSLNLYENQVVSFLGHNGAGKTTTMSILTGLFPPTSGSATI  1050
1051  YGHDIRTEMDEIRKNLGMCPQHNVLFDQLTVEEHLWFYSRLKSMAQEEIR  1100
1101  KEMDKMIEDLELSNKRHSLVQTLSGGMKRKLSVAIAFVGGSRAIILDEPT  1150
1151  AGVDPYARRAIWDLILKYKPGRTILLSTHHMDEADLLGDRIAIISHGKLK  1200
1201  CCGSPLFLKGAYGDGYRLTLVKRPAEPGTSQEPGMASSPSGRPQLSNCSE  1250
1251  MQVSQFIRKHVASSLLVSDTSTELSYILPSEAVKKGAFERLFQQLEHSLD  1300
1301  ALHLSSFGLMDTTLEEVFLKVSEEDQSLENSEADVKESRKDALPGAEGLT  1350
1351  AVESQAGNLARCSELAQSQASLQSASSVGSARGDEGAGYTDGYGDYRPLF  1400
1401  DNLQDPDSVSLQEAEMEALARVGQGSRKLEGWWLKMRQFHGLLVKRFHCA  1450
1451  RRNSKALCSQILLPAFFVCVAMTVALSVPEIGDLPPLVLSPSQYHNYTQP  1500
1501  RGNFIPYANEERREYRLRLSPDASPQQLVSTFRLPSGVGATCVLKSPANG  1550
1551  SLGPMLNLSSGESRLLAARFFDSMCLESFTQGLPLSNFVPPPPSPAPSDS  1600
1601  PLSPDEDSLLAWNTSLPPTAGPETWTWAPSLPRLVHEPVRCTCSAQGTGF  1650
1651  SCPSSVGGHPPQMRVVTGDILTDITGHNVSEYLLFTSDRFRLHRYGAITF  1700
1701  GNIQKSIPAPIGTRTPLMVRKIAVRRVAQVLYNNKGYHSMPTYLNSLNNA  1750
1751  ILRANLPKSKGNPAAYGITVTNHPMNKTSASLSLDYLLQGTDVVIAIFII  1800
1801  VAMSFVPASFVVFLVAEKSTKAKHLQFVSGCNPVIYWLANYVWDMLNYLV  1850
1851  PATCCIIILFVFDLPAYTSPTNFPAVLSLFLLYGWSITPIMYPASFWFEV  1900
1901  PSSAYVFLIVINLFIGITATVATFLLQLFEHDKDLKVVNSYLKSCFLIFP  1950
1951  NYNLGHGLMEIAYNEYINEYYAKIGQFDKMKSPFEWDIVTRGLVAMTVEG  2000
2001  FVGFFLTIMCQYNFLRQPQRLPVSTKPVEDDVDVASERQRVLRGDADNDM  2050
2051  VKIENLTKVYKSRKIGRILAVDRLCLGVRPGECFGLLGVNGAGKTSTFKM  2100
2101  LTGDESTTGGEAFVNGHSVLKDLLQVQQSLGYCPQFDALFDELTAREHLQ  2150
2151  LYTRLRGIPWKDEAQVVRWALEKLELTKCADKPAGSYSGGNKRKLSTAIA  2200
2201  LIGYPAFIFLDEPTTGMDPKARRFLWNLILDLIKTGRSVVLTSHSMEECE  2250
2251  AVCTRLAIMVNGRLRCLGSIQHLKNRFGDGYMITVRTKSSQNVKDVVRFF  2300
2301  NRNFPEAMLKERHHTKVQYQLKSEHISLAQVFSKMEHVVGVLGIEDYSVS  2350
2351  QTTLDNVFVNFAKKQSDNVEQQEAEPSTLPSPLGLLSLLRPRPAPTELRA  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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