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

NucPred

Fetching Q9VEU1 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MDSEAYPMKSSVKISQKKKASQDMAVICVWVMPLAVFGLIAIGQAAKTGQ    50
  51  VQASSGSCAFHTLDGVAAESEGVRFIRLREDAQVGKEILRLQAYPRSTAA   100
 101  LKGADASGDHKYFNLTEHNATTLVVSLARSLERLVDRDVPRNLLKFRILC   150
 151  AGKQEKLEEGSYLSITVYIEDVNDNAPEFLNVPYVVDVDENTSIESIIFE   200
 201  GVQAFDRDKPNTPNSEVHFSMSTVPEQLSADGSPYFALKSPHRPLLILKR   250
 251  ELDFDNGIRQFKLPIFAWDRGTPANQANTTITINVRDVDDLPPKFTEGVY   300
 301  RTRINEFYPMTGVPIRIPLYFAPPIMAFDQDSLNASLVYDIISGNERQLF   350
 351  RVNPHNGVMYLQKEIDLEEESLPGNTFVLQLEARQKDNPLKKALARIEVE   400
 401  VLDLNDNVPEFEADYYNISIVENLPTGFSVLQVNAVDRDQGENSEFLYNL   450
 451  VETKDAAGAFRIDSRTGWITVRDDRLLDREQRRSIQLNVEALERNPSYLD   500
 501  DKHLKKPGPSKVQVEITLLDTNDNTPKFEHGNLYEFKVPINAPTGYVIGQ   550
 551  VVAHDPDEGPNGHLLYELQRPKGSGYIPFRLDNKNGTIYVGGPLRRGRIA   600
 601  VFVEATDQPTNPSERRFSLAVITIEVYATIDDQAIDFVGAPYEFWVGANT   650
 651  PLGTSVGQVRTTLIYEGGDEIMYDLLHTYSEGVPFAIEERSGIITVIREL   700
 701  SEFKRKVYQFEAVANYLFANSSQSLVMSRSSSPLTTIASPAELSDEGVLI   750
 751  TNLTIHIVNKPEQKVPLRPVIEEINMNVIHFHVEENVVGGIIGQLLYKNG   800
 801  INLVNNELGTYREMPSEPTSRNITMGSRFRSRNRSRSSKSKRRLPRRLVG   850
 851  DANIKLRYIIANQQEVVNKISITEDGTLLTLTGLDREQQPSYELTVIVEY   900
 901  STGLVSGAGIYQVNIKVDDVNDNAPKFNALTYVGLINENCVVGTELSMNH   950
 951  AILIQDADEGPNAEFRVQLQGDYSDEFSIEYVNGTSSENSTHHKMPSTTG  1000
1001  AFNIFNLTDQWNDEFKYQELHTTFMQTNFKLSSGPYFRISYTGKRGLDRE  1050
1051  KQQLYNLKIIAADTGGLSGYAHLTVLVADVNDNAPMFERISVFKDSRLEI  1100
1101  REYTTDMEIYFVESSSGMTAPQATAAMMLAPPPYHIPGSPRFNVDRERSV  1150
1151  GAGLGVVARAKSRRRMVRALTTKCPLFAIYEDTPVGTKVLQLSASDEDFG  1200
1201  KNALLHYELQGEQVERTPGMPMLRVHGVKYFAIDKLSGELSVNYPLSANI  1250
1251  EIMLNLTVTDIDGLKDSTCLRFTVMDVNNHAPTFKKSWYSFDTPEGEYKD  1300
1301  SVLGQLTAIDMDFGENANITYTLSDSHLPFTIKPASGVLKIGGQLDRELK  1350
1351  DKYSFQVIATDNAPVMQRMSSSVDVEVNVLDINDNRPEFIGYDDQTKAVK  1400
1401  FIPSVADRTLMLPVYKAYLDRSTQPGTFVRQLTAIDKDNVGNGNGLVLYS  1450
1451  IRHQEMQAPLFQIDSRDGTISTISRINGYNDYEHLNVSVIASDVGSPALS  1500
1501  ATAIVIVNLQGQAVTDPPKSTPKPEPPANVTVFQHAYYEVKLTENNEAPI  1550
1551  EVMRLNLSAGLNPENYRWSLWLEEGLDETDAHPPFEYDAKNMLLYALKPF  1600
1601  DREHISRYQLRIRADRLSREARNYARVSYPVVDERIEGLSLNECRILVHI  1650
1651  ADENDNAPKFRGNGQPIVAVLPQSASFGYPVTRVEANDLDEGLNAEIRYR  1700
1701  LLNEPARLFGIDELSGNIRLLGELSRTEHIYGFDVKATDRMGADDGRSGI  1750
1751  VNVFVYIINEAKQVRLVVAGMPVEVERRIEGLMEALSDAIGKDVRVRLLE  1800
1801  PYSGGLEPATNAYIYAVDPHTNSIMEMEQLQDALAGLQLDALQLQQQKLD  1850
1851  GGKPMPRILELAEFGQLARPAHASASSFMGGLEFVTVVLLALISLGALIA  1900
1901  ACCYVCMRQKRRLWSQRDFSASDAGLTYTIAGIGSPRGQKQRRQRQQRHT  1950
1951  QRCSKGSTGSQRPTSAFMPESVCSSAQTQSTATATEKLEQQLHHHHQQQA  2000
2001  MATQQQHHQYLNEQQRQQKREYIDVPLPKSIAKAAAVTSGGDGAVGVGST  2050
2051  PFVLKYNACQPVNNLNNYETSLFSLHSTGQDSGVEFLSSRELYETSPDSF  2100
2101  QHGGSKRGNNTEVLCPRHAKAHLELRQPNTDSSDTYEDSLKTDEPLVAHN  2150
2151  CRSANCEHRQHQQHPSHHPHYQNTRFEKRSCVRHSFSGVKDDLMQQSPQI  2200
2201  SLRPRGHALRNSMNDLEQRLHNLEQSFRRPLEFSKSNSLF            2240

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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