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

NucPred

Fetching Q9MTH5 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MVNLVYVCMKINNSVVMVGLYYGFISAFSIGSSYLFLLRPRFLNDDPDAI    50
  51  EKKASETAGFFTGQLLIFISILYGPLHLALGRPHTILLLLAPYFFFHYLF   100
 101  SNSGQWPSQRFAFPLLTKSMRNRRFQLVFLNNLLFQLFSLSLLGRPMLTR   150
 151  LSYIYIFRCNNKMLFVLSSFVGWLIGHILVLKWAGLVFVWLLQVIRSKTM   200
 201  KYITCNVLIPATKYIIEKWRNSFVAGLIREILAMKQVESALVRIKNSKLL   250
 251  DDARWWIRGSSLISGLKINIRFYARLILRGFENVYVGAKFRQDMEHLFSI   300
 301  ILFAIFLLYLDQTPLLYADPADKKLQLQRKLSNETQAARAEKKLEERLTK   350
 351  KFEAQRRAQRAAQRQALQEFKQGVVESYLAKQVAKDANQIQAQKDEKQIQ   400
 401  AEQKARRIRAEQVVQYTFWLIEAQRREMEIEAARAMQEAYKGMLAAQEGY   450
 451  VEEGVQEKQEGFPEELISPSPIFHSEEREENPKLLILKEKISILKKKISI   500
 501  LKKKISILKEKNDLFSFEIPIITSLFDPQKPLRPLRYIKTCAGVEKAVKN   550
 551  EMSQYFFYACRSDGKQRICFTYPPSLATFWEMIQRKMASRFPRIYAKAKW   600
 601  RALRWSAPGSYRQWISRNKKKKNSLSTEFQNRIKTLDKKKSLLNVLARRK   650
 651  RSSLLNVLARRKRSSLQNVLETRKRLCNYKTNKTKKEYLPEKEYLPEIAD   700
 701  PFLTGALRGKSDPEVDDGGRKTSDLIKVVFLKNNITMATLRNKNDDDLRE   750
 751  QKNAIALLSRMKNPVNKLHLLFVNERDYPFVKTLVNRINGPAVPKKKKKI   800
 801  SKSKQKNVKSKQKNVKSKQKNVKSKQKNVKSKQNEIKRKVNEIKRKVNEI   850
 851  KRKQNESYPRGVKFGATPKTEINPHGIRFDAATIEKYSFATGYSYSPPSF   900
 901  DDILFHAFVTEPQRNKKAVIELEEEINKKVPRWSYQLIDELEQLEGAEGE   950
 951  TQFSDHEIRILPFKRVAVFTEKDSKKRKPLIDEQGNFVRHRKTYAIRFLG  1000
1001  HMSDFRRGLIKGSARQDRRKAYVCRTTQVNARSPLFALGPRTFLDGLVNL  1050
1051  AVQVKFFYETRIKGEKIVDDDDDNEKDEFKVMIPDTKSIVAETREMLKQA  1100
1101  GAEDGQSYEDVEDDIRIENVTEMWENIDYGQVIRTFILLLHIFLRKKVVF  1150
1151  PAFIIGKNIARMLLLQATEWKIDFARLKRERYAICTYNGMKVSEKIAFDQ  1200
1201  FPPDWADDGIQILVTNPFYLKPWYRSKTRSIQKDPKKEKDPKKEKGPKKE  1250
1251  PWYRFKTRFIQKDPKKEKGPKKEKGPKKEPWYRRFFFQKDPKKEKGPKKG  1300
1301  KAQFEGDRGVRFLTSFGILTDRPFGDLITPDWGVFFNPIRNELKKKIRQF  1350
1351  EKKHSIILSKRFRNVLKKTKKWFIKSFLFLKRARLKRHPIELSGGRETPE  1400
1401  FTRSQKDIDNLKNEQDFRMSRNPRISESLLQGPVRALKDDSLPEEKVADP  1450
1451  EKEPSDLDNELRAVWDEIDKVTKERKKIVFTPKPDSPDKLVQAKKNILKK  1500
1501  LERIKSRRHKFYFLRIRKSYYVLLFFIKRISRNIKRIYLNPLERAISIRK  1550
1551  IHPQRFFEFSKKMIEKSIGIGKTETNKETVYKTKKKKKKKNPFISIFKES  1600
1601  LYDKDIRISENDIKLGDTWNGYKYKRKKATDTSDLASMSQAYVFYKLYQT  1650
1651  QQTQLIHLDKLRYVLQYDGTSRFLKKELKDYFEAQELFHSKLKHKNSLNS  1700
1701  GKNQWKNWLKAQHQYSVSPIIWNSLSPQKWRTKVNQERMDENTDLNKRYS  1750
1751  NEKRKQFFEANSLDDEENVVETYLGQRAGDIKNSIKSYSYDLFSYQSINS  1800
1801  EDKYVCINNKQKNSYNYNRRKVNLVDSPEGIALSNQFLVQNDLLDLYTFP  1850
1851  DRKYVPWRLFPGSLIGGNDKDKDRFVKMWTATNSGNAVKYWTAANGNTSI  1900
1901  KPGVFWTFQNSQRTKKQNPLFDWRGMNTELPNRCISDLKGWFFFSELLKL  1950
1951  DLRYQVKPWILSKNLLFENLIFENQEENPNLIQNPIEDGRKNVIQNENEN  2000
2001  DPIEDGRQNVIQNENENAIQNLIDFFLEKKNSPKDTNQELHAQAKARIWD  2050
2051  ALVASLKQKREQKERKNKRIAQLIEKKKQKEIEKQKRKIEKQKRKKEKIE  2100
2101  NAKKKIENEKKKIETEEEKIEKEKRKKERKKEKLKKKVAKNIEKLKNKVA  2150
2151  KNVAKNIEKLKKQRAKNIARMEEEDKKARKKRKRKVQVQENKIPYTAFGS  2200
2201  DKWQRPIAEYPKSGDIRNFQVILPEDDDEDDEEDRLDELKLNAYELSRIQ  2250
2251  KITDEKRMKRNLLSSIKRERLKMEFSTRNNSLATIMLTHGIFSIEPLRIS  2300
2301  RQNQDASFLIYQLIKISLVEQLDPYDHNDSFELTEKYRARRNFFMPKTNA  2350
2351  ETMHKSDSDLFVPETILSTKRRRELRILISFYSRRGKRKNRIYKNPVFWK  2400
2401  YVKNCGEVVDNSEKKKKKLIKSFLWPNYRLEDLACMNRYWFNAQNGSRFS  2450
2451  MLRIRMYPRLKIR                                       2463

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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