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

NucPred

Fetching Q15878 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MARFGEAVVARPGSGDGDSDQSRNRQGTPVPASGQAAAYKQTKAQRARTM    50
  51  ALYNPIPVRQNCFTVNRSLFIFGEDNIVRKYAKKLIDWPPFEYMILATII   100
 101  ANCIVLALEQHLPEDDKTPMSRRLEKTEPYFIGIFCFEAGIKIVALGFIF   150
 151  HKGSYLRNGWNVMDFIVVLSGILATAGTHFNTHVDLRTLRAVRVLRPLKL   200
 201  VSGIPSLQIVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLEFYSGKLHRA   250
 251  CFMNNSGILEGFDPPHPCGVQGCPAGYECKDWIGPNDGITQFDNILFAVL   300
 301  TVFQCITMEGWTTVLYNTNDALGATWNWLYFIPLIIIGSFFVLNLVLGVL   350
 351  SGEFAKERERVENRRAFMKLRRQQQIERELNGYRAWIDKAEEVMLAEENK   400
 401  NAGTSALEVLRRATIKRSRTEAMTRDSSDEHCVDISSVGTPLARASIKSA   450
 451  KVDGVSYFRHKERLLRISIRHMVKSQVFYWIVLSLVALNTACVAIVHHNQ   500
 501  PQWLTHLLYYAEFLFLGLFLLEMSLKMYGMGPRLYFHSSFNCFDFGVTVG   550
 551  SIFEVVWAIFRPGTSFGISVLRALRLLRIFKITKYWASLRNLVVSLMSSM   600
 601  KSIISLLFLLFLFIVVFALLGMQLFGGRFNFNDGTPSANFDTFPAAIMTV   650
 651  FQILTGEDWNEVMYNGIRSQGGVSSGMWSAIYFIVLTLFGNYTLLNVFLA   700
 701  IAVDNLANAQELTKDEQEEEEAFNQKHALQKAKEVSPMSAPNMPSIERDR   750
 751  RRRHHMSMWEPRSSHLRERRRRHHMSVWEQRTSQLRKHMQMSSQEALNRE   800
 801  EAPTMNPLNPLNPLSSLNPLNAHPSLYRRPRAIEGLALGLALEKFEEERI   850
 851  SRGGSLKGDGGDRSSALDNQRTPLSLGQREPPWLARPCHGNCDPTQQEAG   900
 901  GGEAVVTFEDRARHRQSQRRSRHRRVRTEGKESSSASRSRSASQERSLDE   950
 951  AMPTEGEKDHELRGNHGAKEPTIQEERAQDLRRTNSLMVSRGSGLAGGLD  1000
1001  EADTPLVLPHPELEVGKHVVLTEQEPEGSSEQALLGNVQLDMGRVISQSE  1050
1051  PDLSCITANTDKATTESTSVTVAIPDVDPLVDSTVVHISNKTDGEASPLK  1100
1101  EAEIREDEEEVEKKKQKKEKRETGKAMVPHSSMFIFSTTNPIRRACHYIV  1150
1151  NLRYFEMCILLVIAASSIALAAEDPVLTNSERNKVLRYFDYVFTGVFTFE  1200
1201  MVIKMIDQGLILQDGSYFRDLWNILDFVVVVGALVAFALANALGTNKGRD  1250
1251  IKTIKSLRVLRVLRPLKTIKRLPKLKAVFDCVVTSLKNVFNILIVYKLFM  1300
1301  FIFAVIAVQLFKGKFFYCTDSSKDTEKECIGNYVDHEKNKMEVKGREWKR  1350
1351  HEFHYDNIIWALLTLFTVSTGEGWPQVLQHSVDVTEEDRGPSRSNRMEMS  1400
1401  IFYVVYFVVFPFFFVNIFVALIIITFQEQGDKMMEECSLEKNERACIDFA  1450
1451  ISAKPLTRYMPQNRHTFQYRVWHFVVSPSFEYTIMAMIALNTVVLMMKYY  1500
1501  SAPCTYELALKYLNIAFTMVFSLECVLKVIAFGFLNYFRDTWNIFDFITV  1550
1551  IGSITEIILTDSKLVNTSGFNMSFLKLFRAARLIKLLRQGYTIRILLWTF  1600
1601  VQSFKALPYVCLLIAMLFFIYAIIGMQVFGNIKLDEESHINRHNNFRSFF  1650
1651  GSLMLLFRSATGEAWQEIMLSCLGEKGCEPDTTAPSGQNENERCGTDLAY  1700
1701  VYFVSFIFFCSFLMLNLFVAVIMDNFEYLTRDSSILGPHHLDEFVRVWAE  1750
1751  YDRAACGRIHYTEMYEMLTLMSPPLGLGKRCPSKVAYKRLVLMNMPVAED  1800
1801  MTVHFTSTLMALIRTALDIKIAKGGADRQQLDSELQKETLAIWPHLSQKM  1850
1851  LDLLVPMPKASDLTVGKIYAAMMIMDYYKQSKVKKQRQQLEEQKNAPMFQ  1900
1901  RMEPSSLPQEIIANAKALPYLQQDPVSGLSGRSGYPSMSPLSPQDIFQLA  1950
1951  CMDPADDGQFQERQSLEPEVSELKSVQPSNHGIYLPSDTQEHAGSGRASS  2000
2001  MPRLTVDPQVVTDPSSMRRSFSTIRDKRSNSSWLEEFSMERSSENTYKSR  2050
2051  RRSYHSSLRLSAHRLNSDSGHKSDTHRSGGRERGRSKERKHLLSPDVSRC  2100
2101  NSEERGTQADWESPERRQSRSPSEGRSQTPNRQGTGSLSESSIPSVSDTS  2150
2151  TPRRSRRQLPPVPPKPRPLLSYSSLIRHAGSISPPADGSEEGSPLTSQAL  2200
2201  ESNNACLTESSNSPHPQQSQHASPQRYISEPYLALHEDSHASDCGEEETL  2250
2251  TFEAAVATSLGRSNTIGSAPPLRHSWQMPNGHYRRRRRGGPGPGMMCGAV  2300
2301  NNLLSDTEEDDKC                                       2313

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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