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

NucPred

Fetching Q02343 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MARFGEAAAGRPASGEGDSDQGRNLPGTPVPASGSAAAYKQSKAQRARTM    50
  51  ALYNPIPVRQNCFTVNRSLFIFGEDNIVRKYAKKLIDWPPFEYMILATII   100
 101  ANCIVLALEQHLPEDDKTPMSRRLEKTEPYFIGIFCFEAGIKIVALGFIF   150
 151  HKGSYLRNGWNVMDFIVVLSGILATAGTHFNTHVDLRTLRAVRVLRPLKL   200
 201  VSGIPSLQIVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLEFYSGKLHRA   250
 251  CFVNNSGVLEGFDPPHPCGVQGCPAGYECKDWIGPNDGITQFDNILFAVL   300
 301  TVFQCITMEGWTTVLYNTNDALGATWNWLYFIPLIIIGSFFVLNLVLGVL   350
 351  SGEFAKERERVENRRAFMKLRRQQQIERELNGYRAWIDKAEEVMLAEENK   400
 401  NSGTSALEVLRRATIKRSRTEAMTRDSSDEHCVDISSVGTPLARASIKSA   450
 451  KVDGASYFRHKERLLRISVRHAVKSQVFYWIVLSLVALNTACVAIVHHNQ   500
 501  PQWLTHLLYYAEFLFLGLFLLEMSLKMYGMGPRLYFHSSFNCFDFGVTVG   550
 551  SIFEVVWAIFRPGTSFGISVLRALRLLRIFKITKYWASLRNLVVSLMSSM   600
 601  KSIISLLFLLFLFIVVFALLGMQLFGGRFNFNDGTPSANFDTFPAAIMTV   650
 651  FQILTGEDWNEVMYNGIRSQGGVSSGMWSAVYFIVLTLFGNYTLLNVFLA   700
 701  IAVDNLANAQELTKDEQEEEEAFNQKHALQKAKEVSPMSAPNVPSIERDR   750
 751  RRRHHMSMWEPRSSHLRERRRRHHMSVWEQRTSQLRRHMQMSSQEALNKE   800
 801  EAPPMNPLNPLNPLSPLNPLNAHPSLYRRPRPMEGLALGLEKCEEEHVSR   850
 851  GGSLKGALDCQRSPLSLGRREPPWLARPCHGNCEPALQETAGGETVVTFE   900
 901  DRARHRQSQRRSRHRRVRTEAKESSSASRSRSVSQERSLDEGASTEGERD   950
 951  HEARGSHGGKEPTIHEEERAQDLRRTDSLMVPKGSGLAGGLDEAGTPLVL  1000
1001  SSPEGVGKEAAPTEQHADGSGEPALLGHVQLDVGRAISQSEPDLSCVTAT  1050
1051  TDKVTTESTDVTVAIPDAEPLVDSTVVHIGNKTDGEASPFQEAEMKEAEQ  1100
1101  ETEKQKKKERPASGKAMVPHSSMFIFSTSNPIRRACHYVVNLRYFEMCIL  1150
1151  LVIAASSIALAAEDPVLTNSERNRVLRYFDYVFTGVFTFEMVIKMIDQGL  1200
1201  ILQDGSYFRDLWNILDFVVVVGALVAFALANALGTNKGRDIKTIKSLRVL  1250
1251  RVLRPLKTIKRLPKLKAVFDCVVTSLKNVFNILIVYKLFMFIFAVIAVQL  1300
1301  FKGKFFYCTDSSKDTEKECIGNYVDHEKNKMEVKGREWKRHEFHYDNIIW  1350
1351  ALLTLFTVSTGEGWPQVLQHSVDVTEEDRGPSRSNRMEMSIFYVVYFVVF  1400
1401  PFFFVNIFVALIIITFQEQGDKMMEECSLEKNERACIDFAISAKPLTRYM  1450
1451  PQNRHTFQYRVWHFVVSPSFEYTIMAMIALNTVVLMMKYYSAPCTYELAL  1500
1501  KYLNIAFTMVFSLECVLKVIAFGFVNYFRDTWNIFDFITVIGSITEIVLT  1550
1551  DSKLVNTTGFNMSFLKLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYV  1600
1601  CLLIAMLFFIYAIIGMQVFGNIRLDEESHINRHNNFRSFFGSLMLLFRSA  1650
1651  TGEAWQEIMLSCLGEKGCEPDTTAPSGQQESERCGTDLAYVYFVSFIFFC  1700
1701  SFLMLNLFVAVIMDNFEYLTRDSSILGPHHLDEFVRVWAEYDRAACGRIH  1750
1751  YTEMYEMLTLMSPPLGLGKRCPSKVAYKRLVLMNMPVAEDMTVHFTSTLM  1800
1801  ALIRTALDIKIAKGGADRQQLDSELQKETLAIWPHLSQKMLDLLVPMPKA  1850
1851  SDLTVGKIYAAMMIMDYYKQSKVKKQRRQLEEQKNAPMFQRMEPSSLPQE  1900
1901  IIANAKALPCLPQGPPAGLGGRSGCPAMSPLSPQIFQLTCMDPADDDGQF  1950
1951  QEQRSLVVTDPGSMRRSFSTIRDKRSSSSWLEEFSMERSSDNTYKSRRRS  2000
2001  YHSSLRLSAHRLNSDSGHKSDTHRSGGRERGRSKEREHLLSADVSRCSSE  2050
2051  ERGAQADWDSPERHPSRSPSEGRSQSPSRQGTGSLSESSIPSVSDTSTPR  2100
2101  HSRRQLPPVPPKPRPLLSYSSLKQQPSNFSPPADGSQGGSLLASPALESA  2150
2151  QVGLPESSDSPRRAQGSHASPQRYISEPYLALHEDSHASDCGEEETLTFE  2200
2201  AAVATSLGRSNTIGSAPPLRHSWQMPNGHYRRRRRGGPGAGALCGAVGDL  2250
2251  LSDTEEDKC                                           2259

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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