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

NucPred

Fetching Q61290 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  MARFGEAVVVGRPGSGDGDSDQSRNRQGTPVPASGPAAAYKQSKAQRART    50
  51  MALYNPIPVRQNCFTVNRSLFIFGEDNIVRKYAKKLIDWPPFEYMILATI   100
 101  IANCIVLALEQHLPEDDKTPMSRRLEKTEPYFIGIFCFEAGIKIVALGFI   150
 151  FHKGSYLRNGWNVMDFIVVLSGILATAGTHFNTHVDLRALRAVRVLRPLK   200
 201  LVSGIPSLQIVLKSIMKAMVPLLQIGLLLFFAILMFAIIGLEFYSGKLHR   250
 251  ACFMNNSGILEGFDPPHPCGVQGCPAGYECKDWIGPNDGITQFDNILFAV   300
 301  LTVFQCITMEGWTTVLYNTNDALGATWNWLYFIPLIIIGSFFVLNLVLGV   350
 351  LSGEFAKERERVENRRAFMKLRRQQQIERELNGYRAWIDKAEEVMLAEEN   400
 401  KNSGTSALEVLRRATIKRSRTEAMTRDSSDEHCVDISSVGTPLARASIKS   450
 451  TKVDGASYFRHKERLLRISIRHMVKSQVFYWIVLSVVALNTACVAIVHHN   500
 501  QPQWLTHLLYYAEFLFLGLFLLEMSLKMYGMGPRLYFHSSFNCFDFGVTV   550
 551  GSIFEVVWAIFRPGTSFGISVLRALRLLRIFKITKYWASLRNLVVSLMSS   600
 601  MKSIISLLFLLFLFIVVFALLGMQLFGGRFNFNDGTPSANFDTFPAAIMT   650
 651  VFQILTGEDWNEVMYNGIRSQGGVSSGMWSAIYFIVLTLFGNYTLLNVFL   700
 701  AIAVDNLANAQELTKDEQEEEEAFNQKHALQKAKEVSPMSAPNMPSIERD   750
 751  RRRRHHMSMWEPRSSHLRERRRRHHMSVWEQRTSQLRRHMQMSSQEALNK   800
 801  EEAPPMNPLNPLNPLSPLNPLNAHPSLYRRPRPIEGLALGLGLEKCEEER   850
 851  ISRGGSLKGDIGGLTSALDNQRSPLSLGKREPPWLPRSCHGNCDPIQQEA   900
 901  GGGETVVTFEDRARHRQSQRRSRHRRVRTEGKDSASASRSRSASQERSLD   950
 951  EGVSVEGEKEHEPHSSHRSKEPTIHEEERTQDLRRTNSLMVPRGSGLVGA  1000
1001  LDEAETPLVQPQPELEVGKDAALTEQEAEGSSEQALLGDVQLDVGRGISQ  1050
1051  SEPDLSCMTANMDKATTESTSVTVAIPDVDPLVDSTVVNISNKTDGEASP  1100
1101  LKEAETKEEEEEVEKKKKQKKEKRETGKAMVPHSSMFIFSTTNPIRRACH  1150
1151  YIVNLRYFEMCILLVIAASSIALAAEDPVLTNSERNKVLRYFDYVFTGVF  1200
1201  TFEMVIKMIDQGLILQDGSYFRDLWNILDFVVVVGALVAFALANALGTNK  1250
1251  GRDIKTIKSLRVLRVLRPLKTIKRLPKLKAVFDCVVTSLKNVFNILIVYK  1300
1301  LFMFIFAVIAVQLFKGKFFYCTDSSKDTEKECIGNYVDHEKNKMEVKGRE  1350
1351  WKRHEFHYDNIIWALLTLFTVSTGEGWPQVLQHSVDVTEEDRGPSRSNRM  1400
1401  EMSIFYVVYFVVFPFFFVNIFVALIIITFQEQGDKMMEECSLEKNERACI  1450
1451  DFAISAKPLTRYMPQNRHTFQYRVWHFVVSPSFEYTIMAMIALNTVVLMM  1500
1501  KYYTAPCTYELALKYLNIAFTMVFSLECVLKVIAFGFLNYFRDTWNIFDF  1550
1551  ITVIGSITEIILTDSKLVNTSGFNMSFLKLFRAARLIKLLRQGYTIRILL  1600
1601  WTFVQSFKALPYVCLLIAMLFFIYAIIGMQVFGNIKLDEESHINRHNNFR  1650
1651  SFFGSLMLLFRSATGEAWQEIMLSCLGEKGCEPDTTAPSGQNESERCGTD  1700
1701  LAYVYFVSFIFFCSFLMLNLFVAVIMDNFEYLTRDSSILGPHHLDEFVRV  1750
1751  WAEYDRAACGRIHYTEMYEMLTLMSPPLGLGKRCPSKVAYKRLVLMNMPV  1800
1801  AEDMTVHFTSTLMALIRTALDIKIAKGGADRQQLDSELQKETLAIWPHLS  1850
1851  QKMLDLLVPMPKASDLTVGKIYAAMMIMDYYKQSKVKKQRQQLEEQKNAP  1900
1901  MFQRMEPSSLPQEIIANAKALPYLQQDPVSGLSGRSGYPSMSPLSPQEIF  1950
1951  QLACMDPADDGQFQEQQSLVVTDPSSMRRSFSTIRDKRSNSSWLEEFSME  2000
2001  RSSENTYKSRRRSYHSSLRLSAHRLNSDSGHKSDTHRSGGRERGRSKERK  2050
2051  HLLSPDVSRCNSEERGTQADWESPERRQSRSPSEGRSQTPNRQGTGSLSE  2100
2101  SSIPSISDTSTPRRSRRQLPPVPPKPRPLLSYSSLMRHTGGISPPPDGSE  2150
2151  GGSPLASQALESNSACLTESSNSLHPQQGQHPSPQHYISEPYLALHEDSH  2200
2201  ASDCGEEETLTFEAAVATSLGRSNTIGSAPPLRHSWQMPNGHYRRRRWGA  2250
2251  WAGMMCGAVSDLLSDTEEDDKC                              2272

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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