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

NucPred

Fetching P11029 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MEESSQPAKPLEMNPHSRFIIGSVSEDNSEDETSSLVKLDLLEEKERSLS    50
  51  PVSVCSDSLSDLGLPSAQDGLANHMRPSMSGLHLVKQGRDRKKVDVQRDF   100
 101  TVASPAEFVTRFGGNRVIEKVLIANNGIAAVKCMRSIRRWSYEMFRNERA   150
 151  IRFVVMVTPEDLKANAEYIKMADHYVPVPGGPNNNNYANVELILDIAKRI   200
 201  PVQAVWAGWGHASENPKLPELLHKNGIAFMGPPSQAMWALGDKIASSIVA   250
 251  QTAGIPTLPWNGSGLRVDWQENDLQKRILNVPQELYEKGYVKDADDGLRA   300
 301  AEEVGYPVMIKASEGGGGKGIRKVNNADDFPNLFRQVQAEVPGSPIFVMR   350
 351  LAKQSRHLEVQILADQYGNAISLFGRDCSVQRRHQKIIEEAPASIATSVV   400
 401  FEHMEQCAVKLAKMVGYVSAGTVEYLYSQDGSFYFLELNPRLQVEHPCTE   450
 451  MVADVNLPAAQLQIAMGIPLHRIKDIRVMYGVSPWGDGSIDFENSAHVPC   500
 501  PRGHVIAARITSENPDEGFKPSSGTVQELNFRSNKNVWGYFSVAAAGGLH   550
 551  EFADSQFGHCFSWGENREEAISNMVVALKELSIRGDFRTTVEYLIKLLET   600
 601  ESFQQNRIDTGWLDRLIAEKVQAERPDTMLGVVCGALHVADVSFRNSVSN   650
 651  FLHSLERGQVLPAHTLLNTVDVELIYEGRKYVLKVTRQSPNSYVVIMNSS   700
 701  CVEVDVHRLSDGGLLLSYDGSSYTTYMKEEVDRYRITIGNKTCVFEKEND   750
 751  PSILRSPSAGKLIQYVVEDGGHVFAGQCFAEIEVMKMVMTLTAGESGCIH   800
 801  YVKRPGAVLDPGCVIAKLQLDDPSRVQQAELHTGTLPQIQSTALRGEKLH   850
 851  RIFHYVLDNLVNVMNGYCLPEPYFSSKVKGWVERLMKTLRDPSLPLLELQ   900
 901  DIMTSVSGRIPPNVEKSIKKEMAQYASNITSVLCQFPSQQIANILDSHAA   950
 951  TLNRKSEREVFFMNTQSIVQLVQRYRSGIRGHMKAVVMDLLRQYLKVETQ  1000
1001  FQHGHYDKCVFALREENKSDMNAVLNYIFSHAQVTKKNLLVTMLIDQLCG  1050
1051  RDPTLTDELINILTELTQLSKTTNAKVALRARQVLIASHLPSYELRHNQV  1100
1101  ESIFLSAIDMYGHQFCIENLQKLILSETSIFDVLPNFFYHSNQVVRMAAL  1150
1151  EVYVRRAYIAYELNSVQHRQLKDNTCVVEFQFMLPTSHPNRMSFSSNLNH  1200
1201  YGMVHVASVSDVLLDNSFTPPCQRMGGMVSFRTFEDFVRIFDEVMSCFCD  1250
1251  SPPQSPTFPEAGHASLYDEDKAAREEPIHILNVAIKTDGDVDDDGLAAMF  1300
1301  REFTQSKKSVLIEHGIRRLTFLVAQKREFPKFFTFRARDKFEEDRIYRHL  1350
1351  EPALAFQLELNRMRNFDLTAIPCANHKMHLYLGAAKVEVGTEVTDYRFFV  1400
1401  RAIIRHSDLVTKEASFEYLQNEGERLLLEAMDELEVAFNNTNVRTDCNHI  1450
1451  FLNFVPTVIMDPSKIEESVRSMVMRYGSRLWKLRVLQAELKINIRLTPTG  1500
1501  KAIPIRLFLTNESGYYLDISLYKEVTDSRTGQIMFQAYGDKQGPLHGMLI  1550
1551  NTPYVTKDLLQSKRFQAQSLGTSYVYDIPEMFRQSLIKLWDSMNEHAFLP  1600
1601  TPPLPSDILTYTELVLDDQGQLVHMNRLPGGNEIGMVAWKMTLKTPEYPE  1650
1651  GRDIIVIGNDITYRIGSFGPQEDVLFLRASELARTHGIPRIYVAANSGAR  1700
1701  IGLAEEIRHMFHVAWEDPDDPYKGYKYLYLTPQDYKKVSALNSVHCEHVE  1750
1751  DNGESRYKITDIIGKEDGLGIENLRGSGMIAGESSLAYESIITINLVTCR  1800
1801  AIGIGAYLVRLGQRTIQVENSHIILTGCGALNKVLGREVYTSNNQLGGIQ  1850
1851  IMHNNGVTHGTVCDDFEGVYTILLWLSYMPKSVYSPVPILKVKDPIDRTI  1900
1901  DFVPTKTPYDPRWMLAGRPNPSQKGQWQSGFFDNGSFLEIMQPWAQTVVV  1950
1951  GRARLGGIPVGVVAVETRTVELSIPADPANLDSEAKIIQQAGQVWFPDSA  2000
2001  FKTAQAINDFNREGLPLMVFANWRGFSGGMKDMYDQVLKFGAYIVDGLRE  2050
2051  YRQPVLIYIPPQAELRGGSWAVIDPTINPRHMEMYADRESRGGILEPEGT  2100
2101  VEIKFRRKDLVKTMRRVDPVYMRLAERLGTPELSAADRKDLESKLKEREE  2150
2151  FLIPIYHQVAMQFADLHDTPGRMQEKGAITDILDWKTSRTFFYWRLRRLL  2200
2201  LEDVVKKKIHDANPELTDGQIQAMLRRWFVEVEGTVKAYLWDSNKDLVEW  2250
2251  LEKQLMEEEGVRSVVDENIKYISRDYILKQIRSLVQANPEVAMDSIVHMT  2300
2301  QHISPTQRAEIVRILSTMDSPSST                            2324

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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