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

NucPred

Fetching Q28559 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MGEPSSLAKPLELNQHSRFIIGSVSEDNSEDEISNLVKLDLLEEKEGSLS    50
  51  PASVSSDTLSDLGISSLQDGLALHMRSSMSGLHLVKQGRDRKKIDSQRDF   100
 101  TVASPAEFVTRFGGNKVIEKVLIANNGIAAVKCMRSIRRWSYEMFRNERA   150
 151  IRFVVMVTPEDLKANAEYIKMADHYVPVPGGPNNNNYANVELILDIARRI   200
 201  PVQAVWAGWGHASENPKLPELLLKNGIAFMGPPSQAMWALGDKIASSIVA   250
 251  QTAGIPTLPWSGSGLCVDWHENDFSKRILNVPQELYEKGYVKDVDDGLKA   300
 301  AEEVGYPVMIKASEGGGGKGIRKVNNADDFPNLFRQVQAEVPGSPIFVMR   350
 351  LAKQSRHLEVQILADQYGNAISLFGRDCSVQRRHQKIIEEAPAAIATPAV   400
 401  FEHMEQCAVKLARMVGYVSAGTVEYLYSQDGSFYFLELNPRLQVEHPCTE   450
 451  MVADVNLPAAQLQIAMGIPLYRIKDIRMMYGVSPWGDAPIDFENSAHVPC   500
 501  PRGHVIAARITSENPDEGFKPSSGTVQELNFRSNKNVWGYFSVAAAGGLH   550
 551  EFADSQFGHCFSWGENREEAISNMVVALKELSIRGDFRTTVEYLIKLLET   600
 601  ESFQLNRIDTGWLDRLIAEKVQAERPDTMLGVVCGALHVADVSLRNSISN   650
 651  FLHSLERGQVLSAHTLLNTVDVELIYEGEKIVLKVTRQSPNSYVVIMNGS   700
 701  CVEVDVHRLSDGGLLLSYDGSSYTTYMKEEVDRYRITIGNKTCVFEKEND   750
 751  PSVLRSPSAGKLIQYIVEDGGHVFAGQCYAEIEVMKMVMTLTAAESGCIH   800
 801  YVKRPGAALDPGCVIAKMQLDNPSKVQQAELHTGSLPRIQSTALRGEKLH   850
 851  RVFHYVLDNLVNVMNGYCLPDPFFSSRVKDWVEGLMKTLRDPSLPLLELQ   900
 901  DIMTSVSGRIPPNVEKSIKKEMAQYASNITSVLCQFPSQQIANILDSHAA   950
 951  TLNRKSEREVFFMNTQSIVQLVQRYRSGIRGHMKAVVMDLLRQYLRVETQ  1000
1001  FQNGHYDKCVFALREENKSDMNTVLNYIFSHAQVTKKNLLVTMLIDQLCG  1050
1051  RDPTLTDELLNILTELTQLSKTTNAKVALRARQVLIASHLPSYELRHNQV  1100
1101  ESIFLSAIDMYGHQFCIENLQKLILSETSIFDVLPNFFYHSNQVVRMAAL  1150
1151  EVYVRRAYIAYELNSVQHRQLKDNTCVVEFQFMLPTSHPNRGNIPTLNRM  1200
1201  SFSSNLNHYGMTHVASVSDVLLDNAFTPPCQRMGGMVSFRTFEDFVRIFD  1250
1251  EVMGCFCDSPPQSPTFPEAGHTSLYDEDKVPRDEPIHILNVAIKTDCDIE  1300
1301  DDSLAAMFREFTQQNKATLVEHGIRRLTFLVAQKDFRKQVNYEVDQRFHR  1350
1351  EFPKFFTFRARDKFEEDRIYRHLEPALAFQLELNRMRNFDLTAIPCANHK  1400
1401  MHLYLGAAKVEVGTEVTDYRFFVRAIIRHSDLVTKEASFEYLQNEGERLL  1450
1451  LEAMDELEVAFNNTNVRTDCNHIFLNFVPTVIMDPSKIEESVRSMVMRYG  1500
1501  SRLWKLRVLQAELKINIRLTPTGKAIPIRLFLTNESGYYLDISLYKEVTD  1550
1551  SRTAQIMFQAYGDKQGPLHGMLINTPYVTKDLLQSKRFQAQSLGTTYIYD  1600
1601  IPEMFRQSLIKLWESMSSQAFLPPPPLPSDILTYTELVLDDQGQLVHMNR  1650
1651  LPGGNEIGMVAWKMTLKSPEYPDGRDIIVIGNDITYRIGSFGPQEDLLFL  1700
1701  RASELARAEGIPRIYVAANSGARIGLAEEIRHMFHVAWVDPEDPYKGYKY  1750
1751  LYLTPQDYKRVSALNSVHCEHVEDEGESRYKITDIIGKEEGLGAENLRGS  1800
1801  GMIAGESSLAYDEIITISLVTCRAIGIGAYLVRLGQRTIQVENSHLILTG  1850
1851  AGALNKVLGREVYTSNNQLGGIQIMHNNGVTHSTVCDDFEGVFTVLHWLS  1900
1901  YMPKSVYSSVPLLNSKDPIDRVIEFVPTKAPYDPRWMLAGRPHPTQKGQW  1950
1951  LSGFFDYGSFSEIMQPWAQTVVVGRARLGGIPVGVVAVETRTVELSIPAD  2000
2001  PANLDSEAKIIQQAGQVWFPDSAFKTYQAIKDFNREGLPLMVFANWRGFS  2050
2051  GGMKDMYDQVLKFGAYIVDGLRECSQPVMVYIPPQAELRGGSWVVIDPTI  2100
2101  NPRHMEMYADRESRGSVLEPEGTVEIKFRRKDLVKTMRRVDPVYIHLAER  2150
2151  LGTPELSARERKELESKLKEREEFLLPIYHQVAVQFADLHDTPGRMQEKG  2200
2201  VINDILDWKTSRTFFYWRLRRLLLEDLVKKKIHNANPELTDGQIQAMLRR  2250
2251  WFVEVEGTVKAYVWDNNKDLVEWLEKQLTEEDGVRSVIEENIKYISRDYV  2300
2301  LKQIRSLVQANPEVAMDSIVHMTQHISPTQRAEVVRILSTMDSPST      2346

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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