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

NucPred

Fetching P11497 from www.uniprot.org...

The NucPred score for your sequence is 0.31 (see score help below)

   1  MDEPSPLAKTLELNQHSRFIIGSVSEDNSEDEISNLVKLDLEEKEGSLSP    50
  51  ASVSSDTLSDLGISALQDGLAFHMRSSMSGLHLVKQGRDRKKIDSQRDFT   100
 101  VASPAEFVTRFGGNKVIEKVLIANNGIAAVKCMRSIRRWSYEMFRNERAI   150
 151  RFVVMVTPEDLKANAEYIKMADHYVPVPGGANNNNYANVELILDIAKRIP   200
 201  VQAVWAGWGHASENPKLPELLLKNGIAFMGPPSQAMWALGDKIASSIVAQ   250
 251  TAGIPTLPWSGSGLRVDWQENDFSKRILNVPQDLYEKGYVKDVDDGLKAA   300
 301  EEVGYPVMIKASEGGGGKGIRKVNNADDFPNLFRQVQAEVPGSPIFVMRL   350
 351  AKQSRHLEVQILADQYGNAISLFGRDCSVQRRHQKIIEEAPAAIATPAVF   400
 401  EHMEQCAVKLAKMVGYVSAGTVEYLYSQDGSFYFLELNPRLQVEHPCTEM   450
 451  VADVNLPAAQLQIAMGIPLFRIKDIRMMYGVSPWGDAPIDFENSAHVPCP   500
 501  RGHVIAARITSENPDEGFKPSSGTVQELNFRSNKNVWGYFSVAAAGGLHE   550
 551  FADSQFGHCFSWGENREEAISNMVVALKELSIRGDFRTTVEYLIKLLETE   600
 601  SFQLNRIDTGWLDRLIAEKVQAERPDTMLGVVCGALHVADVNLRNSISNF   650
 651  LHSLERGQVLPAHTLLNTVDVELIYEGIKYVLKVTRQSPNSYVVIMNGSC   700
 701  VEVDVHRLSDGGLLLSYDGSSYTTYMKEEVDRYRITIGNKTCVFEKENDP   750
 751  SVMRSPSAGKLIQYIVEDGGHVFAGQCYAEIEVMKMVMTLTAVESGCIHY   800
 801  VKRPGAALDPGCVIAKMQLDNPSKVQQAELHTGSLPQIQSTALRGEKLHR   850
 851  VFHYVLDNLVNVMNGYCLPDPFFSSKVKDWVERLMKTLRDPSLPLLELQD   900
 901  IMTSVSGRIPLNVEKSIKKEMAQYASNITSVLCQFPSQQIANILDSHAAT   950
 951  LNRKSEREVFFMNTQSIVQLVQRYRSGIRGHMKAVVMDLLRQYLRVETQF  1000
1001  QNGHYDKCVFALREENKSDMNTVLNYIFSHAQVTKKNLLVTMLIDQLCGR  1050
1051  DPTLTDELLNILTELTQLSKTTNAKVALRARQVLIASHLPSYDVRHNQVE  1100
1101  SIFLSAIDMYGHQFCIENLQKLILSETSIFDVLPNFFYHSNQVVRMAALE  1150
1151  VYVRRAYIAYELNSVQHRQLKDNTCVVEFQFMLPTSHPNRGNIPTLNRMS  1200
1201  FASNLNHYGMTHVASVSDVLLDNAFTPPCQRMGGMVSFRTFEDFVRIFDE  1250
1251  VMGCFCDSPPQSPTFPESGHTSLYDEDKVPRDEPIHILNVAIKTDGDIED  1300
1301  DRLAAMFREFTQQNKATLVEHGIRRLTFLVAQKDFRKQVNCEVDQRFHRE  1350
1351  FPKFFTFRARDKFEEDRIYRHLEPALAFQLELNRMRNFDLTAIPCANHKM  1400
1401  HLYLGAAKVEVGTEVTDYRFFVRAIIRHSDLVTKEASFEYLQNEGERLLL  1450
1451  EAMDELEVAFNNTNVRTDCNHIFLNFVPTVIMDPSKIEESVRSMVMRYGS  1500
1501  RLWKLRVLQAELKINIRLTTTGKAIPIRLFLTNESGYYLDISLYKEVTDS  1550
1551  RTAQIMFQAYGDKQGPLHGMLINTPYVTKDLLQSKRFQAQSLGTTYIYDI  1600
1601  PEMFRQSLIKLWESMSTQAFLPSPPLPSDILTYTELVLDDQGQLVHMNRL  1650
1651  PGGNEIGMVAWKMSLKSPEYPDGRDVIVIGNDITYRIGSFGPQEDLLFLR  1700
1701  ASELARAEGIPRIYVAANSGARIGLAEEIRHMFHVAWVDSEDPYKGYKYL  1750
1751  YLTPQDYKRVSALNSVHCEHVEDEGESRYKITDIIGKEEGLGAENLRGSG  1800
1801  MIAGESSLAYDEIITISLVTCRAIGIGAYLVRLGQRTIQVENSHLILTGA  1850
1851  GALNKVLGREVYTSNNQLGGIQIMHNNGVTHCTVCDDFEGVFTVLHWLSY  1900
1901  MPKNVHSSVPLLNSKDPIDRIIEFVPTKAPYDPRWMLAGRPHPTQKGQWL  1950
1951  SGFFDYGSFSEIMQPWAQTVVVGRARLGGIPVGVVAVETRTVELSVPADP  2000
2001  ANLDSEAKIIQQAGQVWFPDSAFKTYQAIKDFNREGLPLMVFANWRGFSG  2050
2051  GMKDMYDQVLKFGAYIVDGLRECSQPVMVYIPPQAELRGGSWVVIDPTIN  2100
2101  PRHMEMYADRESRGSVLEPEGTVEIKFRKKDLVKTMRRVDPVYIRLAERL  2150
2151  GTPELSPTERKELESKLKEREEFLIPIYHQVAVQFADLHDTPGRMQEKGV  2200
2201  INDILDWKTSRTFFYWRLRRLLLEDLVKKKIHSANPELTDGQIQAMLRRW  2250
2251  FVEVEGTVKAYVWDNNKDLVEWLEKQLTEEDGVRSVIEENIKYISRDYVL  2300
2301  KQIRSLVQANPEVAMDSIVHMTQHISPTQRAEVVRILSTMDSPST       2345

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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