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

NucPred

Fetching Q13085 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MDEPSPLAQPLELNQHSRFIIGSVSEDNSEDEISNLVKLDLLEEKEGSLS    50
  51  PASVGSDTLSDLGISSLQDGLALHIRSSMSGLHLVKQGRDRKKIDSQRDF   100
 101  TVASPAEFVTRFGGNKVIEKVLIANNGIAAVKCMRSIRRWSYEMFRNERA   150
 151  IRFVVMVTPEDLKANAEYIKMADHYVPVPGGPNNNNYANVELILDIAKRI   200
 201  PVQAVWAGWGHASENPKLPELLLKNGIAFMGPPSQAMWALGDKIASSIVA   250
 251  QTAGIPTLPWSGSGLRVDWQENDFSKRILNVPQELYEKGYVKDVDDGLQA   300
 301  AEEVGYPVMIKASEGGGGKGIRKVNNADDFPNLFRQVQAEVPGSPIFVMR   350
 351  LAKQSRHLEVQILADQYGNAISLFGRDCSVQRRHQKIIEEAPATIATPAV   400
 401  FEHMEQCAVKLAKMVGYVSAGTVEYLYSQDGSFYFLELNPRLQVEHPCTE   450
 451  MVADVNLPAAQLQIAMGIPLYRIKDIRMMYGVSPWGDSPIDFEDSAHVPC   500
 501  PRGHVIAARITSENPDEGFKPSSGTVQELNFRSNKNVWGYFSVAAAGGLH   550
 551  EFADSQFGHCFSWGENREEAISNMVVALKELSIRGDFRTTVEYLIKLLET   600
 601  ESFQMNRIDTGWLDRLIAEKVQAERPDTMLGVVCGALHVADVSLRNSVSN   650
 651  FLHSLERGQVLPAHTLLNTVDVELIYEGVKYVLKVTRQSPNSYVVIMNGS   700
 701  CVEVDVHRLSDGGLLLSYDGSSYTTYMKEEVDRYRITIGNKTCVFEKEND   750
 751  PSVMRSPSAGKLIQYIVEDGGHVFAGQCYAEIEVMKMVMTLTAVESGCIH   800
 801  YVKRPGAALDPGCVLAKMQLDNPSKVQQAELHTGSLPRIQSTALRGEKLH   850
 851  RVFHYVLDNLVNVMNGYCLPDPFFSSKVKDWVERLMKTLRDPSLPLLELQ   900
 901  DIMTSVSGRIPPNVEKSIKKEMAQYASNITSVLCQFPSQQIANILDSHAA   950
 951  TLNRKSEREVFFMNTQSIVQLVQRYRSGIRGHMKAVVMDLLRQYLRVETQ  1000
1001  FQNGHYDKCVFALREENKSDMNTVLNYIFSHAQVTKKNLLVTMLIDQLCG  1050
1051  RDPTLTDELLNILTELTQLSKTTNAKVALRARQVLIASHLPSYELRHNQV  1100
1101  ESIFLSAIDMYGHQFCIENLQKLILSETSIFDVLPNFFYHSNQVVRMAAL  1150
1151  EVYVRRAYIAYELNSVQHRQLKDNTCVVEFQFMLPTSHPNRGNIPTLNRM  1200
1201  SFSSNLNHYGMTHVASVSDVLLDNSFTPPCQRMGGMVSFRTFEDFVRIFD  1250
1251  EVMGCFSDSPPQSPTFPEAGHTSLYDEDKVPRDEPIHILNVAIKTDCDIE  1300
1301  DDRLAAMFREFTQQNKATLVDHGIRRLTFLVAQKDFRKQVNYEVDRRFHR  1350
1351  EFPKFFTFRARDKFEEDRIYRHLEPALAFQLELNRMRNFDLTAIPCANHK  1400
1401  MHLYLGAAKVEVGTEVTDYRFFVRAIIRHSDLVTKEASFEYLQNEGERLL  1450
1451  LEAMDELEVAFNNTNVRTDCNHIFLNFVPTVIMDPSKIEESVRSMVMRYG  1500
1501  SRLWKLRVLQAELKINIRLTPTGKAIPIRLFLTNESGYYLDISLYKEVTD  1550
1551  SRTAQIMFQAYGDKQGPLHGMLINTPYVTKDLLQSKRFQAQSLGTTYIYD  1600
1601  IPEMFRQSLIKLWESMSTQAFLPSPPLPSDMLTYTELVLDDQGQLVHMNR  1650
1651  LPGGNEIGMVAWKMTFKSPEYPEGRDIIVIGNDITYRIGSFGPQEDLLFL  1700
1701  RASELARAEGIPRIYVSANSGARIGLAEEIRHMFHVAWVDPEDPYKGYRY  1750
1751  LYLTPQDYKRVSALNSVHCEHVEDEGESRYKITDIIGKEEGIGPENLRGS  1800
1801  GMIAGESSLAYNEIITISLVTCRAIGIGAYLVRLGQRTIQVENSHLILTG  1850
1851  AGALNKVLGREVYTSNNQLGGIQIMHNNGVTHCTVCDDFEGVFTVLHWLS  1900
1901  YMPKSVHSSVPLLNSKDPIDRIIEFVPTKTPYDPRWMLAGRPHPTQKGQW  1950
1951  LSGFFDYGSFSEIMQPWAQTVVVGRARLGGIPVGVVAVETRTVELSIPAD  2000
2001  PANLDSEAKIIQQAGQVWFPDSAFKTYQAIKDFNREGLPLMVFANWRGFS  2050
2051  GGMKDMYDQVLKFGAYIVDGLRECCQPVLVYIPPQAELRGGSWVVIDSSI  2100
2101  NPRHMEMYADRESRGSVLEPEGTVEIKFRRKDLVKTMRRVDPVYIHLAER  2150
2151  LGTPELSTAERKELENKLKEREEFLIPIYHQVAVQFADLHDTPGRMQEKG  2200
2201  VISDILDWKTSRTFFYWRLRRLLLEDLVKKKIHNANPELTDGQIQAMLRR  2250
2251  WFVEVEGTVKAYVWDNNKDLAEWLEKQLTEEDGVHSVIEENIKCISRDYV  2300
2301  LKQIRSLVQANPEVAMDSIIHMTQHISPTQRAEVIRILSTMDSPST      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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