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Table 1 The four prion sequences*

From: A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes

  Notable single-residue bias counts for prion determinant domain (Pbias in brackets) Notable LPSs (for whole sequence)
Prion sequence: Ure2p (YNL229C) Prion determinant is residues 1-65   
MM NNNGNQVSNLSNALRQVNIGNRNSNTTTDQSNINFEFSTG VNNNNNNNSSSNNNNVQNNNSGR NGSQNNDNENNIKNTLEQH RQQQQAFSDMSHVEYSRITKFFQEQPLEGYTLFSHRSAPNGFKV AIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGM DNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLF FQTSGHAPMIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVE MALAERREALVMELDTENAAAYSAGTTPMSQSRFFDYPVWLV GDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHMMRRPA VIKALRGE N 27/65 (1.9 × 10-16) N, 33 in 2 to 78 (1.2 × 10-16) Q, 7 in 82 to 108 (5.5 × 10-5) {QN}, 43 in 2 to 88 (1.2 × 10-20) {DERK}, 10 in 2 to 88 (1.6 × 10-3) {VILM}, 4 in 2 to 88 (1.8 × 10-3)
Prion sequence: Sup35p (YDR172W) Prion determinant is residues 1-123   
MSDSNQGNNQQNYQQYSQNGNQQQGNNRYQGYQAYNAQA QPAGGYYQNYQGYSGYQQGGYQQYNPDAGYQQQYNPQGG YQQYNPQGGYQQQFNPQGGRGNYKNFNYNNNLQGYQAGF QPQSQ GMSLNDFQKQQKQAAPKPKKTLKLVSSSGIKLANATKK VGTKPAESDKKEEEKSAETKEPTKEPTKVEEPVKKEEKPVQTEE KTEEKSELPKVEDLKISESTHNTNNANVTSADALIKEQEEEVDDE VVNDMFGGKDHVSLIFMGHVDAGKSTMGGNLLYLTGSVDKRTI EKYEREAKDAGRQGWYLSWVMDTNKEERNDGKTIEVGKAYFE TEKRRYTILDAPGHKMYVSEMIGGASQADVGVLVISARKGEYET GFERGGQTREHALLAKTQGVNKMVVVVNKMDDPTVNWSKER YDQCVSNVSNFLRAIGYNIKTDVVFMPVSGYSGANLKDHVDPK ECPWYTGPTLLEYLDTMNHVDRHINAPFMLPIAAKMKDLGTIVE GKIESGHIKKGQSTLLMPNKTAVEIQNIYNETENEVDMAMCGEQ VKLRIKGVEEEDISPGFVLTSPKNPIKSVTKFVAQIAIVELKSIIAA GFSCVMHVHTAIEEVHIVKLLHKLEKGTNRKSKKPPAFAKKGM KVIAVLETEAPVCVETYQDYPQLGRFTLRDQGTTIAIGKIVKIAE Q 35/123 (9.6 × 10-21) Y 20/123 (4.9 × 10-9) G 21/123 (5.9 × 10-7) N 20/123 (3.7 × 10-5) Q, 39 in 5 to 134 (7.3 × 10-24) Y, 20 in 12 to 112 (1.4 × 10-10) E, 23 in 166 to 248 (1.7 × 10-9) K, 23 in 130 to 218 (5.5 × 10-8) G, 20 in 19 to 122 (1.5 × 10-7) N, 20 in 4 to 108 (3.6 × 10-6) V, 47 in 188 to 653 (4.5 × 10-5) {QN}, 60 in 4 to 134 (6.1 × 10-26) {DERK}, 6 in 4 to 134 (8.0 × 10-9) {VILM}, 2 in 4 to 134 (3.5 × 10-12)
Prion sequence: Rnq1p (YCL028W) Prion determinant is residues 153-405   
MDTDKLISEAESHFSQGNHAEAVAKLTSAAQSNPNDEQMSTIES LIQKIAGYVMDNRSGGSDASQDRAAGGGSSFMNTLMADSKGSS QTQLGKLALLATVMTHSSNKGSSNRGFDVGTVMSMLSGSGGGS QSMGASGLAALASQFFKSGNNSQG QGQGQGQGQGQGQGQG QGSFTALASLASSFMNSNNNNQQGQNQSSGGSSFGALASMAS SFMHSNNNQNSNNSQQGYNQSYQNGNQNSQGYNNQQYQGG NGGYQQQQGQSGGAFSSLASMAQSYLGGGQTQSNQQQYNQ QGQNNQQQYQQQGQNYQHQQQGQQQQQGHSSSFSALASM ASSYLGNNSNSNSSYGGQQQANEYGRPQHNGQQQSNEYGRP QYGGNQNSNGQHESFNFSGNFSQQNNNGNQ NRY Q 66/253 (4.2 × 10-35) G 42/253 (6.6 × 10-12) N 41/253 (7.4 × 10-9) Q, 67 in 152 to 401 (2.1 × 10-36) G, 60 in 50 to 399 (3.1 × 10-17) N, 41 in 185 to 402 (8.3 × 10-11) {QN}, 110 in 149 to 402 (3.2 × 10-43) {DERK}, 5 in 149 to 402 (1.2 × 10-23) {VILM}, 12 in 149 to 402 (8.9 × 10-17)
Prion sequence: New1p (YPL226W) Prion determinant is residues 1-153   
MPPKKFKDLNSFLDDQPKDPNLVASPFGGYFKNPAADAGSN NASKKSSYQQQRNWKQGGNYQQGGYQSY NSNYNNYNNYNN YNNYNNYNNYNKYN GQGYQKSTYKQSAVTPNQSGTPTPSAS TTSLTSLNEKLSNLELTPISQFLSKIPECQSITDCKNQIKLIIEEF GKEGNSTGEKIEEWKIVDVLSKFIKPKNPSLVRESAMLIISNIAQF FSGKPPQEAYLLPFFNVALDCISDKENTVKRAAQHAIDSLLNCFP MEALTCFVLPTILDYLSSGAKWQAKMAALSVVDRIREDSANDL LELTFKDAVPVLTDVATDFKPELAKQGYKTLLDYVSILDNLDLS PRYKLIVDTLQDPSKVPESVKSLSSVTFVAEVTEPSLSLLVPILNR SLNLSSSSQEQLRQTVIVVENLTRLVNNRNEIESFIPLLLPGIQKV VDTASLPEVRELAEKALNVLKEDDEADKENKFSGRLTLEEGRDF LLDHLKDIKADDSCFVKPYMNDETVIKYMSKILTVDSNVNDWK RLEDFLTAVFGGSDSQREFVKQDFIHNLRALFYQEKERADEDEGI EIVNTDFSLAYGSRMLLNKTNLRLLKGHRYGLCGRNGAGKSTL MRAIANGQLDGFPDKDTLRTCFVEHKLQGEEGDLDLVSFIALDE ELQSTSREEIAAALESVGFDEERRAQTVGSLSGGWKMKLELARA MLQKADILLLDEPTNHLDVSNVKWLEEYLLEHTDITSLIVSHDSG FLDTVCTDIIHYENKKLAYYKGNLAAFVEQKPEAKSYYTLTDSN AQMRFPPPGILTGVKSNTRAVAKMTDVTFSYPGAQKPSLSHVSC SLSLSSRVACLGPNGAGKSTLIKLLTGELVPNEGKVEKHPNLRIG YIAQHALQHVNEHKEKTANQYLQWRYQFGDDREVLLKESRKIS EDEKEMMTKEIDIDDGRGKRAIEAIVGRQKLKKSFQYEVKWKY WKPKYNSWVPKDVLVEHGFEKLVQKFDDHEASREGLGYRELIP SVITKHFEDVGLDSEIANHTPLGSLSGGQLVKVVIAGAMWNNPH LLVLDEPTNYLDRDSLGALAVAIRDWSGGVVMISHNNEFVGAL CPEQWIVENGKMVQKGSAQVDQSKFEDGGNADAVGLKASNLA KPSVDDDDSPANIKVKQRKKRLTRNEKKLQAERRRLRYIEWLSS PKGTPKPVDTDDEED N 26/153 (1.4 × 10-6) N, 16 in 69 to 94 (9.8 × 10-14) Y, 13 in 60 to 103 (1.2 × 10-9) L, 74 in 253 to 738 (2.4 × 10-5) Q, 11 in 49 to 112 (2.9 × 10-5) R, 7 in 1149 to 1173 (7.5 × 10-5) {QN}, 27 in 49 to 99 (1.8 × 10-14) {DERK}, 3 in 49 to 99 (5.3 × 10-4) {VILM}, 0 in 49 to 99 (8.1 × 10-7)
  1. *The prion determinant regions (found from experiment) are in bold, the LPSs for the whole protein sequence for the most pronounced single-amino-acid bias, are underlined. All biases with a Pbias = 1 × 10-4 are listed for each prion sequence. As examples, the counts for the sets of residues {DERK} and {VILM} that correspond to the {QN} lowest probability sequence are listed for each prion.