Table 1.

The four prion sequences*

	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
MMNNNGNQVSNLSNALRQVNIGNRNSNTTTDQSNINFEFSTG VNNNNNNNSSSNNNNVQNNNSGRNGSQNNDNENNIKNTLEQH 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 QPQSQGMSLNDFQKQQKQAAPKPKKTLKLVSSSGIKLANATKK 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 QSMGASGLAALASQFFKSGNNSQGQGQGQGQGQGQGQGQG QGSFTALASLASSFMNSNNNNQQGQNQSSGGSSFGALASMAS SFMHSNNNQNSNNSQQGYNQSYQNGNQNSQGYNNQQYQGG NGGYQQQQGQSGGAFSSLASMAQSYLGGGQTQSNQQQYNQ QGQNNQQQYQQQGQNYQHQQQGQQQQQGHSSSFSALASM ASSYLGNNSNSNSSYGGQQQANEYGRPQHNGQQQSNEYGRP QYGGNQNSNGQHESFNFSGNFSQQNNNGNQNRY	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 NASKKSSYQQQRNWKQGGNYQQGGYQSYNSNYNNYNNYNN YNNYNNYNNYNKYNGQGYQKSTYKQSAVTPNQSGTPTPSAS 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)

*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 P_bias = 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.