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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.