Electronic Supplementary Material (ESI) for Molecular BioSystems. This journal is © The Royal Society of Chemistry 2015 Supplementary Table 1. 109 D/E-rich repeats containing proteins in yeast UniProt D/E-rich repeats Protein function Residue pI Start number Length Histone, nucleosome and kinetochore proteins O74515 VQPDADEEEEEEEADEMEEEFDEEGEGDEEEEEEDDGDGDGEGDGDGE ASF1_SCHPO Histone chaperone cia1 262 3.57 170 48 Q759F6 EAEDEYPPEQPGVDDEEVDDEDEDEDEDEEGADEEGADEEGASDG ASF1_ASHGO Histone chaperone ASF1 276 3.62 155 45 RKVQTEDEEDDEAEEIDLEAEEEEDEDEEDEDGDEAEEVDEEEEDDDGEPVGA 206 55 SE Q59MV1 DNEEGADEYPPEQPEDEEEEEEEEEEGEEEEEDEDEEDDDDDEDLNGDAVVDL ASF1_CANAL Histone chaperone ASF1 247 3.62 154 58 EKEEI P32447 EGDLYPPEQPGVDDEEEEDDEEEDDDEDDEDDEDDDQEDGEGEAEEAAEEEEE ASF1_YEAST Histone chaperone ASF1 279 3.73 158 62 EEEKTEDNE Q59RN6 TENNEEGDDDDEDEDDDYEQGKLEDEEEEEDELLEIDES CHZ1_CANAL Histone H2A.Z-specific chaperone CHZ1 167 4.02 73 39 Q5AQ47 SSSSSSDNDQDNDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEESEINGN HST1_CANAL NAD-dependent protein deacetylase HST1 657 4.23 68 57 QISL Q8WZM0 IEDEDFQENGIDDEDEEEEEEEAKDEGDEDDEEKGEDDEEDDEEKEGEDGEGE GCN5_YARLI Histone acetyltransferase GCN5 464 4.67 30 71 EEDEEEDEEKKREEEEKY P34218 KEDEDEDEDFTLDDDIEDEQISEENDEEEDTYEEDSDDDEDG SAS3_YEAST Histone acetyltransferase SAS3 831 6.13 755 42 P53165 DDDNSNDNNNDDDDDDDNDDNEDDDDADDDDD SGF73_YEAST SAGA-associated factor 73 657 9.13 131 32 P32657 MTTIEDDEDEFEDEEGEEDSGEDEDEEDFEEDDDYYGS CHD1_YEAST Chromo domain-containing protein 1 1468 6.15 53 38 P40340 AHDPEEDDESFHEEDVDDDEEEEEADEFEDEYLDEDS TBP7_YEAST Tat-binding homolog 7 1379 4.93 116 37 P25293 AALEFEFEEDEEEADEDEDEEEDDDHGLEDDDGESAEEQDDF NAP1_YEAST Nucleosome assembly protein 417 4.09 363 42 Q9HGN2 TEAMTEEASDEDESVDLEEDEEEEDEEDEEGDEEKQEPPS YO48_SCHPO Putative nucleosome assembly protein 244 4.16 198 40 C36B7.08c Q12386 SVDPRDVADEEDEDEEGEDEDEDEDDNDVDNEDENDNDNANE ARP8_YEAST Actin-like protein ARP8 881 4.54 70 42 P54784 DVSEDMDSGEISADELEEEEDEEEDEDEEEKEA ORC1_YEAST Origin recognition complex subunit 1 914 5.42 267 33 Q6CA87 VEEVEEEEPEEEEGPEEEEAPEEEVEGDDEEEVQ SWR1_YARLI Helicase SWR1 1772 4.68 123 34 LKEEMTAVEEEEEEELVEEEEEEEEEEEQEEDEEQEQQEEEEEEQEEEVTSR 275 52 LDNIKVERAEEEDEEDEENGDDEDEDEEEDDAEIEEETETTTP 718 43 AIEEDEEEDDAFVIKEEEEEVEVEDDEEEEKAD 816 33 P31380 QSEHEDDDYEEEDEDYNDEEEDVEYDDGDDDDDDDDEFVAT FUN30_YEAST ATP-dependent helicase FUN30 1131 5.12 497 41 P53115 SDIINEKDADEDEEDDEDELEDGEEDMEEDEASTG INO80_YEAST Putative DNA helicase INO80 1489 5.47 132 35 DNENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDF 240 50 Q74Z27 RELSGAKLEDEGEGEDDDEEEDEDDEDDEDEDEDEDEEEEEEEELEELEDIQL INO80_ASHGO Putative DNA helicase INO80 1414 6.36 178 62 LDDDNDKDF Q6C931 LDLESDDEDQEEEESEFEVSDDEPEDEDEDSEEFA SPT16_YARLI FACT complex subunit SPT16 1003 5.07 931 35 Transcription factors P38915 ENDSKQDLEGNDDGGEDEEDDDDDDEDDDDDEDEREDDDEQEDDDGEDDAARM SPT8_YEAST Transcription factor SPT8 602 4.13 28 56 DKT Q6C9G2 ALYDDEDEDGDGADGFIDEDDEDDEEDDEEGEGNGFIDDEVEVDEEDQDEDGD BFR2_YARLI Protein BFR2 495 4.18 78 75 EDMEDEQDEDESDEELSENEND Q5ACL9 EELDAESAEEEEDEESEDVADDDEDDQESD BFR2_CANAL Protein BFR2 482 4.24 366 43 Q06631 ENEDEEEEEEEEEEKEEDALSFRTDSEDEEVE BFR2_YEAST Protein BFR2 590 4.34 507 51 P36100 KKQAKLNKEEEEEEEEEEDEEEEEEEEMEDVMDDNDETARENA T2EA_YEAST Transcription initiation factor IIE subunit alpha 990 4.81 91 45 Q05021 RSDAETANNVEEEEEEEEEEEEEDEVDEDEEDDEENDEDEDNVHEREHIQE TAF7_YEAST Transcription initiation factor TFIID subunit 7 956 4.88 58 45 O13936 NDKKEDEDNVEENEEEADANEEEEEDEEDDEEDEEDEDESGGGRR SPT5_SCHPO Transcription elongation factor spt5 1063 4.95 134 44 Q5ALX3 EENNEKEQDQEAGQDEEEQDEDEEEEEDDEEEDEEDEVSSRRKRR SPT5_CANAL Transcription elongation factor SPT5 980 5.02 29 47 P27692 KNSDGDTKDEGDNKDEDDDEDDDDDDDDEDDDDEAPTKRRRQER SPT5_YEAST Transcription elongation factor SPT5 720 5.19 606 45 Q6CC84 IKSEEVDKTQDNVEDEDDEEEEEEEEEEEEEDDDEEDVRQRKKPRRE SPT5_YARLI Transcription elongation factor SPT5 683 6.31 526 36 Q59P39 PNTAENDVPGDDEEEEDDDDDDDDDEEEGEQDDEEEEDGSSTSMS EFH1_CANAL Transcriptional regulator EFH1 719 8.00 541 30 P32432 SQNMVEDQDIDDIDDDDDVDDDDDDDDDDDTENGSS SFP1_YEAST Transcription factor SFP1 512 4.46 106 30 Q03213 EDDDDDGDDEGDGRDNEEDSTAEEDEVDDE HOT1_YEAST High-osmolarity-induced transcription protein 1 534 4.53 96 32 P32351 DVDSEEEGEGNDEDDDDGDGDDMDEEESDEEQ IMPX_YEAST Sugar utilization regulatory protein IMP2 346 4.81 95 32 P08638 DEEEEEDEDEEGEEEEEEEELSSKVPENMD LEUR_YEAST Regulatory protein LEU3 886 5.75 678 30 P38114 SNNNDNDNNINDDDDDDDDDDDDDDDDDDDDDNDDDYSNNGADDDEEDDDYDR TBS1_YEAST Uncharacterized transcriptional regulatory 1094 5.12 981 53 protein TBS1 RNA polymerase subunits P38439 NEYEEDDFLVDDDEEEEAAFDDEEDDNEEEEEEEDADEENASR LEO1_YEAST RNA polymerase-associated protein LEO1 464 4.17 382 43 P36070 QNELDELDDDVDDDDLEEVDLEDDDDLDDDSGDDDDENC RRN3_YEAST RNA polymerase I-specific transcription 627 4.44 245 39 initiation factor RRN3 Q5ALX5 SDNEGGEDIEDDDNDYEDEGDDDEEEEGEEEEEEESDEDEISDIGKS SSN2_CANAL Mediator of RNA polymerase II transcription 1665 4.53 679 47 subunit 13 Q05543 YEVGDGDDDDDDGDNDDDDDDDDDDKNYDDRSND RT103_YEAST Regulator of Ty1 transposition protein 103 409 4.63 263 34 P33441 DEKEESDHEYDDQEDEENEEEDDMEVDVED MFT1_YEAST THO complex subunit MFT1 392 4.27 292 30 Ribosomal proteins Q06672 RVVHIEGDDDEDDEDVEDYDDEDEDEEMDEVVPDLVS TSR2_YEAST Pre-rRNA-processing protein TSR2 205 3.97 146 37 P39520 DYQAVTDGEESENEEEESEEEEEDDDEDDDDDDDDGSDSDSDSETSSDDEN IFH1_YEAST Protein IFH1 1085 4.37 114 51 Q12136 LLEDEDEEEVLAMDEDDESIDEREDEEEEEEEELDG SAS10_YEAST Something about silencing protein 10 610 4.45 54 36 Q59VP7 SDDEDEEEEQEQEEQPQEEENNSDDDDDDDDDDDDN ERB1_CANAL Ribosome biogenesis protein ERB1 849 4.46 51 36 SSQKEEDNKESDNEDEDEEEDNDDDDDDDEPETSS 571 35 RNA processing Q751K8 RARGADDGDVDMLDDDDEEEDDDEDEDDEDSDSDVEIIIG FIP1_ASHGO Pre-mRNA polyadenylation factor FIP1 323 4.06 60 40 P38996 TEEEEEEEHQQKGGNDDDDDDNEEEEEEEEDDDDDDDDDDDDEEEEEEEEEEG NAB3_YEAST Nuclear polyadenylated RNA-binding protein 3 802 4.25 86 63 NDNSSVGSDS Q6C233 DGNGQLVDDYDDDEDDDDEDDEIDEEVDDDLIADENAVDV SQS1_YARLI Protein SQS1 812 4.31 207 40 Q5AFT3 LCFLPFEVIEDDEDEEEEEEEDEEDEDEGEENIDDTKEKKDKK CFT1_CANAL Protein CFT1 1420 4.94 149 43 KIEEKEDNKDDDDNDDDDEDDLYKEEEEEETQ 454 32 P38798 PGKHQAKQDESEDEDDEDDDEDDDDDDDDDDDDGEEGDEDDDEDDDDEDDDDE NMD2_YEAST Nonsense-mediated mRNA decay protein 2 1089 4.85 876 73 EEEDSDSDLEYGGDLDADRD Q9P6R9 GEEDDDENEEDEEDSEETSESEEDESVNDEK CWC22_SCHPO Pre-mRNA-splicing factor cwf22 887 8.66 368 31 Q6C8C5 KEILGDSDDEEEDDSEAEEEADDEEEEEGDEEEEAQAST CWC22_YARLI Pre-mRNA-splicing factor CWC22 954 8.94 464 39 P11745 SKFDDLEVDDFEEVDSEDEEGEDEEDEDEDEKLEEIETERLEKE RNA1_YEAST Ran GTPase-activating protein 1 407 4.39 345 44 P53107 GYEAIEEDEEEDEEEDEEEGKDGEERKEEEEEENKLEDKD YRB30_YEAST Ran-specific GTPase-activating protein 30 440 4.55 337 40 Q6CFG6 APKKAKVEEEESDDDEEDEEDDDDDDDSDDDDSDDSGEPQMEIK EFG1P_YARLI rRNA-processing protein EFG1 305 4.44 218 44 O74363 FADLSVLEEDDDDEDEDEELEGEKEEEEEEKEKPEISN YND2_SCHPO G-patch and R3H domain-containing protein 695 4.65 257 38 C30B4.02c Q6CEW9 KGDDEIDEDEDEEEESENKKDDDNEEAEEDEEDPVIED MRD1_YARLI Multiple RNA-binding domain-containing 828 4.98 192 38 protein 1 Q6CAC9 EQELEEDDIEGAGEEEEEVDEEQEEEEDADDAEEDAEDDSETDKYD UTP25_YARLI U3 small nucleolar RNA-associated protein 25 641 5.14 46 46 C4R2K0 KLEEEQEREEEELQEEDEDEDEEDEEINLEDFESDDESHDD UTP25_PICPG U3 small nucleolar RNA-associated protein 25 697 5.56 102 41 Q6CFT1 DFFELAGKTDDGDDEEEDEEDEEEEEEEKE ESF2_YARLI Pre-rRNA-processing protein ESF2 324 5.33 65 30 Q6C2F4 DFENSEEEGEDDEDEAEDDDDEDVEIHEVDEDEDESGDKS NOP14_YARLI Probable nucleolar complex protein 14 832 5.42 360 40 Q6C2Q7 VDPVRDQQEDKMEVEDEEEDEEEDEEDEEEDEEDEEDEEEKEEDDDDDDDEEE NOP12_YARLI Nucleolar protein 12 509 5.47 30 63 IEEPVIKKSK Q59X38 EKEDGEAVEDTDEEEEEVEIEDGDEDQEDEEEEEDEDLKAQKE PESC_CANAL Pescadillo homolog 587 6.13 458 43 Q6C1W9 EGAEGNDEEDDEDDDDEEEEEEESVSAEPEVVE TRM10_YARLI tRNA (guanine(9)-N1)-methyltransferase 371 5.00 318 33 RNA helicase Q59MW2 DEEEEEEETDESEHESSQDEDINEEEPEEEDED DBP6_CANAL ATP-dependent RNA helicase DBP6 606 4.81 39 33 P32892 MNNGDENQSEEEEEEEEKEEEEEEEEEQEEMTLEKGGKDDE DRS1_YEAST ATP-dependent RNA helicase DRS1 752 5.47 161 41 Q59ZH9 DVEDNETPEVEDEKPTEQEEEEEEEEEEEEEEEEEEEEEEFAGFEDDENNQED MAK5_CANAL ATP-dependent RNA helicase MAK5 782 5.75 97 55 AN Translation Q12532 KVKTSGNEDNGDDDEEEEEEEEEEEEEEEEEEEEEEEEKEEEEKEEEQQQDED TAE2_YEAST Translation-associated element 2 1038 5.47 706 59 DSNEVN Protein-protein interaction Q59S52 KDSGYNSQNLDDEDEDDEDDDEDDEDEEEEDEDDYDDHDLGTINEGI MDM12_CANAL Mitochondrial distribution and morphology 428 3.90 97 47 protein 12 Q12500 EEVGNSEDNEDDDTDEDSEDDDDDGGDDDDSEDDDDDDDGEGDENGDDGEGDE AVL9_YEAST Late secretory pathway protein AVL9 764 4.20 596 57 NGDD P38835 TTKDAEDHGEDDGDGDDGEDDDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDD YHT1_YEAST PH domain-containing protein YHR131C 850 5.02 793 57 GQIT P40021 NDESSENGDGDNDHDDDYDDDDDDDDDDDESE ZRG8_YEAST Zinc-regulated protein 8 1076 4.60 420 32 Q08979 DEDEFEYEDDEEDEDDGEEEQDAGPLEGDEDEESESDDD KEL3_YEAST Kelch repeat-containing protein 3 651 4.88 518 39 Q99299 IFDGVTVRADEEEEEDEDDEDDEEEEEENDDEEDEEDEEDDEDDEEEEEKRKE AIM44_YEAST Altered inheritance of mitochondria protein 44 758 6.31 642 60 GEGRNLA P48362 EEMPSKNAEEEEEEESEEEEDDDEEDEIVE HGH1_YEAST FAM203 family protein HGH1 394 4.48 363 30 Ubiquitin related proteins Q10435 GSESYERDEDVDEEEEEDDDENNDEGDDEDENENDELRSEN YDE1_SCHPO Probable ubiquitin fusion degradation protein 1647 4.82 240 41 C12B10.01c O74201 VRETVENSWNDDDDEEEEEEDEDEAEDEDDDDDDNIDE UBC2_CANAL Ubiquitin-conjugating enzyme E2 2 179 3.92 141 38 P06104 VKETVEKSWEDDMDDMDDDDDDDDDDDDDEA UBC2_YEAST Ubiquitin-conjugating enzyme E2 2 172 4.02 141 31 Q12161