# Complex name	Source	Complex members (systematic name)	Complex members (standard gene name)	known in GO	known in lit.	comments	pubmed
Checkpoint sliding clampandloader	Dave	YOR368W; YLR288C; YPL194W; YER173W					
Yku interactors	Dave	YBR274W; YBR136W; YDL101C; YDR217C; YOR033C; YOR368W; YLR288C; YPL194W; YER173W					
Lydall lab interesting genes	Dave	YBR274W; YBR136W; YDL101C; YDR217C; YOR033C; YOR368W; YLR288C; YPL194W; YER173W; YIL009C-A; YLR233C; TLC1; YLR318W; YMR106C; YMR284W; YDR369C; YMR224C; YNL250W; YBL088C; YHR031C; YML061C; YMR080C; YHR077C; YGR072W; YDR206W					
nuclear telomere cap complex (GO)	Copied from lower down	YBR275C; YDL042C; YDL220C; YDR082W; YDR227W; YGR099W; YLR010C; YLR150W; YLR442C; YLR453C; YNL216W	RIF1; SIR2; CDC13; STN1; SIR4; TEL2; TEN1; STM1; SIR3; RIF2; RAP1	YES			
waif/stray repair proteins	Dave	YJL092W;  YLR032W; YER095W; YML061C; YKL113C;					
Chk1 targets	Greg	YPR145W; YBR252W; YJR082C; YBR177C; 					
MTC/RTCs	Dave	YBR255W; YDR128W; YEL033W; YGL226W; YHR151C;  YJL123C; YKL098W; YNL254C; YOL138C; YOR118W; YPL183W-A;  YBR147W;  YHR087W;  					
SEA complex (RTC1/MTC5 etc)	Dave	YOL138C; YBL104C; YDR128W; YJR138W; 					
adjacent to STN1/TEN1	Dave	YDR083W; YDRO81C; YLR009W; 				adjacent to STN1	
NMD genes	Dave	YMR080C; YHR077C; YGR072W; 					
Unfolded protein response	Dave	YHR079C; YFL031W; YJL034W;					
Spermidine synthase complex	Conor	YKL184W; YOL052C; YPR069C; 	SPE1; SPE2; SPE3				
Spp381-Prp38 complex	curated consensus	YBR152W; YGR075C	SPP381; PRP38	NO	YES	genetic interaction + two-hybrid interaction	9858581
Asf1-Rad53 complex	curated consensus	YJL115W; YPL153C	ASF1; RAD53	NO	YES		11331602; 11172707
Pan1-End3 complex	curated consensus	YIR006C; YNL084C	PAN1; END3	NO	YES		9234686
Sod1-Css1 heterodimer	curated consensus	YJR104C; YMR038C	SOD1; CCS1	NO	YES		11101286
HAT-A4 complex	curated consensus	YBR010W; YBR009C; YNL030W; YEL056W; YPL001W; YLL022C; YOL054W; YNL031C	HHT1; HHF1; HHF2; HAT2; HAT1; HIF1; PSH1; HHT2	NO	YES		9575221
Ste11-Ste50 complex	curated consensus	YLR362W; YCL032W	STE11; STE50	NO	YES		9742096; 9738877
Cdc48-Ufd1-Npl4 complex	curated consensus	YDL126C; YBR170C; YGR048W	CDC48; NPL4; UFD1	NO	YES		11847109
Cdc48-Shp1 complex	curated consensus	YBL058W; YDL126C	SHP1; CDC48	NO	YES		11847109
Sit4-Sap155 complex	curated consensus	YDL047W; YFR040W	SIT4; SAP155	NO	YES		8649382
Ste12-Dig1-Dig2 complex	curated consensus	YPL049C; YHR084W; YDR480W	DIG1; STE12; DIG2	NO	YES		9094309
Rvs161-Rvs167 complex	curated consensus	YCR009C; YDR388W	RVS161; RVS167	NO	YES		9434108; 11096097
She2-She3-Myo4 complex	curated consensus	YAL029C; YBR130C; YKL130C	MYO4; SHE3; SHE2	NO	YES		10792032; 11101531 
Ubp3-Bre5 complex	curated consensus	YNR051C; YER151C	BRE5; UBP3	NO	YES		12778054
Rad6-Rad18 complex	curated consensus	YGL058W; YCR066W	RAD6; RAD18	NO	YES	"in GO only part of large proteasome complex, but literature states that RAD18 and RAD6 form a heterodimer that can associate with the proteasome"	9287349
Rtt109-Vps75 complex	curated consensus	YLL002W; YNL246W	RTT109; VPS75	NO	YES		18036332
Csm3-Tof1 complex	curated consensus	YMR048W; YNL273W	CSM3; TOF1	NO	YES		14742714
Psr2-Psr1-Whi2 complex	curated consensus	YLR019W; YLL010C; YOR043W	PSR2; PSR1; WHI2	NO	YES	Psr2 is functionally redundant with Psr1p	12090248
Rad23-Png1 complex	curated consensus	YEL037C; YPL096W	RAD23; PNG1	NO	YES		15351714
Tim44-Ssc1 heterodimer	curated consensus	YIL022W; YJR045C	TIM44; SSC1	NO	YES		12677068
Dop1-Mon2 complex	curated consensus	YDR141C; YNL297C	DOP1; MON2	NO	YES		16301316
Rsp5-Ubp2-Rup1 deubiquitinating enzyme complex	curated consensus	YER125W; YOR124C; YOR138C	RSP5; UBP2; RUP1	NO	YES		15933713
Pho80-Pho81-Pho85 CDK-cyclin complex	curated consensus	YGR233C; YOL001W; YPL031C	PHO81; PHO80; PHO85	NO	YES		7939631; 17412959
Trm112-Trm11 complex	curated consensus	YNR046W; YOL124C	TRM112; TRM11	NO	YES		18657261
Dug2-Dug3 complex	curated consensus	YBR281C; YNL191W	DUG2; DUG3	NO	YES		17179087
Dph1-Dph2-Dph3 complex	curated consensus	YBL071W-A; YIL103W; YKL191W	KTI11; DPH1; DPH2	NO	YES	Dph3 is not entirely clear whether it is part of the same complex	15485916
Scs2-Opi1 complex	curated consensus	YER120W; YHL020C	SCS2; OPI1	NO	YES		15455074; 15192221
Ula1-Uba3 enzyme complex	curated consensus	YPL003W; YPR066W	ULA1; UBA3	NO	YES	Ula1-Uba3 form an E1 enzyme pair to activate Rub1p	9545234
Nam1-Sls1 complex	curated consensus	YDL044C; YLR139C	MTF2; SLS1	NO	YES		12637560
ER SNARE Use1	curated consensus	YDR498C; YLR440C; YNL258C; YKL196C; YLR268W; YGL145W; YOR075W; YGL098W	SEC20; SEC39; DSL1; YKT6; SEC22; TIP20; UFE1; USE1	NO	YES	"literature seems a bit confusing as to which complexes are specifically formed, but overall it seems that all members associate with oneanother at a given point (although Ykt6 is the most unsure, only shown that it can functionally replace Sec22)"	12853481; 9214619; 15958492; 12221135 
Pba1-Pba2 complex	curated consensus	YKL206C; YLR199C; YBR173C	ADD66; PBA1; UMP1	NO	YES	Ump1 which is loosely associated with Pba1-Pba2 functions as an assembly factor	17431397
Gyl1-Gyp5 complex	curated consensus	YMR192W; YPL249C	GYL1; GYP5	NO	YES		15331637
Rtg1-Rtg3 bHLH-Zip complex	curated consensus	YBL103C; YOL067C	RTG3; RTG1	NO	YES		9032238
Sit4-Sap190 complex	curated consensus	YDL047W; YKR028W	SIT4; SAP190	NO	YES		8649382
Rtt103-Rai1-Rat1 complex	curated consensus	YDR289C; YGL246C; YOR048C	RTT103; RAI1; RAT1	NO	YES		15565157
R2TP complex	curated consensus	YCR060W; YHR034C; YDR190C; YPL235W	TAH1; PIH1; RVB1; RVB2	NO	YES		15766533
adenylyl cyclase complex	curated consensus	YJL005W; YNL138W	CYR1; SRV2	NO	YES		2184942
Ssc1-Mge1 complex	curated consensus	YJR045C; YOR232W	SSC1; MGE1	NO	YES		9048947
Dcs1-Dcs2 heterodimer	curated consensus	YLR270W; YOR173W	DCS1; DCS2	NO	YES		15240832
Kap114-Nap1 histone complex	curated consensus	YBL003C; YGL241W; YBL002W; YOL012C; YKR048C	HTA2; KAP114; HTB2; HTZ1; NAP1	NO	YES		12456659
Grh1-Bug1 complex	curated consensus	YDL099W; YDR517W	BUG1; GRH1	NO	YES		17261844
Mad1-Mad2 complex	curated consensus	YGL086W; YJL030W	MAD1; MAD2	NO	YES		10436016
Ic-CPY complex	curated consensus	YLR178C; YMR297W	TFS1; PRC1	NO	YES		4612529; 9521655
Mlh2-Mlh1 heterodimer	curated consensus	YLR035C; YMR167W	MLH2; MLH1	NO	YES		10570173
Sac3-Thp1 complex	curated consensus	YDR159W; YOL072W	SAC3; THP1	NO	YES		12411502
tRNA methyltransferase complex	curated consensus	YDL201W; YDR165W	TRM8; TRM82	NO	YES		12403464
Tlg1 SNARE complex	curated consensus	YBL050W; YDR468C; YGL095C; YOL018C	SEC17; TLG1; VPS45; TLG2	NO	YES		10397773
ribosome-associated complex	curated consensus	YGR285C; YHR064C; YJL080C	ZUO1; SSZ1; SCP160	NO	YES	Scp160 is not known to be in the complex	11274393
Trm9-Trm112 complex	curated consensus	YML014W; YNR046W	TRM9; TRM112	NO	YES		18657261
prohibitin complex	curated consensus	YGR132C; YGR231C	PHB1; PHB2	NO	YES		15525670
succinyl-CoA ligase	curated consensus	YGR244C; YOR142W	LSC2; LSC1	NO	YES		9874242
Gsp1-Prp20 complex	curated consensus	YGL097W; YLR293C; YOR185C	SRM1; GSP1; GSP2	NO	YES	GSP2 is almost identical to Gsp1p	8455603
Kic1-Sog2 complex	curated consensus	YHR102W; YOR353C	KIC1; SOG2	NO	YES		12972564
Nrd1-Nab3-Sen1 termination complex	curated consensus	YLR430W; YNL251C; YPL190C; YMR239C	SEN1; NRD1; NAB3; RNT1	NO	YES	Rnt1 is not known to be in the complex	18660819
Ssk1-Ssk2 complex	curated consensus	YLR006C; YNR031C	SSK1; SSK2	NO	YES		9482735
Vti1-Pep12 complex	curated consensus	YMR197C; YOR036W	VTI1; PEP12	NO	YES		9199167
Pcl7-Pho85 CDK-cyclin complex	curated consensus	YPL031C; YIL050W	PHO85; PCL7	NO	YES		11069666
Prs1-Prs3 heterodimer	curated consensus	YHL011C; YKL181W	PRS3; PRS1	NO	YES		10212224
Vac14-Fig4 complex	curated consensus	YLR386W; YNL325C	VAC14; FIG4	NO	YES		14528018
Cpr6-Hsc82-Sti1-Hsp82 complex	curated consensus	YLR216C; YMR186W; YOR027W; YPL240C	CPR6; HSC82; STI1; HSP82	NO	YES	not entirely clear whether Cpr6 and Sti1 can bind at the same time to Hsp82p. Hsc82 is 97% identical to Hsp82p	9927435
Bur1-Bur2 CDK-cyclin complex	curated consensus	YPR161C; YLR226W	SGV1; BUR2	NO	YES		10982824
Bub1-Bub3 kinase complex	curated consensus	YGR188C; YOR026W	BUB1; BUB3	NO	YES		7969164
Sis2-Ykl088w-Vhs3 complex	curated consensus	YKR072C; YKL088W; YOR054C	SIS2; CAB3; VHS3	NO	YES		14690591
putative Slu7-Prp18 complex	curated consensus	YDR088C; YGR006W	SLU7; PRP18	NO	YES?	SLU7 seems to recruit PRP18 to the spliceosome	12212850
COMA complex	curated consensus	YBR107C; YBR211C; YDR318W; YJR135C; YGR179C; YDR254W; YPL018W; YLR381W; YDR383C; YLR315W; YPR046W	IML3; AME1; MCM21; MCM22; OKP1; CHL4; CTF19; CTF3; NKP1; NKP2; MCM16	subcomplex not defined in GO	YES	together with MIND and Ndc80 constitutes three independent platforms onto which outer kinetochore protons can assemble	14633972
TEL complex	curated consensus	YDR227W; YDL042C	SIR4; SIR2	subcomplex not defined in GO	YES		11500379
nucleoporin Nup84 subcomplex	curated consensus	YGL100W; YDL116W; YGL092W; YKL057C; YJR042W; YLR208W	SEH1; NUP84; NUP145; NUP120; NUP85; SEC13	subcomplex not defined in GO	YES		8565072
Dcp1-Dcp2 decapping enzyme complex	curated consensus	YBR094W; YEL015W; YOL149W; YNL118C	PBY1; EDC3; DCP1; DCP2	subcomplex not defined in GO	YES	Pby1 is not known to be in the same complex	15225544
Ulp1 nuclear pore complex	curated consensus	YLR347C; YMR308C; YPL020C	KAP95; PSE1; ULP1	subcomplex not defined in GO	YES		12471376
TFIIK complex	curated consensus	YDL108W; YDR460W; YPR025C	KIN28; TFB3; CCL1	subcomplex not defined in GO	YES		8001136
Spt6-Spn1 elongator factor complex	curated consensus	YGR116W; YPR133C	SPT6; SPN1	subcomplex not defined in GO	YES		12242279
cleavage factor I complex	curated consensus	YDR228C; YGL044C; YOR250C; YMR061W	PCF11; RNA15; CLP1; RNA14	subcomplex not defined in GO	YES	missing Hrp1p	11344258
Cln-Cdc28 protein kinase complex	curated consensus	YMR199W; YBR160W; YKR091W; YLR210W; YLR079W; YDL155W; YPL256C; YBR135W	CLN1; CDC28; SRL3; CLB4; SIC1; CLB3; CLN2; CKS1	subcomplex not defined in GO	YES		8402888; 9841670
Isw2-Itc1 complex	curated consensus	YGL133W; YOR304W	ITC1; ISW2	subcomplex not defined in GO	YES		11238944
nucleoporin Nup82 subcomplex	curated consensus	YIL115C; YJL061W; YJL041W; YER107C; YMR047C	NUP159; NUP82; NSP1; GLE2; NUP116	subcomplex not defined in GO	YES	"Nup116-Gle2 complex associates with nucleoporin subcomplex consisting of Nup82p, Nsp1 and Nup159p"	10801828
Snx4-Snx41 heterodimer	curated consensus	YJL036W; YDR425W	SNX4; SNX41	subcomplex not defined in GO	YES		12554655
Nup60-Nup2 nuclear pore complex	curated consensus	YAR002W; YLR335W; YLR347C	NUP60; NUP2; KAP95	subcomplex not defined in GO	YES	Kap60-Kap95 heterodimer dissociates Nup2 from Nup60p	11535617
Erp1-Erp2-Emp24-Erv25 p24 complex	curated consensus	YAL007C; YAR002C-A; YGL200C; YML012W	ERP2; ERP1; EMP24; ERV25	subcomplex not defined in GO	YES		10359606
nucleoporin Nsp1 subcomplex	curated consensus	YFR002W; YGL172W; YGR119C; YJL041W	NIC96; NUP49; NUP57; NSP1	subcomplex not defined in GO	YES		7688296; 9017593
HDA complex	curated consensus	YDR295C; YNL021W; YPR179C	HDA2; HDA1; HDA3	subcomplex not defined in GO	YES		8663039
core H-ACA snoRNP	curated consensus	YDL208W; YHR072W-A; YHR089C; YLR175W; YNL308C	NHP2; NOP10; GAR1; CBF5; KRI1	subcomplex not defined in GO	YES	Kri1 is not known to be in the complex	9843512
Atg11-Atg17-Atg29-Cis1 complex	curated consensus	YPR049C; YPL166W; YDR022C; YLR423C	ATG11; ATG29; CIS1; ATG17	subcomplex not defined in GO	YES	"Atg17 forms a ternary complex with Atg29 and Atg31p(Cis1p), Atg11 can recruit Atg17 and Atg29 to the PAS (pre-autophagosomal structure)"	18287526
Clathrin	curated consensus	YGL206C; YGR167W	CHC1; CLC1	subcomplex not defined in GO	YES		9845372
Ctf18 RFC-like complex	curated consensus	YCL016C; YHR191C; YMR078C	DCC1; CTF8; CTF18	subcomplex not defined in GO	YES		11389843
commitment complex 2	curated consensus	YKL074C; YLR116W	MUD2; MSL5	subcomplex not defined in GO	YES		10376880
Sec24-Sfb2-Sec16-Sec23 complex	curated consensus	YIL109C; YNL049C; YPL085W; YPR181C	SEC24; SFB2; SEC16; SEC23	subcomplex not defined in GO	YES	Sec23-Sec24 seem to participate in three different complex formations. Sfb2 is functionally redundant with Sec24p	10753972; 8930902
"vacuolar proton-transporting V-type ATPase, V0 domain"	curated consensus	YPR149W; YKL119C; YLR447C; YOR270C	NCE102; VPH2; VMA6; VPH1	YES	YES	Nce102 is not known to be in the complex	10224039
Hrd1 ubiquitin ligase ERAD-L complex	curated consensus	YDR057W; YLR207W; YOL013C; YML029W	YOS9; HRD3; HRD1; USA1	YES	YES		16873066
anthranilate synthase complex	curated consensus	YER090W; YKL211C	TRP2; TRP3	YES	YES		3881257
nuclear cohesin complex	curated consensus	YJL074C; YFL008W; YIL026C; YDL003W	SMC3; SMC1; IRR1; MCD1	YES	YES		9990856; 9887095; 10499801
protein kinase CK2 complex	curated consensus	YGL019W; YIL035C; YOR039W; YOR061W	CKB1; CKA1; CKB2; CKA2	YES	YES		9427841
phosphatidylinositol 3-kinase complex II	curated consensus	YBR097W; YLR360W; YPL120W; YLR240W	VPS15; VPS38; VPS30; VPS34	YES	YES		11157979
mitochondrial proton-transporting ATP synthase complex	curated consensus	YBL099W; YBR039W; YDR298C; YKL016C	ATP1; ATP3; ATP5; ATP7	YES	YES		10066811
GINS complex	curated consensus	YDR013W; YJL072C; YDR489W; YOL146W	PSF1; PSF2; SLD5; PSF3	YES	YES		12730134
mitochondtrial large ribosomal subunit	curated consensus	YGR076C; YDR405W; YBR282W; YHR147C; YBL038W; YDR462W; YOR150W; YBR122C; YCR071C; YDR237W; YDR116C; YDR322W; YLR439W; YDR296W; YCR046C; YNL252C; YMR193W; YGR220C; YKL167C; YKR006C; YJL063C; YKR085C; YML025C; YMR024W; YNL005C; YLR312W-A; YPL183W-A; YMR098C; YML009C; YMR225C; YNL177C; YNL284C; YPR100W	MRPL25; MRP20; MRPL27; MRPL6; MRPL16; MRPL28; MRPL23; MRPL36; IMG2; MRPL7; MRPL1; MRPL35; MRPL4; MHR1; IMG1; MRPL17; MRPL24; MRPL9; MRP49; MRPL13; MRPL8; MRPL20; YML6; MRPL3; MRP7; MRPL15; RTC6; ATP25; MRPL39; MRPL44; MRPL22; MRPL10; MRPL51	YES	YES		12392552; 9151978
ribonuclease H2 complex	curated consensus	YDR279W; YNL072W	RNH202; RNH201	YES	YES		14734815
SUMO activating enzyme complex	curated consensus	YDR390C; YPR180W	UBA2; AOS1	YES	YES		9312010
tRNA (m1A) methyltransferase complex	curated consensus	YJL125C; YNL062C	GCD14; GCD10	YES	YES		10779558
polarisome	curated consensus	YER149C; YLL021W	PEA2; SPA2	YES	YES		
TRAMP complex	curated consensus	YDL175C; YJL050W; YOL115W	AIR2; MTR4; PAP2	YES	YES		15828860
transcription factor TFIIA complex	curated consensus	YKL058W; YOR194C	TOA2; TOA1	YES	YES		7862117
CPF complex	curated consensus	YMR061W; YER133W; YDR195W; YGR156W; YAL043C; YNL222W; YDR301W; YKL059C; YJR093C; YPR107C; YLR115W; YLR277C; YKR002W; YNL317W; YKL018W; YOR179C	RNA14; GLC7; REF2; PTI1; PTA1; SSU72; CFT1; MPE1; FIP1; YTH1; CFT2; YSH1; PAP1; PFS2; SWD2; SYC1	YES	YES	Rna14 is not known to be in the complex	10523662; 12819204
serine C-palmitoyltransferase complex	curated consensus	YDR062W; YMR296C	LCB2; LCB1	YES	YES		1556076
Cyc8-Tup1 corepressor complex	curated consensus	YCR084C; YBR112C	TUP1; CYC8	YES	YES		9111019; 8943325
delta DNA polymerase complex	curated consensus	YDL102W; YJR006W; YJR043C	POL3; POL31; POL32	YES	YES		
snRNP U2	curated consensus	YDL043C; YJL203W; YMR240C; YDL030W; YPL213W; YML049C; YMR288W	PRP11; PRP21; CUS1; PRP9; LEA1; RSE1; HSH155	YES	YES		11804584; 16314500
AP-3 adaptor complex	curated consensus	YBR288C; YGR261C; YJL024C; YPL195W	APM3; APL6; APS3; APL5	YES	YES		9335339
Ric1-Rgp1 complex	curated consensus	YDR137W; YLR039C	RGP1; RIC1	YES	YES		10990452
Ndc80 complex	curated consensus	YER018C; YIL144W; YOL069W; YMR117C	SPC25; TID3; NUF2; SPC24	YES	YES		11266451; 11179222
Rpd3L complex	curated consensus	YDR207C; YDL076C; YAL013W; YBR095C; YNL097C; YIL084C; YMR263W; YPL181W; YOL004W; YNL330C; YPL139C; YMR075W	UME6; RXT3; DEP1; RXT2; PHO23; SDS3; SAP30; CTI6; SIN3; RPD3; UME1; RCO1	YES	YES		16286007
methionyl glutamyl tRNA synthetase complex	curated consensus	YGL245W; YGL105W; YGR264C	GUS1; ARC1; MES1	YES	YES		11069915; 9659920
protein phosphatase type 2A complex	curated consensus	YAL016W; YDL188C; YGL190C; YDL134C; YMR273C; YML109W; YOR014W	TPD3; PPH22; CDC55; PPH21; ZDS1; ZDS2; RTS1	YES	YES		
TORC1 complex	curated consensus	YHR186C; YJR066W	KOG1; TOR1	YES	YES		12408816
epsilon DNA polymerase complex	curated consensus	YDR121W; YBR278W; YNL262W; YPR175W	DPB4; DPB3; POL2; DPB2	YES	YES		2406268; 11024162
mitochondrial oxoglutarate dehydrogenase complex	curated consensus	YFR049W; YFL018C; YDR148C; YIL125W	YMR31; LPD1; KGD2; KGD1	YES	YES	Ymr31 is not known to bind	2072900
NatC complex	curated consensus	YPR051W; YCR020C-A; YEL053C	MAK3; MAK31; MAK10	YES	YES		10504710
SWR1 complex	curated consensus	YAL011W; YDR485C; YLR085C; YBR231C; YDR334W; YLR385C; YLR399C; YML041C; YFL039C; YDR190C; YPL235W; YJL081C; YGR002C; YNL107W	SWC3; VPS72; ARP6; SWC5; SWR1; SWC7; BDF1; VPS71; ACT1; RVB1; RVB2; ARP4; SWC4; YAF9	YES	YES		
transcription factor TFIIE complex	curated consensus	YKL028W; YKR062W	TFA1; TFA2	YES	YES		
mRNA capping enzyme complex	curated consensus	YPL228W; YGL130W	CET1; CEG1	YES	YES		9710603
Set3C	curated consensus	YBR103W; YDR155C; YIL112W; YKR029C; YGL194C; YOL068C; YCR033W	SIF2; CPR1; HOS4; SET3; HOS2; HST1; SNT1	YES	YES		11711434
ESCRT II complex	curated consensus	YJR102C; YLR417W; YPL002C	VPS25; VPS36; SNF8	YES	YES		12194858
MutSalpha complex	curated consensus	YOL090W; YDR097C	MSH2; MSH6	YES	YES		8816473
Cdc73-Paf1 complex	curated consensus	YBR279W; YGL244W; YOR123C; YOL145C; YLR418C	PAF1; RTF1; LEO1; CTR9; CDC73	YES	YES		9891041
mitochondrial small ribosomal subunit	curated consensus	YER050C; YNR037C; YBR251W; YGR215W; YBR146W; YPL118W; YMR158W; YDR036C; YGR084C; YDL045W-A; YHR059W; YDR041W; YGL129C; YPL013C; YKL155C; YIL093C; YNL137C; YDR337W; YJR101W; YJR113C; YBL090W; YMR188C; YNL081C; YDR175C; YOR158W; YHL004W; YDR347W; YNR036C; YNL306W; YGR165W; YKL003C	RSM18; RSM19; MRPS5; RSM27; MRPS9; MRP51; MRPS8; EHD3; MRP13; MRP10; FYV4; RSM10; RSM23; MRPS16; RSM22; RSM25; NAM9; MRPS28; RSM26; RSM7; MRP21; MRPS17; SWS2; RSM24; PET123; MRP4; MRP1; MRPS12; MRPS18; MRPS35; MRP17	YES	YES		9151978; 9445368; 11278769
AP-1 adaptor complex	curated consensus	YFL034W; YHL019C; YKL135C; YLR170C; YPR029C; YPL259C	YFL034W; APM2; APL2; APS1; APL4; APM1	YES	YES		10564262
U4-U6 x U5 tri-snRNP complex	curated consensus	YGR074W; YER029C; YLR147C; YLR275W; YER172C; YKL173W; YHR165C; YDL098C; YGR091W; YDR473C; YOR308C; YBR055C; YPR178W; YPR082C	SMD1; SMB1; SMD3; SMD2; BRR2; SNU114; PRP8; SNU23; PRP31; PRP3; SNU66; PRP6; PRP4; DIB1	YES	YES		10377396; 10449419
GET complex	curated consensus	YDL100C; YER083C; YGL020C	GET3; GET2; GET1	YES	YES		16269340
NatB complex	curated consensus	YOL076W; YPR131C	MDM20; NAT3	YES	YES		12890471
heterotrimeric G-protein complex	curated consensus	YHR005C; YOR212W	GPA1; STE4	YES	YES		11394869; 2105453
ribonuclease MRP complex	curated consensus	YBL018C; YAL033W; YBR167C; YBR257W; YGR030C; YNL221C; YNL282W; YDR478W; YHR062C	POP8; POP5; POP7; POP4; POP6; POP1; POP3; SNM1; RPP1	YES	YES		9620854; 15637077; 9353260; 9029160
DASH complex	curated consensus	YDR201W; YDR016C; YKL052C; YGR113W; YGL061C; YKR083C; YKR037C; YKL138C-A; YBR233W-A	SPC19; DAD1; ASK1; DAM1; DUO1; DAD2; SPC34; HSK3; DAD3	YES	YES		11799062; 15640796; 15664196
COPI vesicle coat	curated consensus	YER122C; YGL137W; YDL145C; YDR238C; YNL287W; YFR051C; YIL076W; YPL010W	GLO3; SEC27; COP1; SEC26; SEC21; RET2; SEC28; RET3	YES	YES		15254269; 8617224; 7929113
GID complex	curated consensus	YCL039W; YDL176W; YDR255C; YBR105C; YGL227W; YIL097W; YIL017C; YMR135C	GID7; YDL176W; RMD5; VID24; VID30; FYV10; VID28; GID8	YES	YES	"Only recently found in literature (2008), YDL176W not part of this"	18508925
alpha-glucosidase II complex	curated consensus	YBR229C; YDR221W	ROT2; GTB1	YES	YES		
Golgi transport complex	curated consensus	YNL041C; YPR105C; YGL005C; YGL223C; YER157W; YNL051W; YGR120C; YML071C	COG6; COG4; COG7; COG1; COG3; COG5; COG2; COG8	YES	YES		11703943
mitochondrial processing peptidase complex	curated consensus	YHR024C; YLR163C	MAS2; MAS1	YES	YES		2905264
carbamoyl-phosphate synthase complex	curated consensus	YJR109C; YOR303W	CPA2; CPA1	YES	YES		6086650; 6358221
mitochondrial pyruvate dehydrogenase complex	curated consensus	YBR221C; YER178W; YNL071W; YGR193C	PDB1; PDA1; LAT1; PDX1	YES	YES		9123965; 2007123
Srb-mediator complex	curated consensus	YBL093C; YDL005C; YGL127C; YCR081W; YGR104C; YDR308C; YER022W; YGL025C; YOL051W; YPR168W; YMR112C; YDR443C; YBR253W; YOL135C; YLR071C; YPL042C; YHR041C; YHR058C; YBR193C; YOR174W; YPR070W; YNR010W; YGL151W; YNL236W	ROX3; MED2; SOH1; SRB8; SRB5; SRB7; SRB4; PGD1; GAL11; NUT2; MED11; SSN2; SRB6; MED7; RGR1; SSN3; SRB2; MED6; MED8; MED4; MED1; CSE2; NUT1; SIN4	YES	YES		9420330; 16885025
CCR4-NOT complex	curated consensus	YGR134W; YCR093W; YAL021C; YNL288W; YNR052C; YER068W	CAF130; CDC39; CCR4; CAF40; POP2; MOT2	YES	YES		10490603
ubiquitin conjugating enzyme complex	curated consensus	YGL087C; YMR140W; YDR092W	MMS2; SIP5; UBC13	YES	YES	Sip5 not known to be part of complex	10089880
MBF transcription complex	curated consensus	YDL056W; YLR182W	MBP1; SWI6	YES	YES		9719633
mitochondrial respiratory chain complex II	curated consensus	YKL148C; YLL041C	SDH1; SDH2	YES	YES		
snf1 protein kinase complex	curated consensus	YDR028C; YDR422C; YER027C; YER129W; YDR477W; YGL115W; YGL208W	REG1; SIP1; GAL83; SAK1; SNF1; SNF4; SIP2	YES	YES	Reg1 and Sak1 are not known to be in the complex. Sak1 is an upstream kinase that can activate Snf1p	12393914
m-AAA complex	curated consensus	YER017C; YMR089C	AFG3; YTA12	YES	YES		8681382
ESCRT-0 complex	curated consensus	YHL002W; YNR006W	HSE1; VPS27	YES	YES		12055639
TREX complex	curated consensus	YDR381W; YDL084W; YDR138W; YHR167W; YML062C; YNL139C; YNL253W; YNL004W	YRA1; SUB2; HPR1; THP2; MFT1; THO2; TEX1; HRB1	YES	YES	Hrb1 is not known to be in the complex	11979277
alpha DNA polymerase:primase complex	curated consensus	YBL035C; YNL102W; YIR008C; YKL045W	POL12; POL1; PRI1; PRI2	YES	YES		3888995
NatA complex	curated consensus	YDL040C; YHR013C; YOR253W	NAT1; ARD1; NAT5	YES	YES		14517307
signal recognition particle	curated consensus	YDL051W; YKL122C; YML105C; YPR088C; YDL092W; YPL210C; YPL243W	LHP1; SRP21; SEC65; SRP54; SRP14; SRP72; SRP68	YES	YES	Lhp1 is not known to be in the complex	
NEF4 complex	curated consensus	YJR052W; YPL046C	RAD7; ELC1	YES	YES	missing Abf1 and Rad16	15226437
CCAAT-binding factor complex	curated consensus	YBL021C; YGL237C; YOR358W	HAP3; HAP2; HAP5	YES	YES		9618445
"vacuolar proton-transporting V-type ATPase, V1 domain"	curated consensus	YJR033C; YDL185W; YBR127C; YGR020C; YHR039C-A; YEL051W; YPR036W; YOR332W; YKL080W	RAV1; TFP1; VMA2; VMA7; VMA10; VMA8; VMA13; VMA4; VMA5	YES	YES		9442887
PAN complex	curated consensus	YGL094C; YKL025C	PAN2; PAN3	YES	YES		8816488
cytosolic small ribosomal subunit	curated consensus	YDR025W; YER102W; YBR048W; YBR189W; YBL072C; YDR064W; YOR096W; YJR145C; YHR203C; YJL190C; YIL069C; YLR367W; YML024W; YPL081W; YOR204W	RPS11A; RPS8B; RPS11B; RPS9B; RPS8A; RPS13; RPS7A; RPS4A; RPS4B; RPS22A; RPS24B; RPS22B; RPS17A; RPS9A; DED1	YES	YES		9559554; 3533916
"gamma-tubulin small complex, spindle pole body"	curated consensus	YAL047C; YHR172W; YNL126W; YLR212C	SPC72; SPC97; SPC98; TUB4	YES	YES		9384578
Elg1 RFC-like complex	curated consensus	YBR087W; YOL094C; YNL290W; YJR068W; YOR217W; YOR144C	RFC5; RFC4; RFC3; RFC2; RFC1; ELG1	YES	YES		12912927
tRNA-intron endonuclease complex	curated consensus	YLR105C; YPL083C	SEN2; SEN54	YES	YES		9200603
ISW1 complex	curated consensus	YBR245C; YKR001C; YPL082C; YLR095C; YMR044W	ISW1; VPS1; MOT1; IOC2; IOC4	YES	YES		12482963
EKC-KEOPS protein complex	curated consensus	YGR262C; YJL184W; YKR038C; YML036W	BUD32; GON7; KAE1; CGI121	YES	YES		16874308
FACT complex	curated consensus	YGL207W; YML069W	SPT16; POB3	YES	YES		11432837
HOPS complex	curated consensus	YMR231W; YAL002W; YLR396C; YLR148W; YDR080W; YDL077C; YPL045W	PEP5; VPS8; VPS33; PEP3; VPS41; VAM6; VPS16	YES	YES	"shares many subunits with CORVET complex, HOPS and CORVET complex can interconvert"	10944212; 17488625
MutSBeta complex	curated consensus	YOL090W; YCR092C	MSH2; MSH3	YES	YES		8805366
"cytochome c oxidase complex, subunits IV, Va, VI and VIIa"	curated consensus	YNL052W; YGL187C; YDL067C; YHR051W	COX5A; COX4; COX9; COX6	YES	YES	"total number of cytochrom c oxidase amounts to 12, but most are easily lost due to purification techniques"	1331058
SCF ubiquitin ligase complex	curated consensus	YDL132W; YDR054C; YJL047C; YGL252C; YOL133W	CDC53; CDC34; RTT101; RTG2; HRT1	YES	YES		9346238; 10385629
nucleotide-excision repair factor 1 complex	curated consensus	YAL027W; YML095C; YPL022W	SAW1; RAD10; RAD1	YES	YES		8621533
carboxy-terminal domain protein kinase complex	curated consensus	YKL139W; YJL006C; YML112W	CTK1; CTK2; CTK3	YES	YES		
eukaryotic translation elongation factor 1 complex	curated consensus	YAL003W; YPL048W; YKL081W; YPR080W	EFB1; CAM1; TEF4; TEF1	YES	YES		8420802; 3026912; 8041634 
NuA4 histone acetyltransferase complex	curated consensus	YDR359C; YEL018W; YFL024C; YOR244W; YJR082C; YHR090C; YNL136W; YPR023C; YJL081C; YGR002C; YNL107W; YFL039C	EAF1; EAF5; EPL1; ESA1; EAF6; YNG2; EAF7; EAF3; ARP4; SWC4; YAF9; ACT1	YES	YES		10487762
RNA polymerase I complex	curated consensus	YNL113W; YPR110C; YHR143W-A; YBR154C; YPR187W; YOR224C; YOR210W; YDR156W; YJL148W; YJR063W; YNL248C; YOR340C; YOR341W; YPR010C	RPC19; RPC40; RPC10; RPB5; RPO26; RPB8; RPB10; RPA14; RPA34; RPA12; RPA49; RPA43; RPA190; RPA135	YES	YES		9774381; 8246845
90S preribosome	curated consensus	YBR247C; YDR324C; YPL126W; YOR310C; YGR145W; YLR222C; YNL075W; YJL109C; YDR398W; YCR057C; YPR144C; YLR409C; YNL132W; YLL011W; YDL148C; YOR145C; YBL004W; YLR186W; YCL059C; YJR145C; YDR449C; YPR112C; YMR128W; YJR002W; YDR299W; YOR096W; YPL217C; YLR197W; YOR078W; YDL014W; YPR137W; YMR093W; YOL010W; YPL266W; YLR003C; YJL069C; YGR128C; YLR129W; YGR090W; YPL012W; YER127W; YKR060W; YER082C; YEL055C; YDR064W; YHR196W; YGL171W; YHR148W	ENP1; UTP4; NAN1; NOP58; ENP2; UTP13; IMP4; UTP10; UTP5; PWP2; NOC4; UTP21; KRE33; SOF1; NOP14; PNO1; UTP20; EMG1; KRR1; RPS4A; UTP6; MRD1; ECM16; MPP10; BFR2; RPS7A; BMS1; NOP56; BUD21; NOP1; RRP9; UTP15; RCL1; DIM1; CMS1; UTP18; UTP8; DIP2; UTP22; RRP12; LCP5; UTP30; UTP7; POL5; RPS13; UTP9; ROK1; IMP3	YES	YES		12150911
RSC complex	curated consensus	YMR091C; YGL013C; YNR023W; YHR056C; YLR357W; YML127W; YDR303C; YDR225W; YOR156C; YGR056W; YFR037C; YOR290C; YIL126W; YHL025W; YJL176C; YMR033W; YDR073W; YCR020W-B; YPR034W; YCR052W; YBR289W; YLR321C; YLR033W; YGR275W; YFL049W; YPL016W; YKR008W	NPL6; PDR1; SNF12; RSC30; RSC2; RSC9; RSC3; HTA1; NFI1; RSC1; RSC8; SNF2; STH1; SNF6; SWI3; ARP9; SNF11; HTL1; ARP7; RSC6; SNF5; SFH1; RSC58; RTT102; SWP82; SWI1; RSC4	YES	YES		12183366; 10619019
CAAX-protein geranylgeranyltransferase complex	curated consensus	YKL019W; YGL155W	RAM2; CDC43	YES	YES		1400380
Arp2-3 protein complex	curated consensus	YDL029W; YBR234C; YIL062C; YNR035C; YKL013C; YLR370C; YJR065C	ARP2; ARC40; ARC15; ARC35; ARC19; ARC18; ARP3	YES	YES		
SAGA complex	curated consensus	YBR198C; YDR167W; YDR145W; YMR236W; YDR448W; YGR252W; YGL112C; YDR392W; YCL010C; YOL148C; YBR081C; YDR176W; YGL066W; YPL254W; YLR055C; YMR223W; YPL047W; YHR099W	TAF5; TAF10; TAF12; TAF9; ADA2; GCN5; TAF6; SPT3; SGF29; SPT20; SPT7; NGG1; SGF73; HFI1; SPT8; UBP8; SGF11; TRA1	YES	YES		9674426
TRAPP complex	curated consensus	YGR166W; YKR068C; YOR115C; YDR108W; YDR246W; YML077W; YDR407C; YBR254C; YDR472W; YMR218C	KRE11; BET3; TRS33; GSG1; TRS23; BET5; TRS120; TRS20; TRS31; TRS130	YES	YES		10727015
AP-2 adaptor complex	curated consensus	YBL037W; YJR058C; YJR005W; YOL062C	APL3; APS2; APL1; APM4	YES	YES		10564262
CAF-1 complex	curated consensus	YBR195C; YML102W; YPR018W	MSI1; CAC2; RLF2	YES	YES		9030687
GARP complex	curated consensus	YDR484W; YDR027C; YJL029C; YJL034W; YKR020W	VPS52; VPS54; VPS53; KAR2; VPS51	YES	YES		10637310
CCR4-NOT Not2-Not5 subcomplex	curated consensus	YDL165W; YPR072W	CDC36; NOT5	YES	YES	Not2 and Not5 are known to have a strong physical association	10490603
origin recognition complex	curated consensus	YBR060C; YML065W; YLL004W; YPR162C; YHR118C; YNL261W	ORC2; ORC1; ORC3; ORC4; ORC6; ORC5	YES	YES		
Smc5-Smc6 complex	curated consensus	YEL019C; YDR288W; YOL034W; YDL105W	MMS21; NSE3; SMC5; NSE4	YES	YES		15738391
RNA polymerase III complex	curated consensus	YDR045C; YDL150W; YJL011C; YKL144C; YKR025W; YNL151C; YPR190C; YNR003C; YOR207C; YOR116C; YNL113W; YPR110C; YBR154C; YPR187W; YOR224C; YOR210W	RPC11; RPC53; RPC17; RPC25; RPC37; RPC31; RPC82; RPC34; RET1; RPO31; RPC19; RPC40; RPB5; RPO26; RPB8; RPB10	YES	YES		9774381; 8246845
proteasome regulatory particle	curated consensus	YDL147W; YHL030W; YDR363W-A; YFR010W; YGR232W; YDR394W; YER021W; YDR427W; YDL007W; YHR200W; YFR004W; YFR052W; YOR259C; YOR261C; YDL097C; YGL048C; YLR421C; YHR027C; YOR117W; YPR108W; YIL075C; YKL145W	RPN5; ECM29; SEM1; UBP6; NAS6; RPT3; RPN3; RPN9; RPT2; RPN10; RPN11; RPN12; RPT4; RPN8; RPN6; RPT6; RPN13; RPN1; RPT5; RPN7; RPN2; RPT1	YES	YES		
Ski complex	curated consensus	YGL213C; YLR398C; YKL023W; YPR189W	SKI8; SKI2; YKL023W; SKI3	YES	YES	Ykl023w is not known to be in the complex	
eukaryotic translation initiation factor 2B complex	curated consensus	YDR211W; YLR215C; YOR260W; YLR291C; YGR083C; YJR007W; YER025W; YKR026C; YPL237W	GCD6; CDC123; GCD1; GCD7; GCD2; SUI2; GCD11; GCN3; SUI3	YES	YES	eIF-2B phosphorylates eIF-2 and is stably associated with eIF-2 alpha	8506384; 8336705
exomer complex	curated consensus	YLR330W; YJL099W; YKR027W; YOR299W; YMR237W	CHS5; CHS6; BCH2; BUD7; BCH1	YES	YES		
INO80 complex	curated consensus	YFL039C; YER092W; YGL150C; YDL002C; YFL013C; YOR141C; YLR052W; YNL059C; YNL215W; YDR190C; YPL235W; YJL081C	ACT1; IES5; INO80; NHP10; IES1; ARP8; IES3; ARP5; IES2; RVB1; RVB2; ARP4	YES	YES		10952318
MIND complex	curated consensus	YAL034W-A; YPL233W; YIR010W; YJR112W	MTW1; NSL1; DSN1; NNF1	YES	YES		14633972
Elongator holoenzyme complex	curated consensus	YLR384C; YGR200C; YPL086C; YHR187W; YPL101W; YMR312W	IKI3; ELP2; ELP3; IKI1; ELP4; ELP6	YES	YES		
retromer complex	curated consensus	YHR012W; YJL154C; YJL053W; YOR069W; YOR132W; YPL070W	VPS29; VPS35; PEP8; VPS5; VPS17; MUK1	YES	YES		9700157
anaphase-promoting complex	curated consensus	YDR260C; YFR036W; YIR025W; YGL240W; YBL084C; YDR118W; YOR249C; YHR166C; YKL022C; YLR127C; YNL172W; YLR102C	SWM1; CDC26; MND2; DOC1; CDC27; APC4; APC5; CDC23; CDC16; APC2; APC1; APC9	YES	YES		9469814; 12574115; 15797379
proteasome core complex	curated consensus	YFL007W; YER012W; YGL011C; YBL041W; YOL038W; YFR050C; YGR135W; YER094C; YJL001W; YOR362C; YPR103W; YGR253C; YML092C; YOR157C; YMR314W	BLM10; PRE1; SCL1; PRE7; PRE6; PRE4; PRE9; PUP3; PRE3; PRE10; PRE2; PUP2; PRE8; PUP1; PRE5	YES	YES	Evidence based on computational method	
"alpha-1,6-mannosyltransferase complex"	curated consensus	YDR245W; YEL036C; YJL183W; YPL050C; YJR075W	MNN10; ANP1; MNN11; MNN9; HOC1	YES	YES		9430634; 10037752
ESCRT I complex	curated consensus	YCL008C; YLR119W; YGR206W; YPL065W	STP22; SRN2; MVB12; VPS28	YES	YES		11511343
cAMP-dependent protein kinase complex	curated consensus	YKL166C; YIL033C; YJL164C; YPL203W	TPK3; BCY1; TPK1; TPK2	YES	YES		3036373
translation release factor complex	curated consensus	YBR143C; YDR172W	SUP45; SUP35	YES	YES		7556078
Ku70:Ku80 complex	curated consensus	YMR106C; YMR284W	YKU80; YKU70	YES	YES		8754818
transcription factor TFIIIC complex	curated consensus	YGR047C; YAL001C; YDR362C; YBR123C; YOR110W; YPL007C	TFC4; TFC3; TFC6; TFC1; TFC7; TFC8	YES	YES		10384303
fatty acid synthase complex	curated consensus	YKL182W; YPL231W	FAS1; FAS2	YES	YES		65153
RENT complex	curated consensus	YDL042C; YJL076W	SIR2; NET1	YES	YES		10219244
septin complex	curated consensus	YJR092W; YJR076C; YCR002C; YHR107C; YDL225W; YLR314C	BUD4; CDC11; CDC10; CDC12; SHS1; CDC3	YES	YES	Bud4 is not known to be part of the complex	9813094; 18550837
exocyst	curated consensus	YPR055W; YER008C; YJL085W; YIL068C; YDR166C; YLR166C; YBR102C; YGL233W	SEC8; SEC3; EXO70; SEC6; SEC5; SEC10; EXO84; SEC15	YES	YES		8978675
signalosome	curated consensus	YDR179C; YDL216C; YOL117W; YIL071C; YMR025W	CSN9; RRI1; RRI2; PCI8; CSI1	YES	YES		12446563
"preribosome, large subunit precursor"	curated consensus	YLL008W; YER006W; YPL211W; YBR142W; YNL061W; YNL110C; YOL077C; YDR496C; YHR052W; YMR290C; YKR081C; YLL034C; YOR272W; YKL172W; YPR016C; YDR087C; YGL111W; YHR088W; YLR002C; YFL002C; YKL009W; YCL054W; YDL031W; YPL093W; YOR206W; YLR449W; YMR049C; YNL002C; YMR229C; YGR103W	DRS1; NUG1; NIP7; MAK5; NOP2; NOP15; BRX1; PUF6; CIC1; HAS1; RPF2; RIX7; YTM1; EBP2; TIF6; RRP1; NSA1; RPF1; NOC3; SPB4; MRT4; SPB1; DBP10; NOG1; NOC2; FPR4; ERB1; RLP7; RRP5; NOP7	YES	YES		
nucleotide-excision repair factor 2 complex	curated consensus	YEL037C; YER162C	RAD23; RAD4	YES	YES		7768886
calcineurin complex	curated consensus	YKL190W; YML057W	CNB1; CMP2	YES	YES		1321337
mitochondrial isocitrate dehydrogenase complex (NAD+)	curated consensus	YOR136W; YNL037C	IDH2; IDH1	YES	YES		16884682
Mre11 complex	curated consensus	YDR369C; YMR224C; YNL250W	XRS2; MRE11	YES	YES	DL put Rad50 therein	9845372
Rab-protein geranylgeranyltransferase complex	curated consensus	YJL031C; YPR176C	BET4; BET2	YES	YES		8756702
signal recognition particle receptor complex	curated consensus	YDR292C; YKL154W	SRP101; SRP102	YES	YES		9679135
endoplasmic reticulum Sec complex	curated consensus	YBR171W; YLR292C; YOR254C; YPL094C	SEC66; SEC72; SEC63; SEC62	YES	YES		2000150; 8257795 ; 8051213
eukaryotic translation initiation factor 3 complex	curated consensus	YAL035W; YDR091C; YBR079C; YMR309C; YLR192C; YDR429C; YMR146C; YPR041W; YOR361C; YNL244C	FUN12; RLI1; RPG1; NIP1; HCR1; TIF35; TIF34; TIF5; PRT1; SUI1	YES	YES	Fun12 and Rli1 are not known to be in the complex but are required for translation initiation	9660829
HIR complex	curated consensus	YBL008W; YOR038C; YBR215W; YJR140C	HIR1; HIR2; HPC2; HIR3	YES	YES		16303565; 16264190
MutLalpha complex	curated consensus	YMR167W; YNL082W	MLH1; PMS1	YES	YES		10570173
RNA polymerase II complex	curated consensus	YGL043W; YDL115C; YDL140C; YGL070C; YGR005C; YGR186W; YIL021W; YDR404C; YOL005C; YJL140W; YOR151C; YGR063C; YML010W; YPL129W; YBR154C; YPR187W; YOR224C; YOR210W	DST1; IWR1; RPO21; RPB9; TFG2; TFG1; RPB3; RPB7; RPB11; RPB4; RPB2; SPT4; SPT5; TAF14; RPB5; RPO26; RPB8; RPB10	YES	YES		9774381; 8246845
chaperonin-containing T-complex	curated consensus	YJL014W; YDL143W; YDR188W; YIL142W; YJL111W; YOR281C; YNL212W; YJL008C; YJR064W	CCT3; CCT4; CCT6; CCT2; CCT7; PLP2; VID27; CCT8; CCT5	YES	YES	Plp1 and Vid27 are not known to be in the complex	15704212
transcription factor TFIID complex	curated consensus	YBR198C; YDR167W; YDR145W; YMR236W; YGL112C; YGR274C; YMR227C; YML015C; YPL011C; YMR005W; YML098W	TAF5; TAF10; TAF12; TAF9; TAF6; TAF1; TAF7; TAF11; TAF3; TAF4; TAF13	YES	YES		15448131; 10788514
nascent polypeptide-associated complex	curated consensus	YHR193C; YPL037C; YDR252W	EGD2; EGD1; BTT1	YES	YES		
cytosolic large ribosomal subunit	curated consensus	YBL092W; YGL014W; YBR191W; YHR141C; YLR287C-A; YFR032C-A; YGR118W; YNL302C; YNL096C; YGL031C; YDR418W; YGL123W; YDR382W; YDL083C; YCR031C; YDR447C; YER074W; YBL027W; YDL136W; YHL001W; YJL177W; YGR034W; YMR194W; YKL180W; YBR181C; YOL040C; YHL033C; YFR031C-A; YNL069C; YML073C; YLR448W; YNL301C; YLR075W; YML063W; YLR441C; YJR123W; YNL178W; YPL090C; YLR150W; YGL147C; YBR031W; YGL030W; YDL075W; YGL103W; YDL082W; YDR471W; YMR242C; YOL127W; YGL135W; YGR085C; YIL133C; YLR029C; YDR012W; YOR312C; YGL076C; YLL045C; YOR063W; YPL198W; YPL249C-A; YLR340W; YIL018W; YPL220W; YMR142C; YOL039W	RPL32; PUF4; RPL21A; RPL42B; RPS30A; RPL29; RPS23A; RPS19B; RPS7B; RPL24A; RPL12B; RPS2; RPP2B; RPS16B; RPS14A; RPS17B; RPS24A; RPL19B; RPL35B; RPL14B; RPL17B; RPL26B; RPL36A; RPL17A; RPS6B; RPS15; RPL8A; RPL2A; RPL16B; RPL6A; RPL6B; RPL18B; RPL10; RPS1B; RPS1A; RPS5; RPS3; RPS6A; STM1; RPL9A; RPL4A; RPL30; RPL31A; RPL28; RPL13A; RPL27B; RPL20A; RPL25; RPL1B; RPL11B; RPL16A; RPL15A; RPL4B; RPL20B; RPL7A; RPL8B; RPL3; RPL7B; RPL36B; RPP0; RPL2B; RPL1A; RPL13B; RPP2A	YES	YES		9559554; 10690410
RAVE complex	curated consensus	YDR202C; YJR033C; YDR328C	RAV2; RAV1; SKP1	YES	YES		11283612
prefoldin complex	curated consensus	YJL179W; YEL003W; YGR078C; YNL153C; YML094W; YLR200W	PFD1; GIM4; PAC10; GIM3; GIM5; YKE2	YES	YES		9463374; 9630229
eukaryotic translation initiation factor 4F complex	curated consensus	YER165W; YGL049C; YGR162W; YOL139C	PAB1; TIF4632; TIF4631; CDC33	YES	YES	"Pab1 is known to be associated with TIF4632-1, but not officially annotated as part of the complex. missing Tif1-2p"	8336723; 9841679
core TFIIH complex	curated consensus	YDR311W; YLR005W; YPR056W	TFB1; SSL1; TFB4	YES	YES	missing Rad3 and Tfb2p	14500720
phenylalanine-tRNA ligase complex	curated consensus	YLR060W; YFL022C	FRS1; FRS2	YES	YES		9812975
DNA replication factor A complex	curated consensus	YAR007C; YNL312W; YJL173C; YHR164C	RFA1; RFA2; RFA3; DNA2	YES	YES	Dna2 not known to be part of the complex	2554144
"alpha,alpha-trehalose-phosphate synthase complex (UDP-forming)"	curated consensus	YBR126C; YDR074W; YMR261C; YML100W	TPS1; TPS2; TPS3; TSL1	YES	YES		
GPI-anchor transamidase complex	curated consensus	YDR331W; YHR188C; YLR088W; YDR434W	GPI8; GPI16; GAA1; GPI17	YES	YES		
ribonucleoside-diphosphate reductase complex	curated consensus	YGR180C; YJL026W; YOR230W	RNR4; RNR2; WTM1	YES	YES	Wtm1 is transcriptional modulator of RNR genes	10716984
exosome (RNase complex)	curated consensus	YHR081W; YCR035C; YGR195W; YDL111C; YDR280W; YOR076C; YGR158C; YHR069C; YGR095C; YOL142W; YNL232W; YOL021C; YOR001W; YNR024W; YNL189W	LRP1; RRP43; SKI6; RRP42; RRP45; SKI7; MTR3; RRP4; RRP46; RRP40; CSL4; DIS3; RRP6; MPP6; SRP1	YES	YES		10465791
COMPASS complex	curated consensus	YBR175W; YBR258C; YDR469W; YHR119W; YAR003W; YLR015W; YPL138C; YKL018W	SWD3; SHG1; SDC1; SET1; SWD1; BRE2; SPP1; SWD2	YES	YES		11687631
SBF transcription complex	curated consensus	YER111C; YLR182W	SWI4; SWI6	YES	YES		8423776
protein farnesyltransferase complex	curated consensus	YDL090C; YKL019W	RAM1; RAM2	YES	YES		1763050
nuclear condensin complex	curated consensus	YFR031C; YDR325W; YLR272C; YLR086W; YBL097W	SMC2; YCG1; YCS4; SMC4; BRN1	YES	YES		10811823
snRNP U6	curated consensus	YER146W; YDL160C; YER112W; YCR077C; YJL124C; YBL026W; YDR378C; YNL147W; YJR022W; YMR268C; YLR438C-A	LSM5; DHH1; LSM4; PAT1; LSM1; LSM2; LSM6; LSM7; LSM8; PRP24; LSM3	YES	YES		10369684; 11720284; 10580475
subunit VII of the cytochrome bc1 complex	curated consensus	YDL189W; YDR529C; YBL045C; YPR191W	RBS1; QCR7; COR1; QCR2	"YES, not split u in subunits"	YES	Rbs1 not known to be in the same complex	10873857
putatie Saf1-Aah1 complex	curated consensus	YNL141W; YBR280C	AAH1; SAF1	NO	"NO, double check!"	Aah1 is specifically degraded through Saf1 and has been suggested as a bonafide subunit of Skp1-Cullin-F-box	17517885
putative Tkl2-Tkl1 isozyme complex	curated consensus	YBR117C; YPR074C	TKL2; TKL1	NO	NO		
putative Trm7-Ymr259c complex	curated consensus	YBR061C; YMR259C	TRM7; YMR259C	NO	NO		
putative Atg18-Atg2 complex	curated consensus	YFR021W; YNL242W	ATG18; ATG2	NO	NO	Atg2 is recruited by Atg18	
putative Trm7-Rtt10 complex	curated consensus	YBR061C; YPL183C	TRM7; RTT10	NO	NO		
putative Nuc1-Trz1-Ymr099c complex	curated consensus	YJL208C; YKR079C; YMR099C	NUC1; TRZ1; YMR099C	NO	NO		
putative Sas5-Wtm2 complex	curated consensus	YOR213C; YOR229W	SAS5; WTM2	NO	NO		
putative Cdc47-Erg26 complex	curated consensus	YBR202W; YGL001C	MCM7; ERG26	NO	NO		
putative Flc2-Tcb3 complex	curated consensus	YAL053W; YML072C	FLC2; TCB3	NO	NO		
putative Rpl23a-Rpl23b-Bcp1-Rkm1 complex	curated consensus	YBL087C; YER117W; YDR361C; YPL208W	RPL23A; RPL23B; BCP1; RKM1	NO	NO	Rpl23a and Rpl23b are identical. Rkm1 methylates lysine residues of Rpl23a-bp	
putative Rsa3-Urb1-Urb2-Nop8 complex	curated consensus	YLR221C; YKL014C; YJR041C; YOL144W	RSA3; URB1; URB2; NOP8	NO	NO	most proteins involed in pre-60S ribosome biogenesis	
putative Ybr225w-Mds3-Cdc25 complex	curated consensus	YBR225W; YGL197W; YLR310C	YBR225W; MDS3; CDC25	NO	NO		
putative Tom71-Ylr072w complex	curated consensus	YHR117W; YLR072W	TOM71; YLR072W	NO	NO		
putative Flc2-Pdr5 complex	curated consensus	YAL053W; YOR153W	FLC2; PDR5	NO	NO		
putative Ecm30-Ubp15 complex	curated consensus	YLR436C; YMR304W	ECM30; UBP15	NO	NO		
putative Cox20-Chs1 complex	curated consensus	YDR231C; YNL192W	COX20; CHS1	NO	NO		
putative Hca4-Esf1-Esf2 complex	curated consensus	YJL033W; YDR365C; YNR054C	HCA4; ESF1; ESF2	NO	NO	all proteins are involved in 18S rRNA synthesis	
putative Hsp42-Gln1 complex	curated consensus	YDR171W; YPR035W	HSP42; GLN1	NO	NO		
putative Bud6-Yor304c-a complex	curated consensus	YLR319C; YOR304C-A	BUD6; YOR304C-A	NO	NO		
putative Skp1-Ypt52-Ymr258c complex	curated consensus	YDR328C; YKR014C; YMR258C	SKP1; YPT52; YMR258C	NO	NO	Skp1 and Ymr258c are known to interact	11283612
putative Bat1-Bat2 complex	curated consensus	YHR208W; YJR148W	BAT1; BAT2	NO	NO	"Bat1, Bat2 encode for the mitochondrial and cytosolic branched-chain amino acid aminotransferases respectively"	
putative Nfs1-Isd11 complex	curated consensus	YCL017C; YER048W-A	NFS1; ISD11	NO	NO		
putative Ser3-Ser33 isozyme complex	curated consensus	YER081W; YIL074C	SER3; SER33	NO	NO	Ser3 is an isozyme of Ser33	12525494
putative Slx5-Swa2 complex	curated consensus	YDL013W; YDR320C	SLX5; SWA2	NO	NO		
putative Yjl070c-Amd1 complex	curated consensus	YJL070C; YML035C	YJL070C; AMD1	NO	NO		
putative Yer071c-Aim21-Cap1-Cap2 complex	curated consensus	YER071C; YIR003W; YIL034C; YKL007W	TDA2; AIM21; CAP2; CAP1	NO	NO	Cap1 and Cap2 are known to form heterodimers	
putative Mob1-Dbf20 complex	curated consensus	YIL106W; YPR111W	MOB1; DBF20	NO	NO	Mob1 is known to form a kinase complex with Dbf2 which shares 80% sequence homology with Dbf20p	
putative Psy2-Rrd1 complex	curated consensus	YNL201C; YIL153W	PSY2; RRD1	NO	NO		
putative Nvj1-Tos4 complex	curated consensus	YHR195W; YLR183C	NVJ1; TOS4	NO	NO		
putative Ark1-Ste4 complex	curated consensus	YDR264C; YOR212W	AKR1; STE4	NO	NO	"Akr1 acts as a negative regulator of the pheromone response pathway, potentially through Ste4p"	8524293; 8649369
putative Sla2-Lsb3 complex	curated consensus	YNL243W; YFR024C-A	SLA2; LSB3	NO	NO		
putative Cyc3-Yat1 complex	curated consensus	YAL039C; YAR035W	CYC3; YAT1	NO	NO		
putative Uba1-Ydr415c complex	curated consensus	YKL210W; YDR415C	UBA1; YDR415C	NO	NO		
putative Las17-Sla1-Vrp1 complex	curated consensus	YLR337C; YBL007C; YOR181W	VRP1; SLA1; LAS17	NO	NO		
putative Ela1-Tys1 complex	curated consensus	YNL230C; YGR185C	ELA1; TYS1	NO	NO		
putative Dre2-Tah18 complex	curated consensus	YKR071C; YPR048W	DRE2; TAH18	NO	NO	Both Dre2 and Tah18 show synthetic lethal interactions with pol3-13 allele	
putative Kex2-Sil1 complex	curated consensus	YNL238W; YOL031C	KEX2; SIL1	NO	NO		
putative Ssl2-Yor352w complex	curated consensus	YIL143C; YOR352W	SSL2; YOR352W	NO	NO		
putative Tdh3-Pgk1-Eno2-Fba1-Pgm1 complex	curated consensus	YGR192C; YCR012W; YHR174W; YKL060C; YKL152C	TDH3; PGK1; ENO2; FBA1; GPM1	NO	NO	All proteins are involved in gluconeogenesis	
putative Cin8-Zwf1 complex	curated consensus	YEL061C; YNL241C	CIN8; ZWF1	NO	NO		
putative Pcm1-Mgs1 complex	curated consensus	YEL058W; YNL218W	PCM1; MGS1	NO	NO		
putative Yef1-Utr1 complex	curated consensus	YEL041W; YJR049C	YEF1; UTR1	NO	NO	both ATP-NAD kinases	
putative Ost1-Stt3 complex	curated consensus	YJL002C; YGL022W	OST1; STT3	NO	NO	Both proteins are part of the bigger oligosaccharyltransferase complex	
putative Osh2-Swh1 complex	curated consensus	YDL019C; YAR042W	OSH2; SWH1	NO	NO		
putative Sit4-Sap185-Rts3-Hrk1 complex	curated consensus	YDL047W; YJL098W; YGR161C; YOR267C	SIT4; SAP185; RTS3; HRK1	NO	NO	Sit4 and Sap185 are known to be in a complex with eachother	
putative Grh1-Fmp38 complex	curated consensus	YDR517W; YOR205C	GRH1; LRC5	NO	NO		
putative Tif1-Tif2 complex	curated consensus	YKR059W; YJL138C	TIF1; TIF2	NO	NO	Tif1 and Tif2 are identical	
putative Sah1-Caf16 complex	curated consensus	YER043C; YFL028C	SAH1; CAF16	NO	NO	Caf16 is a member of CCR4-NOT complex	
putative Bre1-Lge1 complex	curated consensus	YDL074C; YPL055C	BRE1; LGE1	NO	NO		
putative Fmc1-Atp12 complex	curated consensus	YIL098C; YJL180C	FMC1; ATP12	NO	NO	Fmc1 is thought to hel the folding-stability or functioning of At12p	
putative Fpr3-Ssb2 complex	curated consensus	YML074C; YNL209W	FPR3; SSB2	NO	NO		
putative Ptc7-Sec14 complex	curated consensus	YHR076W; YMR079W	PTC7; SEC14	NO	NO		
putative Faa4-Ygl082w complex	curated consensus	YGL082W; YMR246W	YGL082W; FAA4	NO	NO		
putative Ykl088w-Ppz1 complex	curated consensus	YKL088W; YML016C	CAB3; PPZ1	NO	NO		
putative Hmt1-Scd6-Psp2 complex	curated consensus	YBR034C; YPR129W; YML017W	HMT1; SCD6; PSP2	NO	NO	Scd6 (Lsm13p) associates with methyltransferases (such as Hmt1p)	
putative Eft1-Eft2 complex	curated consensus	YOR133W; YDR385W	EFT1; EFT2	NO	NO	Both Eft1 and Eft2 encode for Elongation factor 2	
putative Mnl1-Pdi1 complex	curated consensus	YHR204W; YCL043C	MNL1; PDI1	NO	NO	"both proteins located in the ER lumen, Pdi1 involved in formation disulfide bonds for secretory and cell-surface proteins, Mnl1 involved in degradation of glycoproteins"	
putative Nnf2-Yel043w complex	curated consensus	YEL043W; YGR089W	YEL043W; NNF2	NO	NO		
putative Yae1-Ynl260c complex	curated consensus	YJR067C; YNL260C	YAE1; YNL260C	NO	NO		
putative Erv46-Erv41-Ero1 complex	curated consensus	YAL042W; YML067C; YML130C	ERV46; ERV41; ERO1	NO	NO	Erv46 and Erv41 are known to be in the same complex	11157978
putative Sok1-Rtn1-Crp1-Ids2-Pep4 complex	curated consensus	YDR006C; YDR233C; YHR146W; YJL146W; YPL154C	SOK1; RTN1; CRP1; IDS2; PEP4	NO	NO		
putative Vac8-Nce102 complex	curated consensus	YEL013W; YPR149W	VAC8; NCE102	NO	NO		
putative Tma20-Tma22 complex	curated consensus	YER007C-A; YJR014W	TMA20; TMA22	NO	NO		
putative Wbp1-Swp1 complex	curated consensus	YEL002C; YMR149W	WBP1; SWP1	NO	NO	Both proteins are part of the bigger oligosaccharyltransferase complex	
putative Ubc4-Ufd4 complex	curated consensus	YBR082C; YKL010C	UBC4; UFD4	NO	NO		
putative Sfp1-Mrs6 complex	curated consensus	YLR403W; YOR370C	SFP1; MRS6	NO	NO		
putative Trm3-Fas1 complex	curated consensus	YDL112W; YKL182W	TRM3; FAS1	NO	NO		
putative Ste23-Mrn1 complex	curated consensus	YLR389C; YPL184C	STE23; MRN1	NO	NO		
putative Drn1-Dbr1 complex	curated consensus	YGR093W; YKL149C	DRN1; DBR1	NO	NO		
putative Yak1-Ypl247c complex	curated consensus	YJL141C; YPL247C	YAK1; YPL247C	NO	NO		
putative Fap1-Fpr1-Yil161w complex	curated consensus	YNL135C; YNL023C; YIL161W	FPR1; FAP1; YIL161W	NO	NO		
putative Crn1-Inp52-Bsp1 complex	curated consensus	YLR429W; YNL106C; YPR171W	CRN1; INP52; BSP1	NO	NO		
putative Uga1-Ndt80 complex	curated consensus	YGR019W; YHR124W	UGA1; NDT80	NO	NO		
putative Ptc6-Pro2 complex	curated consensus	YCR079W; YOR323C	PTC6; PRO2	NO	NO		
putative Tub3-Gcn1-Gcn20-Gfa1-Mae1-Sam1-Clu1 complex	curated consensus	YML124C; YGL195W; YFR009W; YKL104C; YKL029C; YLR180W; YMR012W	TUB3; GCN1; GCN20; GFA1; MAE1; SAM1; CLU1	NO	NO		
putative Pex5-Mmt1 complex	curated consensus	YDR244W; YMR177W	PEX5; MMT1	NO	NO		
putative Pcl8-Pho85 CDK-cyclin complex	curated consensus	YPL031C; YPL219W	PHO85; PCL8	NO	NO	Pcl8 is known to regulate glycogen synthase through interaction with Pho85p	9032248; 11602261
putative Mba1-Ste50 complex	curated consensus	YBR185C; YCL032W	MBA1; STE50	NO	NO		
putative Ura5-Ura10 isozyme complex	curated consensus	YML106W; YMR271C	URA5; URA10	NO	NO	major and mnior isozymes	
putative Pmr1-Psd1 complex	curated consensus	YGL167C; YNL169C	PMR1; PSD1	NO	NO		
putative Kem1-Gbp2-Sro9-Sbp1 complex	curated consensus	YGL173C; YCL011C; YCL037C; YHL034C	KEM1; GBP2; SRO9; SBP1	NO	NO		
putative Ipp1-Tus1-Ypl066w complex	curated consensus	YBR011C; YLR425W; YPL066W	IPP1; TUS1; YPL066W	NO	NO		
putative Ede1-Syp1 complex	curated consensus	YBL047C; YCR030C	EDE1; SYP1	NO	NO		
putative Pex14-Pex17 complex	curated consensus	YGL153W; YNL214W	PEX14; PEX17	NO	NO	"Pex14 and Pex17 are known to associate with eachother but also include Pex13p, Pex5 and Pex7p"	
putative Sum1-Rfm1 complex	curated consensus	YDR310C; YOR279C	SUM1; RFM1	NO	NO		
putative Ptc4-Ydr186c complex	curated consensus	YBR125C; YDR186C	PTC4; YDR186C	NO	NO		
putative Ybr137w-Sgt2-Mdy2-Yor164c complex	curated consensus	YBR137W; YOR007C; YOL111C; YOR164C	YBR137W; SGT2; MDY2; GET4	NO	NO	interaction between Mdy2 and YOR164c has been shown (16702403)	
putative Ygr071c-Vid22-Tbf1 complex	curated consensus	YGR071C; YLR373C; YPL128C	YGR071C; VID22; TBF1	NO	NO		
putative Yhb1-Aco1 complex	curated consensus	YGR234W; YLR304C	YHB1; ACO1	NO	NO		
putative Yjr136c-Ykl033w complex	curated consensus	YJR136C; YKL033W	TTI2; TTI1	NO	NO		
putative Lys20-Lys21 isozyme complex	curated consensus	YDL131W; YDL182W	LYS21; LYS20	NO	NO		
putative Nth1-Bmh1-Bmh2 complex	curated consensus	YDR001C; YDR099W; YER177W	NTH1; BMH2; BMH1	NO	NO	Bmh1 is the major isoform of Bmh2p	
putative Met13-Yml082w complex	curated consensus	YGL125W; YML082W	MET13; YML082W	NO	NO		
putative Pyc1-Pyc2 isozyme complex	curated consensus	YGL062W; YBR218C	PYC1; PYC2	NO	NO	"Pyc2 is an isozyme of Pyc1, only double deletion shows phenotype"	
putative Gir2-Rbg2 complex	curated consensus	YDR152W; YGR173W	GIR2; RBG2	NO	NO		
putative Yhr131c-Rsp5 complex	curated consensus	YHR131C; YER125W	YHR131C; RSP5	NO	NO		
putative Ptc3-Paa1 complex	curated consensus	YBL056W; YDR071C	PTC3; PAA1	NO	NO		
putative Aro3-Bcs1 complex	curated consensus	YDR035W; YDR375C	ARO3; BCS1	NO	NO		
putative Yor251c-Rev1 complex	curated consensus	YOR251C; YOR346W	TUM1; REV1	NO	NO		
putative Cmd1-Mlc1-Myo2-Myo1-Mlc2 complex	curated consensus	YBR109C; YGL106W; YOR326W; YHR023W; YPR188C	CMD1; MLC1; MYO2; MYO1; MLC2	NO	NO		
putative Efg1-Bud22 complex	curated consensus	YMR014W; YGR271C-A	BUD22; EFG1	NO	NO		
putative Hsp42-Sis1 complex	curated consensus	YDR171W; YNL007C	HSP42; SIS1	NO	NO		
putative Ygr017w-Vip1 complex	curated consensus	YGR017W; YLR410W	YGR017W; VIP1	NO	NO		
putative Ygr130c-Ymr031c complex	curated consensus	YGR130C; YMR031C	YGR130C; YMR031C	NO	NO		
putative Put1-Ymr315w complex	curated consensus	YLR142W; YMR315W	PUT1; YMR315W	NO	NO		
putative Crm1-Mir1-Erd2-Tub1-Gea2-Mtr10-Kap104 complex	curated consensus	YGR218W; YJR077C; YBL040C; YML085C; YEL022W; YOR160W; YBR017C	CRM1; MIR1; ERD2; TUB1; GEA2; MTR10; KAP104	NO	NO		
putative Kap95-Nup1 nuclear pore subcomplex	curated consensus	YLR347C; YOR098C	KAP95; NUP1	NO	NO	contains only part of the nuclear pore complex	
putative Emp24-Erv25-Erp3-Erp5 complex	curated consensus	YGL200C; YML012W; YDL018C; YHR110W	EMP24; ERV25; ERP3; ERP5	NO	NO	"Erp3p, Erp5 have protein similarity with Emp24 and Erv25p"	
putative Gdh1-Gdh3 isozyme complex	curated consensus	YOR375C; YAL062W	GDH1; GDH3	NO	NO		
putative Sas3-Nto1-Ylr455w complex	curated consensus	YBL052C; YPR031W; YLR455W	SAS3; NTO1; YLR455W	NO	NO	Sas3 and Nto1 are part of the NuA3 complex	
putative Cwc2-Spp382-Ntr2 complex	curated consensus	YDL209C; YLR424W; YKR022C	CWC2; SPP382; NTR2	NO	NO		
putative Heh2-Erg24 complex	curated consensus	YDR458C; YNL280C	HEH2; ERG24	NO	NO		
putative Sgn1-Ygr250c complex	curated consensus	YGR250C; YIR001C	YGR250C; SGN1	NO	NO		
putative Oca6-Oca5-Oca4-Oca3-Oca1-Oca2 complex	curated consensus	YDR067C; YHL029C; YCR095C; YNL032W; YNL099C; YNL056W	OCA6; OCA5; OCA4; SIW14; OCA1; OCA2	NO	NO		
putative Yll032c-Yml119w complex	curated consensus	YLL032C; YML119W	YLL032C; YML119W	NO	NO		
putative Map1-Ybr030w complex	curated consensus	YBR030W; YLR244C	RKM3; MAP1	NO	NO		
putative core TFIIH Tfb5-Tfb2 subcomplex	curated consensus	YDR079C-A; YPL122C	TFB5; TFB2	NO	NO		
putative Gsy1-Gsy2 complex	curated consensus	YLR258W; YFR015C	GSY2; GSY1	NO	NO	Gsy1 and Gsy2 are similar	
putative Ycp4-Rfs1-Pst2 complex	curated consensus	YCR004C; YBR052C; YDR032C	YCP4; RFS1; PST2	NO	NO	all proteins are members of the flavodoxin-like proteins	
putative Dhr2-Ubp10 complex	curated consensus	YKL078W; YNL186W	DHR2; UBP10	NO	NO		
putative Ats1-Kti11 complex	curated consensus	YAL020C; YBL071W-A	ATS1; KTI11	NO	NO		
putative Yer140w-Slp1 complex	curated consensus	YER140W; YOR154W	YER140W; SLP1	NO	NO		
putative Ipp1-Ack1-Rom2 complex	curated consensus	YBR011C; YDL203C; YLR371W	IPP1; ACK1; ROM2	NO	NO		
putative Ypk1-Ypk2 complex	curated consensus	YKL126W; YMR104C	YPK1; YPK2	NO	NO	Ypk1 and Ypk2 are functionally redundant	
putative Tao3-Yml081w complex	curated consensus	YIL129C; YML081W	TAO3; TDA9	NO	NO		
putative Hrr25-Ltv1-Rio2-Tsr1 complex	curated consensus	YKL143W; YDL060W; YPL204W; YNL207W	LTV1; TSR1; HRR25; RIO2	NO	NO		
putative Arx1-Rsa4-Sda1-Ipi3-Nsa2-Nog2-Bud20-Ipi1-Mdn1 complex	curated consensus	YDR101C; YCR072C; YGR245C; YNL182C; YER126C; YNR053C; YLR074C; YHR085W; YLR106C	ARX1; RSA4; SDA1; IPI3; NSA2; NOG2; BUD20; IPI1; MDN1	NO	NO	most proteins are associated with pre-60S ribosomal particles	
putative Hog1-Rck2 complex	curated consensus	YLR113W; YLR248W	HOG1; RCK2	NO	NO	Hog1 is known to phosphorylate Rck2p	11344302
putative Nup170-Nup53-Hms1 complex	curated consensus	YBL079W; YMR153W; YOR032C	NUP170; NUP53; HMS1	NO	NO		
putative Ade16-Ade17-Sol2 complex	curated consensus	YMR120C; YCR073W-A; YLR028C	ADE17; SOL2; ADE16	NO	NO	Ade17 and Ade17 encode isoforms	
putative Rgd1-Fyv8 complex	curated consensus	YBR260C; YGR196C	RGD1; FYV8	NO	NO		
putative Pet112-Ymr293c complex	curated consensus	YBL080C; YMR293C	PET112; HER2	NO	NO	"petite formation, decreased metabolite accumulation"	
putative Cul3-Yil001w complex	curated consensus	YGR003W; YIL001W	CUL3; YIL001W	NO	NO		
putative Paa1-Ptc2 complex	curated consensus	YDR071C; YER089C	PAA1; PTC2	NO	NO		
putative Ypt1-Dss4 complex	curated consensus	YFL038C; YPR017C	YPT1; DSS4	NO	NO	all proteins involved in post-Golgi vesicle mediated transport	
putative Nma2-Nma1 complex	curated consensus	YGR010W; YLR328W	NMA2; NMA1	NO	NO	both proteins are involved in the NAD salvage pathway	
putative Cia1-Yhr122w-Met18-Nar1 complex	curated consensus	YDR267C; YHR122W; YIL128W; YNL240C	CIA1; YHR122W; MET18; NAR1	NO	NO		
putative Ddi1-Pmt4 complex	curated consensus	YER143W; YJR143C	DDI1; PMT4	NO	NO		
putative Ygr283c-Idp3 complex	curated consensus	YGR283C; YNL009W	YGR283C; IDP3	NO	NO		
putative Abp1-Crn1 complex	curated consensus	YCR088W; YLR429W	ABP1; CRN1	NO	NO	"Abp1 is an activator of the Arp2-3 complex, whereas Crn1 inhibits its function"	
putative Met13-Met12 isozyme complex	curated consensus	YGL125W; YPL023C	MET13; MET12	NO	NO		
putative Boi2-Cdc24 complex	curated consensus	YAL041W; YER114C	CDC24; BOI2	NO	NO		
putative Fun19-Kap123 complex	curated consensus	YAL034C; YER110C	FUN19; KAP123	NO	NO		
putative Ygr283c-Ymr310c complex	curated consensus	YGR283C; YMR310C	YGR283C; YMR310C	NO	NO		
putative Trr1-Trr2 complex	curated consensus	YDR353W; YHR106W	TRR1; TRR2	NO	NO	"Trr1 is part of the cytoplasmic thioredoxin system, Trr2 is part of the mitochondrial thioredoxin system (both thioredoxin reductases)"	
putative Fbp26-Ylr345w complex	curated consensus	YJL155C; YLR345W	FBP26; YLR345W	NO	NO	"Ylr345w show similarity to 6-phosphofructo-2-kinase-fructose-2,6-bisphosphatase enzymes"	
putative Pck1-Eno1 complex	curated consensus	YBL105C; YGR254W	PKC1; ENO1	NO	NO		
putative Tdh1-Tdh2 isozyme complex	curated consensus	YJL052W; YJR009C	TDH1; TDH2	NO	NO		
putative Gdi1-Ypt6-Ypt1 complex	curated consensus	YER136W; YLR262C; YFL038C	GDI1; YPT6; YPT1	NO	NO	all proteins involved in post-Golgi vesicle mediated transport	
putative Bdh1-Bdh2 complex	curated consensus	YAL060W; YAL061W	BDH1; BDH2	NO	NO	"BDH2 has 51% homology with BDH1, putative alcohol dehydrogenase"	
putative Rps0a-Rps0b complex	curated consensus	YGR214W; YLR048W	RPS0A; RPS0B	NO	NO	Rps0a and Rps0b are nearly identical	
putative Ubp13-Yol087c complex	curated consensus	YBL067C; YOL087C	UBP13; DUF1	NO	NO		
putative Pol4-Rpn5 complex	curated consensus	YCR014C; YDL147W	POL4; RPN5	NO	NO		
putative Erg7-Erg27 complex	curated consensus	YHR072W; YLR100W	ERG7; ERG27	NO	NO	both proteins are involved in ergosterol biosynthesis	
putative Rrp7-Ifh1 complex	curated consensus	YCL031C; YLR223C	RRP7; IFH1	NO	NO		
putative Asn1-Asn2 isozyme complex	curated consensus	YGR124W; YPR145W	ASN2; ASN1	NO	NO		
putative Mdm10-Mpm1-Tom40-Yhm2 complex	curated consensus	YAL010C; YJL066C; YMR203W; YMR241W	MDM10; MPM1; TOM40; YHM2	NO	NO		
putative Ybt1-Dak1 complex	curated consensus	YLL048C; YML070W	YBT1; DAK1	NO	NO		
putative Cdc19-Pyk2 isozyme complex	curated consensus	YAL038W; YOR347C	CDC19; PYK2	NO	NO	Cdc19 and Pyk2 both encode pyruvate kinases and can compensate eachothers loss	
putative Pkh1-Mrp8-Pil1-Lsp1 complex	curated consensus	YDR490C; YKL142W; YGR086C; YPL004C	PKH1; MRP8; PIL1; LSP1	NO	NO	Pil1 and Lsp1 are known to be in the same complex (eiosome)	
putative Lsg1-Nmd3-Rei1 complex	curated consensus	YGL099W; YBR267W; YHR170W	LSG1; REI1; NMD3	NO	NO		
putative Taf8-Taf14-Taf2 TFIID subcomplex	curated consensus	YML114C; YPL129W; YCR042C	TAF8; TAF14; TAF2	NO	NO	"All proteins are part of a bigger complex, TFIID"	
putative Ssd1-Psy4-Pph3-Psy2 complex	curated consensus	YDR293C; YBL046W; YDR075W; YNL201C	SSD1; PSY4; PPH3; PSY2	NO	NO		
putative Rim1-Rad52 complex	curated consensus	YCR028C-A; YML032C	RIM1; RAD52	NO	NO		
putative Nqm1-Tal1 complex	curated consensus	YGR043C; YLR354C	NQM1; TAL1	NO	NO		
putative Vab2-Ydr357c-Ykl061w-YGL079w-Ynl086w complex	curated consensus	YDR357C; YKL061W; YEL005C; YGL079W; YNL086W	YDR357C; YKL061W; VAB2; YGL079W; YNL086W	NO	NO		
putative Kap123-Ypr174c complex	curated consensus	YER110C; YPR174C	KAP123; YPR174C	NO	NO		
putative Spe3-Spe4 complex	curated consensus	YLR146C; YPR069C	SPE4; SPE3	NO	NO	both proteins are part of the pantothenic acid biosynthesis pathway	11154694
putative Leu4-Leu9 isozyme complex	curated consensus	YNL104C; YOR108W	LEU4; LEU9	NO	NO		
putative Snf7-Vps4 complex	curated consensus	YLR025W; YPR173C	SNF7; VPS4	NO	NO	Vps4 is needed for dissociation of the ESCRT II complex (of which Snf7 is part of)	
putative Hmg1-Hmg2 isozyme complex	curated consensus	YLR450W; YML075C	HMG2; HMG1	NO	NO		
putative Oye2-Oye3 complex	curated consensus	YHR179W; YPL171C	OYE2; OYE3	NO	NO	Oye2 and Oye3 are homologous	
putative Glt1-Ylr257w complex	curated consensus	YDL171C; YLR257W	GLT1; YLR257W	NO	NO		
spliceosome	curated consensus	YGL120C; YBR065C; YJR050W; YAL032C; YDR364C; YGR278W; YCR063W; YMR213W; YDL209C; YDR416W; YLL036C; YLR117C; YPL151C; YPR101W; YGL128C; YLR424W	PRP43; ECM2; ISY1; PRP45; CDC40; CWC22; BUD31; CEF1; CWC2; SYF1; PRP19; CLF1; PRP46; SNT309; CWC23; SPP382	"NO, not specific enough"	NO	"Different compositions around Ntc20 and Cef1 complexes are known, which overla to a large degree"	
"1,3-beta-glucan synthase complex (GO)"	GeneOntology	YGR032W; YLR342W; YPR165W	GSC2; FKS1; RHO1	YES			
6-phosphofructokinase complex (GO)	GeneOntology	YGR240C; YMR205C	PFK1; PFK2	YES			
90S preribosome (GO)	GeneOntology	YCR057C; YGR081C; YGR103W; YJL010C; snR17a; snR17b	PWP2; SLX9; NOP7; NOP9; SNR17A; SNR17B	YES			
acetolactate synthase complex (GO)	GeneOntology	YCL009C; YMR108W	ILV6; ILV2	YES			
box C/D snoRNP complex (GO)	GeneOntology	YDL014W; YEL026W; YLR197W; YOR310C; snR128; snR13; snR17a; snR17b; snR18; snR190; snR24; snR38; snR39; snR39B; snR4; snR40; snR41; snR47; snR48; snR50; snR51; snR52; snR53; snR54; snR55; snR56; snR57; snR58; snR59; snR60; snR61; snR62; snR63; snR64; snR65; snR66; snR67; snR68; snR69; snR70; snR71; snR72; snR73; snR74; snR75; snR76; snR77; snR78; snR79; snR87	NOP1; SNU13; NOP56; NOP58; SNR128; SNR13; SNR17A; SNR17B; SNR18; SNR190; SNR24; SNR38; SNR39; SNR39B; SNR4; SNR40; SNR41; SNR47; SNR48; SNR50; SNR51; SNR52; SNR53; SNR54; SNR55; SNR56; SNR57; SNR58; SNR59; SNR60; SNR61; SNR62; SNR63; SNR64; SNR65; SNR66; SNR67; SNR68; SNR69; SNR70; SNR71; SNR72; SNR73; SNR74; SNR75; SNR76; SNR77; SNR78; SNR79; SNR87	YES			
box H/ACA snoRNP complex (GO)	GeneOntology	YHR089C; YLR175W; snR10; snR11; snR161; snR189; snR191; snR3; snR30; snR31; snR32; snR33; snR34; snR35; snR36; snR37; snR42; snR43; snR44; snR46; snR49; snR5; snR8; snR80; snR81; snR82; snR83; snR84; snR85; snR86; snR9	GAR1; CBF5; SNR10; SNR11; SNR161; SNR189; SNR191; SNR3; SNR30; SNR31; SNR32; SNR33; SNR34; SNR35; SNR36; SNR37; SNR42; SNR43; SNR44; SNR46; SNR49; SNR5; SNR8; SNR80; SNR81; SNR82; SNR83; SNR84; SNR85; SNR86; SNR9	YES			
calcineurin complex (GO)	GeneOntology	YKL159C; YKL190W; YLR433C; YML057W	RCN1; CNB1; CNA1; CMP2	YES			
CBF3 complex (GO)	GeneOntology	YDR328C; YGR140W; YMR094W; YMR168C	SKP1; CBF2; CTF13; CEP3	YES			
CCR4-NOT complex (GO)	GeneOntology	YFL028C; YGR134W; YKR036C; YNL278W; YNL288W	CAF16; CAF130; CAF4; CAF120; CAF40	YES			
chromatin accessibility complex (GO)	GeneOntology	YDR121W; YGL133W; YJL065C; YOR304W	DPB4; ITC1; DLS1; ISW2	YES			
chromatin assembly complex (GO)	GeneOntology	YER030W; YJL115W; YOL012C	CHZ1; ASF1; HTZ1	YES			
chromatin silencing complex (GO)	GeneOntology	YBR195C; YDR227W; YKR101W; YLR442C	MSI1; SIR4; SIR1; SIR3	YES			
cohesin loading complex (GO)	GeneOntology	YDR180W; YER147C	SCC2; SCC4	YES			
commitment complex (GO)	GeneOntology	YDR240C; YGR074W; YHR086W; YIL061C; YKL074C; YLR116W; YLR147C; YLR298C; YML046W; YMR125W; YPL178W; snR19	SNU56; SMD1; NAM8; SNP1; MUD2; MSL5; SMD3; YHC1; PRP39; STO1; CBC2; SNR19	YES			
Cul3-RING ubiquitin ligase complex (GO)	GeneOntology	YBR114W; YGR003W; YJR052W; YNL230C; YPL046C	RAD16; CUL3; RAD7; ELA1; ELC1	YES			
CURI complex (GO)	GeneOntology	YCL031C; YGR090W; YLR223C; YOR039W; YPR104C	RRP7; UTP22; IFH1; CKB2; FHL1	YES			
cyclin-dependent protein kinase holoenzyme complex (GO)	GeneOntology	YBR135W; YBR160W; YDL127W; YDL179W; YER059W; YGL134W; YGL215W; YHR071W; YIL050W; YNL289W; YOL001W; YPL219W; YPL256C	CKS1; CDC28; PCL2; PCL9; PCL6; PCL10; CLG1; PCL5; PCL7; PCL1; PHO80; PCL8; CLN2	YES			
cytoplasmic dynein complex (GO)	GeneOntology	YDR424C; YDR488C; YKR054C; YMR299C	DYN2; PAC11; DYN1; DYN3	YES			
Dbf4-dependent protein kinase complex (GO)	GeneOntology	YDL017W; YDR052C	CDC7; DBF4	YES			
DNA ligase IV complex (GO)	GeneOntology	YGL090W; YLR265C; YOR005C	LIF1; NEJ1; DNL4	YES			
"DNA-directed RNA polymerase II, holoenzyme (GO)"	GeneOntology	YBR236C; YDL115C; YGR097W	ABD1; IWR1; ASK10	YES			
DSIF complex (GO)	GeneOntology	YGR063C; YML010W	SPT4; SPT5	YES			
dynactin complex (GO)	GeneOntology	YDR106W; YHR129C; YMR294W; YPL174C	ARP10; ARP1; JNM1; NIP100	YES			
ESCRT III complex (GO)	GeneOntology	YKL002W; YKL041W; YLR025W; YMR077C	DID4; VPS24; SNF7; VPS20	YES			
exosome (RNase complex) (GO)	GeneOntology	YOR076C	SKI7	YES			
F-actin capping protein complex (GO)	GeneOntology	YIL034C; YKL007W	CAP2; CAP1	YES			
glutamate synthase complex (GO)	GeneOntology	YDL171C	GLT1	YES			
glycine cleavage complex (GO)	GeneOntology	YAL044C; YDR019C; YFL018C; YMR189W	GCV3; GCV1; LPD1; GCV2	YES			
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO)	GeneOntology	YDR437W; YGR216C; YNL038W; YPL076W; YPL096C-A; YPL175W	GPI19; GPI1; GPI15; GPI2; ERI1; SPT14	YES			
heterogeneous nuclear ribonucleoprotein complex (GO)	GeneOntology	YNL004W; YNL016W	HRB1; PUB1	YES			
heterotrimeric G-protein complex (GO)	GeneOntology	YHR005C; YJR086W; YOR212W	GPA1; STE18; STE4	YES			
high affinity iron permease complex (GO)	GeneOntology	YER145C; YMR058W	FTR1; FET3	YES			
Holliday junction resolvase complex (GO)	GeneOntology	YBR098W; YDR386W	MMS4; MUS81	YES			
i-AAA complex (GO)	GeneOntology	YCL044C; YPR024W	MGR1; YME1	YES			
kinesin complex (GO)	GeneOntology	YBL063W; YEL061C; YGL216W; YMR198W; YPL155C; YPL253C	KIP1; CIN8; KIP3; CIK1; KIP2; VIK1	YES			
mannosyltransferase complex (GO)	GeneOntology	YBR004C; YNL158W	GPI18; PGA1	YES			
MCM complex (GO)	GeneOntology	YBL023C; YBR202W; YEL032W; YGL201C; YLR274W; YPR019W	MCM2; MCM7; MCM3; MCM6; MCM5; MCM4	YES			
Mdm10/Mdm12/Mmm1 complex (GO)	GeneOntology	YAL010C; YLL006W; YOL009C	MDM10; MMM1; MDM12	YES			
mitochondrial inner membrane peptidase complex (GO)	GeneOntology	YEL059C-A; YMR035W; YMR150C	SOM1; IMP2; IMP1	YES			
mitochondrial inner membrane presequence translocase complex (GO)	GeneOntology	YGR033C; YJL104W; YJL143W; YLR008C; YNR017W; YPL063W	TIM21; PAM16; TIM17; PAM18; TIM23; TIM50	YES			
mitochondrial inner membrane protein insertion complex (GO)	GeneOntology	YBR091C; YDL217C; YJL054W; YOR297C	TIM12; TIM22; TIM54; TIM18	YES			
mitochondrial intermembrane space protein transporter complex (GO)	GeneOntology	YEL020W-A; YGR181W; YHR005C-A; YJR135W-A	TIM9; TIM13; TIM10; TIM8	YES			
mitochondrial outer membrane translocase complex (GO)	GeneOntology	YGR082W; YKL195W; YMR203W; YNL070W; YNL121C; YNL131W; YOR045W; YPR133W-A	TOM20; MIA40; TOM40; TOM7; TOM70; TOM22; TOM6; TOM5	YES			
mitochondrial proton-transporting ATP synthase complex (GO)	GeneOntology	YDL130W-A; YDL181W; YGR008C	STF1; INH1; STF2	YES			
"mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO)"	GeneOntology	Q0080; Q0085; Q0130; YDR322C-A; YDR377W; YLR295C; YML081C-A; YOL077W-A; YPR020W	ATP8; ATP6; OLI1; TIM11; ATP17; ATP14; ATP18; ATP19; ATP20	YES			
mitochondrial respiratory chain complex II (GO)	GeneOntology	YDR178W; YKL141W; YKL148C; YLL041C	SDH4; SDH3; SDH1; SDH2	YES			
mitochondrial ribonuclease P complex (GO)	GeneOntology	YML091C	RPM2	YES			
mitochondrial ribosome (GO)	GeneOntology	YDL069C; YGL068W; YKL142W; YPL132W	CBS1; MNP1; MRP8; COX11	YES			
mitochondrial sorting and assembly machinery complex (GO)	GeneOntology	YAL010C; YHR083W; YMR060C; YNL026W	MDM10; SAM35; SAM37; SAM50	YES			
mitotic checkpoint complex (GO)	GeneOntology	YGL116W; YJL013C; YJL030W; YOR026W	CDC20; MAD3; MAD2; BUB3	YES			
monopolin complex (GO)	GeneOntology	YCR086W; YDR439W; YER106W; YPL204W	CSM1; LRS4; MAM1; HRR25	YES			
Mre11 complex (GO)	GeneOntology	YDR369C; YMR224C; YNL250W	XRS2; MRE11; RAD50	YES			
mRNA cap complex (GO)	GeneOntology	YJL124C; YKL204W; YOR276W	LSM1; EAP1; CAF20	YES			
MutLbeta complex (GO)	GeneOntology	YMR167W; YPL164C	MLH1; MLH3	YES			
myosin II complex (GO)	GeneOntology	YHR023W	MYO1	YES			
myosin V complex (GO)	GeneOntology	YAL029C; YOR326W	MYO4; MYO2	YES			
Noc1p-Noc2p complex (GO)	GeneOntology	YDR060W; YOR206W	MAK21; NOC2	YES			
Noc2p-Noc3p complex (GO)	GeneOntology	YLR002C; YOR206W	NOC3; NOC2	YES			
Noc4p-Nop14p complex (GO)	GeneOntology	YDL148C; YPR144C	NOP14; NOC4	YES			
NuA3 histone acetyltransferase complex (GO)	GeneOntology	YBL052C; YJR082C; YOR064C; YPL129W; YPR031W	SAS3; EAF6; YNG1; TAF14; NTO1	YES			
nuclear cap binding complex (GO)	GeneOntology	YMR125W; YPL178W	STO1; CBC2	YES			
nuclear RNA export factor complex (GO)	GeneOntology	YKL186C; YPL169C	MTR2; MEX67	YES			
nuclear SCF ubiquitin ligase complex (GO)	GeneOntology	YFL009W; YIL046W	CDC4; MET30	YES			
nuclear telomere cap complex (GO)	GeneOntology	YBR275C; YDL042C; YDL220C; YDR082W; YDR227W; YGR099W; YLR010C; YLR150W; YLR442C; YLR453C; YNL216W	RIF1; SIR2; CDC13; STN1; SIR4; TEL2; TEN1; STM1; SIR3; RIF2; RAP1	YES			
"nucleolar preribosome, large subunit precursor (GO)"	GeneOntology	YER126C; YGR103W; YLR022C; YLR221C; YNR038W; YPL093W	NSA2; NOP7; SDO1; RSA3; DBP6; NOG1	YES			
"nucleolar preribosome, small subunit precursor (GO)"	GeneOntology	YBR247C; YGR081C; YJL010C; YKL143W; YNL178W	ENP1; SLX9; NOP9; LTV1; RPS3	YES			
nucleotide-excision repair factor 1 complex (GO)	GeneOntology	YML095C; YMR201C; YPL022W	RAD10; RAD14; RAD1	YES			
nucleotide-excision repair factor 3 complex (GO)	GeneOntology	YDR460W; YGR258C	TFB3; RAD2	YES			
nucleotide-excision repair factor 4 complex (GO)	GeneOntology	YBR114W; YJR052W; YKL112W; YPL046C	RAD16; RAD7; ABF1; ELC1	YES			
oligosaccharyl transferase complex (GO)	GeneOntology	YDL232W; YEL002C; YGL022W; YGL226C-A; YJL002C; YML019W; YMR149W; YOR085W; YOR103C	OST4; WBP1; STT3; OST5; OST1; OST6; SWP1; OST3; OST2	YES			
palmitoyltransferase complex (GO)	GeneOntology	YLR246W; YOL110W	ERF2; SHR5	YES			
PCNA complex (GO)	GeneOntology	YBR088C	POL30	YES			
phosphopyruvate hydratase complex (GO)	GeneOntology	YGR254W; YHR174W	ENO1; ENO2	YES			
preribosome (GO)	GeneOntology	YDL166C; YOR056C	FAP7; NOB1	YES			
proteasome complex (GO)	GeneOntology	YBR082C; YDR059C; YDR069C; YDR177W; YEL037C; YGL058W; YGR184C; YHL030W; YHR052W	UBC4; UBC5; DOA4; UBC1; RAD23; RAD6; UBR1; ECM29; CIC1	YES			
proteasome core complex (GO)	GeneOntology	YFL007W	BLM10	YES			
proteasome regulatory particle (GO)	GeneOntology	YDL020C; YFR010W; YGR232W	RPN4; UBP6; NAS6	YES			
protein phosphatase type 1 complex (GO)	GeneOntology	YBR045C; YBR050C; YDR028C; YER054C; YER133W; YLR273C; YOR178C	GIP1; REG2; REG1; GIP2; GLC7; PIG1; GAC1	YES			
RecQ helicase-Topo III complex (GO)	GeneOntology	YLR234W; YMR190C; YPL024W	TOP3; SGS1; RMI1	YES			
RENT complex (GO)	GeneOntology	YDL042C; YFR028C; YJL076W; YPL126W	SIR2; CDC14; NET1; NAN1	YES			
repairosome (GO)	GeneOntology	YBR114W; YEL037C; YER162C; YJR052W	RAD16; RAD23; RAD4; RAD7	YES			
"retromer complex, outer shell (GO)"	GeneOntology	YOR069W; YOR132W	VPS5; VPS17	YES			
Rhp55-Rhp57 complex (GO)	GeneOntology	YDR004W; YDR076W	RAD57; RAD55	YES			
ribonuclease H2 complex (GO)	GeneOntology	YDR279W; YLR154C; YNL072W	RNH202; RNH203; RNH201	YES			
ribonucleoprotein complex (GO)	GeneOntology	YIL149C; YKR095W; YOR198C	MLP2; MLP1; BFR1	YES			
ribonucleoside-diphosphate reductase complex (GO)	GeneOntology	YER070W; YGR180C; YIL066C; YJL026W	RNR1; RNR4; RNR3; RNR2	YES			
RNA polymerase I transcription factor complex (GO)	GeneOntology	YBL014C; YER148W; YJL025W; YKL125W; YML043C	RRN6; SPT15; RRN7; RRN3; RRN11	YES			
RNA polymerase I upstream activating factor complex (GO)	GeneOntology	YBL025W; YLR141W; YMR270C; YOR295W	RRN10; RRN5; RRN9; UAF30	YES			
signal peptidase complex (GO)	GeneOntology	YIR022W; YJR010C-A; YLR066W; YML055W	SEC11; SPC1; SPC3; SPC2	YES			
Sin3 complex (GO)	GeneOntology	YMR053C; YNL309W; YOL004W	STB2; STB1; SIN3	YES			
Slx1-Slx4 complex (GO)	GeneOntology	YBR228W; YLR135W	SLX1; SLX4	YES			
small nuclear ribonucleoprotein complex (GO)	GeneOntology	YER127W; YPR057W; YPR137W	LCP5; BRR1; RRP9	YES			
SNARE complex (GO)	GeneOntology	YAL030W; YGR009C; YPL232W	SNC1; SEC9; SSO1	YES			
sulfite reductase complex (NADPH) (GO)	GeneOntology	YFR030W; YJR137C	MET10; ECM17	YES			
synaptonemal complex (GO)	GeneOntology	YGL249W; YNL088W	ZIP2; TOP2	YES			
telomerase catalytic core complex (GO)	GeneOntology	TLC1; YLR318W	TLC1; EST2	YES			
telomerase holoenzyme complex (GO)	GeneOntology	YIL009C-A; YLR233C	EST3; EST1	YES			
TORC1 complex (GO)	GeneOntology	YHR186C; YJR066W; YKL203C; YNL006W; YPL180W	KOG1; TOR1; TOR2; LST8; TCO89	YES			
TORC2 complex (GO)	GeneOntology	YER093C; YIL105C; YJL058C; YKL203C; YMR068W; YNL006W; YNL047C; YOL078W	TSC11; SLM1; BIT61; TOR2; AVO2; LST8; SLM2; AVO1	YES			
transcription elongation factor complex (GO)	GeneOntology	YER164W; YGR116W; YNL230C; YPL046C; YPR133C	CHD1; SPT6; ELA1; ELC1; SPN1	YES			
transcription factor complex (GO)	GeneOntology	YCR081W; YDR443C; YNL025C; YPL042C; YPR186C	SRB8; SSN2; SSN8; SSN3; PZF1	YES			
transcription factor TFIIIB complex (GO)	GeneOntology	YER148W; YGR246C; YNL039W	SPT15; BRF1; BDP1	YES			
translocon complex (GO)	GeneOntology	YBR283C; YDR086C; YER019C-A; YER087C-B; YLR378C	SSH1; SSS1; SBH2; SBH1; SEC61	YES			
tRNA-intron endonuclease complex (GO)	GeneOntology	YAR008W; YLR105C; YMR059W; YPL083C	SEN34; SEN2; SEN15; SEN54	YES			
ubiquitin conjugating enzyme complex (GO)	GeneOntology	YDR092W; YGL087C	UBC13; MMS2	YES			
ubiquitin ligase complex (GO)	GeneOntology	YDL013W; YDR219C; YDR306C; YER116C; YER125W; YLR224W; YML111W; YMR275C; YNL311C; YOR057W	SLX5; MFB1; YDR306C; SLX8; RSP5; YLR224W; BUL2; BUL1; YNL311C; SGT1	YES			
UDP-N-acetylglucosamine transferase complex (GO)	GeneOntology	YBR070C; YGL047W	ALG14; ALG13	YES			
vacuolar transporter chaperone complex (GO)	GeneOntology	YER072W; YFL004W; YJL012C; YPL019C	VTC1; VTC2; VTC4; VTC3	YES			
zeta DNA polymerase complex (GO)	GeneOntology	YIL139C; YPL167C	REV7; REV3	YES			
