Cul3p-RING ubiquitin ligase complex	GO:0031463	CUL3 ELA1 ELC1 RAD16 RAD7
Nfs1p/Isd11p complex	-	ISD11 NFS1
box C/D snoRNP complex	GO:0032040	NOP58 NOP1 SNU13 SIK1
Rvs161p/Rvs167p complex	-	RVS161 RVS167
Tup1p/Ssn6p complex	GO:0017053	CYC8 TUP1
tRNA Methyltransferase Complex	-	TRM8 TRM82
cytoplasmic ribosomal small subunit	GO:0022627	ASC1 RPS0A RPS0B RPS10A RPS10B RPS11A RPS11B RPS12 RPS13 RPS14A RPS14B RPS15 RPS16A RPS16B RPS17A RPS17B RPS18A RPS18B RPS19A RPS19B RPS1A RPS1B RPS2 RPS20 RPS21A RPS21B RPS22A RPS22B RPS23A RPS23B RPS24A RPS24B RPS25A RPS25B RPS26A RPS26B RPS27A RPS27B RPS28A RPS28B RPS29A RPS29B RPS3 RPS30A RPS30B RPS31 RPS4A RPS4B RPS5 RPS6A RPS6B RPS7A RPS7B RPS8A RPS8B RPS9A RPS9B
Ribosome-associated complex (RAC)	GO:0005840	SSZ1 ZUO1
transcription factor TFIIIC complex	GO:0000127	TFC1 TFC3 TFC4 TFC6 TFC7 TFC8
Cdc28p/Clb1p complex	GO:0000307	CDC28 CLB1
Rix1p complex	-	IPI1 IPI3 RIX1
Phenylalaninine-tRNA-ligase	GO:0009328	FRS1 FRS2
Signal recognition particle (SRP)	GO:0005786	SEC65 SRP14 SRP21 SRP54 SRP68 SRP72
"1,3-beta-glucan synthase complex (Gsc2p/Smk1p)"	GO:0000148	GSC2 SMK1
CCR4-NOT core complex	GO:0030015	CAF130 CAF40 CCR4 CDC36 CDC39 MOT2 NOT3 NOT5 POP2
phosphatidylinositol (PtdIns) 3-kinase complex (functions in CPY sorting)	-	VPS15 VPS30 VPS34 VPS38
Decapping Enzyme Complex	GO:0000932	DCP1 DCP2
"actin cytoskeleton-regulatory complex, Pan1p/Sla1p/End3p complex"	-	END3 PAN1 SLA1
Bi4p/Nam2p complex	-	BI4 NAM2
Cytochrome c oxidase (complex IV)	GO:0005751	COX1 COX12 COX13 COX2 COX3 COX4 COX5A COX6 COX7 COX8 COX9
CCAAT-binding factor complex	GO:0016602	HAP2 HAP3 HAP4 HAP5
protein kinase CK2 complex	GO:0005956	CKA1 CKA2 CKB1 CKB2
Pho85p/Pcl1p complex	GO:0000307	PCL1 PHO85
ribonucleoside-diphosphate reductase complex	GO:0005971	RNR1 RNR2 RNR4
Cdc7p/Dbf4p complex	GO:0031431	CDC7 DBF4
Lge1p/Bre1p complex	-	LGE1 BRE1
Bi3 ribonucleoprotein complex	-	BI3 MRS1
mitochondrial ribosomal large subunit	GO:0005762	IMG1 IMG2 MNP1 MRP20 MRP49 MRP7 MRPL1 MRPL10 MRPL11 MRPL13 MRPL15 MRPL16 MRPL17 MRPL19 MRPL20 MRPL22 MRPL23 MRPL24 MRPL25 MRPL27 MRPL28 MRPL3 MRPL31 MRPL32 MRPL33 MRPL35 MRPL36 MRPL37 MRPL38 MRPL39 MRPL4 MRPL40 MRPL44 MRPL49 MRPL50 MRPL51 MRPL6 MRPL7 MRPL8 MRPL9 RML2 YDR115W YML6 YPL183W-A
Sro1p/Sec4p/Sec9p complex	GO:0031201	SEC4 SEC9 SRO7
eEF1	GO:0005853	CAM1 EFB1 TEF1 TEF2 TEF4
"1,3-beta-glucan synthase complex (Fks1p/Rho1p)"	GO:0000148	FKS1 RHO1
Tof1p/Mrc1p/Csm3p complex	-	CSM3 MRC1 TOF1
CAAX-protein geranylgeranyltransferase complex	GO:0005953	CDC43 RAM2
DNA-directed RNA polymerase III complex	GO:0005666	RET1 RPB10 RPB5 RPB8 RPC10 RPC11 RPC17 RPC19 RPC25 RPC31 RPC34 RPC37 RPC40 RPC53 RPC82 RPO26 RPO31
TORC 2 complex	GO:0031932	AVO1 AVO2 BIT61 LST8 SLM1 SLM2 TOR2 TSC11
polarisome complex	GO:0000133	BUD6 PEA2 SPA2
mRNA cleavage and polyadenylation specificity factor complex	GO:0005847	CFT1 CFT2 FIP1 GLC7 MPE1 PAP1 PFS2 PTA1 PTI1 REF2 SSU72 SWD2 SYC1 YSH1 YTH1
calcineurin complex	GO:0005955	CMP2 CNA1 CNB1
karyopherin docking subcomplex of the Nuclear Pore Complex (NPC)	GO:0005643	ASM4 NUP170 NUP53
ubiquitin conjugating enzyme complex	GO:0031371	MMS2 UBC13
Mps2p/Bbp1p complex	-	BBP1 MPS2 NBP1
Cdc28p/Clb6p complex	GO:0000307	CDC28 CLB6
RNA Degradation Complex	-	RAI1 RAT1 RTT103
nucleotide-excision repair factor 3 complex	GO:0000442	RAD2 RAD3 SSL1 SSL2 TFB1 TFB2 TFB4
HMC Complex	GO:0005844	HSC82 SRO9 SSA3 YDJ1
nascent polypeptide-associated complex	GO:0005854	BTT1 EGD1 EGD2
Ume6p/Ime1p complex	GO:0000508	IME1 UME6
Gip1p/Glc7p complex	GO:0000164	GIP1 GLC7
MBF complex	-	MBP1 SWI6
"alpha-1,6-mannosyltransferase complex(Anp1p/Mnn9p)"	GO:0000136	ANP1 HOC1 MNN10 MNN11 MNN9
protein farnesyltransferase complex	GO:0005965	RAM1 RAM2
FACT complex	GO:0035101	POB3 SPT16
Ubp3p/Bre5p complex	-	BRE5 UBP3
Mto1p/Mss1p complex	-	MSS1 MTO1
nucleotide-excision repair factor 2 complex	GO:0000111	RAD23 RAD4
DNA polymerase epsilon complex	GO:0008622	DPB2 DPB3 DPB4 POL2
Erv41p/Erv46p complex	-	ERV41 ERV46
Rtt109p/Vps75p complex	-	RTT109 VPS75
CBF3 complex	GO:0031518	CBF2 CEP3 CTF13 SKP1
Mlh1p/Mlh3p complex	GO:0032390	MLH1 MLH3
carbamoyl-phosphate synthase complex	GO:0005951	CPA1 CPA2
"H+-transporting ATPase, vacuolar"	GO:0000221	CUP5 PPA1 TFP1 TFP3 VMA10 VMA13 VMA2 VMA4 VMA5 VMA6 VMA7 VMA8 VPH1
Ula1p/Uba3p complex	-	UBA3 ULA1
COMPASS complex	GO:0048188	BRE2 SDC1 SET1 SHG1 SPP1 SWD1 SWD2 SWD3
Sfb3p/Sec23p complex	GO:0030127	SFB3 SEC23
other DNA repair complexes	GO:0033062	RAD55 RAD57
nuclear ubiquitin ligase complex	GO:0019005	CDC53 GRR1 HRT1 SKP1
CURI complex	GO:0032545	CKB2 IFH1 RRP7 UTP22
acetolactate synthase complex	GO:0005948	ILV2 ILV6
Ino2p/Ino4p basic helix-loop-helix heteromeric complex	-	INO2 INO4
ESCRT II complex	GO:0000814	SNF8 VPS25 VPS36
GSE Complex	GO:0030688	GTR1 GTR2 LTV1 MEH1 SLM4
Ntr1p/Ntr2p/Prp43p complex	GO:0005681	SPP382 NTR2 PRP43
Cdc28p/Cln3p complex	GO:0000307	CDC28 CLN3
mitochondrial intermembrane space protein transporter complex	GO:0042719	MRS11 TIM9
Fig4p/Vac14p complex	-	FIG4 VAC14
GINS complex	GO:0000811	PSF1 PSF2 PSF3 SLD5
smc5p-Smc6p complex	GO:0030915	KRE29 MMS21 NSE1 NSE3 NSE4 NSE5 SMC5 SMC6
Def1p/Rad26p complex	-	DEF1 RAD26
F0/F1 ATP synthase (complex V)	GO:0000276	ATP1 ATP14 ATP15 ATP16 ATP17 ATP18 ATP19 ATP2 ATP20 ATP3 ATP4 ATP5 ATP6 ATP7 ATP8 INH1 OLI1 TIM11
mitochondrial sorting and assembly machinery complex	GO:0001401	MDM10 SAM35 SAM37 SAM50
"Cytochrome bc1 complex (Ubiquinol-cytochrome c reductase complex, complex III)"	GO:0005750	COB COR1 CYT1 QCR10 QCR2 QCR6 QCR7 QCR8 QCR9 RIP1
Swr1p complex	GO:0000812	ACT1 ARP4 ARP6 RVB1 RVB2 SWC3 SWC4 SWC5 SWC7 SWR1 VPS71 VPS72 YAF9
retromer complex	GO:0030904	PEP8 VPS17 VPS29 VPS35 VPS5
Hse1p/Vps27p complex	GO:0033565	HSE1 VPS27
6-phosphofructokinase complex	GO:0005945	PFK1 PFK2
RSC complex	GO:0016586	ARP7 ARP9 HTL1 LDB7 NPL6 RSC1 RSC2 RSC3 RSC30 RSC4 RSC58 RSC6 RSC8 RSC9 RTT102 SFH1 STH1
SLIK (SAGA-like) complex	GO:0046695	ADA2 CHD1 GCN5 HFI1 NGG1 RTG2 SGF73 SPT20 SPT3 SPT7 TAF10 TAF12 TAF5 TAF6 TAF9 TRA1 UBP8
Npa2p-containing subcomplex	GO:0030687	DBP6 NOP8 RSA3 URB1 URB2
Sds22p/Glc7p complex	GO:0000164	SDS22 GLC7
Gcn1p/Gcn20p complex	GO:0022626	GCN1 GCN20
luminal surveillance complex	GO:0034099	HRD3 KAR2 YOS9
EKC/KEOPS protein complex	GO:0000408	BUD32 CGI121 GON7 KAE1 PCC1
Nup82 nuclear pore subcomplex	GO:0005643	GLE1 NUP159 NUP82
SF3b complex	GO:0005686	YSF3 CUS1 HSH155 HSH49 RDS3 RSE1
signal peptidase complex	GO:0005787	SEC11 SPC1 SPC2 SPC3
Grh1p/Bug1p complex	-	GRH1 BUG1
methionyl glutamyl tRNA synthetase complex	GO:0017102	ARC1 GUS1 MES1
Cytoplasmic exosome complex	GO:0000177	CSL4 DIS3 MTR3 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 SKI6
Mei5p/Sae3p complex	-	MEI5 SAE3
Kel1p/Kel2p/Lte1p complex	-	KEL2 KEL1 LTE1
DNA replication factor A complex	GO:0005662	RFA1 RFA2 RFA3
Mgm1p/Ugo1p/Fzo1p complex	-	FZO1 MGM1 UGO1
Cdc42p/Ste20p complex	-	CDC42 STE20
Snf1p/Snf4p/Sip1p complex	GO:0031588	SIP1 SNF1 SNF4
Mcm2-7 complex	GO:0042555	MCM5 MCM7 MCM4 MCM2 MCM3 MCM6
mitochondrial inner membrane peptidase complex	GO:0042720	IMP1 IMP2 SOM1
Permease-Oxidase Complex	GO:0033573	FET3 FTR1
TRAMP complex (Air1p)	GO:0031499	AIR1 MTR4 PAP2
Psr1p/Whi2p complex	-	PSR1 WHI2
Hop2p/Mnd1p complex	-	HOP2 MND1
Prp9p/Prp11p/Prp21p complex(SF3a complex)	GO:0005686	PRP11 PRP21 PRP9
Succinate dehydrogenase complex (complex II)	GO:0005749	SDH1 SDH2 SDH3 SDH4
transcription factor TFIIH complex	GO:0000442	CCL1 KIN28 TFB3 RAD3 SSL1 SSL2 TFB1 TFB2 TFB4 TFB5
Cdc28p/Cln2p complex	GO:0000307	CDC28 CLN2
MRX complex	GO:0030870	MRE11 RAD50 XRS2
anthranilate synthase complex	GO:0005950	TRP2 TRP3
Bud14p/Glc7p complex	GO:0000164	BUD14 GLC7
GAL4p/GAL80p complex	-	GAL4 GAL80
NC2 complex	-	BUR6 NCB2
Aurora B-INCENP protein kinase complex	GO:0000778	IPL1 SLI15
Ssh1p translocon complex	GO:0005784	SBH2 SSH1 SSS1
ribonuclease MRP complex	GO:0000172	POP1 POP3 POP4 POP5 POP6 POP7 POP8 RMP1 RPP1 SNM1
SAGA complex	GO:0000124	ADA2 CHD1 GCN5 HFI1 NGG1 SGF11 SGF29 SGF73 SPT20 SPT3 SPT7 SPT8 SUS1 TAF10 TAF12 TAF5 TAF6 TAF9 TRA1 UBP8
PAM complex	GO:0001405	MGE1 PAM16 PAM17 PAM18 SSC1 TIM44
Gcd10p/Gcd14p complex	GO:0031515	GCD10 GCD14
chromatin silencing complex	GO:0005677	SIR2 SIR3 SIR4
mitochondrial ribosomal small subunit	GO:0005763	MRP1 MRP10 MRP13 MRP17 MRP2 MRP21 MRP4 MRP51 MRPS16 MRPS17 MRPS18 MRPS28 MRPS35 MRPS5 MRPS8 MRPS9 NAM9 PET123 PPE1 RSM10 RSM18 RSM19 RSM22 RSM23 RSM24 RSM25 RSM26 RSM27 RSM7 VAR1 YMR31 SWS2
cytoplasmic dynein complex	GO:0005868	DYN1 DYN2 DYN3 PAC11
NatA complex	GO:0031415	ARD1 NAT1 NAT5
RING finger peroxin complex	-	PEX10 PEX12 PEX2
ESCRT I complex	GO:0000813	MVB12 SRN2 STP22 VPS28
nucleotide-excision repair factor 1 complex	GO:0000110	RAD1 RAD10 RAD14
VTC heterotetrameric complex	GO:0033254	VTC1 VTC2 VTC3 VTC4
nucleolar ribonuclease P complex	GO:0005655	POP1 POP3 POP4 POP5 POP6 POP7 POP8 RPR2 RPP1
Nonsense-mediated mRNA decay pathway complex	GO:0005844	NAM7 NMD2 UPF3
Mon1p/Ccz1p complex	-	CCZ1 MON1
ubiquitin ligase ERAD-M complex	GO:0000838	HRD1 HRD3
TRAMP complex (Air2p)	GO:0031499	AIR2 MTR4 PAP2
Sec62p/Sec63p complex	GO:0031207	SEC62 SEC63 SEC66 SEC72
DNA ligase IV	GO:0032807	DNL4 LIF1
DSIF complex	GO:0032044	SPT4 SPT5
Cdc28p/Clb3p complex	GO:0000307	CDC28 CLB3
Pho85p/Pho80p complex	GO:0000307	PHO80 PHO85
Tim8p/Tim13p complex	GO:0042719	TIM13 TIM8
Pho85p/Pcl2p complex	GO:0000307	PCL2 PHO85
chromatin assembly complex	GO:0033186	CAC2 MSI1 RLF2
UTP A complex	GO:0032040	POL5 NAN1 UTP4 UTP8 UTP9 UTP10 UTP15
transcription factor TFIIE complex	GO:0005673	TFA1 TFA2
Sec61p translocon complex	GO:0005784	SBH1 SEC61 SSS1
U4/U6 x U5 tri-snRNP complex	GO:0046540	BRR2 DIB1 LSM2 LSM3 LSM4 LSM5 LSM6 LSM7 LSM8 PRP18 PRP3 PRP31 PRP38 PRP4 PRP6 PRP8 SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3 SNU114 SNU13 SNU23 SNU66 SPP381
GAL3p/GAL80p complex	-	GAL3 GAL80
Noc2p/Noc3p complex	GO:0030691	NOC2 NOC3
Bub2p/Bfa1p complex	-	BUB2 BFA1
Reg1p/Glc7p complex	GO:0000164	REG1 GLC7
mRNA cleavage factor complex (CFI)	GO:0005849	CLP1 HRP1 PCF11 RNA14 RNA15
SAS Complex	-	SAS2 SAS4 SAS5
Ctf3p protein complex	GO:0000778	CTF3 MCM16 MCM22
Mtr2p/Mex67p complex	GO:0042272	MEX67 MTR2
Ela1p/Elc1p complex	GO:0031463	ELA1 ELC1
Golgi transport complex	GO:0017119	COG1 COG2 COG3 COG4 COG5 COG6 COG7 COG8
prohibitin complex	-	PHB1 PHB2
"alpha,alpha-trehalose-phosphate synthase complex (UDP-forming)"	GO:0005946	TPS1 TPS2 TPS3 TSL1
mitotic checkpoint complex	GO:0033597	BUB3 CDC20 MAD2 MAD3
Cbp1p/Pet309p complex	-	CBP1 PET309
heterotrimeric G-protein complex	GO:0005834	GPA1 STE18 STE4
RES complex	GO:0005686	BUD13 PML1 IST3
Cdc24p/Far1p/Gbetagamma protein complex	GO:0005834	CDC24 FAR1 STE18 STE4
multi-eIF complex	GO:0043614	GCD11 NIP1 PRT1 SUI1 SUI2 SUI3 TIF34 TIF5
Set3p complex	GO:0000118	HOS2 HOS4 CPR1 HST1 SET3 SIF2 SNT1
commitment complex	GO:0005685	CBC2 MSL5 MUD2 STO1 SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3 LUC7 MUD1 NAM8 PRP39 PRP40 PRP42 SNP1 SNU56 SNU71 YHC1
RENT complex	GO:0030869	CDC14 NET1 SIR2
MIND complex	GO:0000818	DSN1 MTW1 NNF1 NSL1
Sod1p/Ccs1p complex	-	CCS1 SOD1
Prp19-associated complex	GO:0005681	PRP19 CEF1 ISY1 CLF1 SYF1 SYF2 NTC20 SNT309
Nucleosomal protein complex	GO:0000788	HHF1 HHF2 HHT1 HHT2 HTA1 HTA2 HTB1 HTB2
Rad6p/Rad18p complex	GO:0000502	RAD18 RAD6
U2 snRNP complex	GO:0005686	LEA1 MSL1 RSE1 HSH155 IST3 HSH49 PRP9 PRP11 PRP21 CUS1 CUS2 SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3
Apg12p/Apg5p/Apg16 multimeric complex	-	ATG12 ATG16 ATG5
gamma-tubulin complex	GO:0000928	SPC97 SPC98 TUB4
Exocyst complex	GO:0000145	EXO70 EXO84 SEC10 SEC15 SEC3 SEC5 SEC6 SEC8
Car1p/Arg3p complex	-	ARG3 CAR1
Sgv1p/Bur2p complex	-	BUR2 SGV1
Pho85p/Pcl8p complex	GO:0000307	PCL8 PHO85
SBF complex	-	SWI4 SWI6
i-AAA complex	GO:0031942	MGR1 YME1
DNA-directed RNA polymerase II complex	GO:0005665	RPB10 RPB11 RPB2 RPB3 RPB4 RPB5 RPB7 RPB8 RPB9 RPC10 RPO21 RPO26
DNA polymerase delta complex	GO:0043625	POL3 POL31 POL32
Protein O-mannosyltransferase(Pmt1p/Pmt2p)	-	PMT1 PMT2
COPI	GO:0030126	COP1 GLO3 RET2 RET3 SEC21 SEC26 SEC27 SEC28
ISW1b complex	GO:0016587	IOC2 IOC4 ISW1
transcription factor TFIIA complex	GO:0005672	TOA1 TOA2
Cdc28p/Clb4p complex	GO:0000307	CDC28 CLB4
Vam3p/Vam7 vacuolar tSNARE complex	-	VAM3 VAM7
sulfite reductase complex (NADPH)	GO:0009337	MET10 ECM17
Bni4p/Glc7p complex	GO:0000164	BNI4 GLC7
Mlh1p/Pms1p complex	GO:0032389	MLH1 PMS1
Pxa1p/Pxa2p complex	-	PXA1 PXA2
Mot1p complex	GO:0000126	MOT1 SPT15
Fth1p/Fet5p complex	-	FET5 FTH1
nucleotide-excision repair factor 4 complex	GO:0000113	ABF1 ELC1 RAD16 RAD7
SWI/SNF complex	GO:0016514	ARP7 ARP9 RTT102 SNF11 SNF12 SNF2 SNF5 SNF6 SWI1 SWI3 TAF14 SWP82
signal recognition particle receptor complex	GO:0005785	SRP101 SRP102
SPB components	-	CMD1 CNM67 NUD1 SPC110 SPC29 SPC42 SPC72
Elongator complex	GO:0033588	ELP2 ELP3 ELP4 ELP6 IKI1 IKI3
Gac1p/Glc7p complex	GO:0000164	GAC1 GLC7
Nsp1p complex	GO:0005643	NSP1 NIC96 NUP49 NUP57
eIF1/eIF1A/40S complex	GO:0043614	SUI1 TIF11
Dsl1p complex	-	DSL1 TIP20 SEC20 SEC39 USE1 UFE1
Sko1p/Cyc8p/Tup1 repressor complex	GO:0017053	CYC8 SKO1 TUP1
chaperonin-containing T-complex	GO:0005832	CCT2 CCT3 CCT4 CCT5 CCT6 CCT7 CCT8 TCP1
Met4p/Met28p/Met31p complex	-	MET28 MET31 MET4
palmitoyltransferase complex	GO:0031211	ERF2 SHR5
signalosome complex	GO:0008180	CSI1 CSN12 CSN9 PCI8 RRI1 RRI2
"H+-transporting ATPase, Golgi"	GO:0000221	CUP5 PPA1 STV1 TFP1 TFP3 VMA10 VMA13 VMA2 VMA4 VMA5 VMA6 VMA7 VMA8
OCA complex	-	OCA1 OCA2 SIW14 YCR095C YHL029C YDR067C
Synaptonemal complex (SC)	-	HOP1 RED1 ZIP1 ZIP2
zeta DNA polymerase complex	GO:0016035	REV3 REV7
Tap42p/Pph21p/Rrd2p complex	GO:0000159	TAP42 PPH21 RRD2
Ku complex	GO:0043564	YKU70 YKU80
HAT-B complex	GO:0000123	HAT1 HAT2 HIF1
mitochondrial processing peptidase complex	GO:0017087	MAS1 MAS2
mitochondrial ATPase inhibitor complex	GO:0005753	INH1 STF1 STF2
Ski Complex	-	SKI2 SKI3 SKI8
Geranylgeranyltransferase II (GGTase II)	GO:0005968	BET2 BET4
eIF2	GO:0005850	GCD11 SUI2 SUI3
eIF3	GO:0005852	CLU1 HCR1 NIP1 PRT1 RPG1 TIF34 TIF35
Kornberg's mediator (SRB) complex	GO:0000119	SSN3 SSN8 SRB8 SSN2 CSE2 GAL11 MED1 MED11 MED2 MED4 MED6 MED7 MED8 NUT1 NUT2 PGD1 RGR1 ROX3 SIN4 SRB2 SRB4 SRB5 SRB6 SRB7 SOH1
nuclear cohesin complex	GO:0000798	IRR1 MCD1 REC8 SMC1 SMC3
Rad53p/Asf1p complex	GO:0005678	ASF1 RAD53
histone H2A phosphatase complex	-	PPH3 PSY2 PSY4
U5 snRNP complex	GO:0005682	SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3 SNU114 AAR2 BRR2 PRP8 PRP28 LIN1 DIB1
ER V-ATPase assembly complex	-	VMA22 VPH2
guanyl-nucleotide exchange factor complex	GO:0034066	RGP1 RIC1
Rad17p/Ddc1p/Mec3p complex	-	DDC1 MEC3 RAD17
Sap190p/Sit4p complex	-	SAP190 SIT4
AP-2 adaptor complex	GO:0030122	APL1 APL3 APM4 APS2
UTP C complex	GO:0005956	RRP7 UTP22 CKA1 CKA2 CKB1 CKB2
NatC complex	GO:0031417	MAK10 MAK3 MAK31
"Arg2p/Arg5,6p complex"	-	ARG2 "ARG5,6"
TRAPP complex	GO:0030008	BET3 BET5 GSG1 KRE11 TRS120 TRS130 TRS20 TRS23 TRS31 TRS33
dynactin complex	GO:0005869	ARP1 ARP10 JNM1 NIP100
fatty acid synthase complex	GO:0005835	FAS1 FAS2
Csh1p/Csg2p complex	-	CSG2 CSH1
FBP degradation complex	-	RMD5 GID7 GID8 VID24 VID28 VID30 FYV10 YDL176W
Sap185p/Sit4p complex	-	SAP185 SIT4
Telomerase	GO:0005697	EST1 EST2 EST3
mitochondrial inner membrane protein insertion complex	GO:0042721	MRS5 TIM18 TIM22 TIM54
Mtk1p/Pbp1p complex	GO:0005844	MKT1 PBP1
Sum1p/Rfm1p/Hst1p complex	GO:0000118	HST1 RFM1 SUM1
CORVET complex	GO:0033263	PEP3 PEP5 VPS3 VPS16 VPS33 VPS8
Eisosome	GO:0032126	LSP1 PIL1
Cdc73p/Paf1p complex	GO:0016593	CDC73 CTR9 HPR1 LEO1 PAF1 RTF1 CCR4
transcription factor TFIIIB complex	GO:0000126	BDP1 BRF1 SPT15
mitochondrial pyruvate dehydrogenase complex	GO:0005967	LAT1 LPD1 PDA1 PDB1 PDX1 PKP1 PTC5
cohesin loading factor complex	GO:0032116	SCC2 SCC4
OAF complex	-	OAF1 PIP2
Rtg1p/Rtg3p complex	-	RTG1 RTG3
DNA replication factor C complex (Rcf1p)	GO:0005663	RFC1 RFC2 RFC3 RFC4 RFC5
ARGR complex	-	ARG80 ARG81 ARG82 MCM1
Reg2p/Glc7p complex	GO:0000164	REG2 GLC7
Dop1p/Mon2p complex	-	DOP1 MON2
Nsp1p/Nup82p complex	GO:0005643	NSP1 NUP82
Uba2p/Aos1p complex	GO:0031510	AOS1 UBA2
Esp1p/Pds1p complex	-	ESP1 PDS1
mRNA guanylyl transferase (capping complex)	GO:0031533	CEG1 CET1
RNA polymerase I upstream activating factor complex	GO:0000500	RRN10 RRN5 RRN9 UAF30 HHT1 HHF1
Isocitrate dehydrogenase	GO:0005962	IDH1 IDH2
Kel1p/Kel2p complex	-	KEL1 KEL2
heterodimeric G-protein complex	GO:0005834	STE18 STE4
DNA-directed RNA polymerase I complex	GO:0005736	RPA12 RPA135 RPA14 RPA190 RPA34 RPA43 RPA49 RPB10 RPB5 RPB8 RPC10 RPC19 RPC40 RPO26
transcription factor TFIID complex	GO:0005669	SPT15 TAF1 TAF10 TAF11 TAF12 TAF13 TAF14 TAF2 TAF3 TAF4 TAF5 TAF6 TAF7 TAF8 TAF9
Holliday junction resolvase complex	GO:0048476	MMS4 MUS81
COPII	GO:0030127	EMP24 ERP1 ERP2 ERV25 ERV46 SAR1 SEC13 SEC16 SEC23 SEC24 SEC31
mitochondrial inner membrane presequence translocase complex	GO:0005744	TIM23 PAM16 PAM18 TIM17 TIM21 TIM50
STE5-MAPK complex	-	FUS3 STE11 STE5 STE7
COMA complex	GO:0000817	AME1 CTF19 MCM21 OKP1
Mst27p/Mst28p complex	-	MST27 MST28
mitochondrial oxoglutarate dehydrogenase complex	GO:0009353	KGD1 KGD2 LPD1
Ada2p/Gcn5p/Ada3 transcription activator complex	GO:0005671	ADA2 AHC1 GCN5 HFI1 NGG1
Hym1p/Kic1p/Sog2p complex	-	HYM1 KIC1 SOG2
Swh1p/Nvj1p complex	-	NVJ1 SWH1
DASH complex	GO:0042729	ASK1 DAD1 DAD2 DAD3 DAD4 DAM1 DUO1 HSK3 SPC19 SPC34
Rsp5p/Bul1 ubiquitin ligase complex	GO:0000151	BUL1 RSP5
NuA3 histone acetyltransferase complex	GO:0033100	EAF6 SAS3 TAF14 YNG1 NTO1
Clathrin	GO:0030125	CHC1 CLC1
cAMP-dependent protein kinase	GO:0005952	BCY1 TPK1 TPK2 TPK3
Nem1p/Spo7p complex	-	NEM1 SPO7
Cbf1p/Met4p/Met28p complex	GO:0000776	CBF1 MET28 MET4
Ndc80p complex	GO:0031262	NUF2 SPC24 SPC25 TID3
MSH2p/MSH3p complex	GO:0032302	MSH2 MSH3
UDP-N-acetylglucosamine transferase complex	GO:0043541	ALG13 ALG14
eIF2B	GO:0005851	GCD1 GCD2 GCD6 GCD7 GCN3
Succinyl-CoA ligase	-	LSC1 LSC2
Chs5p/Arf-1binding proteins (ChAPs)	GO:0034044	ARF1 BCH1 BCH2 BUD7 CHS5 CHS6
anaphase-promoting complex	GO:0005680	APC1 APC11 APC2 APC4 APC5 APC9 CDC16 CDC20 CDC23 CDC26 CDC27 CDH1 DOC1 MND2 SWM1
meiotic recombination initiation complex	-	REC102 REC104 SPO11
Protein O-mannosyltransferase(Pmt3p/Pmt5p)	-	PMT3 PMT5
Rpd3L complex	GO:0000508	ASH1 CTI6 DEP1 PHO23 RPD3 RXT2 RXT3 SAP30 SDS3 SIN3 UME1 UME6
Pho85p/Pcl10p complex	GO:0000307	PCL10 PHO85
DNA replication factor C complex (Elg1p)	GO:0031391	ELG1 RFC2 RFC3 RFC4 RFC5
UTP B complex	GO:0034388	DIP2 PWP2 UTP6 UTP13 UTP18 UTP21
cytoplasmic ribosomal large subunit	GO:0022625	RPL10 RPL11A RPL11B RPL12A RPL12B RPL13A RPL13B RPL14A RPL14B RPL15A RPL15B RPL16A RPL16B RPL17A RPL17B RPL18A RPL18B RPL19A RPL19B RPL1A RPL1B RPL20A RPL20B RPL21A RPL21B RPL22A RPL22B RPL23A RPL23B RPL24A RPL24B RPL25 RPL26A RPL26B RPL27A RPL27B RPL28 RPL29 RPL2A RPL2B RPL3 RPL30 RPL31A RPL31B RPL32 RPL33A RPL33B RPL34A RPL34B RPL35A RPL35B RPL36A RPL36B RPL37A RPL37B RPL38 RPL39 RPL40A RPL40B RPL41A RPL41B RPL42A RPL42B RPL43A RPL43B RPL4A RPL4B RPL5 RPL6A RPL6B RPL7A RPL7B RPL8A RPL8B RPL9A RPL9B RPP0 RPP1A RPP1B RPP2A RPP2B
transcription export complex	GO:0000346	SUB2 TEX1 YRA1
U6 snRNP complex	GO:0005688	LSM2 LSM3 LSM4 LSM5 LSM6 LSM7 LSM8 PRP24
DNA replication factor C complex (Ctf18p/Ctf8p/dcc1p)	GO:0031390	CTF18 CTF8 DCC1 RFC2 RFC3 RFC4 RFC5
RAVE complex	GO:0043291	RAV1 RAV2 SKP1
Tap42p/Sit4p/Rrd1p complex	-	RRD1 SIT4 TAP42
RecQ helicase-Topo III complex	GO:0031422	RMI1 SGS1 TOP3
DNA replication factor C complex (Rad24p)	GO:0005663	RAD24 RFC2 RFC3 RFC4 RFC5
Ino80p complex	GO:0031011	ACT1 ARP4 ARP5 ARP8 IES1 IES3 IES4 INO80 NHP10 RVB1 RVB2 TAF14
alpha DNA polymerase:primase complex	GO:0005658	POL1 POL12 PRI1 PRI2
Noc1p/Noc2p complex	GO:0030690	MAK21 NOC2
Polzeta-Rev1p complex	GO:0016035	REV1 REV3 REV7
ESCRT III complex	GO:0000815	DID4 SNF7 VPS20 VPS24
GCR complex	-	GCR1 GCR2
"alpha-1,6-mannosyltransferase complex(Van1p/Mnn9p)"	GO:0000136	MNN9 VAN1
Rpd3S complex	GO:0000509	EAF3 RCO1 RPD3 SIN3 UME1
histone deacetylase complex	GO:0000118	HDA1 HDA2 HDA3
phosphatidylinositol (PtdIns) 3-kinase complex (functions in autophagy)	-	ATG14 VPS15 VPS30 VPS34
mitochondrial outer membrane translocase complex	GO:0005742	TOM20 TOM22 TOM40 TOM5 TOM6 TOM7 TOM70
Mdm12p/Mmm1p/Mdm10p complex	GO:0032865	MDM10 MDM12 MMM1
Mad1p/Mad2p complex	GO:0033597	MAD1 MAD2
Nup84p complex	GO:0005643	NUP84 NUP85 NUP120 NUP145 SEC13 SEH1
chromatin accessibility complex	GO:0008623	DLS1 DPB4 ISW2 ITC1
GARP complex	GO:0000938	VPS51 VPS52 VPS53 VPS54
Mob2p/Cbk1p complex	-	MOB2 CBK1
TORC 1 complex	GO:0031931	KOG1 LST8 TCO89 TOR1
MSH2p/MSH6p complex	GO:0032301	MSH2 MSH6
Png1p/Rad23p complex	GO:0000111	PNG1 RAD23
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex	GO:0000506	ERI1 GPI1 GPI15 GPI19 GPI2 SPT14
Rot2p/Gtb1p complex	GO:0017177	GTB1 ROT2
Rsp5p/Bul2 ubiquitin ligase complex	GO:0000151	BUL2 RSP5
GSH degradosomal complex	-	DUG1 DUG2 DUG3
protein phosphatase type 2A complex (Rts1p)	GO:0000159	PPH21 RTS1 TPD3
Nuclear exosome complex	GO:0000176	CSL4 DIS3 LRP1 MTR3 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SKI6
ribonuclease H2 complex	GO:0032299	RNH201 RNH202 RNH203
Snf1p/Snf4p/Sip2p complex	GO:0031588	SIP2 SNF1 SNF4
Dpb11p/Sld2p complex	GO:0008622	DPB11 SLD2
HOPS complex	GO:0030897	PEP3 PEP5 VAM6 VPS16 VPS33 VPS41
Dcs1p/Dcs2 heterodimer	GO:0000932	DCS1 DCS2
LMA1 complex	-	PBI2 TRX1
Atg20p/Snx4p/Snx41p complex	-	ATG20 SNX4 SNX41
Fatty Acid Import Complex	-	FAA1 FAA4 FAT1
m-AAA complex	GO:0005745	AFG3 YTA12
degradosome	-	DSS1 SUV3
Sac3p/Thp1p complex	GO:0005643	SAC3 THP1
Cdc28p/Cln1p complex	GO:0000307	CDC28 CLN1
translation release factor complex	GO:0018444	SUP35 SUP45
Cdc28p/Clb2p complex	GO:0000307	CDC28 CLB2
Far3p/Far7p/Far8p/Far9p/Far10p/Far11p complex	-	FAR10 FAR11 FAR3 FAR7 FAR8 VPS64
GPI-anchor transamidase complex	GO:0042765	GAA1 GAB1 GPI16 GPI17 GPI8
Noc4p/Nop14p complex	GO:0030692	NOC4 NOP14
Cdc48p complex	GO:0034098	CDC48 UFD1 NPL4
monopolin complex	GO:0033551	LRS4 MAM1 CSM1 HRR25
oligosaccharyl transferase complex	GO:0008250	OST1 OST2 OST3 OST4 OST5 OST6 STT3 SWP1 WBP1
Origin recognition complex	GO:0005664	ORC1 ORC2 ORC3 ORC4 ORC5 ORC6
19/22S regulator	GO:0008541	SEM1 ECM29 UBP6 NAS6 RPN1 RPN10 RPN11 RPN12 RPN13 RPN2 RPN3 RPN5 RPN6 RPN7 RPN8 RPN9 RPT1 RPT2 RPT3 RPT4 RPT5 RPT6
Chz1p/Htz1p/Htb1p complex	GO:0005678	CHZ1 HTB1 HTZ1
THO complex	GO:0000446	HPR1 MFT1 RLR1 THP2
GET complex	GO:0043529	GET1 GET2 GET3
Mlh1p/Mlh2p complex	GO:0032390	MLH1 MLH2
Sli15p/Bir1p complex	GO:0000778	BIR1 SLI15
Cdc28p/Clb5p complex	GO:0000307	CDC28 CLB5
peroxin docking complex	-	PEX13 PEX14 PEX17
RNA polymerase I transcription factor complex	GO:0000120	RRN11 RRN6 RRN7
AP-1 adaptor complex	GO:0030121	APL2 APL4 APM1 APM2 APS1
Slx1p/Slx4p complex	GO:0033557	SLX1 SLX4
PAN complex	GO:0031251	PAN2 PAN3
ISW1a complex	GO:0016587	IOC3 ISW1
HIR complex	GO:0000417	HIR1 HIR2 HIR3 HPC2
EGO complex	-	GTR2 MEH1 SLM4
Gyl1p/Gyp5p complex	-	GYL1 GYP5
Arp2/3 protein complex	GO:0005885	ARC15 ARC18 ARC19 ARC35 ARC40 ARP2 ARP3
transcription factor TFIIF complex	GO:0005674	TAF14 TFG1 TFG2
20S proteasome	GO:0019774	PRE1 PRE10 PRE2 PRE3 PRE4 PRE5 PRE6 PRE7 PRE8 PRE9 PUP1 PUP2 PUP3 SCL1
tRNA-intron endonuclease complex	GO:0000214	SEN15 SEN2 SEN34 SEN54
NatB complex	GO:0031416	MDM20 NAT3
ubiquitin ligase ERAD-L complex	GO:0000839	USA1 DER1 YOS9 HRD1 HRD3
SCF-CDC4 complex	GO:0019005	CDC34 CDC4 CDC53 SGT1 SKP1
nuclear condensin complex	GO:0000799	BRN1 SMC2 SMC4 YCG1 YCS4
AP-3 adaptor complex	GO:0030123	APL5 APL6 APM3 APS3
Slx5p/Slx8p complex	GO:0000151	SLX5 SLX8
Shq1p/Naf1p complex	-	NAF1 SHQ1
Bub1p/Bub3p complex	GO:0033597	BUB1 BUB3
SNARE complex	GO:0031201	SEC9 SSO1 SNC1
Met4p/Met28p/Met32p complex	-	MET28 MET32 MET4
Dig1p/Ste12p/Dig2p complex	-	DIG1 DIG2 STE12
protein phosphatase type 2A complex (Cdc55p)	GO:0000159	CDC55 PPH21 TPD3
U1 snRNP complex	GO:0005685	SMB1 SMD1 SMD2 SMD3 SME1 SMX2 SMX3 LUC7 MUD1 NAM8 PRP39 PRP40 PRP42 SNP1 SNU56 SNU71 YHC1
eIF4F	GO:0016281	CDC33 TIF1 TIF4631
carboxy-terminal domain protein kinase complex	GO:0032806	CTK1 CTK2 CTK3
NuA4 histone acetyltransferase complex	GO:0035267	ACT1 ARP4 EAF3 EAF5 EAF6 EAF7 EPL1 ESA1 SWC4 TRA1 EAF1 YAF9 YNG2
Cox14p/Cox1p/Mss51p complex	GO:0005751	COX1 COX14 MSS51
glycine cleavage complex	GO:0005960	GCV1 GCV2 GCV3 LPD1
adoMet-dependent tRNA methyltransferase (Mtase) Complex	-	TRM11 TRM112
Sno1p/Snz1p complex	-	SNO1 SNZ1
Tubulins	GO:0045298	TUB1 TUB2
serine C-palmitoyltransferase complex	GO:0017059	LCB1 LCB2
Q-biosynthetic Coq polypeptide complex	-	COQ3 COQ4
Mks1p/Rtg2p complex	GO:0046695	MKS1 RTG2
Snf1p/Snf4p/Gal83p complex	GO:0031588	GAL83 SNF1 SNF4
Mob1p/Dbf2p complex	-	DBF2 MOB1
Sap155p/Sit4p complex	-	SAP155 SIT4
prefoldin complex	GO:0016272	GIM3 GIM4 GIM5 PAC10 PFD1 YKE2
Sur1p/Csg2p complex	-	CSG2 SUR1
adenylyl cyclase complex	-	CYR1 SRV2
Csm1p/Lrs4p complex	GO:0033551	CSM1 LRS4
