Table S3. Members of selected mitochondrial protein complexes.
Yeast
ORF
YAL044C
YDR019C
YMR189W
YBR221C
YER178W
YGR193C
YNL071W
YER017C
YGR132C
YGR231C
YMR089C
YPR024W
YDL085W
YML120C
YMR145C
YDR178W
YKL141W
YKL148C
YLL041C
YBR044C
Q0105
YBL045C
YDR529C
YEL024W
YFR033C
YGR183C
YHR001W-A
YJL166W
YOR065W
YPR191W
YPL215W
Q0045
Q0250
Q0275
YDL067C
YGL187C
YGL191W
YHR051W
YIL111W
YLR038C
YLR395C
YMR256C
YNL052W
YBR024W
Gene Mitochondrial Proteome MitoP2
Protein
NF
F
a
b
c
d
localization ranking score
complex
max maxe
GCV3
MATRIX
H_115
98
GlycineDC
8
8
GCV1
MATRIX
H_078
98
GlycineDC
12
11
GCV2
MATRIX
H_122
97
GlycineDC
22
31
PDB1
MATRIX
H_065
98
PDH
18
20
PDA1
MATRIX
H_061
98
PDH
14
16
PDX1
MATRIX
H_151
98
PDH
10
11
LAT1
MATRIX
H_045
98
PDH
21
27
AFG3
MIM
M_026
98
PROTEASE
4
3
PHB1
MIM
H_064
98
PROTEASE
9
10
PHB2
MIM
H_081
97
PROTEASE
6
9
YTA12
MIM
M_007
98
PROTEASE
4
1
YME1
MIM
H_182
98 PROTEASE (I-AAA) 4
6
MIM
M_027
95
RCC1
5
0
NDI1
MIM
H_050
98
RCC1
24
23
MIM
H_051
98
RCC1
18
18
SDH4
MIM
H_107
98
RCC2
3
2
SDH3
MIM
H_074
98
RCC2
3
3
SDH1
MIM
H_007
98
RCC2
17
14
SDH2
MIM
H_056
98
RCC2
12
6
TCM62
MIM
98
RCC2_Asy
1
1
COB
MIM
97
RCC3
1
0
COR1
MIM
H_006
98
RCC3
29
27
QCR7
MIM
H_019
98
RCC3
10
10
RIP1
MIM
H_028
98
RCC3
12
9
QCR6
MIM
M_158
98
RCC3
2
1
QCR9
MIM
98
RCC3
1
0
QCR10
MIM
H_130
89
RCC3
4
2
QCR8
MIM
H_132
98
RCC3
4
2
CYT1
MIM
H_069
98
RCC3
8
7
QCR2
MIM
H_005
98
RCC3
32
29
CBP3
MITO
H_159
98
RCC3_Asy
7
6
COX1
MIM
H_133
97
RCC4
3
3
COX2
MIM
H_040
97
RCC4
8
5
COX3
MIM
97
RCC4
0
0
COX9
MIM
H_120
97
RCC4
2
2
COX4
MIM
H_018
98
RCC4
9
8
COX13
MIM
H_083
98
RCC4
10
6
COX6
MIM
H_013
98
RCC4
10
12
COX5B
MIM
H_136
98
RCC4
2
3
COX12
MIM
H_108
98
RCC4
3
1
COX8
MIM
M_018
98
RCC4
2
1
COX7
MIM
H_171
97
RCC4
3
2
COX5A
MIM
H_055
98
RCC4
9
9
SCO2
MIM
98
RCC4_Asy
1
1
YBR037C
YBR185C
YDR079W
YDR231C
YER058W
YER141W
YGR062C
YGR112W
YJL003W
YJR034W
YLL009C
YLL018C-A
YML129C
YPL132W
YPL172C
Q0080
Q0085
Q0130
YBL099W
YBR039W
YDL004W
YDL130W-A
YDL181W
YDR298C
YDR322C-A
YDR377W
YGR008C
YJR121W
YKL016C
YLR295C
YML081C-A
YOL077W-A
YPL078C
YPL271W
YPR020W
YIL098C
YJL180C
YLR393W
YNL315C
YDR148C
YFL018C
YGR244C
YIL125W
YKL085W
YLR304C
YNL037C
YNR001C
YOR136W
SCO1
MBA1
PET100
COX20
PET117
COX15
COX18
SHY1
PET191
COX17
COX19
COX14
COX11
COX10
AAP1
ATP6
OLI1
ATP1
ATP3
ATP16
STF1
INH1
ATP5
TIM11
ATP17
STF2
ATP2
ATP7
ATP14
ATP18
ATP19
ATP4
ATP15
ATP20
FMC1
ATP12
ATP10
ATP11
KGD2
LPD1
LSC2
KGD1
MDH1
ACO1
IDH1
CIT1
IDH2
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIMS
MIMS
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MIM
MATRIX
MATRIX
MIM
MATRIX
MATRIX
MATRIX
MATRIX
MATRIX
MATRIX
MATRIX
MATRIX
MATRIX
MATRIX
M_103
M_209
H_145
M_132
M_102
H_208
H_002
H_011
H_070
H_157
H_124
H_012
H_073
H_117
H_008
H_017
H_087
H_109
H_162
H_026
H_071
H_135
M_215
M_147
M_201
H_027
H_021
H_024
H_015
H_020
H_001
H_010
H_004
H_035
98
98
98
97
98
98
97
98
97
98
98
92
98
98
98
51
97
97
98
98
98
93
98
98
89
98
18
98
98
98
98
81
98
98
97
98
98
98
98
98
98
98
98
98
98
98
98
98
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC4_Asy
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5
RCC5_Asy
RCC5_Asy
RCC5_Asy
RCC5_Asy
TCA
TCA
TCA
TCA
TCA
TCA
TCA
TCA
TCA
2
1
0
2
1
4
0
4
1
0
0
0
1
3
1
1
2
0
50
22
9
7
8
13
8
6
0
61
13
5
3
4
17
6
3
2
1
2
2
18
31
19
44
34
67
28
54
19
2
0
0
0
1
4
0
0
0
0
0
0
1
1
0
1
1
0
49
20
9
3
4
10
7
6
0
74
13
5
1
2
17
5
3
1
1
1
1
12
27
19
30
31
47
29
47
17
YOR142W
YPL262W
YPR001W
YBR091C
YDL217C
YEL020W-A
YGR181W
YHR005C-A
YJL054W
YJR135W-A
YOR297C
YFL016C
YIL022W
YJL143W
YJR045C
YNR017W
YOR232W
YPL063W
YGR082W
YHR117W
YMR060C
YMR203W
YNL070W
YNL121C
YNL131W
YOR045W
YPR133W-A
a
LSC1
FUM1
CIT3
MRS5
TIM22
TIM9
TIM13
MRS11
TIM54
TIM8
TIM18
MDJ1
TIM44
TIM17
SSC1
MAS6
MGE1
TOM20
TOM71
TOM37
TOM40
TOM7
TOM70
TOM22
TOM6
TOM5
MATRIX
MATRIX
MATRIX
MIMS
MIM
MIMS
MIMS
MIMS
MIM
MIMS
MIM
MIM
MATRIX
MIM
MATRIX
MIM
MATRIX
MIM
MOM
MOM
MOM
MOM
MOM
MOM
MOM
MOM
MOM
H_034
H_037
H_155
M_064
H_174
M_077
H_141
H_125
H_009
H_183
H_102
H_181
H_206
M_039
H_032
M_017
H_039
H_105
H_147
98
98
98
97
93
94
87
49
97
80
97
98
97
96
98
97
98
89
98
90
98
94
97
97
93
91
97
TCA
TCA
TCA
TIM22/8/13
TIM22/8/13
TIM22/8/13
TIM22/8/13
TIM22/8/13
TIM22/8/13
TIM22/8/13
TIM22/8/13
TIM23
TIM23
TIM23
TIM23
TIM23
TIM23
TIM23
TOM
TOM
TOM
TOM
TOM
TOM
TOM
TOM
TOM
17
21
8
0
0
3
1
3
2
1
1
10
8
0
57
5
8
4
3
3
1
7
2
16
2
0
2
16
14
3
0
0
0
0
1
1
0
0
11
7
0
55
5
10
6
2
2
1
6
2
13
5
0
1
Mitochondrial localization: MITO, mitochondrial with unspecified sub-localization; MOM,
mitochondrial outer membrane; MIMS, mitochondrial intermembrane space; MIM,
mitochondrial inner membrane; MATRIX, mitochondrial matrix.
b
Proteome Ranking: H, High confidence class in proteomics; M, Medium confidence class; L,
Low confidence class; the number indicates the ranking position within each confidence class
according to number of experiments in which the protein was detected; dash by itself means not
detected.
c
Protein complex: GlycineDC, Glycine decarboxylase; NDH, NADH-oxidoreductase; PDH,
Pyruvate dehydrogenase; PROTEASE, mitochondrial protease complex; RCC, mitochondrial
respiratory chain complex (1-5); Asy, assembly factors of the respiratory chain complex;
TIM22/8/13 and TIM23, transport across inner membrane; TOM, transport across outer
membrane.
d
NF max: maximum number of tags detected under non-fermentable growth conditions. eF max:
maximum tag number detected under fermentable media conditions.