Table S4. Members of selected mitochondrial protein complexes.

Yeast

ORF

Gene

 

Mitochondrial

localizationa

Proteome rankingb

MitoP2

score

Protein

complexc

NF

maxd

F

maxe

YAL044C

GCV3

MATRIX

H_115

98

GlycineDC

8

8

YDR019C

GCV1

MATRIX

H_078

98

GlycineDC

12

11

YMR189W

GCV2

MATRIX

H_122

97

GlycineDC

22

31

YBR221C

PDB1

MATRIX

H_065

98

PDH

18

20

YER178W

PDA1

MATRIX

H_061

98

PDH

14

16

YGR193C

PDX1

MATRIX

H_151

98

PDH

10

11

YNL071W

LAT1

MATRIX

H_045

98

PDH

21

27

YER017C

AFG3

MIM

M_026

98

PROTEASE

4

3

YGR132C

PHB1

MIM

H_064

98

PROTEASE

9

10

YGR231C

PHB2

MIM

H_081

97

PROTEASE

6

9

YMR089C

YTA12

MIM

M_007

98

PROTEASE

4

1

YPR024W

YME1

MIM

H_182

98

PROTEASE (I-AAA)

4

6

YDL085W

 

MIM

M_027

95

RCC1

5

0

YML120C

NDI1

MIM

H_050

98

RCC1

24

23

YMR145C

 

MIM

H_051

98

RCC1

18

18

YDR178W

SDH4

MIM

H_107

98

RCC2

3

2

YKL141W

SDH3

MIM

H_074

98

RCC2

3

3

YKL148C

SDH1

MIM

H_007

98

RCC2

17

14

YLL041C

SDH2

MIM

H_056

98

RCC2

12

6

YBR044C

TCM62

MIM

-

98

RCC2_Asy

1

1

Q0105

COB

MIM

-

97

RCC3

1

0

YBL045C

COR1

MIM

H_006

98

RCC3

29

27

YDR529C

QCR7

MIM

H_019

98

RCC3

10

10

YEL024W

RIP1

MIM

H_028

98

RCC3

12

9

YFR033C

QCR6

MIM

M_158

98

RCC3

2

1

YGR183C

QCR9

MIM

-

98

RCC3

1

0

YHR001W-A

QCR10

MIM

H_130

89

RCC3

4

2

YJL166W

QCR8

MIM

H_132

98

RCC3

4

2

YOR065W

CYT1

MIM

H_069

98

RCC3

8

7

YPR191W

QCR2

MIM

H_005

98

RCC3

32

29

YPL215W

CBP3

MITO

H_159

98

RCC3_Asy

7

6

Q0045

COX1

MIM

H_133

97

RCC4

3

3

Q0250

COX2

MIM

H_040

97

RCC4

8

5

Q0275

COX3

MIM

-

97

RCC4

0

0

YDL067C

COX9

MIM

H_120

97

RCC4

2

2

YGL187C

COX4

MIM

H_018

98

RCC4

9

8

YGL191W

COX13

MIM

H_083

98

RCC4

10

6

YHR051W

COX6

MIM

H_013

98

RCC4

10

12

YIL111W

COX5B

MIM

H_136

98

RCC4

2

3

YLR038C

COX12

MIM

H_108

98

RCC4

3

1

YLR395C

COX8

MIM

M_018

98

RCC4

2

1

YMR256C

COX7

MIM

H_171

97

RCC4

3

2

YNL052W

COX5A

MIM

H_055

98

RCC4

9

9

YBR024W

SCO2

MIM

-

98

RCC4_Asy

1

1

YBR037C

SCO1

MIM

M_103

98

RCC4_Asy

2

2

YBR185C

MBA1

MIM

-

98

RCC4_Asy

1

0

YDR079W

PET100

MIM

-

98

RCC4_Asy

0

0

YDR231C

COX20

MIM

M_209

97

RCC4_Asy

2

0

YER058W

PET117

MIM

-

98

RCC4_Asy

1

1

YER141W

COX15

MIM

H_145

98

RCC4_Asy

4

4

YGR062C

COX18

MIM

-

97

RCC4_Asy

0

0

YGR112W

SHY1

MIM

M_132

98

RCC4_Asy

4

0

YJL003W

 

MIM

-

97

RCC4_Asy

1

0

YJR034W

PET191

MIM

-

98

RCC4_Asy

0

0

YLL009C

COX17

MIMS

-

98

RCC4_Asy

0

0

YLL018C-A

COX19

MIMS

-

92

RCC4_Asy

0

0

YML129C

COX14

MIM

-

98

RCC4_Asy

1

1

YPL132W

COX11

MIM

M_102

98

RCC4_Asy

3

1

YPL172C

COX10

MIM

-

98

RCC4_Asy

1

0

Q0080

AAP1

MIM

-

51

RCC5

1

1

Q0085

ATP6

MIM

H_208

97

RCC5

2

1

Q0130

OLI1

MIM

-

97

RCC5

0

0

YBL099W

ATP1

MIM

H_002

98

RCC5

50

49

YBR039W

ATP3

MIM

H_011

98

RCC5

22

20

YDL004W

ATP16

MIM

H_070

98

RCC5

9

9

YDL130W-A

STF1

MIM

H_157

93

RCC5

7

3

YDL181W

INH1

MIM

H_124

98

RCC5

8

4

YDR298C

ATP5

MIM

H_012

98

RCC5

13

10

YDR322C-A

TIM11

MIM

H_073

89

RCC5

8

7

YDR377W

ATP17

MIM

H_117

98

RCC5

6

6

YGR008C

STF2

MIM

-

18

RCC5

0

0

YJR121W

ATP2

MIM

H_008

98

RCC5

61

74

YKL016C

ATP7

MIM

H_017

98

RCC5

13

13

YLR295C

ATP14

MIM

H_087

98

RCC5

5

5

YML081C-A

ATP18

MIM

H_109

98

RCC5

3

1

YOL077W-A

ATP19

MIM

H_162

81

RCC5

4

2

YPL078C

ATP4

MIM

H_026

98

RCC5

17

17

YPL271W

ATP15

MIM

H_071

98

RCC5

6

5

YPR020W

ATP20

MIM

H_135

97

RCC5

3

3

YIL098C

FMC1

MATRIX

M_215

98

RCC5_Asy

2

1

YJL180C

ATP12

MATRIX

-

98

RCC5_Asy

1

1

YLR393W

ATP10

MIM

M_147

98

RCC5_Asy

2

1

YNL315C

ATP11

MATRIX

M_201

98

RCC5_Asy

2

1

YDR148C

KGD2

MATRIX

H_027

98

TCA

18

12

YFL018C

LPD1

MATRIX

H_021

98

TCA

31

27

YGR244C

LSC2

MATRIX

H_024

98

TCA

19

19

YIL125W

KGD1

MATRIX

H_015

98

TCA

44

30

YKL085W

MDH1

MATRIX

H_020

98

TCA

34

31

YLR304C

ACO1

MATRIX

H_001

98

TCA

67

47

YNL037C

IDH1

MATRIX

H_010

98

TCA

28

29

YNR001C

CIT1

MATRIX

H_004

98

TCA

54

47

YOR136W

IDH2

MATRIX

H_035

98

TCA

19

17

YOR142W

LSC1

MATRIX

H_034

98

TCA

17

16

YPL262W

FUM1

MATRIX

H_037

98

TCA

21

14

YPR001W

CIT3

MATRIX

H_155

98

TCA

8

3

YBR091C

MRS5

MIMS

-

97

TIM22/8/13

0

0

YDL217C

TIM22

MIM

-

93

TIM22/8/13

0

0

YEL020W-A

TIM9

MIMS

M_064

94

TIM22/8/13

3

0

YGR181W

TIM13

MIMS

-

87

TIM22/8/13

1

0

YHR005C-A

MRS11

MIMS

H_174

49

TIM22/8/13

3

1

YJL054W

TIM54

MIM

M_077

97

TIM22/8/13

2

1

YJR135W-A

TIM8

MIMS

-

80

TIM22/8/13

1

0

YOR297C

TIM18

MIM

-

97

TIM22/8/13

1

0

YFL016C

MDJ1

MIM

H_141

98

TIM23

10

11

YIL022W

TIM44

MATRIX

H_125

97

TIM23

8

7

YJL143W

TIM17

MIM

-

96

TIM23

0

0

YJR045C

SSC1

MATRIX

H_009

98

TIM23

57

55

YNR017W

MAS6

MIM

H_183

97

TIM23

5

5

YOR232W

MGE1

MATRIX

H_102

98

TIM23

8

10

YPL063W

 

MIM

H_181

89

TIM23

4

6

YGR082W

TOM20

MOM

H_206

98

TOM

3

2

YHR117W

TOM71

MOM

M_039

90

TOM

3

2

YMR060C

TOM37

MOM

-

98

TOM

1

1

YMR203W

TOM40

MOM

H_032

94

TOM

7

6

YNL070W

TOM7

MOM

M_017

97

TOM

2

2

YNL121C

TOM70

MOM

H_039

97

TOM

16

13

YNL131W

TOM22

MOM

H_105

93

TOM

2

5

YOR045W

TOM6

MOM

-

91

TOM

0

0

YPR133W-A

TOM5

MOM

H_147

97

TOM

2

1

 

aMitochondrial localization: MITO, mitochondrial with unspecified sub-localization; MOM, mitochondrial outer membrane; MIMS, mitochondrial intermembrane space; MIM, mitochondrial inner membrane; MATRIX, mitochondrial matrix.

bProteome 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.

cProtein 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.

dNF max: maximum number of tags detected under non-fermentable growth conditions. eF max: maximum tag number detected under fermentable media conditions.