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Conserved domains on  [gi|586765|sp|P38460|]
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RecName: Full=Uncharacterized mitochondrial protein ymf17; AltName: Full=ORF86A

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SdhD super family cl43620
Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];
8-77 1.28e-06

Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];


The actual alignment was detected with superfamily member COG2142:

Pssm-ID: 441745  Cd Length: 124  Bit Score: 42.90  E-value: 1.28e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586765     8 LGHWLLQRITAAFLIPTILI-----------------------ANVSTLILLNILLFWHIHVGIEEILADYVHHEVTRNW 64
Cdd:COG2142  20 THHWLLQRVTAVALVVLVLWflffllslpgadyaevaawfaspFWAILTLLFLLSALYHAWLGLRVVIEDYVHGTGLRLA 99

                        90
                ....*....|...
gi 586765    65 ILILLRVFCLIII 77
Cdd:COG2142 100 LLLLLTLALVALA 112
 
Name Accession Description Interval E-value
SdhD COG2142
Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];
8-77 1.28e-06

Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];


Pssm-ID: 441745  Cd Length: 124  Bit Score: 42.90  E-value: 1.28e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586765     8 LGHWLLQRITAAFLIPTILI-----------------------ANVSTLILLNILLFWHIHVGIEEILADYVHHEVTRNW 64
Cdd:COG2142  20 THHWLLQRVTAVALVVLVLWflffllslpgadyaevaawfaspFWAILTLLFLLSALYHAWLGLRVVIEDYVHGTGLRLA 99

                        90
                ....*....|...
gi 586765    65 ILILLRVFCLIII 77
Cdd:COG2142 100 LLLLLTLALVALA 112
SQR_TypeC_SdhD_like cd03495
Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) ...
 9-77 2.96e-05

Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. E. coli SQR is classified as Type C SQRs because it contains two transmembrane subunits and one heme group. The SdhD and SdhC subunits are membrane anchor subunits containing heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.


Pssm-ID: 239575  Cd Length: 100  Bit Score: 38.73  E-value: 2.96e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586765     9 GHWLLQRITAAFLIPTILIA-----------------------NVSTLILLNILLFWHIHVGIEEILADYVHHEVTRNWI 65
Cdd:cd03495   1 HHWWAQRVTAVALVPLVLWFvfsvalllgasyaevvawlahpfNAILLILTLVSAFYHARLGMQVVIEDYVHSEGLRLAL 80

                        90
                ....*....|..
gi 586765    66 LILLRVFCLIII 77
Cdd:cd03495  81 IIAVKLFAIATA 92
CybS pfam05328
CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several ...
 10-64 2.48e-03

CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterized by the development of benign, vascularised tumours in the head and neck.


Pssm-ID: 461624  Cd Length: 131  Bit Score: 34.13  E-value: 2.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 586765      10 HWLLQRITAAFLIPTILIA----NVSTLI--LLNILLFWHIHVGIEEILADYVHHEVTRNW 64
Cdd:pfam05328  33 HWTFERIVAVGLLPLTPAPfaagSPSPVLdaVLASSLLGHCHIGFQSCIIDYIPKRVYGKW 93
 
Name Accession Description Interval E-value
SdhD COG2142
Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];
8-77 1.28e-06

Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion];


Pssm-ID: 441745  Cd Length: 124  Bit Score: 42.90  E-value: 1.28e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586765     8 LGHWLLQRITAAFLIPTILI-----------------------ANVSTLILLNILLFWHIHVGIEEILADYVHHEVTRNW 64
Cdd:COG2142  20 THHWLLQRVTAVALVVLVLWflffllslpgadyaevaawfaspFWAILTLLFLLSALYHAWLGLRVVIEDYVHGTGLRLA 99

                        90
                ....*....|...
gi 586765    65 ILILLRVFCLIII 77
Cdd:COG2142 100 LLLLLTLALVALA 112
SQR_TypeC_SdhD_like cd03495
Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) ...
 9-77 2.96e-05

Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. E. coli SQR is classified as Type C SQRs because it contains two transmembrane subunits and one heme group. The SdhD and SdhC subunits are membrane anchor subunits containing heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes.


Pssm-ID: 239575  Cd Length: 100  Bit Score: 38.73  E-value: 2.96e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 586765     9 GHWLLQRITAAFLIPTILIA-----------------------NVSTLILLNILLFWHIHVGIEEILADYVHHEVTRNWI 65
Cdd:cd03495   1 HHWWAQRVTAVALVPLVLWFvfsvalllgasyaevvawlahpfNAILLILTLVSAFYHARLGMQVVIEDYVHSEGLRLAL 80

                        90
                ....*....|..
gi 586765    66 LILLRVFCLIII 77
Cdd:cd03495  81 IIAVKLFAIATA 92
CybS pfam05328
CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several ...
 10-64 2.48e-03

CybS, succinate dehydrogenase cytochrome B small subunit; This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterized by the development of benign, vascularised tumours in the head and neck.


Pssm-ID: 461624  Cd Length: 131  Bit Score: 34.13  E-value: 2.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 586765      10 HWLLQRITAAFLIPTILIA----NVSTLI--LLNILLFWHIHVGIEEILADYVHHEVTRNW 64
Cdd:pfam05328  33 HWTFERIVAVGLLPLTPAPfaagSPSPVLdaVLASSLLGHCHIGFQSCIIDYIPKRVYGKW 93
SQR_TypeC_CybS cd03496
SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to ...
 10-57 3.16e-03

SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Eukaryotic SQRs reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. CybS and CybL are the two transmembrane proteins of eukaryotic SQRs. They contain heme and quinone binding sites. CybS is the eukaryotic homolog of the bacterial SdhD subunit. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the transmembrane subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. Mutations in human Complex II result in various physiological disorders including hereditary paraganglioma and pheochromocytoma tumors. The gene encoding for the SdhD subunit is classified as a tumor suppressor gene.


Pssm-ID: 239576  Cd Length: 104  Bit Score: 33.75  E-value: 3.16e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 586765    10 HWLLQRITAAFLIPTILIANVSTLI------LLNILLFWHIHVGIEEILADYVH 57
Cdd:cd03496   6 HWTFERILAVSLLPLTPAAFFAPGLspvmdaALAAALLLHSHWGFESCIIDYVP 59
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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