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Conserved domains on  [gi|472377084|ref|XP_004407975|]
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PREDICTED: succinate dehydrogenase cytochrome b560 subunit, mitochondrial isoform X1 [Odobenus rosmarus divergens]

Protein Classification

succinate:quinone oxidoreductase subunit C( domain architecture ID 10131276)

succinate:quinone oxidoreductase transmembrane subunit C, together with the D subunit, acts to anchor the catalytic components of succinate dehydrogenase to the cytoplasmic membrane

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SQR_TypeC_SdhC cd03499
Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) ...
 50-168 4.05e-39

Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family 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. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. 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: 239579  Cd Length: 117  Bit Score: 128.81  E-value: 4.05e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  50 RPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLFG---LSALLIPGNFEShlelvKSLCLGPSLIYTAKFALVFPLMY 126
Cdd:cd03499    1 RPLSPHLTIYRPPLTAILSILHRITGVALFLGLPLLLwwlLASLSSPESFES-----VSALLGSWLGKLVLFGLTWALFY 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 472377084 127 HTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAA 168
Cdd:cd03499   76 HLLNGIRHLIWDLGKGLELKTVYKSGYAVLVLSVVLTVLLGI 117
 
Name Accession Description Interval E-value
SQR_TypeC_SdhC cd03499
Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) ...
 50-168 4.05e-39

Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family 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. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. 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: 239579  Cd Length: 117  Bit Score: 128.81  E-value: 4.05e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  50 RPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLFG---LSALLIPGNFEShlelvKSLCLGPSLIYTAKFALVFPLMY 126
Cdd:cd03499    1 RPLSPHLTIYRPPLTAILSILHRITGVALFLGLPLLLwwlLASLSSPESFES-----VSALLGSWLGKLVLFGLTWALFY 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 472377084 127 HTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAA 168
Cdd:cd03499   76 HLLNGIRHLIWDLGKGLELKTVYKSGYAVLVLSVVLTVLLGI 117
SdhC COG2009
Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and ...
 49-168 4.22e-25

Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion];


Pssm-ID: 441612  Cd Length: 128  Bit Score: 93.69  E-value: 4.22e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  49 NRPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLF--GLSALLI-PGNFESHLELVKSLclgpsLIYTAKFALVFPLM 125
Cdd:COG2009    6 NRPLSPHLQIYRLPLTMIVSILHRITGVALFLGLPLLvwWLAASASsPEAFAAVQAFLGSP-----LGKLVLLGLTWALL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 472377084 126 YHTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAA 168
Cdd:COG2009   81 YHLLAGIRHLLWDFGYGFELETARRSAWVVLVLSVVLTVLLGV 123
Sdh_cyt pfam01127
Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a ...
 46-166 4.04e-24

Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.


Pssm-ID: 426067  Cd Length: 122  Bit Score: 90.91  E-value: 4.04e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084   46 TDLNRPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLFGLSALLIPGNFESHLELVKSLCLGPSLIYTAK-FALVFPL 124
Cdd:pfam01127   1 MRKNRPLSPHLGLYRAHLTTWLSILHRITGVALAVLGLIFLLLWLLLLLSLLGPESYATVVAWLASPVKLILlLLLLLAL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 472377084  125 MYHTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGL 166
Cdd:pfam01127  81 FYHAANGIRHLIWDVGFGLELKTVRKSGAAVLALSVVLVIVL 122
succ_dehyd_cytB TIGR02970
succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two ...
 49-168 1.14e-21

succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex. In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see TIGR02046). [Energy metabolism, TCA cycle]


Pssm-ID: 274370  Cd Length: 120  Bit Score: 84.54  E-value: 1.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084   49 NRPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLF--GLSALLIpgnFESHLELVKSLCLGPsLIYTAKFALVFPLMY 126
Cdd:TIGR02970   2 QRPLSPHLQIYRFPITAILSILHRITGVLLFFGLPFLlwWLSLSLS---SPESFATVHALLSSP-LGKLILWGLLWALLY 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 472377084  127 HTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAA 168
Cdd:TIGR02970  78 HLLAGIRHLLWDLGYGLELKSARISAWVVLVLSLVLTILAGI 119
PLN00127 PLN00127
succinate dehydrogenase (ubiquinone) cytochrome b subunit; Provisional
 50-169 1.44e-17

succinate dehydrogenase (ubiquinone) cytochrome b subunit; Provisional


Pssm-ID: 177738  Cd Length: 178  Bit Score: 75.69  E-value: 1.44e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  50 RPLSPHI-------TIYSWSLPMAMSICHRGTGVALSAGVSLFGLSALL-IPGNFESHLELVKSLclGPSLIYTAKFALV 121
Cdd:PLN00127  52 RPLSPDVmdidgksTHYKFPVVALSSITNRVTGCVLSGGAAGGGVLALVgGSEAVPATMEGFKSG--GPLIVFPAKFAVS 129

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 472377084 122 FPLMYHTWNGIRHLIWD-LGKGLKIPQLYQSGVAVLVLTVLSSVGLAAM 169
Cdd:PLN00127 130 FPFVYHTLGGLRHLVWDkTTEGLDNPSVEASSYGLFGASAALSAAAAVL 178
 
Name Accession Description Interval E-value
SQR_TypeC_SdhC cd03499
Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) ...
 50-168 4.05e-39

Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family 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. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. 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: 239579  Cd Length: 117  Bit Score: 128.81  E-value: 4.05e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  50 RPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLFG---LSALLIPGNFEShlelvKSLCLGPSLIYTAKFALVFPLMY 126
Cdd:cd03499    1 RPLSPHLTIYRPPLTAILSILHRITGVALFLGLPLLLwwlLASLSSPESFES-----VSALLGSWLGKLVLFGLTWALFY 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 472377084 127 HTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAA 168
Cdd:cd03499   76 HLLNGIRHLIWDLGKGLELKTVYKSGYAVLVLSVVLTVLLGI 117
SdhC COG2009
Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and ...
 49-168 4.22e-25

Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion];


Pssm-ID: 441612  Cd Length: 128  Bit Score: 93.69  E-value: 4.22e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  49 NRPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLF--GLSALLI-PGNFESHLELVKSLclgpsLIYTAKFALVFPLM 125
Cdd:COG2009    6 NRPLSPHLQIYRLPLTMIVSILHRITGVALFLGLPLLvwWLAASASsPEAFAAVQAFLGSP-----LGKLVLLGLTWALL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 472377084 126 YHTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAA 168
Cdd:COG2009   81 YHLLAGIRHLLWDFGYGFELETARRSAWVVLVLSVVLTVLLGV 123
Sdh_cyt pfam01127
Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a ...
 46-166 4.04e-24

Succinate dehydrogenase/Fumarate reductase transmembrane subunit; This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.


Pssm-ID: 426067  Cd Length: 122  Bit Score: 90.91  E-value: 4.04e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084   46 TDLNRPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLFGLSALLIPGNFESHLELVKSLCLGPSLIYTAK-FALVFPL 124
Cdd:pfam01127   1 MRKNRPLSPHLGLYRAHLTTWLSILHRITGVALAVLGLIFLLLWLLLLLSLLGPESYATVVAWLASPVKLILlLLLLLAL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 472377084  125 MYHTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGL 166
Cdd:pfam01127  81 FYHAANGIRHLIWDVGFGLELKTVRKSGAAVLALSVVLVIVL 122
succ_dehyd_cytB TIGR02970
succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two ...
 49-168 1.14e-21

succinate dehydrogenase, cytochrome b556 subunit; In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex. In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see TIGR02046). [Energy metabolism, TCA cycle]


Pssm-ID: 274370  Cd Length: 120  Bit Score: 84.54  E-value: 1.14e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084   49 NRPLSPHITIYSWSLPMAMSICHRGTGVALSAGVSLF--GLSALLIpgnFESHLELVKSLCLGPsLIYTAKFALVFPLMY 126
Cdd:TIGR02970   2 QRPLSPHLQIYRFPITAILSILHRITGVLLFFGLPFLlwWLSLSLS---SPESFATVHALLSSP-LGKLILWGLLWALLY 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 472377084  127 HTWNGIRHLIWDLGKGLKIPQLYQSGVAVLVLTVLSSVGLAA 168
Cdd:TIGR02970  78 HLLAGIRHLLWDLGYGLELKSARISAWVVLVLSLVLTILAGI 119
PLN00127 PLN00127
succinate dehydrogenase (ubiquinone) cytochrome b subunit; Provisional
 50-169 1.44e-17

succinate dehydrogenase (ubiquinone) cytochrome b subunit; Provisional


Pssm-ID: 177738  Cd Length: 178  Bit Score: 75.69  E-value: 1.44e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  50 RPLSPHI-------TIYSWSLPMAMSICHRGTGVALSAGVSLFGLSALL-IPGNFESHLELVKSLclGPSLIYTAKFALV 121
Cdd:PLN00127  52 RPLSPDVmdidgksTHYKFPVVALSSITNRVTGCVLSGGAAGGGVLALVgGSEAVPATMEGFKSG--GPLIVFPAKFAVS 129

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 472377084 122 FPLMYHTWNGIRHLIWD-LGKGLKIPQLYQSGVAVLVLTVLSSVGLAAM 169
Cdd:PLN00127 130 FPFVYHTLGGLRHLVWDkTTEGLDNPSVEASSYGLFGASAALSAAAAVL 178
SQR_QFR_TM cd03493
Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, ...
 69-168 1.68e-14

Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQRs may reduce either high or low potential quinones while QFRs oxidize only low potential quinols. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit(s) containing the electron donor/acceptor (quinol or quinone). The reversible reduction of quinone is an essential feature of respiration, allowing the transfer of electrons between respiratory complexes. SQRs and QFRs can be classified into five types (A-E) according to the number of their hydrophobic subunits and heme groups. This classification is consistent with the characteristics and phylogeny of the catalytic and iron-sulfur subunits. Type E proteins, e.g. non-classical archael SQRs, contain atypical transmembrane subunits and are not included in this hierarchy. The heme and quinone binding sites reside in the transmembrane subunits. Although succinate oxidation and fumarate reduction are carried out by separate enzymes in most organisms, some bifunctional enzymes that exhibit both SQR and QFR activities exist.


Pssm-ID: 239573  Cd Length: 98  Bit Score: 65.38  E-value: 1.68e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472377084  69 ICHRGTGVALSAGVSLFGLSALLIPGNFESHLELVksLCLGPSLIYTAKFALVFPLMYHTWNGIRHLIWDLGKGLKIPQL 148
Cdd:cd03493    1 ILHRITGVALLLFLPLHLLGLLALLGGPYAFAEVV--AFLSSPLGKLLYLLLLLALLYHALNGIRHLIWDYGKGLELKLR 78

                         90       100
                 ....*....|....*....|
gi 472377084 149 YQSGVAVLVLTVLSSVGLAA 168
Cdd:cd03493   79 KALGYAVLALSVLLTVLLLF 98
PLN00126 PLN00126
succinate dehydrogenase, cytochrome b subunit family; Provisional
 49-82 4.04e-03

succinate dehydrogenase, cytochrome b subunit family; Provisional


Pssm-ID: 165695  Cd Length: 129  Bit Score: 35.51  E-value: 4.04e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 472377084  49 NRPLSPHITIYSWSLPMAMSICHRGTGVALSAGV 82
Cdd:PLN00126  81 NRPLSPHLPLKKPQLSATFSISHRIFGAALGAAI 114
 
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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