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Conserved domains on  [gi|947109853|gb|KRH58179|]
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hypothetical protein GLYMA_05G110100v4 [Glycine max]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cyt_c_Oxidase_VIa super family cl00017
Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 1-102 5.54e-48

Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform. Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip in CcO, depending on the presence of cardiolipin and palmitate.


The actual alignment was detected with superfamily member PLN02595:

Pssm-ID: 444654  Cd Length: 102  Bit Score: 148.44  E-value: 5.54e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947109853   1 MATSLVRSGFLRSALRGSARGSQVPKRNFASSGHHDDAYETAKWEKITYLGIVSCTGLAVYNLSKGHPHFKEPPAYPYLH 80
Cdd:PLN02595   1 MATAIVRSALSRAVTRAAPKTSVAPKRNFSSSAGHDDAYEAAKWEKITYLGIASCTALAVYVLSKGHHHGEDPPAYPYMH 80

                         90       100
                 ....*....|....*....|..
gi 947109853  81 IRNKEFPWGPDGLFETKHHEEH 102
Cdd:PLN02595  81 IRNKEFPWGPDGLFEVKHNKEH 102
 
Name Accession Description Interval E-value
PLN02595 PLN02595
cytochrome c oxidase subunit VI protein
 1-102 5.54e-48

cytochrome c oxidase subunit VI protein


Pssm-ID: 178205  Cd Length: 102  Bit Score: 148.44  E-value: 5.54e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947109853   1 MATSLVRSGFLRSALRGSARGSQVPKRNFASSGHHDDAYETAKWEKITYLGIVSCTGLAVYNLSKGHPHFKEPPAYPYLH 80
Cdd:PLN02595   1 MATAIVRSALSRAVTRAAPKTSVAPKRNFSSSAGHDDAYEAAKWEKITYLGIASCTALAVYVLSKGHHHGEDPPAYPYMH 80

                         90       100
                 ....*....|....*....|..
gi 947109853  81 IRNKEFPWGPDGLFETKHHEEH 102
Cdd:PLN02595  81 IRNKEFPWGPDGLFEVKHNKEH 102
COX6A pfam02046
Cytochrome c oxidase subunit VIa;
27-92 1.60e-09

Cytochrome c oxidase subunit VIa;


Pssm-ID: 426579 [Multi-domain]  Cd Length: 112  Bit Score: 50.77  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947109853   27 RNFASSGHH-----------------DDAYETAK-WEKITYLGIVSC---TGLAVYNLSKGH-------PHFKEPPAYPY 78
Cdd:pfam02046   6 RRFASSAAGhaaaaenefvrereavkEHAAGTTDlWRKISYYVAIPAlilAGINAYNLENEHwehwehlPPLEERTEYPY 85

                          90
                  ....*....|....
gi 947109853   79 LHIRNKEFPWGpDG 92
Cdd:pfam02046  86 QNIRTKNFFWG-DG 98
Cyt_c_Oxidase_VIa cd00925
Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 30-98 4.72e-09

Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform. Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip in CcO, depending on the presence of cardiolipin and palmitate.


Pssm-ID: 238465 [Multi-domain]  Cd Length: 86  Bit Score: 48.91  E-value: 4.72e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 947109853  30 ASSGHHddAYETAK-WEKITYLGIVSCTGLAVYNLSKGHPHFK-----EPPAYPYLHIRNKEFPWGpDG---LFETKH 98
Cdd:cd00925    3 AAKGEH--AAGTSElWKKISFYVALPAVALCMLNAYLKHKEHEeherpEFVEYEHLNIRTKPFPWG-DGnktLFHNPH 77
 
Name Accession Description Interval E-value
PLN02595 PLN02595
cytochrome c oxidase subunit VI protein
 1-102 5.54e-48

cytochrome c oxidase subunit VI protein


Pssm-ID: 178205  Cd Length: 102  Bit Score: 148.44  E-value: 5.54e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947109853   1 MATSLVRSGFLRSALRGSARGSQVPKRNFASSGHHDDAYETAKWEKITYLGIVSCTGLAVYNLSKGHPHFKEPPAYPYLH 80
Cdd:PLN02595   1 MATAIVRSALSRAVTRAAPKTSVAPKRNFSSSAGHDDAYEAAKWEKITYLGIASCTALAVYVLSKGHHHGEDPPAYPYMH 80

                         90       100
                 ....*....|....*....|..
gi 947109853  81 IRNKEFPWGPDGLFETKHHEEH 102
Cdd:PLN02595  81 IRNKEFPWGPDGLFEVKHNKEH 102
COX6A pfam02046
Cytochrome c oxidase subunit VIa;
27-92 1.60e-09

Cytochrome c oxidase subunit VIa;


Pssm-ID: 426579 [Multi-domain]  Cd Length: 112  Bit Score: 50.77  E-value: 1.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947109853   27 RNFASSGHH-----------------DDAYETAK-WEKITYLGIVSC---TGLAVYNLSKGH-------PHFKEPPAYPY 78
Cdd:pfam02046   6 RRFASSAAGhaaaaenefvrereavkEHAAGTTDlWRKISYYVAIPAlilAGINAYNLENEHwehwehlPPLEERTEYPY 85

                          90
                  ....*....|....
gi 947109853   79 LHIRNKEFPWGpDG 92
Cdd:pfam02046  86 QNIRTKNFFWG-DG 98
Cyt_c_Oxidase_VIa cd00925
Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 30-98 4.72e-09

Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform. Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip in CcO, depending on the presence of cardiolipin and palmitate.


Pssm-ID: 238465 [Multi-domain]  Cd Length: 86  Bit Score: 48.91  E-value: 4.72e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 947109853  30 ASSGHHddAYETAK-WEKITYLGIVSCTGLAVYNLSKGHPHFK-----EPPAYPYLHIRNKEFPWGpDG---LFETKH 98
Cdd:cd00925    3 AAKGEH--AAGTSElWKKISFYVALPAVALCMLNAYLKHKEHEeherpEFVEYEHLNIRTKPFPWG-DGnktLFHNPH 77
 
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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