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Conserved domains on  [gi|42562709|ref|NP_175680|]
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Rubredoxin-like superfamily protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cyt_c_Oxidase_Vb super family cl00016
Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 4-90 4.38e-55

Cytochrome c oxidase subunit Vb. 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 Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.


The actual alignment was detected with superfamily member PLN02294:

Pssm-ID: 444653  Cd Length: 174  Bit Score: 168.12  E-value: 4.38e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562709    4 LDKEYSGRRLLDIDHPESPFGTKESPAVVQSYFDKRNIGCRGGEGEDGHDVVWFWLDKGKSFECPVCSQYFE------HG 77
Cdd:PLN02294  81 LEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFElevvgpGG 160

                         90
                 ....*....|...
gi 42562709   78 PPDGHGDDEDHHH 90
Cdd:PLN02294 161 PPDGHGDDDDHHH 173
 
Name Accession Description Interval E-value
PLN02294 PLN02294
cytochrome c oxidase subunit Vb
 4-90 4.38e-55

cytochrome c oxidase subunit Vb


Pssm-ID: 177931  Cd Length: 174  Bit Score: 168.12  E-value: 4.38e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562709    4 LDKEYSGRRLLDIDHPESPFGTKESPAVVQSYFDKRNIGCRGGEGEDGHDVVWFWLDKGKSFECPVCSQYFE------HG 77
Cdd:PLN02294  81 LEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFElevvgpGG 160

                         90
                 ....*....|...
gi 42562709   78 PPDGHGDDEDHHH 90
Cdd:PLN02294 161 PPDGHGDDDDHHH 173
Cyt_c_Oxidase_Vb cd00924
Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 10-79 1.45e-21

Cytochrome c oxidase subunit Vb. 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 Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.


Pssm-ID: 238464  Cd Length: 97  Bit Score: 80.81  E-value: 1.45e-21
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42562709 10 GRRLLDIDHPESPFGTKESPAVVQSYFDKRNIGCRGGEGEdgHDVVWFWLDKGKSFECPVCSQYF---EHGPP 79
Cdd:cd00924 27 GIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDS--HDVIWMWLEKGKPKRCPECGHVFklvDVGPP 97
COX5B pfam01215
Cytochrome c oxidase subunit Vb;
24-90 3.16e-12

Cytochrome c oxidase subunit Vb;


Pssm-ID: 426131  Cd Length: 128  Bit Score: 57.74  E-value: 3.16e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42562709    24 GTKESPAVVQSYFDKRNIGCRGGEgEDGHDVVWFWLDKGKSFECPVCSQYFEHGPPdghGDDEDHHH 90
Cdd:pfam01215  65 GTMEDPILVPSYDDYRYVGCTGSP-ADSHTVMWLKVSVGKVARCWECGSVYKLNYV---GVPDDDHH 127
 
Name Accession Description Interval E-value
PLN02294 PLN02294
cytochrome c oxidase subunit Vb
 4-90 4.38e-55

cytochrome c oxidase subunit Vb


Pssm-ID: 177931  Cd Length: 174  Bit Score: 168.12  E-value: 4.38e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42562709    4 LDKEYSGRRLLDIDHPESPFGTKESPAVVQSYFDKRNIGCRGGEGEDGHDVVWFWLDKGKSFECPVCSQYFE------HG 77
Cdd:PLN02294  81 LEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFElevvgpGG 160

                         90
                 ....*....|...
gi 42562709   78 PPDGHGDDEDHHH 90
Cdd:PLN02294 161 PPDGHGDDDDHHH 173
Cyt_c_Oxidase_Vb cd00924
Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 10-79 1.45e-21

Cytochrome c oxidase subunit Vb. 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 Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.


Pssm-ID: 238464  Cd Length: 97  Bit Score: 80.81  E-value: 1.45e-21
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42562709 10 GRRLLDIDHPESPFGTKESPAVVQSYFDKRNIGCRGGEGEdgHDVVWFWLDKGKSFECPVCSQYF---EHGPP 79
Cdd:cd00924 27 GIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDS--HDVIWMWLEKGKPKRCPECGHVFklvDVGPP 97
COX5B pfam01215
Cytochrome c oxidase subunit Vb;
24-90 3.16e-12

Cytochrome c oxidase subunit Vb;


Pssm-ID: 426131  Cd Length: 128  Bit Score: 57.74  E-value: 3.16e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42562709    24 GTKESPAVVQSYFDKRNIGCRGGEgEDGHDVVWFWLDKGKSFECPVCSQYFEHGPPdghGDDEDHHH 90
Cdd:pfam01215  65 GTMEDPILVPSYDDYRYVGCTGSP-ADSHTVMWLKVSVGKVARCWECGSVYKLNYV---GVPDDDHH 127
PTZ00043 PTZ00043
cytochrome c oxidase subunit; Provisional
 22-76 1.55e-08

cytochrome c oxidase subunit; Provisional


Pssm-ID: 240240  Cd Length: 268  Bit Score: 49.82  E-value: 1.55e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 42562709   22 PFGTKESPAVVQSYFDKRNIGCRGGEGEDGHDVVWFWLDKGKSFECPVCSQYFEH 76
Cdd:PTZ00043 139 PFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYRCGECDQIFML 193
 
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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