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Conserved domains on  [gi|145332591|ref|NP_001078161|]
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Rubredoxin-like superfamily protein [Arabidopsis thaliana]

Protein Classification

cytochrome c oxidase subunit Vb family protein( domain architecture ID 10010759)

cytochrome c oxidase subunit Vb (COXVb) family protein such as mammalian COXVb (also known as COX5B) and yeast subunit cytochrome c oxidase polypeptide IV (also known as Cox4p), which are components of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN02294 PLN02294
cytochrome c oxidase subunit Vb
 1-175 1.40e-96

cytochrome c oxidase subunit Vb


:

Pssm-ID: 177931  Cd Length: 174  Bit Score: 276.74  E-value: 1.40e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591   1 MWRRIVSSQLKTLAADVVAASPRRSIAATTRPvgFYLAANRSAISASSFVIPRRFSSDS-ETPATKKVEDVMPIATGHEK 79
Cdd:PLN02294   1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRP--LYLSRSRSSISASSSVFSRYFSSESaDTAVKKRVEDVMPIATGHER 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591  80 EELEAELEGRRLDDIDFPEGPFGTKEAPAIVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGP 159
Cdd:PLN02294  79 EELEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGP 158

                        170
                 ....*....|....*.
gi 145332591 160 GGPPDGHGDEDDEHHH 175
Cdd:PLN02294 159 GGPPDGHGDDDDHHHH 174
 
Name Accession Description Interval E-value
PLN02294 PLN02294
cytochrome c oxidase subunit Vb
 1-175 1.40e-96

cytochrome c oxidase subunit Vb


Pssm-ID: 177931  Cd Length: 174  Bit Score: 276.74  E-value: 1.40e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591   1 MWRRIVSSQLKTLAADVVAASPRRSIAATTRPvgFYLAANRSAISASSFVIPRRFSSDS-ETPATKKVEDVMPIATGHEK 79
Cdd:PLN02294   1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRP--LYLSRSRSSISASSSVFSRYFSSESaDTAVKKRVEDVMPIATGHER 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591  80 EELEAELEGRRLDDIDFPEGPFGTKEAPAIVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGP 159
Cdd:PLN02294  79 EELEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGP 158

                        170
                 ....*....|....*.
gi 145332591 160 GGPPDGHGDEDDEHHH 175
Cdd:PLN02294 159 GGPPDGHGDDDDHHHH 174
Cyt_c_Oxidase_Vb cd00924
Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 65-157 1.88e-31

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: 108.93  E-value: 1.88e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591  65 KKVEDVMPIATGHEKEELEAELEGRRLDDIDFPEGPFGTKEAPAIVKSYYDKRIVGCPGgeGEDEHDVVWFWLEKGKSFE 144
Cdd:cd00924    4 GEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCIC--EPDSHDVIWMWLEKGKPKR 81

                         90
                 ....*....|...
gi 145332591 145 CPVCTQYFELEVV 157
Cdd:cd00924   82 CPECGHVFKLVDV 94
COX5B pfam01215
Cytochrome c oxidase subunit Vb;
102-175 4.37e-15

Cytochrome c oxidase subunit Vb;


Pssm-ID: 426131  Cd Length: 128  Bit Score: 67.75  E-value: 4.37e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 145332591  102 GTKEAPAIVKSYYDKRIVGCPGGEgEDEHDVVWFWLEKGKSFECPVCTQYFELEVVgpggppdghGDEDDEHHH 175
Cdd:pfam01215  65 GTMEDPILVPSYDDYRYVGCTGSP-ADSHTVMWLKVSVGKVARCWECGSVYKLNYV---------GVPDDDHHH 128
 
Name Accession Description Interval E-value
PLN02294 PLN02294
cytochrome c oxidase subunit Vb
 1-175 1.40e-96

cytochrome c oxidase subunit Vb


Pssm-ID: 177931  Cd Length: 174  Bit Score: 276.74  E-value: 1.40e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591   1 MWRRIVSSQLKTLAADVVAASPRRSIAATTRPvgFYLAANRSAISASSFVIPRRFSSDS-ETPATKKVEDVMPIATGHEK 79
Cdd:PLN02294   1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRP--LYLSRSRSSISASSSVFSRYFSSESaDTAVKKRVEDVMPIATGHER 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591  80 EELEAELEGRRLDDIDFPEGPFGTKEAPAIVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGP 159
Cdd:PLN02294  79 EELEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGP 158

                        170
                 ....*....|....*.
gi 145332591 160 GGPPDGHGDEDDEHHH 175
Cdd:PLN02294 159 GGPPDGHGDDDDHHHH 174
Cyt_c_Oxidase_Vb cd00924
Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 65-157 1.88e-31

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: 108.93  E-value: 1.88e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145332591  65 KKVEDVMPIATGHEKEELEAELEGRRLDDIDFPEGPFGTKEAPAIVKSYYDKRIVGCPGgeGEDEHDVVWFWLEKGKSFE 144
Cdd:cd00924    4 GEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCIC--EPDSHDVIWMWLEKGKPKR 81

                         90
                 ....*....|...
gi 145332591 145 CPVCTQYFELEVV 157
Cdd:cd00924   82 CPECGHVFKLVDV 94
COX5B pfam01215
Cytochrome c oxidase subunit Vb;
102-175 4.37e-15

Cytochrome c oxidase subunit Vb;


Pssm-ID: 426131  Cd Length: 128  Bit Score: 67.75  E-value: 4.37e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 145332591  102 GTKEAPAIVKSYYDKRIVGCPGGEgEDEHDVVWFWLEKGKSFECPVCTQYFELEVVgpggppdghGDEDDEHHH 175
Cdd:pfam01215  65 GTMEDPILVPSYDDYRYVGCTGSP-ADSHTVMWLKVSVGKVARCWECGSVYKLNYV---------GVPDDDHHH 128
PTZ00043 PTZ00043
cytochrome c oxidase subunit; Provisional
 99-154 3.04e-12

cytochrome c oxidase subunit; Provisional


Pssm-ID: 240240  Cd Length: 268  Bit Score: 62.91  E-value: 3.04e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 145332591  99 GPFGTKEAPAIVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFEL 154
Cdd:PTZ00043 138 GPFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYRCGECDQIFML 193
zf-CHCC pfam10276
Zinc-finger domain; This is a short zinc-finger domain conserved from fungi to humans. It is ...
 117-148 3.30e-03

Zinc-finger domain; This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C.


Pssm-ID: 463041  Cd Length: 37  Bit Score: 34.05  E-value: 3.30e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 145332591  117 RIVGCPGGEGEDEHDVVWFWLEKGKSFECPVC 148
Cdd:pfam10276   2 RRVACDGGGGALGHPRVYINLDKPGPVECPYC 33
 
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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