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Conserved domains on  [gi|225442833|ref|XP_002285331|]
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cytochrome c oxidase subunit 5b-1, mitochondrial [Vitis vinifera]

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
1-166 6.10e-113

cytochrome c oxidase subunit Vb


:

Pssm-ID: 177931  Cd Length: 174  Bit Score: 318.35  E-value: 6.10e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833   1 MWRGRLSAQLQTLARSRSAANLTRLVTGDINRSFISPSPAPFRRTASLFSRQFSAESADNAVskeKKRVEDVMPIATGHE 80
Cdd:PLN02294   1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAV---KKRVEDVMPIATGHE 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833  81 REELEAALDGRDILDADHPVGPFGTKEAPAVVQSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSHECPVCSQYFTLEVIG 160
Cdd:PLN02294  78 REELEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVG 157

                 ....*.
gi 225442833 161 PGGPPP 166
Cdd:PLN02294 158 PGGPPD 163
 
Name Accession Description Interval E-value
PLN02294 PLN02294
cytochrome c oxidase subunit Vb
1-166 6.10e-113

cytochrome c oxidase subunit Vb


Pssm-ID: 177931  Cd Length: 174  Bit Score: 318.35  E-value: 6.10e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833   1 MWRGRLSAQLQTLARSRSAANLTRLVTGDINRSFISPSPAPFRRTASLFSRQFSAESADNAVskeKKRVEDVMPIATGHE 80
Cdd:PLN02294   1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAV---KKRVEDVMPIATGHE 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833  81 REELEAALDGRDILDADHPVGPFGTKEAPAVVQSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSHECPVCSQYFTLEVIG 160
Cdd:PLN02294  78 REELEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVG 157

                 ....*.
gi 225442833 161 PGGPPP 166
Cdd:PLN02294 158 PGGPPD 163
Cyt_c_Oxidase_Vb cd00924
Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
64-161 2.56e-40

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: 131.65  E-value: 2.56e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833  64 KEKKRVEDVMPIATGHEREELEAALDGRDILDADHPVGPFGTKEAPAVVQSYYDKRIVGCPGgeGEDEHDVVWFWLEKGK 143
Cdd:cd00924    1 AAEGEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCIC--EPDSHDVIWMWLEKGK 78
                         90
                 ....*....|....*...
gi 225442833 144 SHECPVCSQYFTLEVIGP 161
Cdd:cd00924   79 PKRCPECGHVFKLVDVGP 96
COX5B pfam01215
Cytochrome c oxidase subunit Vb;
76-166 1.77e-20

Cytochrome c oxidase subunit Vb;


Pssm-ID: 426131  Cd Length: 128  Bit Score: 82.00  E-value: 1.77e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833   76 ATGHEREELEAALDGRDILDaDHPVGP--FGTKEAPAVVQSYYDKRIVGCPGGEgEDEHDVVWFWLEKGKSHECPVCSQY 153
Cdd:pfam01215  36 ATGLERLELLGKLEGIDVFD-MKPLDSsrKGTMEDPILVPSYDDYRYVGCTGSP-ADSHTVMWLKVSVGKVARCWECGSV 113
                          90
                  ....*....|...
gi 225442833  154 FTLEVIGPGGPPP 166
Cdd:pfam01215 114 YKLNYVGVPDDDH 126
 
Name Accession Description Interval E-value
PLN02294 PLN02294
cytochrome c oxidase subunit Vb
1-166 6.10e-113

cytochrome c oxidase subunit Vb


Pssm-ID: 177931  Cd Length: 174  Bit Score: 318.35  E-value: 6.10e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833   1 MWRGRLSAQLQTLARSRSAANLTRLVTGDINRSFISPSPAPFRRTASLFSRQFSAESADNAVskeKKRVEDVMPIATGHE 80
Cdd:PLN02294   1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAV---KKRVEDVMPIATGHE 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833  81 REELEAALDGRDILDADHPVGPFGTKEAPAVVQSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSHECPVCSQYFTLEVIG 160
Cdd:PLN02294  78 REELEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVG 157

                 ....*.
gi 225442833 161 PGGPPP 166
Cdd:PLN02294 158 PGGPPD 163
Cyt_c_Oxidase_Vb cd00924
Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
64-161 2.56e-40

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: 131.65  E-value: 2.56e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833  64 KEKKRVEDVMPIATGHEREELEAALDGRDILDADHPVGPFGTKEAPAVVQSYYDKRIVGCPGgeGEDEHDVVWFWLEKGK 143
Cdd:cd00924    1 AAEGEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCIC--EPDSHDVIWMWLEKGK 78
                         90
                 ....*....|....*...
gi 225442833 144 SHECPVCSQYFTLEVIGP 161
Cdd:cd00924   79 PKRCPECGHVFKLVDVGP 96
COX5B pfam01215
Cytochrome c oxidase subunit Vb;
76-166 1.77e-20

Cytochrome c oxidase subunit Vb;


Pssm-ID: 426131  Cd Length: 128  Bit Score: 82.00  E-value: 1.77e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225442833   76 ATGHEREELEAALDGRDILDaDHPVGP--FGTKEAPAVVQSYYDKRIVGCPGGEgEDEHDVVWFWLEKGKSHECPVCSQY 153
Cdd:pfam01215  36 ATGLERLELLGKLEGIDVFD-MKPLDSsrKGTMEDPILVPSYDDYRYVGCTGSP-ADSHTVMWLKVSVGKVARCWECGSV 113
                          90
                  ....*....|...
gi 225442833  154 FTLEVIGPGGPPP 166
Cdd:pfam01215 114 YKLNYVGVPDDDH 126
PTZ00043 PTZ00043
cytochrome c oxidase subunit; Provisional
100-156 9.21e-13

cytochrome c oxidase subunit; Provisional


Pssm-ID: 240240  Cd Length: 268  Bit Score: 64.46  E-value: 9.21e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 225442833 100 VGPFGTKEAPAVVQSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSHECPVCSQYFTL 156
Cdd:PTZ00043 137 VGPFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYRCGECDQIFML 193
zf-CHCC pfam10276
Zinc-finger domain; This is a short zinc-finger domain conserved from fungi to humans. It is ...
119-154 7.57e-05

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: 38.29  E-value: 7.57e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 225442833  119 RIVGCPGGEGEDEHDVVWFWLEKGKSHECPVCSQYF 154
Cdd:pfam10276   2 RRVACDGGGGALGHPRVYINLDKPGPVECPYCGLRF 37
 
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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