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Conserved domains on  [gi|1279104030|ref|XP_022876142.1|]
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cytochrome c oxidase subunit 6b-1-like [Olea europaea var. sylvestris]

Protein Classification

cytochrome c oxidase subunit 6B family protein( domain architecture ID 10097107)

cytochrome c oxidase subunit 6B family protein similar to cytochrome c oxidase subunit 6B (also known as subunit VIb), which is a component of cytochrome c oxidase, the terminal oxidase in the respiratory chains of eukaryotes and most bacteria which catalyzes the reduction of O2 and simultaneously pumps protons across the membrane; subunit 6B may bind heme

CATH:  1.10.10.140
Gene Ontology:  GO:0045333|GO:0004129|GO:0022900
PubMed:  20233836
SCOP:  4000996

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cyt_c_Oxidase_VIb cd00926
Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 121-195 5.02e-45

Cytochrome c oxidase subunit VIb. 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 VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex.


:

Pssm-ID: 238466  Cd Length: 75  Bit Score: 143.60  E-value: 5.02e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1279104030 121 PEIKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEDAPECNKFAKYYRSLCPGEWIERWNEQRENGTFPGP 195
Cdd:cd00926     1 DAGPLTTAPFDPRFPNQNQTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYESLCPQEWLEKWDEQREEGTFPGK 75
Agg_substance super family cl41491
LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, ...
 42-136 6.77e-04

LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, are LPXTG-anchored large surface proteins that contribute to virulence. Several closely related paralogs may be found in a single strain.


The actual alignment was detected with superfamily member NF033875:

Pssm-ID: 411439 [Multi-domain]  Cd Length: 1306  Bit Score: 40.08  E-value: 6.77e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279104030   42 NAVAKEVVEQPEETPVSVDS--------DVSPAVAEESGKDSDSASGESK-ENIPVDESTGEVSPAASEESTDSAEPEDA 112
Cdd:NF033875    40 NVQAAELDTQPGTTTVQPDNpdpqsgseTPKTAVSEEATVQKDTTSQPTKvEEVASEKNGAEQSSATPNDTTNAQQPTVG 119

                           90       100
                   ....*....|....*....|....
gi 1279104030  113 GEQEAEETPEIKLETAPADFRFPT 136
Cdd:NF033875   120 AEKSAQEQPVVSPETTNEPLGQPT 143
 
Name Accession Description Interval E-value
Cyt_c_Oxidase_VIb cd00926
Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 121-195 5.02e-45

Cytochrome c oxidase subunit VIb. 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 VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex.


Pssm-ID: 238466  Cd Length: 75  Bit Score: 143.60  E-value: 5.02e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1279104030 121 PEIKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEDAPECNKFAKYYRSLCPGEWIERWNEQRENGTFPGP 195
Cdd:cd00926     1 DAGPLTTAPFDPRFPNQNQTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYESLCPQEWLEKWDEQREEGTFPGK 75
COX6B pfam02297
Cytochrome oxidase c subunit VIb; Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is ...
 133-193 1.40e-26

Cytochrome oxidase c subunit VIb; Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase.


Pssm-ID: 426708  Cd Length: 65  Bit Score: 96.27  E-value: 1.40e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1279104030 133 RFPTTNQTRHCFTRYIEYHRCVAAKGEDAPECNKFAKYYRSLCPGEWIERWNEQR---ENGTFP 193
Cdd:pfam02297   2 RFPNQNQRKHCWQARDDFFKCLDKNGIDNSPCKKEKKNYESLCPASWVEYFDEQRvyrEEGTFP 65
Agg_substance NF033875
LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, ...
 42-136 6.77e-04

LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, are LPXTG-anchored large surface proteins that contribute to virulence. Several closely related paralogs may be found in a single strain.


Pssm-ID: 411439 [Multi-domain]  Cd Length: 1306  Bit Score: 40.08  E-value: 6.77e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279104030   42 NAVAKEVVEQPEETPVSVDS--------DVSPAVAEESGKDSDSASGESK-ENIPVDESTGEVSPAASEESTDSAEPEDA 112
Cdd:NF033875    40 NVQAAELDTQPGTTTVQPDNpdpqsgseTPKTAVSEEATVQKDTTSQPTKvEEVASEKNGAEQSSATPNDTTNAQQPTVG 119

                           90       100
                   ....*....|....*....|....
gi 1279104030  113 GEQEAEETPEIKLETAPADFRFPT 136
Cdd:NF033875   120 AEKSAQEQPVVSPETTNEPLGQPT 143
 
Name Accession Description Interval E-value
Cyt_c_Oxidase_VIb cd00926
Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the ...
 121-195 5.02e-45

Cytochrome c oxidase subunit VIb. 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 VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex.


Pssm-ID: 238466  Cd Length: 75  Bit Score: 143.60  E-value: 5.02e-45
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1279104030 121 PEIKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEDAPECNKFAKYYRSLCPGEWIERWNEQRENGTFPGP 195
Cdd:cd00926     1 DAGPLTTAPFDPRFPNQNQTKHCWQRYVDYHRCIKAKGEDASPCKKFRRVYESLCPQEWLEKWDEQREEGTFPGK 75
COX6B pfam02297
Cytochrome oxidase c subunit VIb; Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is ...
 133-193 1.40e-26

Cytochrome oxidase c subunit VIb; Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase.


Pssm-ID: 426708  Cd Length: 65  Bit Score: 96.27  E-value: 1.40e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1279104030 133 RFPTTNQTRHCFTRYIEYHRCVAAKGEDAPECNKFAKYYRSLCPGEWIERWNEQR---ENGTFP 193
Cdd:pfam02297   2 RFPNQNQRKHCWQARDDFFKCLDKNGIDNSPCKKEKKNYESLCPASWVEYFDEQRvyrEEGTFP 65
Agg_substance NF033875
LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, ...
 42-136 6.77e-04

LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, are LPXTG-anchored large surface proteins that contribute to virulence. Several closely related paralogs may be found in a single strain.


Pssm-ID: 411439 [Multi-domain]  Cd Length: 1306  Bit Score: 40.08  E-value: 6.77e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279104030   42 NAVAKEVVEQPEETPVSVDS--------DVSPAVAEESGKDSDSASGESK-ENIPVDESTGEVSPAASEESTDSAEPEDA 112
Cdd:NF033875    40 NVQAAELDTQPGTTTVQPDNpdpqsgseTPKTAVSEEATVQKDTTSQPTKvEEVASEKNGAEQSSATPNDTTNAQQPTVG 119

                           90       100
                   ....*....|....*....|....
gi 1279104030  113 GEQEAEETPEIKLETAPADFRFPT 136
Cdd:NF033875   120 AEKSAQEQPVVSPETTNEPLGQPT 143
 
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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