SUPERFAMILY 1.75 HMM library and genome assignments server


Cytochrome c oxidase subunit I-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   Cytochrome c oxidase subunit I-like [ 81443]
Superfamily:   Cytochrome c oxidase subunit I-like [ 81442]
Families:   Cytochrome c oxidase subunit I-like [ 81441] (4)


Superfamily statistics
Genomes (2,009) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,954 0 8
Proteins 4,944 0 8


Functional annotation
General category Metabolism
Detailed category Energy

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism metabolic process10.8711Least InformativeInherited
Biological Process (BP)oxidation-reduction process0.0025314.02e-06Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.8950.9711Moderately InformativeInherited
Biological Process (BP)energy derivation by oxidation of organic compounds0.0071620.003157InformativeInherited
Biological Process (BP)phosphorylation0.060320.1533InformativeInherited
Biological Process (BP)oxidative phosphorylation2.768e-063.494e-07Highly InformativeDirect
Biological Process (BP)electron transport chain1.734e-051.538e-05Highly InformativeDirect
Molecular Function (MF)transporter activity00Moderately InformativeDirect
Molecular Function (MF)oxidoreductase activity00Moderately InformativeDirect
Molecular Function (MF)inorganic cation transmembrane transporter activity00InformativeDirect
Molecular Function (MF)hydrogen ion transmembrane transporter activity00Highly InformativeDirect
Molecular Function (MF)heme-copper terminal oxidase activity00Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor10Highly InformativeInherited
Cellular Component (CC)membrane00Least InformativeDirect
Cellular Component (CC)protein complex00Least InformativeDirect
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)mitochondrial part3.763e-051.088e-05Moderately InformativeDirect
Cellular Component (CC)organelle envelope9.124e-055.545e-05Moderately InformativeDirect
Cellular Component (CC)organelle membrane0.82540.5824Moderately InformativeInherited
Cellular Component (CC)respiratory chain00InformativeDirect
Cellular Component (CC)respiratory chain complex IV00Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8711 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 4.02e-06 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.9711 Moderately Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0001104 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.003157 Informative Inherited
Biological Process (BP) phosphorylation 0.1533 Informative Inherited
Biological Process (BP) oxidative phosphorylation 3.494e-07 Highly Informative Direct
Biological Process (BP) electron transport chain 1.538e-05 Highly Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.04376 Moderately Informative Inherited
Molecular Function (MF) inorganic cation transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) nuclease activity 9.379e-06 Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 0 Highly Informative Direct
Molecular Function (MF) heme-copper terminal oxidase activity 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor 0 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 1.088e-05 Moderately Informative Direct
Cellular Component (CC) organelle envelope 5.545e-05 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.5824 Moderately Informative Inherited
Cellular Component (CC) respiratory chain 0 Informative Direct
Cellular Component (CC) respiratory chain complex IV 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on a heme group of donors0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on a heme group of donors0Highly InformativeDirect
Enzyme Commission (EC)Acting on diphenols and related substances as donors0.194Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processRespiratory chain0Highly InformativeDirect
Biological processIntron homing0Highly InformativeDirect
Biological processHydrogen ion transport1.245e-11Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Molecular functionHeme0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)energy metabolism0Moderately InformativeDirect
UniPathway (UP)oxidative phosphorylation0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR000883 SSF81442 Protein matches
Abstract Cytochrome c oxidase is a key enzyme in aerobic metabolism. Proton pumping heme-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-heme a3 (or heme o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases , is directly involved in the coupling between dioxygen reduction and proton pumping [PubMed8083153, PubMed8049679]. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes).

The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (CO I)) is found in all heme-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin heme and copper B) as well as a low-spin heme, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members [PubMed8013452, PubMed6307356, PubMed2824194]. In contrast to eukaryotes the respiratory chain of prokaryotes is branched to multiple terminal oxidases. The enzyme complexes vary in heme and copper composition, substrate type and substrate affinity. The different respiratory oxidases allow the cells to customize their respiratory systems according to a variety of environmental growth conditions [PubMed8083153].

It has been shown that eubacterial quinol oxidase was derived from cytochrome c oxidase in Gram-positive bacteria and that archaebacterial quinol oxidase has an independent origin. A considerable amount of evidence suggests that proteobacteria (Purple bacteria) acquired quinol oxidase through a lateral gene transfer from Gram-positive bacteria [PubMed8083153].

Nitric oxide reductase (NOR) exists in denitrifying species of archae and eubacteria and is a heterodimer of cytochromes b and c. Phenazine methosulphate can act as acceptor. The prosite signature in this entry recognises the heme-copper site of the nitric oxidases.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 5 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Cytochrome c oxidase subunit I-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 5 hidden Markov models representing the Cytochrome c oxidase subunit I-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]