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Cytochrome c superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Cytochrome c [ 46625]
Superfamily:   Cytochrome c [ 46626] (8)
Families:   monodomain cytochrome c [ 46627] (15)
  N-terminal (heme c) domain of cytochrome cd1-nitrite reductase [ 46671]
  Quinoprotein alcohol dehydrogenase, C-terminal domain [ 68952]
  Cytochrome bc1 domain [ 46676]
  Two-domain cytochrome c [ 46680] (2)
  Di-heme cytochrome c SoxA [ 81677]
  Di-heme cytochrome c peroxidase [ 46685]
  Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 [ 68956]


Superfamily statistics
Genomes (2,136) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 23,570 159,168 122
Proteins 17,330 114,964 113


Functional annotation
General category Metabolism
Detailed category E- transfer

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 process0.00023770.0000000003758Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.21340.3309Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.12060.7013Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.33681Least InformativeInherited
Biological Process (BP)single-organism cellular process0.35021Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.11950.798Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.12180.8905Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)generation of precursor metabolites and energy0.0000000000042340.0000000000001294Moderately InformativeDirect
Biological Process (BP)nucleoside phosphate metabolic process0.0000064380.0000001819Moderately InformativeDirect
Biological Process (BP)oxidation-reduction process0.00000000000041910Moderately InformativeDirect
Biological Process (BP)purine-containing compound metabolic process0.00000074040.000000007571Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.00065120.0003383Moderately InformativeDirect
Biological Process (BP)phosphorylation0.0000025580.0005393InformativeDirect
Biological Process (BP)electron transport chain0.00000000000024920InformativeDirect
Biological Process (BP)cellular respiration0.000000022280.0000000001943InformativeDirect
Biological Process (BP)ATP metabolic process0.00000000082740.0000000000003926InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)tetrapyrrole binding0.00001720InformativeDirect
Molecular Function (MF)heme binding0.000012780Highly InformativeDirect
Cellular Component (CC)membrane0.47441Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.11481Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.79631Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0000050730.3164Least InformativeInherited
Cellular Component (CC)mitochondrial envelope0.000003140.000000000003055Moderately InformativeDirect
Cellular Component (CC)organelle inner membrane0.0028050.00000000003497Moderately InformativeInherited

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) single-organism metabolic process 0.0000000003758 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.3309 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.7013 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.798 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8905 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.0000000000001294 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000001819 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.000003794 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000000007571 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0003383 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.578 Moderately Informative Inherited
Biological Process (BP) phosphorylation 0.0005393 Informative Direct
Biological Process (BP) electron transport chain 0 Informative Direct
Biological Process (BP) cellular respiration 0.0000000001943 Informative Direct
Biological Process (BP) ATP metabolic process 0.0000000000003926 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.0002348 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.06898 Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.02059 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.004679 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0.0000000001529 Informative Direct
Molecular Function (MF) tetrapyrrole binding 0 Informative Direct
Molecular Function (MF) peroxidase activity 0.000000164 Highly Informative Direct
Molecular Function (MF) iron ion binding 0.000008419 Highly Informative Direct
Molecular Function (MF) heme-copper terminal oxidase activity 0.0009158 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0.0000001072 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor 0.0000000002706 Highly Informative Direct
Molecular Function (MF) heme binding 0 Highly Informative Direct
Cellular Component (CC) protein complex 0.1875 Least Informative Inherited
Cellular Component (CC) membrane 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) cytoplasmic part 0.3164 Least Informative Inherited
Cellular Component (CC) mitochondrial envelope 0.000000000003055 Moderately Informative Direct
Cellular Component (CC) organelle inner membrane 0.00000000003497 Moderately Informative Direct
Cellular Component (CC) mitochondrial protein complex 0.0009339 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.3996 Moderately Informative Inherited
Cellular Component (CC) membrane protein complex 0.01718 Moderately Informative Inherited
Cellular Component (CC) mitochondrial respiratory chain 0.0001898 Informative Direct
Cellular Component (CC) cytochrome complex 0.000000000000008837 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.00001708 Informative Direct
Cellular Component (CC) transporter complex 0.0003979 Informative Direct
Cellular Component (CC) respiratory chain complex 0.03223 Informative Inherited
Cellular Component (CC) inner mitochondrial membrane protein complex 0.01215 Informative Inherited
Cellular Component (CC) mitochondrial respiratory chain complex III 0.00002344 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

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis0.000000000009657Moderately InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processPhotosynthesis0InformativeDirect
Biological processElectron transport0InformativeDirect
Biological processHydrogen ion transport0.000003478Highly InformativeDirect
Cellular componentMembrane0.00006577Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPlastid0.0004227Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentPhotosystem II0Highly InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Post-translational modificationOxidoreductase0.00000006462Moderately InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009056 SSF46626 Protein matches
Abstract

After cytochrome c is synthesized in the cytoplasm as apocytochrome c, it is transported through the outer mitochondrial membrane to the intermembrane space, where haem is covalently attached by thioester bonds to two cysteine residues located in the cytochrome c centre. Cytochrome c is required during oxidative phosphorylation as an electron shuttle between Complex III (cytochrome c reductase) and IV (cytochrome c oxidase). In addition, cytochrome c is involved in apoptosis in more complex organisms such as Xenopus, rats and humans. Cellular stress can induce cytochrome c release from the mitochondrial membrane. In mammals, cytochrome c triggers the assembly of the apoptosome, consisting of cytochrome c, Apaf-1 and dATP, which activates caspase-9, leading to cell death [PubMed12729583, PubMed10707095]. There are several different members of the cytochrome c family with different functional roles, for instance cytochrome c549 is associated with photosystem II [PubMed11315568].

The known structures of c-type cytochromes have six different classes of fold. Of these, four are unique to c-type cytochromes [PubMed12594933, PubMed2166169]. The consensus sequence for the cytochrome c centre is Cys-X-X-Cys-His, where the histidine residue is one of the two axial ligands of the haem iron [PubMed10647174]. This arrangement is shared by all proteins known to belong to the cytochrome c family, which presently includes both mono-haem proteins and multi-haem proteins. This entry represents mono-haem cytochrome c proteins (excluding class II and f-type cytochromes), such as cytochromes c, c1, c2, c5, c555, c550 to c553, c556, and c6.

Cytochrome c-type centres are also found in the active sites of many enzymes, including cytochrome cd1-nitrite reductase as the N-terminal haem c domain, in quinoprotein alcohol dehydrogenase as the C-terminal domain, in Quinohemoprotein amine dehydrogenase A chain as domains 1 and 2, and in the cytochrome bc1 complex as the cytochrome bc1 domain.


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) · UniProtKB KeyWords (KW) ]

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 72 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 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 72 hidden Markov models representing the Cytochrome c 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) · UniProtKB KeyWords (KW) · Internal database links ]