SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (2,127) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,508 81,775 122
Proteins 17,268 57,671 113


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)heterocycle metabolic process0.13011Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.66550.0006509Least InformativeInherited
Biological Process (BP)single-organism cellular process0.34381Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.00027660.811Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.22531Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.00091850.6466Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.13561Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.58861Least InformativeInherited
Biological Process (BP)organic cyclic compound catabolic process0.0000000029230.00003468Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process0.025030.3362Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.0024290.02933Moderately InformativeInherited
Biological Process (BP)DNA metabolic process0.00000000000020690.00007174InformativeDirect
Biological Process (BP)apoptotic process00.0000000008881InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.0000000000058490.000003534InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process0.00000000000015060.00000004529InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis00.00000000004564InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds0.098490.9372InformativeInherited
Biological Process (BP)phosphorylation0.000011960.01081InformativeInherited
Biological Process (BP)oxidative phosphorylation0.000000071350.0000000005547Highly InformativeDirect
Biological Process (BP)DNA catabolic process00Highly InformativeDirect
Biological Process (BP)cellular component disassembly00.00000000000002782Highly InformativeDirect
Biological Process (BP)electron transport chain0.0000010320.0003393Highly InformativeDirect
Biological Process (BP)execution phase of apoptosis00Highly InformativeDirect
Molecular Function (MF)binding0.92331Least InformativeInherited
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)tetrapyrrole binding0.00011480InformativeDirect
Molecular Function (MF)heme binding0.000091930Highly InformativeDirect
Cellular Component (CC)membrane0.38650.9589Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.00000013850.02534Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.64220.928Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.17371Least InformativeInherited
Cellular Component (CC)organelle envelope0.0000096690.00000001501Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.0011560.00000000109Moderately InformativeInherited
Cellular Component (CC)organelle membrane0.0047850.0003189Moderately InformativeInherited
Cellular Component (CC)respiratory chain0.00002990.000000002519InformativeDirect
Cellular Component (CC)mitochondrial membrane part0.0015710.0000001558InformativeInherited

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 0.0006509 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.811 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.6466 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0000007087 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 0.00003468 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.3362 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02933 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.00007174 Informative Direct
Biological Process (BP) apoptotic process 0.0000000008881 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.000003534 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000004529 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.00000000004564 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.9372 Informative Inherited
Biological Process (BP) phosphorylation 0.01081 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.03229 Informative Inherited
Biological Process (BP) oxidative phosphorylation 0.0000000005547 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.00000000000002782 Highly Informative Direct
Biological Process (BP) electron transport chain 0.0003393 Highly Informative Direct
Biological Process (BP) execution phase of apoptosis 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0003033 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.04308 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 0.000003783 Informative Direct
Molecular Function (MF) tetrapyrrole binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.03892 Informative Inherited
Molecular Function (MF) iron ion binding 0.000006617 Highly Informative Direct
Molecular Function (MF) heme-copper terminal oxidase activity 0.0008898 Highly Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 0.000000000008887 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0.000000001083 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor 0.000000000947 Highly Informative Direct
Molecular Function (MF) heme binding 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001394 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.928 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02534 Least Informative Inherited
Cellular Component (CC) membrane 0.9589 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.0003189 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.00000001501 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.00000000109 Moderately Informative Direct
Cellular Component (CC) mitochondrial membrane part 0.0000001558 Informative Direct
Cellular Component (CC) respiratory chain 0.000000002519 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP 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 the CH-OH group of donors0.0752Moderately InformativeInherited
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0.00179InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.008082InformativeInherited
Enzyme Commission (EC)Acting on a peroxide as acceptor0.02728InformativeInherited
Enzyme Commission (EC)With a cytochrome as acceptor0.000000000000004743Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0.000000000007746Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.00000000003003Highly InformativeDirect
Enzyme Commission (EC)Peroxidases0.00002235Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis0.000000000007476Moderately InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processHydrogen ion transport0.000003512Highly InformativeDirect
Cellular componentMembrane0.00001476Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPlastid0.0003523Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentPhotosystem II0Highly InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Post-translational modificationOxidoreductase0.00003155Moderately InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid0InformativeDirect

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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Arabidopsis Plant Ontology (AP) · 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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]