SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,128) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,527 81,775 122
Proteins 17,287 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)single-organism metabolic process0.088730.00001035Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.00000045290.02403Least InformativeInherited
Biological Process (BP)single-organism cellular process0.062790.2411Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.000088840.1115Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.000080180.1496Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.011120.8019Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.00032020.8683Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.2091Least InformativeInherited
Biological Process (BP)oxidation-reduction process0.000000000000240Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.021770.01044Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.03240.4061Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.010490.001999Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.0024260.02776Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.033750.03273Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.00010590.0067Moderately InformativeInherited
Biological Process (BP)apoptotic process00.000000000877InformativeDirect
Biological Process (BP)nucleoside monophosphate metabolic process0.0000000190.0003322InformativeDirect
Biological Process (BP)purine ribonucleotide metabolic process0.0000054180.00009507InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds0.0000024760.0000000432InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.00010070.0004466InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process0.00000000000016760.00000005137InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.0000084820.00005806InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis00.00000000004255InformativeDirect
Biological Process (BP)phosphorylation0.000037810.02365InformativeInherited
Biological Process (BP)nucleoside triphosphate metabolic process0.0000027320.004548InformativeInherited
Biological Process (BP)oxidative phosphorylation0.000000021110.00000000009485Highly InformativeDirect
Biological Process (BP)DNA catabolic process00Highly InformativeDirect
Biological Process (BP)cellular component disassembly00.00000000000004385Highly InformativeDirect
Biological Process (BP)electron transport chain0.00000000000037470Highly InformativeDirect
Biological Process (BP)execution phase of apoptosis00Highly InformativeDirect
Molecular Function (MF)binding0.9291Least InformativeInherited
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)tetrapyrrole binding0.00012060InformativeDirect
Molecular Function (MF)heme binding0.000096710Highly InformativeDirect
Cellular Component (CC)membrane0.39680.9631Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.64350.9Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.13451Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.00000012520.02695Least InformativeInherited
Cellular Component (CC)organelle envelope0.000009540.00000001453Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.0011960.000000001043Moderately InformativeInherited
Cellular Component (CC)respiratory chain0.000027150.000000002467InformativeDirect
Cellular Component (CC)mitochondrial membrane part0.0015350.0000001461InformativeInherited

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 0.00001035 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.2411 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.02403 Least Informative Inherited
Biological Process (BP) localization 0.973 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.1115 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1496 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.8019 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8683 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.000003548 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.01044 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4061 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.002531 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.001999 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02776 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.03273 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.0067 Moderately Informative Inherited
Biological Process (BP) apoptotic process 0.000000000877 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0003322 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.00009507 Informative Direct
Biological Process (BP) monovalent inorganic cation transport 0.00000001426 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.0000000432 Informative Direct
Biological Process (BP) ion transmembrane transport 0.000002027 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0004466 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.00000005137 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.00005806 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.00000000004255 Informative Direct
Biological Process (BP) phosphorylation 0.02365 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.03372 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.004548 Informative Inherited
Biological Process (BP) oxidative phosphorylation 0.00000000009485 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0.00000000000004385 Highly Informative Direct
Biological Process (BP) electron transport chain 0 Highly Informative Direct
Biological Process (BP) execution phase of apoptosis 0 Highly Informative Direct
Biological Process (BP) hydrogen ion transmembrane transport 0.0000000000002151 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 0.0003137 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.04249 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) monovalent inorganic cation transmembrane transporter activity 0.00000004703 Informative Direct
Molecular Function (MF) tetrapyrrole binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.03974 Informative Inherited
Molecular Function (MF) iron ion binding 0.000007798 Highly Informative Direct
Molecular Function (MF) heme-copper terminal oxidase activity 0.0008641 Highly Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 0.000000000008765 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 0.000000001142 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor 0.0000000009427 Highly Informative Direct
Molecular Function (MF) heme binding 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001439 Highly Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02695 Least Informative Inherited
Cellular Component (CC) membrane 0.9631 Least Informative Inherited
Cellular Component (CC) organelle envelope 0.00000001453 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.000000001043 Moderately Informative Direct
Cellular Component (CC) mitochondrial membrane part 0.0000001461 Informative Direct
Cellular Component (CC) respiratory chain 0.000000002467 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 donors0.07302Moderately InformativeInherited
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0.003356InformativeInherited
Enzyme Commission (EC)Acting on a sulfur group of donors0.007899InformativeInherited
Enzyme Commission (EC)Acting on a peroxide as acceptor0.02678InformativeInherited
Enzyme Commission (EC)With a cytochrome as acceptor0.000000000000004754Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor0.000000000007688Highly InformativeDirect
Enzyme Commission (EC)With other acceptors0.0000000008452Highly InformativeDirect
Enzyme Commission (EC)Peroxidases0.00002222Highly InformativeDirect

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)alimentary tract and metabolism0Least InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis0.000000000007572Moderately InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processHydrogen ion transport0.000004339Highly InformativeDirect
Cellular componentMembrane0.00002833Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPlastid0.0004339Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentPhotosystem II0Highly InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Post-translational modificationOxidoreductase0.000003379Moderately 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)one-carbon metabolism0.00004897Moderately InformativeDirect
UniPathway (UP)oxidative phosphorylation0Highly InformativeDirect
UniPathway (UP)methylamine degradation0.0000000000003297Highly 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) · DrugBank ATC (DB) · 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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]