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 (2,079) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 23,375 49,005 122
Proteins 17,122 35,181 113


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 process0.12741Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.80240.006307Least InformativeInherited
Biological Process (BP)single-organism cellular process0.33661Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.00016750.6802Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.22781Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.00062390.553Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.13551Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.44831Least InformativeInherited
Biological Process (BP)macromolecule catabolic process1.281e-115.165e-07Moderately InformativeDirect
Biological Process (BP)organic cyclic compound catabolic process3.177e-092.136e-05Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process0.020670.2736Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.0026630.03016Moderately InformativeInherited
Biological Process (BP)DNA metabolic process1.825e-134.666e-05InformativeDirect
Biological Process (BP)cell death09.171e-09InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process4.024e-122.213e-06InformativeDirect
Biological Process (BP)cellular macromolecule catabolic process1.023e-132.574e-08InformativeDirect
Biological Process (BP)nucleic acid phosphodiester bond hydrolysis03.474e-11InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds0.044690.662InformativeInherited
Biological Process (BP)phosphorylation9.095e-060.008509InformativeInherited
Biological Process (BP)oxidative phosphorylation7.678e-086.071e-10Highly InformativeDirect
Biological Process (BP)DNA catabolic process00Highly InformativeDirect
Biological Process (BP)cellular component disassembly01.431e-14Highly InformativeDirect
Biological Process (BP)electron transport chain2.277e-076.531e-05Highly InformativeDirect
Biological Process (BP)execution phase of apoptosis00Highly InformativeDirect
Molecular Function (MF)binding0.83881Least InformativeInherited
Molecular Function (MF)electron carrier activity00InformativeDirect
Molecular Function (MF)tetrapyrrole binding8.036e-050InformativeDirect
Molecular Function (MF)heme binding6.274e-050Highly InformativeDirect
Cellular Component (CC)intracellular organelle part0.83490.8153Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.25771Least InformativeInherited
Cellular Component (CC)cytoplasmic part7.303e-070.03639Least InformativeInherited
Cellular Component (CC)organelle envelope0.0003853.602e-08Moderately InformativeDirect
Cellular Component (CC)mitochondrial part0.015245.113e-09Moderately InformativeInherited
Cellular Component (CC)periplasmic space8.841e-090Highly 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) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.006307 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 0.6802 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.553 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 6.733e-07 Moderately Informative Direct
Biological Process (BP) macromolecule catabolic process 5.165e-07 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 2.136e-05 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.2736 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.03016 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 4.666e-05 Informative Direct
Biological Process (BP) cell death 9.171e-09 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 2.213e-06 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 2.574e-08 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 3.474e-11 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.662 Informative Inherited
Biological Process (BP) phosphorylation 0.008509 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.02603 Informative Inherited
Biological Process (BP) oxidative phosphorylation 6.071e-10 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0 Highly Informative Direct
Biological Process (BP) cellular component disassembly 1.431e-14 Highly Informative Direct
Biological Process (BP) electron transport chain 6.531e-05 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 0.0001324 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.02805 Moderately Informative Inherited
Molecular Function (MF) electron carrier activity 0 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 2.166e-06 Informative Direct
Molecular Function (MF) tetrapyrrole binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.03003 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.04673 Informative Inherited
Molecular Function (MF) iron ion binding 5.11e-06 Highly Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 5.744e-12 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on a sulfur group of donors 8.706e-07 Highly Informative Direct
Molecular Function (MF) heme binding 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0001044 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.8153 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.9327 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.03639 Least Informative Inherited
Cellular Component (CC) membrane 0.9321 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.0005269 Moderately Informative Direct
Cellular Component (CC) organelle envelope 3.602e-08 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 5.113e-09 Moderately Informative Direct
Cellular Component (CC) mitochondrial membrane part 9.38e-07 Informative Direct
Cellular Component (CC) respiratory chain 3.128e-08 Informative Direct
Cellular Component (CC) mitochondrial respiratory chain 0.0001554 Highly Informative Direct
Cellular Component (CC) periplasmic space 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

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

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six 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 donors0.02193Moderately InformativeInherited
Enzyme Commission (EC)Acting on other nitrogenous compounds as donors0.0007992InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor0.01534InformativeInherited
Enzyme Commission (EC)With a cytochrome as acceptor3.361e-12Highly InformativeDirect
Enzyme Commission (EC)With other acceptors1.16e-11Highly InformativeDirect
Enzyme Commission (EC)With a cytochrome as acceptor3.759e-11Highly InformativeDirect
Enzyme Commission (EC)Peroxidases1.181e-05Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processApoptosis6.74e-12Moderately InformativeDirect
Biological processIon transport1Moderately InformativeInherited
Biological processElectron transport0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processHydrogen ion transport3.468e-06Highly InformativeDirect
Cellular componentMembrane3.52e-05Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPlastid0.0003246Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
Cellular componentThylakoid0InformativeDirect
Cellular componentPhotosystem II0Highly InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect
Post-translational modificationOxidoreductase2.744e-05Moderately 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) · 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]