SUPERFAMILY 1.75 HMM library and genome assignments server

Please note: Superfamily is currently under maintenance and some functionality may be limited. Please bear with us as we fix these problems.

Cytochromes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Four-helical up-and-down bundle [ 47161] (28)
Superfamily:   Cytochromes [ 47175] (2)
Families:   Cytochrome b562 [ 47176]
  Cytochrome c'-like [ 47179] (2)

Superfamily statistics
Genomes (644) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 830 6,197 16
Proteins 830 6,197 16

Functional annotation
General category Metabolism
Detailed category E- transfer

Function annotation of SCOP domain superfamilies

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processElectron transport0InformativeDirect
Cellular componentPeriplasm0InformativeDirect
DomainSignal0.00000000002238Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionHeme0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010980 SSF47175 Protein matches

Cytochromes are haem-containing proteins that function as electron carriers during electron transfer reactions. Cytochromes can be divided into types depending upon how the haem atom is bound: in c-type cytochromes the haem is covalently attached to the polypeptide, while in b-type cytochromes the haem is not covalently attached. A four-helical bundle motif is found in several cytochromes, including the cytochrome c family , cytochrome b562 , and cytochrome b559, despite having very low sequence similarities. Cytochromes c and b562 are found in many bacteria and are probably involved in nitric oxide transfer [PubMed12215425]. These proteins exhibit a reduction potential in the range of around żżż8mV to 400mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [PubMed11914078].

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 · 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 9 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 Cytochromes 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 9 hidden Markov models representing the Cytochromes 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 · UniProtKB KeyWords (KW) · Internal database links ]