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0  structures 4477  species 0  interactions 8917  sequences 16  architectures

Family: Cytochrom_C_asm (PF01578)

Summary: Cytochrome C assembly protein

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This is the Wikipedia entry entitled "Cytochrome c assembly protein family". More...

Cytochrome c assembly protein family Edit Wikipedia article

Cytochrome C assembly protein
Identifiers
Symbol Cytochrom_C_asm
Pfam PF01578
Pfam clan CL0328
InterPro IPR002541
TCDB 9.B.14

In molecular biology, the cytochrome c assembly protein family includes various proteins involved in cytochrome c assembly from mitochondria and bacteria. Members of this family include: CycK from Rhizobium leguminosarum,[1] CcmC from Escherichia coli and Paracoccus denitrificans,[2][3] and orf240 from Triticum aestivum (Wheat) mitochondria.[4] The members of this family are probably integral membrane proteins with six predicted transmembrane helices that may comprise the membrane component of an ABC (ATP binding cassette) transporter complex. This transporter may be necessary for transport of some component needed for cytochrome c assembly. One member, R. leguminosarum CycK, contains a putative haem-binding motif.[1] Wheat orf240 also contains a putative haem-binding motif and is a proposed ABC transporter with c-type haem as its proposed substrate.[4] However it seems unlikely that all members of this family transport haem or c-type apocytochromes because P. denitrificans CcmC transports neither.[3]

References[edit]

  1. ^ a b Delgado MJ, Yeoman KH, Wu G, Vargas C, Davies AE, Poole RK, Johnston AW, Downie JA (September 1995). "Characterization of the cycHJKL genes involved in cytochrome c biogenesis and symbiotic nitrogen fixation in Rhizobium leguminosarum". J. Bacteriol. 177 (17): 4927–34. PMC 177267. PMID 7665469. 
  2. ^ Thony-Meyer L, Fischer F, Künzler P, Ritz D, Hennecke H (August 1995). "Escherichia coli genes required for cytochrome c maturation". J. Bacteriol. 177 (15): 4321–6. PMC 177179. PMID 7635817. 
  3. ^ a b Page MD, Pearce DA, Norris HA, Ferguson SJ (February 1997). "The Paracoccus denitrificans ccmA, B and C genes: cloning and sequencing, and analysis of the potential of their products to form a haem or apo- c-type cytochrome transporter". Microbiology (Reading, Engl.) 143 (2): 563–76. PMID 9043133. 
  4. ^ a b Bonnard G, Grienenberger JM (January 1995). "A gene proposed to encode a transmembrane domain of an ABC transporter is expressed in wheat mitochondria". Mol. Gen. Genet. 246 (1): 91–9. PMID 7529870. 

This article incorporates text from the public domain Pfam and InterPro IPR002541

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cytochrome C assembly protein Provide feedback

This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from [3] CcmC from E. coli and Paracoccus denitrificans [2,1] and orf240 from wheat mitochondria [4]. The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family comprise a membrane component of an ABC (ATP binding cassette) transporter complex. It is also proposed that this transporter is necessary for transport of some component needed for cytochrome c assembly. One member CycK contains a putative heme-binding motif [3] orf240 also contains a putative heme-binding motif and is a proposed ABC transporter with c-type heme as its proposed substrate [4]. However it seems unlikely that all members of this family transport heme nor c-type apocytochromes because CcmC in the putative CcmABC transporter transports neither [1].

Literature references

  1. Page D, Pearce DA, Norris HA, Ferguson SJ; , Microbiology 1997;143:563-576.: The Paracoccus denitrificans ccmA, B and C genes: cloning and sequencing, and analysis of the potential of their products to form a haem or apo-c-type cytochrome transporter. PUBMED:9043133 EPMC:9043133

  2. Thony-Meyer L, Fischer F, Kunzler P, Ritz D, Hennecke H; , J Bacteriol 1995;177:4321-4326.: Escherichia coli genes required for cytochrome c maturation. PUBMED:7635817 EPMC:7635817

  3. Delgado MJ, Yeoman KH, Wu G, Vargas C, Davies A, Poole RK, Johnston AWB, Downie JA; , J bacteriol 1995;177:4927-4934.: Characterization of the cycHJKL genes involved in cytochrome c biogenesis and symbiotic nitrogen fixation in Rhizobium leguminosarum. PUBMED:7665469 EPMC:7665469

  4. Bonnard G, Grienenberger JM; , Mol Gen Genet 1995;246:91-99.: A gene proposed to encode a transmembrane domain of an ABC transporter is expressed in wheat mitochondria. PUBMED:7529870 EPMC:7529870


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002541

This entry consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium leguminosarum [PUBMED:7665469], CcmC from Escherichia coli and Paracoccus denitrificans [PUBMED:7635817, PUBMED:9043133] and orf240 from Triticum aestivum (Wheat) mitochondria [PUBMED:7529870]. The members of this family are probably integral membrane proteins with six predicted transmembrane helices that may comprise the membrane component of an ABC (ATP binding cassette) transporter complex. This transporter may be necessary for transport of some component needed for cytochrome c assembly.

One member, R. leguminosarum CycK, contains a putative haem-binding motif [PUBMED:7665469]. Wheat orf240 also contains a putative haem-binding motif and is a proposed ABC transporter with c-type haem as its proposed substrate [PUBMED:7529870]. However it seems unlikely that all members of this family transport haem or c-type apocytochromes because P. denitrificans CcmC transports neither [PUBMED:9043133].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan 2heme_cytochrom (CL0328), which has the following description:

This superfamily includes a variety of different heme binding cytochromes.

The clan contains the following 10 members:

COX15-CtaA Cytochrom_B561 Cytochrom_B_N Cytochrom_B_N_2 Cytochrom_C_asm DUF2427 DUF4405 Ferric_reduct Ni_hydr_CYTB PCRF

Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(39)
Full
(8917)
Representative proteomes NCBI
(6398)
Meta
(4666)
RP15
(525)
RP35
(1095)
RP55
(1442)
RP75
(1718)
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Format an alignment

  Seed
(39)
Full
(8917)
Representative proteomes NCBI
(6398)
Meta
(4666)
RP15
(525)
RP35
(1095)
RP55
(1442)
RP75
(1718)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(39)
Full
(8917)
Representative proteomes NCBI
(6398)
Meta
(4666)
RP15
(525)
RP35
(1095)
RP55
(1442)
RP75
(1718)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_114 (release 4.1) Pfam-B_8014 (Release 8.0)
Previous IDs: CytC_asm;
Type: Family
Author: Bashton M, Bateman A
Number in seed: 39
Number in full: 8917
Average length of the domain: 196.50 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 51.54 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.2
Noise cut-off 20.8 20.9
Model length: 214
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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