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0  structures 1028  species 0  interactions 1201  sequences 7  architectures

Family: FixO (PF02433)

Summary: Cytochrome C oxidase, mono-heme subunit/FixO

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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 oxidase, mono-heme subunit/FixO Provide feedback

The bacterial oxidase complex, fixNOPQ or cytochrome cbb3, is thought to be required for respiration in endosymbiosis. FixO is a membrane bound mono-heme constituent of the fixNOPQ complex.

Literature references

  1. Marchal K, Sun J, Keijers V, Haaker H, Vanderleyden J; , J Bacteriol 1998;180:5689-5696.: A cytochrome cbb3 (cytochrome c) terminal oxidase in Azospirillum brasilense Sp7 supports microaerobic growth. PUBMED:9791120 EPMC:9791120


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003468

Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO) [PUBMED:15100055]. Cytochrome cbb3 oxidases are required both to support symbiotic nitrogen fixation, whilst ensuring that the oxygen-labile nitrogenase is not compromised. Cytochrome cbb3 oxidases consist of four subunits: FixN (or CcoN), FixO (or CcoO), FixP (or CcoP) and FixQ (or CcoQ). The catalytic core is comprised of subunits FixN, FixO and FixP, where FixN acts as the catalytic subunit, and Fix O and FixP are membrane-bound mono- and di-haem cytochromes c, respectively. The FixQ subunit protects the core complex in the presence of oxygen from proteolytic degradation [PUBMED:11864982]. This entry represents the mono-haem FixO subunit.

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 Cytochrome-c (CL0318), which contains the following 10 members:

CCP_MauG Cytochrom_C Cytochrom_C1 Cytochrom_C550 Cytochrome_CBB3 Dehyd-heme_bind DUF1111 DUF1924 FixO PSCyt1

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(56)
Full
(1201)
Representative proteomes NCBI
(915)
Meta
(226)
RP15
(111)
RP35
(233)
RP55
(301)
RP75
(361)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(56)
Full
(1201)
Representative proteomes NCBI
(915)
Meta
(226)
RP15
(111)
RP35
(233)
RP55
(301)
RP75
(361)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(56)
Full
(1201)
Representative proteomes NCBI
(915)
Meta
(226)
RP15
(111)
RP35
(233)
RP55
(301)
RP75
(361)
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:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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_2045 (release 5.4)
Previous IDs: none
Type: Family
Author: Mian N. Bateman A
Number in seed: 56
Number in full: 1201
Average length of the domain: 199.50 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 74.82 %

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 24.2 24.2
Trusted cut-off 24.3 24.7
Noise cut-off 23.8 23.2
Model length: 226
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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