Summary: CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
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CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit Provide feedback
This family consists of Carbon monoxide dehydrogenase I/II beta subunit EC:18.104.22.168 and acetyl-CoA synthase epsilon subunit. Carbon monoxide beta subunit catalyses the reaction: CO + H2O + acceptor <=> CO2 + reduced acceptor.
Eggen RIL, van Kranenburg R, Vriesema AJ, Geerling AC, Verhagen MF, Hagen WR, de Vos WM; , J Biol Chem 1996;271:14256-14263.: Carbon monoxide dehydrogenase from Methanosarcina frisia Go1. Characterization of the enzyme and the regulated expression of two operon-like cdh gene clusters. PUBMED:8662887 EPMC:8662887
Maupin-Furlow J, Ferry JG; , J Bacteriol 1996;178:340-346.: Characterization of the cdhD and cdhE genes encoding subunits of the corrinoid/iron-sulfur enzyme of the CO dehydrogenase complex from Methanosarcina thermophila. PUBMED:8550451 EPMC:8550451
Internal database links
|Similarity to PfamA using HHSearch:||TPP_enzyme_M|
This tab holds annotation information from the InterPro database.
InterPro entry IPR003704
Carbon monoxide dehydrogenase (Cdh) from Methanosarcina mazei (Methanosarcina frisia) Go1 is a Ni2+-, Fe2+-, and S2-containing alpha2beta2 heterotetramer [ PUBMED:8662887 ]. The CO dehydrogenase enzyme complex from Methanosarcina thermophila contains a corrinoid/iron-sulphur enzyme composed of two subunits (delta and gamma) [ PUBMED:8550451 ]. This family consists of carbon monoxide dehydrogenase I/II beta subunit EC and CO dehydrogenase (acetyl-CoA synthase epsilon subunit).
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||methanogenesis, from acetate (GO:0019385)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This family is a member of clan FAD_DHS (CL0085), which has the following description:
The members of this family adopt a Rossmann fold, similar to CLAN:CL0063. However, the members of this family are distinguished in that the FAD/NAD cofactor is bound in the opposite direction. In this arrangement, the adenosine moiety is found bound at the second half of the fold. In addition, the conserved GxGxxG motif found in classical NADP binding Rossmann folds is absent. Finally, another distinguishing characteristic is the formation of an internal hydrogen bond in the FAD molecule .
The clan contains the following 10 members:CO_dh DS DUF4917 ETF_alpha PNTB PPS_PS SIR2 SIR2_2 TPP_enzyme_M TPP_enzyme_M_2
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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You can see the alignments as HTML or in three different sequence viewers:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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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.
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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.
|Author:||Bashton M , Bateman A|
|Number in seed:||6|
|Number in full:||146|
|Average length of the domain:||159.2 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||70.83 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CO_dh domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.