!!

Powering down the Pfam website
On October 5th, we began redirecting traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will remain available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
144  structures 4307  species 0  interactions 13182  sequences 197  architectures

Family: CO_deh_flav_C (PF03450)

Summary: CO dehydrogenase flavoprotein C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

CO dehydrogenase flavoprotein C-terminal domain Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005107

Proteins containing this domain form structural complexes with other known families, such as INTERPRO and INTERPRO . The carbon monoxide (CO) dehydrogenase of Oligotropha carboxidovorans is a heterotrimeric complex composed of a apoflavoprotein, a molybdoprotein, and an iron-sulphur protein. It can be dissociated with sodium dodecylsulphate [ PUBMED:10636886 ]. CO dehydrogenase catalyzes the oxidation of CO according to the following equation [ PUBMED:11076018 ]: CO + H2O = CO2 + 2e + 2H+

Subunit S represents the iron-sulphur protein of CO dehydrogenase and is clearly divided into a C- and an N-terminal domain, each binding a [2Fe-2S] cluster [ PUBMED:10430865 ].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan SufE_NifU (CL0233), which has the following description:

This clan includes iron sulfur cluster assembly proteins.

The clan contains the following 4 members:

CO_deh_flav_C Lip_prot_lig_C NifU_N SufE

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(93)
Full
(13182)
Representative proteomes UniProt
(51988)
RP15
(1560)
RP35
(5590)
RP55
(12639)
RP75
(21412)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(93)
Full
(13182)
Representative proteomes UniProt
(51988)
RP15
(1560)
RP35
(5590)
RP55
(12639)
RP75
(21412)
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
(93)
Full
(13182)
Representative proteomes UniProt
(51988)
RP15
(1560)
RP35
(5590)
RP55
(12639)
RP75
(21412)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: SCOP
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Griffiths-Jones SR
Number in seed: 93
Number in full: 13182
Average length of the domain: 101.9 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 15.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.5 25.5
Trusted cut-off 25.5 25.5
Noise cut-off 25.4 25.4
Model length: 102
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Structures

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_deh_flav_C domain has been found. There are 144 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.

Loading structure mapping...

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.

Protein Predicted structure External Information
A0A077YWP9 View 3D Structure Click here
A0A0D2DJ52 View 3D Structure Click here
A0A0K0E478 View 3D Structure Click here
A0A0K0E8Z9 View 3D Structure Click here
A0A0R0G5H5 View 3D Structure Click here
A0A175VSC0 View 3D Structure Click here
A0A1C1C6R0 View 3D Structure Click here
A0A1D6GFT6 View 3D Structure Click here
A0A1D6HSW8 View 3D Structure Click here
A0A1D6HX68 View 3D Structure Click here
A0A1D6K6B9 View 3D Structure Click here
A0A1D6L715 View 3D Structure Click here
A0A1D6L725 View 3D Structure Click here
A0A1D6L755 View 3D Structure Click here
A0A1U8QNG8 View 3D Structure Click here
A0A2R8Q1T4 View 3D Structure Click here
C0NJY1 View 3D Structure Click here
C0P187 View 3D Structure Click here
C1GVU5 View 3D Structure Click here
C1GXQ5 View 3D Structure Click here
C4NYZ3 View 3D Structure Click here
F1Q5R8 View 3D Structure Click here
F4JLI5 View 3D Structure Click here
G3X982 View 3D Structure Click here
H9TB17 View 3D Structure Click here
H9TB18 View 3D Structure Click here
H9TB19 View 3D Structure Click here
I1JIN7 View 3D Structure Click here
I1M510 View 3D Structure Click here
I1M7D9 View 3D Structure Click here
I6Y7N2 View 3D Structure Click here
K0ENK1 View 3D Structure Click here
K0F5V3 View 3D Structure Click here
K7KB27 View 3D Structure Click here
M1ZMM0 View 3D Structure Click here
O17892 View 3D Structure Click here
O23887 View 3D Structure Click here
O23888 View 3D Structure Click here
O54754 View 3D Structure Click here
P10351 View 3D Structure Click here