Summary: BadF/BadG/BcrA/BcrD ATPase family
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BadF/BadG/BcrA/BcrD ATPase family Provide feedback
This family includes the BadF O07462 and BadG O07463 proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase P11568. The protein O66634 contains two copies of this region suggesting that the family may structurally dimerise. This family appears to be related to PF00370.
Literature references
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Bendrat K, Muller U, Klees AG, Buckel W; , FEBS Lett 1993;329:329-331.: Identification of the gene encoding the activator of (R)-2- hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans by gene expression in Escherichia coli. PUBMED:8365476 EPMC:8365476
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Breese K, Boll M, Alt-Morbe J, Schagger H, Fuchs G; , Eur J Biochem 1998;256:148-154.: Genes coding for the benzoyl-CoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica. PUBMED:9746358 EPMC:9746358
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Egland PG, Pelletier DA, Dispensa M, Gibson J, Harwood CS; , Proc Natl Acad Sci U S A 1997;94:6484-6489.: A cluster of bacterial genes for anaerobic benzene ring biodegradation. PUBMED:9177244 EPMC:9177244
Internal database links
SCOOP: | Acetate_kinase Carbam_trans_N DEDD_Tnp_IS110 FGGY_C FGGY_N FtsA Fumble Glucokinase Hydant_A_N Hydantoinase_A MreB_Mbl MutL PilM_2 ROK SHS2_FTSA TsaD |
Similarity to PfamA using HHSearch: | FGGY_N ROK |
External database links
SCOP: | 1hux |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002731
This domain is found in the BadF (SWISSPROT) and BadG (SWISSPROT) proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase (SWISSPROT). The hypothetical protein AQ_278 from Aquifex aeolicus SWISSPROT contains two copies of this region suggesting that the family may structurally dimerise.
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 Actin_ATPase (CL0108), which has the following description:
The actin-like ATPase domain forms an alpha/beta canonical fold. The domain can be subdivided into 1A, 1B, 2A and 2B subdomains. Subdomains 1A and 1B share the same RNAseH-like fold (a five-stranded beta-sheet decorated by a number of alpha-helices). Domains 1A and 2A are conserved in all members of this superfamily, whereas domain 1B and 2B have a variable structure and are even missing from some homologues [1]. Within the actin-like ATPase domain the ATP-binding site is highly conserved. The phosphate part of the ATP is bound in a cleft between subdomains 1A and 2A, whereas the adenosine moiety is bound to residues from domains 2A and 2B[1].
The clan contains the following 34 members:
Acetate_kinase Actin Actin_micro ALP_N AnmK BcrAD_BadFG Carbam_trans_N DDR DUF1464 DUF2229 EutA FGGY_C FGGY_N FtsA Fumble GDA1_CD39 Glucokinase Hexokinase_1 Hexokinase_2 HGD-D HSP70 Hydant_A_N Hydantoinase_A HypF_C MreB_Mbl MutL Pan_kinase PilM_2 Ppx-GppA RACo_C_ter ROK StbA T2SSL TsaDAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (16) |
Full (7715) |
Representative proteomes | UniProt (31659) |
NCBI (45139) |
Meta (201) |
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RP15 (1241) |
RP35 (4221) |
RP55 (7721) |
RP75 (12150) |
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PP/heatmap | 1 |
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.
Seed (16) |
Full (7715) |
Representative proteomes | UniProt (31659) |
NCBI (45139) |
Meta (201) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1241) |
RP35 (4221) |
RP55 (7721) |
RP75 (12150) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Enright A & Pfam-B_5854 (Release 7.5) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Enright A |
Number in seed: | 16 |
Number in full: | 7715 |
Average length of the domain: | 266.00 aa |
Average identity of full alignment: | 19 % |
Average coverage of the sequence by the domain: | 61.27 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 267 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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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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Interactions
There is 1 interaction for this family. More...
BcrAD_BadFGStructures
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 BcrAD_BadFG domain has been found. There are 25 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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