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.
127  structures 5931  species 0  interactions 19476  sequences 141  architectures

Family: ABM (PF03992)

Summary: Antibiotic biosynthesis monooxygenase

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

This is the Wikipedia entry entitled "ABM domain". More...

ABM domain Edit Wikipedia article

PDB 1tz0 EBI.jpg
crystal structure of putative antibiotic biosynthesis monooxygenase from bacillus cereus
Pfam clanCL0032

In molecular biology, the ABM domain is a protein domain that is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species, which can carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. The structure of ActVA-Orf6 monooxygenase from Streptomyces coelicolor, which is involved in actinorhodin biosynthesis, reveals a dimeric alpha+beta barrel topology.[1] There is also a conserved histidine that is likely to be an active site residue. In the S. coelicolor protein SCO1909 this domain occurs as a repeat.


  1. ^ Sciara G, Kendrew SG, Miele AE, Marsh NG, Federici L, Malatesta F, Schimperna G, Savino C, Vallone B (January 2003). "The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis". EMBO J. 22 (2): 205–15. doi:10.1093/emboj/cdg031. PMC 140106. PMID 12514126.
This article incorporates text from the public domain Pfam and InterPro: IPR007138

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.

Antibiotic biosynthesis monooxygenase Provide feedback

This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. It's occurrence as a repeat in Streptomyces coelicolor SCO1909 (Q9X9W3) is suggestive that the other proteins function as multimers. There is also a conserved histidine which is likely to be an active site residue.

Literature references

  1. Yeats C, Bentley S, Bateman A; , BMC Microbiol 2003;3:3-3.: New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. PUBMED:12625841 EPMC:12625841

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007138

The antibiotic biosynthesis monooxygenase (ABM) domain is found in proteins involved in a diverse range of biological processes, including metabolism, transcription, translation and biosynthesis of secondary metabolites:

  • Streptomyces coelicolor ActVA-Orf6 monooxygenase, plays a role in the biosynthesis of aromatic polyketides, specifically the antibiotic actinorhodin, by oxidizing phenolic groups to quinones [ PUBMED:12514126 ].
  • Escherichia coli probable quinol monooxygenase YgiN, can oxidize menadiol to menadione [ PUBMED:15613473 ].
  • Staphylococcus aureus heme-degrading enzymes IsdG and IsdI [ PUBMED:15520015 , PUBMED:18713745 ].
  • Staphylococci signal transduction protein TRAP (target of RNAIII- activating protein) [ PUBMED:22750855 ].
  • Mycobacterium tuberculosis heme-degrading monooxygenase MhuD (or Rv3592) [ PUBMED:19917297 ].
  • Mycobacterium tuberculosis putative monooxygenase Rv0793, might be involved in antibiotic biosynthesis, or may act as reactive oxygen species scavenger that could help in evading host defenses [ PUBMED:16496224 ].
  • Thermus thermophilus hypothetical protein TT1380 [ PUBMED:15103643 ].

The ABM domain has only moderate sequence homology while sharing a high degree of structural similarity. The ABM domain crystallizes as a homodimer. Each monomer is composed of three alpha-helices (H1-3) and four beta-strands (S1-4) and has a ferredoxin-like split BetaAlphaBeta-fold with an antiparallel beta- sheet [ PUBMED:15103643 ]. The beta-sheets of two monomers form a 10-strand, anti- parallel beta-barrel. The barrel is built of two smaller sheets that are connected by long C-terminal strands crossing over from one monomer to the other providing important interactions within the dimer. The core of the barrel is mainly hydrophobic [ PUBMED:12514126 , PUBMED:15613473 , PUBMED:15520015 , PUBMED:22750855 , PUBMED:16496224 , PUBMED:15103643 ].

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 Dim_A_B_barrel (CL0032), which has the following description:

This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel. The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases.

The clan contains the following 28 members:

ABM AsnC_trans_reg AsnC_trans_reg2 Chalcone_N Chlor_dismutase Cyclase_polyket Dabb Dehydratase_hem DUF1330 DUF1428 DUF3291 DUF4188 DUF4242 DUF4937 Dyp_perox EthD FtsX_ECD GYD HapK MIase MmlI NapD NIPSNAP rhaM SchA_CurD SOR YCII ydhR


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.

Representative proteomes UniProt
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

Representative proteomes UniProt

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.

Representative proteomes UniProt
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...


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: Yeats C
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Yeats C
Number in seed: 86
Number in full: 19476
Average length of the domain: 76.60 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 56.80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.1 20.9
Trusted cut-off 23.1 20.9
Noise cut-off 23.0 20.8
Model length: 78
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

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


Align selected sequences to HMM

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


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


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.


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 ABM domain has been found. There are 127 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...