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181  structures 3810  species 0  interactions 33357  sequences 408  architectures

Family: FMO-like (PF00743)

Summary: Flavin-binding monooxygenase-like

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 "Flavin-containing monooxygenase". More...

Flavin-containing monooxygenase Edit Wikipedia article

The flavin-containing monooxygenase (FMO) protein family consists of a group of enzymes that catalyze chemical reactions via the bound cofactor flavin. These reactions involve oxidation of heteroatoms, particularly nucleophilic atoms such as the nitrogen of amines.[1]

The best-known such protein is called FMO3 and is mutated in the vast majority of cases of trimethylaminuria, a genetic disease that causes deficiencies in breakdown of trimethylamine and gives the patient a fishy body odor.[2] In yeast, FMO proteins are associated with redox cycling of glutathione to glutathione disulfide, a system that maintains the redox state of the cell and heavily influences the protein folding rates of disulfide bond-containing proteins.[3]


  1. ^ Cashman JR. (1995). Structural and catalytic properties of the mammalian flavin-containing monooxygenase. Chem Res Toxicol 8(2):166-81. PMID 7766799
  2. ^ Hernandez D, Addou S, Lee D, Orengo C, Shephard EA, Phillips IR (2003). Trimethylaminuria and a human FMO3 mutation database. Hum Mutat 22 (3): 209-13. PMID 12938085
  3. ^ Suh JK, Poulsen LL, Ziegler DM, Robertus JD. (1999). Yeast flavin-containing monooxygenase generates oxidizing equivalents that control protein folding in the endoplasmic reticulum. Proc Natl Acad Sci 96(6):2687-91. PMID 10077572

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.

Flavin-binding monooxygenase-like Provide feedback

This family includes FMO proteins, cyclohexanone mono-oxygenase and a number of different mono-oxygenases.

Literature references

  1. Stehr M, Diekmann H, Smau L, Seth O, Ghisla S, Singh M, Macheroux P; , Trends Biochem Sci 1998;23:56-57.: A hydrophobic sequence motif common to N-hydroxylating enzymes. PUBMED:9538688 EPMC:9538688

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020946

Flavin-containing monooxygenases (FMOs) constitute a family of xenobiotic-metabolising enzymes [ PUBMED:8311461 ]. Using an NADPH cofactor and FAD prosthetic group, these microsomal proteins catalyse the oxygenation of nucleophilic nitrogen, sulphur, phosphorus and selenium atoms in a range of structurally diverse compounds. FMOs have been implicated in the metabolism of a number of pharmaceuticals, pesticides and toxicants. In man, lack of hepatic FMO-catalysed trimethylamine metabolism results in trimethylaminuria (fish odour syndrome). Five mammalian forms of FMO are now known and have been designated FMO1-FMO5 [ PUBMED:1712018 , PUBMED:2318837 , PUBMED:1542660 , PUBMED:1417778 , PUBMED:8486656 ]. This is a recent nomenclature based on comparison of amino acid sequences, and has been introduced in an attempt to eliminate confusion inherent in multiple, laboratory-specific designations and tissue-based classifications [ PUBMED:8311461 ]. Following the determination of the complete nucleotide sequence of Saccharomyces cerevisiae (Baker's yeast) [ PUBMED:8091229 ], a novel gene was found to encode a protein with similarity to mammalian monooygenases. In Aspergillus, flavin-containing monooxygenases ustF1 and ustF2 are components in the biosynthesis of the antimitotic tetrapeptide ustiloxin B, a secondary metabolite. The monooxygenases modify the side chain of the intermediate S-deoxyustiloxin H [ PUBMED:27166860 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 209 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 BMT5-like BpsA_C CARME CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF268 DUF2855 DUF3410 DUF364 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C KR LCM Ldh_1_N LpxI_N Lycopene_cycl Lys_Orn_oxgnase Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MmeI_Mtase MOLO1 Mqo MT-A70 MTS Mur_ligase N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall OpcA_G6PD_assem Orbi_VP4 PALP PARP_regulatory PCMT PDH_N PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth SRR1 TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N


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...

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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.

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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: Pfam-B_437 (release 2.1)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 5
Number in full: 33357
Average length of the domain: 257.7 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 59.09 %

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 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 532
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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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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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 FMO-like domain has been found. There are 181 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.

Protein Predicted structure External Information
A0A044T008 View 3D Structure Click here
A0A044UI80 View 3D Structure Click here
A0A077YYU9 View 3D Structure Click here
A0A077Z9H7 View 3D Structure Click here
A0A084R1J7 View 3D Structure Click here
A0A0A2V5R6 View 3D Structure Click here
A0A0D2DD95 View 3D Structure Click here
A0A0D2DHK5 View 3D Structure Click here
A0A0D2DKA2 View 3D Structure Click here
A0A0D2DLR5 View 3D Structure Click here
A0A0D2DNE6 View 3D Structure Click here
A0A0D2DNZ2 View 3D Structure Click here
A0A0D2DQJ0 View 3D Structure Click here
A0A0D2DQL2 View 3D Structure Click here
A0A0D2DS58 View 3D Structure Click here
A0A0D2DTM8 View 3D Structure Click here
A0A0D2DV44 View 3D Structure Click here
A0A0D2E102 View 3D Structure Click here
A0A0D2E3E5 View 3D Structure Click here
A0A0D2E442 View 3D Structure Click here
A0A0D2E496 View 3D Structure Click here
A0A0D2E4Z9 View 3D Structure Click here
A0A0D2EKG7 View 3D Structure Click here
A0A0D2ELC0 View 3D Structure Click here
A0A0D2EMV3 View 3D Structure Click here
A0A0D2EPD8 View 3D Structure Click here
A0A0D2EQ39 View 3D Structure Click here
A0A0D2ESF8 View 3D Structure Click here
A0A0D2EST1 View 3D Structure Click here
A0A0D2ETN2 View 3D Structure Click here
A0A0D2EU55 View 3D Structure Click here
A0A0D2EU68 View 3D Structure Click here
A0A0D2EUX5 View 3D Structure Click here
A0A0D2EYZ4 View 3D Structure Click here
A0A0D2F0M8 View 3D Structure Click here
A0A0D2F242 View 3D Structure Click here
A0A0D2F394 View 3D Structure Click here
A0A0D2F3W7 View 3D Structure Click here
A0A0D2F6N5 View 3D Structure Click here
A0A0D2F8R9 View 3D Structure Click here