Summary: FMN-dependent dehydrogenase
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.
FMN-dependent dehydrogenase Provide feedback
No Pfam abstract.
Literature references
-
Lindqvist Y; , J Mol Biol 1989;209:151-166.: Refined structure of spinach glycolate oxidase at 2 A resolution. PUBMED:2681790 EPMC:2681790
-
Xia ZX, Mathews FS; , J Mol Biol 1990;212:837-863.: Molecular structure of flavocytochrome b2 at 2.4 A resolution. PUBMED:2329585 EPMC:2329585
Internal database links
SCOOP: | Aldolase B12-binding CBS DHO_dh DUF561 Dus F_bP_aldolase G3P_antiterm Glu_syn_central Glu_synthase His_biosynth IGPS IMPDH NanE NMO OMPdecase Oxidored_FMN PcrB PEP_mutase QRPTase_C ThiG TMP-TENI Trp_syntA |
Similarity to PfamA using HHSearch: | IMPDH Dus Dus Glu_synthase NMO ThiG |
External database links
HOMSTRAD: | flavbb |
PROSITE: | PDOC00482 |
SCOP: | 1gox |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000262
A number of oxidoreductases that act on alpha-hydroxy acids and which are FMN-containing flavoproteins have been shown [PUBMED:2324094, PUBMED:2271624, PUBMED:1939137] to be structurally related. These enzymes are:
- Lactate dehydrogenase (EC), which consists of a dehydrogenase domain and a haem-binding domain called cytochrome b2 and which catalyses the conversion of lactate into pyruvate.
- Glycolate oxidase (EC) ((S)-2-hydroxy-acid oxidase), a peroxisomal enzyme that catalyses the conversion of glycolate and oxygen to glyoxylate and hydrogen peroxide.
- Long chain alpha-hydroxy acid oxidase from rat (EC), a peroxisomal enzyme.
- Lactate 2-monooxygenase (EC) (lactate oxidase) from Mycobacterium smegmatis, which catalyses the conversion of lactate and oxygen to acetate, carbon dioxide and water.
- (S)-mandelate dehydrogenase from Pseudomonas putida (gene mdlB), which catalyses the reduction of (S)-mandelate to benzoylformate.
The first step in the reaction mechanism of these enzymes is the abstraction of the proton from the alpha-carbon of the substrate producing a carbanion which can subsequently attach to the N5 atom of FMN. A conserved histidine has been shown [PUBMED:2644287] to be involved in the removal of the proton. The region around this active site residue is highly conserved and contains an arginine residue which is involved in substrate binding.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | oxidoreductase activity (GO:0016491) |
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 TIM_barrel (CL0036), which has the following description:
This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].
The clan contains the following 60 members:
4HFCP_synth Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD ComA CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF2090 DUF4862 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm GatZ_KbaZ-like Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH KDGP_aldolase Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI PRMT5_TIM Pterin_bind QRPTase_C Radical_SAM RhaA Ribul_P_3_epim SOR_SNZ TAL_FSA ThiC_Rad_SAM ThiG TIM TMP-TENI Trp_syntA UvdE UxuAAlignments
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...
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 (174) |
Full (14853) |
Representative proteomes | UniProt (49762) |
NCBI (140662) |
Meta (8459) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1460) |
RP35 (6092) |
RP55 (12478) |
RP75 (21571) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (174) |
Full (14853) |
Representative proteomes | UniProt (49762) |
NCBI (140662) |
Meta (8459) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1460) |
RP35 (6092) |
RP55 (12478) |
RP75 (21571) |
||||||
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: | Pfam-B_829 (release 3.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 174 |
Number in full: | 14853 |
Average length of the domain: | 292.70 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 82.19 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 348 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
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...
Tree controls
HideThe 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 FMN_dh domain has been found. There are 241 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...