Summary: Methionine gamma-lyase
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Methionine gamma-lyase Provide feedback
This is a putative pyridoxal 5'-phosphate-dependent methionine gamma-lyase enzyme involved in methionine catabolism.
Literature references
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Inoue H, Inagaki K, Eriguchi SI, Tamura T, Esaki N, Soda K, Tanaka H;, J Bacteriol. 1997;179:3956-3962.: Molecular characterization of the mde operon involved in L-methionine catabolism of Pseudomonas putida. PUBMED:9190812 EPMC:9190812
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McKie AE, Edlind T, Walker J, Mottram JC, Coombs GH;, J Biol Chem. 1998;273:5549-5556.: The primitive protozoon Trichomonas vaginalis contains two methionine gamma-lyase genes that encode members of the gamma-family of pyridoxal 5'-phosphate-dependent enzymes. PUBMED:9488680 EPMC:9488680
Internal database links
SCOOP: | Alliinase_C Aminotran_1_2 Aminotran_5 Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P SelA |
Similarity to PfamA using HHSearch: | Aminotran_1_2 Aminotran_5 Cys_Met_Meta_PP Beta_elim_lyase |
This tab holds annotation information from the InterPro database.
InterPro entry IPR009651
This is a putative pyridoxal 5'-phosphate-dependent methionine gamma-lyase enzyme involved in methionine catabolism [PUBMED:9190812, PUBMED:9488680].
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 PLP_aminotran (CL0061), which has the following description:
This superfamily contains a variety of PLP-dependent enzymes.
The clan contains the following 16 members:
Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Aminotran_MocR Beta_elim_lyase ComK Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SepSecS SHMTAlignments
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 (13) |
Full (1636) |
Representative proteomes | UniProt (6092) |
NCBI (16485) |
Meta (403) |
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RP15 (238) |
RP35 (965) |
RP55 (1617) |
RP75 (2494) |
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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 (13) |
Full (1636) |
Representative proteomes | UniProt (6092) |
NCBI (16485) |
Meta (403) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (238) |
RP35 (965) |
RP55 (1617) |
RP75 (2494) |
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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: | Pfam-B_5307 (release 10.0) |
Previous IDs: | Alum_res; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Vella Briffa B |
Number in seed: | 13 |
Number in full: | 1636 |
Average length of the domain: | 383.70 aa |
Average identity of full alignment: | 50 % |
Average coverage of the sequence by the domain: | 94.46 % |
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: | 405 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
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...
Met_gamma_lyaseStructures
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 Met_gamma_lyase domain has been found. There are 22 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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