Summary: Antitoxin Phd_YefM, type II toxin-antitoxin system
Antitoxin Phd_YefM, type II toxin-antitoxin system Provide feedback
Members of this family act as antitoxins in type II toxin-antitoxin systems . When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin . This domain complexes with Txe toxins containing PF06769 Fic/DOC toxins containing PF02661 and YafO toxins containing PF13957.
Anantharaman V, Aravind L; , Genome Biol 2003;4:R81.: New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. PUBMED:14659018 EPMC:14659018
Garcia-Pino A, Balasubramanian S, Wyns L, Gazit E, De Greve H, Magnuson RD, Charlier D, van Nuland NA, Loris R;, Cell. 2010;142:101-111.: Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. PUBMED:20603017 EPMC:20603017
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR006442
Members of this family act as antitoxins in type II toxin-antitoxin systems [PUBMED:14659018]. When bound to their toxin partners, they can bind DNA via the N terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [PUBMED:20603017].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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The families in this clan are plasmid encoded toxins involved in plasmid maintenance. The plasmid encodes both a toxin and an antitoxin. Upon loss of the plasmid the antitoxin is inactivated more rapidly than the toxin. This allows the toxin to interact with its target thus killing the cell or impeding growth.
The clan contains the following 7 members:DUF1044 Gp49 PhdYeFM_antitox Plasmid_killer Plasmid_stabil Plasmid_Txe RelB_N
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Seed source:||COG2161 and |
|Previous IDs:||DUF172; PhdYeFM;|
|Author:||Mian N, Bateman A, Eberhardt R|
|Number in seed:||156|
|Number in full:||5612|
|Average length of the domain:||70.50 aa|
|Average identity of full alignment:||18 %|
|Average coverage of the sequence by the domain:||79.79 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 PhdYeFM_antitox domain has been found. There are 47 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 seqence.
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