Summary: AefR-like transcriptional repressor, C-terminal region
AefR-like transcriptional repressor, C-terminal region Provide feedback
This family comprises the C-terminal domain of transcriptional regulators of the TetR family. It includes the AefR transcriptional regulator from P. syringae . It is found in association with PF00440.
Quinones B, Pujol CJ, Lindow SE;, Mol Plant Microbe Interact. 2004;17:521-531.: Regulation of AHL production and its contribution to epiphytic fitness in Pseudomonas syringae. PUBMED:15141956 EPMC:15141956
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This clan features families of transcriptional regulators for multidrug efflux pumps, which belong to the TetR superfamily. They are induced by the presence of a variety of factors, such as antibiotics or organic solvents. The C-terminal region featured in these families is thought to contain the inducer-binding site; the divergent sequences in this region allow for the binding of a variety of different inducers [1-4].
The clan contains the following 12 members:DUF1956 TetR_C TetR_C_10 TetR_C_11 TetR_C_13 TetR_C_2 TetR_C_3 TetR_C_4 TetR_C_5 TetR_C_6 TetR_C_7 TetR_C_9
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- 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
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Curation and family details
|Number in seed:||92|
|Number in full:||4356|
|Average length of the domain:||53.70 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||24.94 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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There is 1 interaction 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 TetR_C_7 domain has been found. There are 4 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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