Summary: YcdC-like protein, C-terminal region
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YcdC-like protein, C-terminal region Provide feedback
This family comprises proteins that belong to the TetR family of transcriptional regulators. They bear particular similarity to YcdC (P75899), a putative HTH-containing protein. This family features the C-terminal region of these sequences, which does not include the helix-turn-helix.
Internal database links
SCOOP: | TetR_C_21 TetR_C_24 TetR_C_29 TetR_C_9 |
Similarity to PfamA using HHSearch: | TetR_C_29 |
External database links
SCOP: | 1pb6 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013573
This entry represents the C-terminal domain found in the hypothetical transcriptional regulators RutR and YcdC (SWISSPROT) from Escherichia coli. Both of these proteins are member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. RutR negatively controls the transcription of the rut operon involved in pyrimidine utilization. The C-terminal domains of RutR, YsiA and TetR share a multi-helical, interlocking structure. These proteins also contain helix-turn-helix (HTH) DNA-binding domains.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Biological process | negative regulation of transcription, DNA-templated (GO:0045892) |
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 TetR_C (CL0174), which has the following description:
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 36 members:
CecR_C TetR_C_1 TetR_C_10 TetR_C_11 TetR_C_13 TetR_C_14 TetR_C_15 TetR_C_16 TetR_C_17 TetR_C_18 TetR_C_19 TetR_C_2 TetR_C_20 TetR_C_21 TetR_C_22 TetR_C_23 TetR_C_24 TetR_C_25 TetR_C_26 TetR_C_27 TetR_C_28 TetR_C_29 TetR_C_3 TetR_C_30 TetR_C_31 TetR_C_33 TetR_C_34 TetR_C_35 TetR_C_36 TetR_C_37 TetR_C_4 TetR_C_5 TetR_C_6 TetR_C_7 TetR_C_8 TetR_C_9Alignments
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 (15) |
Full (1370) |
Representative proteomes | UniProt (9658) |
NCBI (11475) |
Meta (128) |
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RP15 (92) |
RP35 (478) |
RP55 (1325) |
RP75 (3138) |
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HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (15) |
Full (1370) |
Representative proteomes | UniProt (9658) |
NCBI (11475) |
Meta (128) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (92) |
RP35 (478) |
RP55 (1325) |
RP75 (3138) |
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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_4012 (release 17.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Fenech M |
Number in seed: | 15 |
Number in full: | 1370 |
Average length of the domain: | 139.60 aa |
Average identity of full alignment: | 36 % |
Average coverage of the sequence by the domain: | 64.85 % |
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: | 143 | ||||||||||||
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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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 TetR_C_3 domain has been found. There are 12 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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