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].
This clan contains 36 families and the total number of domains in the clan is 74094. The clan was built by M Fenech.
- Rouch DA, Cram DS, DiBerardino D, Littlejohn TG, Skurray RA; , Mol Microbiol 1990;4:2051-2062.: Efflux-mediated antiseptic resistance gene qacA from Staphylococcus aureus: common ancestry with tetracycline- and sugar-transport proteins. PUBMED:2089219 EPMC:2089219
- Grkovic S, Brown MH, Roberts NJ, Paulsen IT, Skurray RA; , J Biol Chem 1998;273:18665-18673.: QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. PUBMED:9660841 EPMC:9660841
- Godsey MH, Zheleznova Heldwein EE, Brennan RG; , J Biol Chem 2002;277:40169-40172.: Structural biology of bacterial multidrug resistance gene regulators. PUBMED:12186881 EPMC:12186881
- Hillen W, Berens C; , Annu Rev Microbiol 1994;48:345-369.: Mechanisms underlying expression of Tn10 encoded tetracycline resistance. PUBMED:7826010 EPMC:7826010
This clan contains the following 36 member families: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_32 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_9
External database links
Below is a listing of the unique domain organisations or architectures from this clan. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- 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
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by
clicking on the graphic. You can also choose to see all sequences which
have a given architecture by clicking on the
in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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The table below shows the number of occurrences of each domain throughout the sequence database. More...
In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this domain. The rightmost column provides a link to the alignments tab for each domain. Finally, the last row in the table provides a link to the HTML representation of the alignment for the seed alignments for all members of this clan.
Please note: the clan alignment can be extremely large and the resulting HTML file is often too large to be rendered by web-browsers. Please consider downloading the alignment (by right-clicking the link) rather than viewing it in your browser.
|Pfam family||Num. domains||Alignment|
|TetR_C_24 (PF17932)||8098 (10.9%)||View|
|TetR_C_33 (PF13305)||7957 (10.7%)||View|
|TetR_C_6 (PF13977)||7477 (10.1%)||View|
|TetR_C_1 (PF02909)||7013 (9.5%)||View|
|TetR_C_11 (PF16859)||6479 (8.7%)||View|
|TetR_C_7 (PF14246)||4732 (6.4%)||View|
|TetR_C_8 (PF14278)||3807 (5.1%)||View|
|TetR_C_14 (PF17754)||3616 (4.9%)||View|
|TetR_C_13 (PF16925)||2903 (3.9%)||View|
|TetR_C_16 (PF17920)||2122 (2.9%)||View|
|TetR_C_29 (PF17938)||1849 (2.5%)||View|
|TetR_C_31 (PF17940)||1818 (2.5%)||View|
|TetR_C_30 (PF17939)||1607 (2.2%)||View|
|TetR_C_3 (PF08362)||1523 (2.1%)||View|
|TetR_C_28 (PF17937)||1306 (1.8%)||View|
|TetR_C_15 (PF17918)||1140 (1.5%)||View|
|TetR_C_20 (PF17925)||1075 (1.5%)||View|
|TetR_C_22 (PF17928)||1007 (1.4%)||View|
|TetR_C_27 (PF17935)||970 (1.3%)||View|
|Pfam family||Num. domains||Alignment|
|TetR_C_4 (PF08359)||955 (1.3%)||View|
|TetR_C_2 (PF08361)||937 (1.3%)||View|
|TetR_C_32 (PF09209)||772 (1.0%)||View|
|TetR_C_23 (PF17931)||735 (1.0%)||View|
|TetR_C_21 (PF17926)||725 (1.0%)||View|
|TetR_C_34 (PF17929)||628 (0.8%)||View|
|TetR_C_35 (PF18556)||595 (0.8%)||View|
|TetR_C_10 (PF16295)||481 (0.6%)||View|
|TetR_C_25 (PF17933)||371 (0.5%)||View|
|TetR_C_19 (PF17924)||270 (0.4%)||View|
|TetR_C_17 (PF17922)||217 (0.3%)||View|
|TetR_C_5 (PF08360)||215 (0.3%)||View|
|TetR_C_36 (PF18598)||193 (0.3%)||View|
|TetR_C_18 (PF17923)||170 (0.2%)||View|
|TetR_C_9 (PF14514)||136 (0.2%)||View|
|TetR_C_26 (PF17934)||106 (0.1%)||View|
|TetR_C_37 (PF18665)||89 (0.1%)||View|
|Total: 36||Total: 74094||Clan alignment|
Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.
This diagram shows the relationships between members of this clan. More...
Relationships between families in a clan are determined using HHsearch. Families are deemed to be closely related if their E-value is less than 10-3 and these relationships are shown with a solid line. Less closely related family pairs, with an E-value of between 10-3 and 10-1, are shown with a dashed line.
The E-value for each pair of closely or partially related families is shown next to the line linking the families. You can see the information regarding a Pfam family by clicking on the family box.
This tree shows the occurrence of the domains in this clan across different species. More...
For all of the domain matches in a full alignment we count the number of domains that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There are 25 interactions for this clan. 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 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 MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.
Loading structure mapping...