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3  structures 1461  species 0  interactions 12982  sequences 291  architectures

Family: TLD (PF07534)

Summary: TLD

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

TLD Provide feedback

This domain is predicted to be an enzyme [1] and is often found associated with PF01476. It's structure consists of a beta-sandwich surrounded by two helices and two one-turn helices [2].

Literature references

  1. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P; , Genome Res 2002;12:47-56.: Systematic identification of novel protein domain families associated with nuclear functions. PUBMED:11779830 EPMC:11779830

  2. Blaise M, Alsarraf HM, Wong JE, Midtgaard SR, Laroche F, Schack L, Spaink H, Stougaard J, Thirup S;, Proteins. 2012;80:1694-1698.: Crystal structure of the TLDc domain of oxidation resistance protein 2 from zebrafish. PUBMED:22434723 EPMC:22434723


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006571

The Tre2/Bub2/Cdc16 (TBC), lysin motif (LysM), domain catalytic (TLDc) domain is present in all eukaryotes, and its primary sequence is highly conserved among species. The TLDc domain is present in several proteins that share a protective function against oxidative stress (OS). The TLDc domain alone is able to confer oxidative resistance properties to all the TLDc members. The TLDc domain-containing proteins could influence the expression of key oxygen free-radical scavengers that, in turn, reduce the levels of ROS in the cell [ PUBMED:28707022 , PUBMED:26668325 , PUBMED:20567517 , PUBMED:22434723 ].

The TLDc domain is a conserved protein motif of ~200 amino acids whose overall structure is globular. Two antiparallel beta-sheets form a central beta- sandwich, surrounded by two helices and two one-turn helices. Each beta-sheet is composed of six and four strands. The two sheets organize as a pseudo-orthogonal beta-sandwich and interact with each other only by hydrophobic interactions [ PUBMED:22434723 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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 and the UniProtKB 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
(97)
Full
(12982)
Representative proteomes UniProt
(23250)
RP15
(3886)
RP35
(6192)
RP55
(10805)
RP75
(14065)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(97)
Full
(12982)
Representative proteomes UniProt
(23250)
RP15
(3886)
RP35
(6192)
RP55
(10805)
RP75
(14065)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(97)
Full
(12982)
Representative proteomes UniProt
(23250)
RP15
(3886)
RP35
(6192)
RP55
(10805)
RP75
(14065)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

Seed source: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Studholme DJ , Eberhardt R
Number in seed: 97
Number in full: 12982
Average length of the domain: 133.80 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 28.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 139
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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 TLD domain has been found. There are 3 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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