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0  structures 1483  species 0  interactions 11568  sequences 193  architectures

Family: TRAM_LAG1_CLN8 (PF03798)

Summary: TLC domain

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.

TLC domain Provide feedback

No Pfam abstract.

Literature references

  1. Winter E, Ponting CP; , Trends Biochem Sci. 2002;27:381-383.: TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains?. PUBMED:12151215 EPMC:12151215


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006634

TLC is a protein domain with at least 5 transmembrane alpha-helices. Lag1p and Lac1p are essential for acyl-CoA-dependent ceramide synthesis [ PUBMED:11694577 ], TRAM is a subunit of the translocon and the CLN8 gene is mutated in Northern epilepsy syndrome. Proteins containing this domain may possess multiple functions such as lipid trafficking, metabolism, or sensing. Trh homologues possess additional homeobox domains [ PUBMED:9872981 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(134)
Full
(11568)
Representative proteomes UniProt
(21239)
RP15
(2116)
RP35
(5111)
RP55
(9519)
RP75
(12516)
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
(134)
Full
(11568)
Representative proteomes UniProt
(21239)
RP15
(2116)
RP35
(5111)
RP55
(9519)
RP75
(12516)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(134)
Full
(11568)
Representative proteomes UniProt
(21239)
RP15
(2116)
RP35
(5111)
RP55
(9519)
RP75
(12516)
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: Pfam-B_1398 (release 7.0)
Previous IDs: LAG1;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD
Number in seed: 134
Number in full: 11568
Average length of the domain: 190.80 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 56.64 %

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 24.6 24.6
Trusted cut-off 24.6 24.6
Noise cut-off 24.5 24.5
Model length: 197
Family (HMM) version: 18
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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A061AD30 View 3D Structure Click here
A0A096SS31 View 3D Structure Click here
A0A0G2KHZ9 View 3D Structure Click here
A0A0P0V1A2 View 3D Structure Click here
A0A0R0JEU3 View 3D Structure Click here
A0A0R0L3B1 View 3D Structure Click here
A0A0R0L423 View 3D Structure Click here
A0A0R4IJ79 View 3D Structure Click here
A0A0R4IS61 View 3D Structure Click here
A0A140LFW4 View 3D Structure Click here
A0A1D6HBL9 View 3D Structure Click here
A0A1D6I3C9 View 3D Structure Click here
A0A1D6LCY5 View 3D Structure Click here
A0A1D6Q3T5 View 3D Structure Click here
A0A1D8PKA5 View 3D Structure Click here
A0A1I9LNG5 View 3D Structure Click here
A0A1P8AW96 View 3D Structure Click here
A0A368UHU5 View 3D Structure Click here
A4I6V5 View 3D Structure Click here
A6NGC4 View 3D Structure Click here
A8E7D4 View 3D Structure Click here
A8WGS4 View 3D Structure Click here
B1H294 View 3D Structure Click here
B1WBX0 View 3D Structure Click here
B4FBX8 View 3D Structure Click here
B4FHS8 View 3D Structure Click here
B4FM98 View 3D Structure Click here
B4FRP7 View 3D Structure Click here
B4G0X2 View 3D Structure Click here
B6TCE5 View 3D Structure Click here
B6TCF6 View 3D Structure Click here
B6UA21 View 3D Structure Click here
B6UE85 View 3D Structure Click here
C0H4D2 View 3D Structure Click here
C0HH61 View 3D Structure Click here
C0PA08 View 3D Structure Click here
C0PFX9 View 3D Structure Click here
D3ZKW7 View 3D Structure Click here
D3ZNW9 View 3D Structure Click here
D3ZPC3 View 3D Structure Click here
D3ZU86 View 3D Structure Click here
D4A038 View 3D Structure Click here
D4AA91 View 3D Structure Click here
D4AAE5 View 3D Structure Click here
E7F142 View 3D Structure Click here
E7F9X7 View 3D Structure Click here
E7FCM3 View 3D Structure Click here
E7FG14 View 3D Structure Click here
F1LTP8 View 3D Structure Click here
F1LUA2 View 3D Structure Click here
F1Q640 View 3D Structure Click here
F1QF55 View 3D Structure Click here
F1QPF3 View 3D Structure Click here
F1QSW8 View 3D Structure Click here
F1QVG1 View 3D Structure Click here
F1QW88 View 3D Structure Click here
F4HWQ7 View 3D Structure Click here
G5ED45 View 3D Structure Click here
G5EF48 View 3D Structure Click here
I1JEN4 View 3D Structure Click here
I1JHP6 View 3D Structure Click here
I1JJ09 View 3D Structure Click here
I1JZ62 View 3D Structure Click here
I1KAA0 View 3D Structure Click here
I1LM10 View 3D Structure Click here
I1M706 View 3D Structure Click here
I1M885 View 3D Structure Click here
I1MBN3 View 3D Structure Click here
I1MLN2 View 3D Structure Click here
I1MMA9 View 3D Structure Click here
I1MXY9 View 3D Structure Click here
I1N7F6 View 3D Structure Click here
K7L9X3 View 3D Structure Click here
K7MPZ5 View 3D Structure Click here
K7MRC9 View 3D Structure Click here
O13752 View 3D Structure Click here
O59735 View 3D Structure Click here
P27544 View 3D Structure Click here
P27545 View 3D Structure Click here
P28496 View 3D Structure Click here
P38703 View 3D Structure Click here
P47153 View 3D Structure Click here
P78970 View 3D Structure Click here
Q06107 View 3D Structure Click here
Q0DJC1 View 3D Structure Click here
Q0JIZ9 View 3D Structure Click here
Q15035 View 3D Structure Click here
Q15629 View 3D Structure Click here
Q1A3B0 View 3D Structure Click here
Q1HL14 View 3D Structure Click here
Q1L8N1 View 3D Structure Click here
Q1LXV8 View 3D Structure Click here
Q20297 View 3D Structure Click here
Q2QV58 View 3D Structure Click here
Q3T1K1 View 3D Structure Click here
Q3TYE7 View 3D Structure Click here
Q4CUX8 View 3D Structure Click here
Q4DB03 View 3D Structure Click here
Q4DN32 View 3D Structure Click here
Q4DSX0 View 3D Structure Click here
Q54S87 View 3D Structure Click here
Q550S9 View 3D Structure Click here
Q550T0 View 3D Structure Click here
Q55BP8 View 3D Structure Click here
Q5A879 View 3D Structure Click here
Q5AI01 View 3D Structure Click here
Q5N944 View 3D Structure Click here
Q5ND56 View 3D Structure Click here
Q5U2T1 View 3D Structure Click here
Q5XI41 View 3D Structure Click here
Q5XIY2 View 3D Structure Click here
Q6AYM9 View 3D Structure Click here
Q6EUN0 View 3D Structure Click here
Q6IDJ6 View 3D Structure Click here
Q6L537 View 3D Structure Click here
Q6NQI8 View 3D Structure Click here
Q6P4U7 View 3D Structure Click here
Q6YWS8 View 3D Structure Click here
Q6ZMG9 View 3D Structure Click here
Q6ZRR5 View 3D Structure Click here
Q71RH2 View 3D Structure Click here
Q75HA3 View 3D Structure Click here
Q75J74 View 3D Structure Click here
Q7TNV1 View 3D Structure Click here
Q7Z139 View 3D Structure Click here
Q802X7 View 3D Structure Click here
Q84QC0 View 3D Structure Click here
Q8C172 View 3D Structure Click here
Q8CGF5 View 3D Structure Click here
Q8GSI6 View 3D Structure Click here
Q8GYK7 View 3D Structure Click here
Q8IM57 View 3D Structure Click here
Q8IU89 View 3D Structure Click here
Q8N5B7 View 3D Structure Click here
Q8N609 View 3D Structure Click here
Q8QZR0 View 3D Structure Click here
Q8TBR7 View 3D Structure Click here
Q8VC26 View 3D Structure Click here
Q8VZR3 View 3D Structure Click here
Q90YY7 View 3D Structure Click here
Q91V04 View 3D Structure Click here
Q924Z4 View 3D Structure Click here
Q924Z5 View 3D Structure Click here
Q93VP0 View 3D Structure Click here
Q93Z82 View 3D Structure Click here
Q93ZA9 View 3D Structure Click here
Q96CP7 View 3D Structure Click here
Q96G23 View 3D Structure Click here
Q96MV1 View 3D Structure Click here
Q99JT6 View 3D Structure Click here
Q9BL09 View 3D Structure Click here
Q9D6J1 View 3D Structure Click here
Q9D6K9 View 3D Structure Click here
Q9HA82 View 3D Structure Click here
Q9LDF2 View 3D Structure Click here
Q9LJK3 View 3D Structure Click here
Q9N5G9 View 3D Structure Click here
Q9QUK3 View 3D Structure Click here
Q9UBY8 View 3D Structure Click here
Q9V3S7 View 3D Structure Click here
Q9W423 View 3D Structure Click here
Q9W5C2 View 3D Structure Click here
Q9XHZ7 View 3D Structure Click here
Q9XWE9 View 3D Structure Click here
Q9XXK7 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;