Summary: GDSL-like Lipase/Acylhydrolase family
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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.
GDSL-like Lipase/Acylhydrolase family Provide feedback
This family of presumed lipases and related enzymes are similar to PF00657.
Literature references
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Upton C, Buckley JT; , Trends Biochem Sci 1995;20:178-179.: A new family of lipolytic enzymes? PUBMED:7610479 EPMC:7610479
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Molgaard A, Kauppinen S, Larsen S; , Structure Fold Des 2000;8:373-383.: Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. PUBMED:10801485 EPMC:10801485
Internal database links
SCOOP: | ALGX DUF459 DUF4886 GSCFA Lipase_GDSL Lipase_GDSL_3 Lipase_GDSL_lke OSK PC-Esterase SASA SGNH |
Similarity to PfamA using HHSearch: | Lipase_GDSL GSCFA Lipase_GDSL_3 Lipase_GDSL_lke OSK |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013830
This entry represents the SGNH hydrolase-type esterase domain, which has a similar fold to flavoproteins, namely a three-layer alpha/beta/alpha structure, where the beta-sheets are composed of five parallel strands. Enzymes containing this domain act as esterases and lipases, but have little sequence homology to true lipases [ PUBMED:10801485 , PUBMED:15522763 ]. Proteins containing this type of esterase domain have been found in a variety of hydrolases; those with structural information include an esterase from Streptomyces scabies [ PUBMED:7773790 ]; the esterase domain of viral haemagglutinin-esterase surface glycoproteins (influenza C virus, coronaviruses and toroviruses) [ PUBMED:9817207 ]; mammalian acetylhydrolases [ PUBMED:11522926 ]; fungal rhamnogalacturonan acetylesterase [ PUBMED:11752785 ]; and the multifunctional enzyme thioesterase I (TAP) from Escherichia coli [ PUBMED:12842470 ]. SGNH hydrolase-type esterase domains contain unique hydrogen bond network that stabilises their catalytic centres; they usually contain the catalytic triad Ser/Acid/His.
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 SGNH_hydrolase (CL0264), which has the following description:
This superfamily contains a diversity of hydrolytic enzyme activities.
The clan contains the following 16 members:
ALGX DHHW DltD DUF1574 DUF459 DUF4886 GSCFA Hema_esterase Lipase_GDSL Lipase_GDSL_2 Lipase_GDSL_3 Lipase_GDSL_lke OSK PC-Esterase SASA SGNHAlignments
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 (1326) |
Full (38435) |
Representative proteomes | UniProt (137280) |
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RP15 (4205) |
RP35 (16916) |
RP55 (37076) |
RP75 (63003) |
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Jalview | |||||||
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 (1326) |
Full (38435) |
Representative proteomes | UniProt (137280) |
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---|---|---|---|---|---|---|---|
RP15 (4205) |
RP35 (16916) |
RP55 (37076) |
RP75 (63003) |
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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: | Jackhmmer:A0LCN0 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 1326 |
Number in full: | 38435 |
Average length of the domain: | 188.40 aa |
Average identity of full alignment: | 16 % |
Average coverage of the sequence by the domain: | 55.67 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 179 | ||||||||||||
Family (HMM) version: | 8 | ||||||||||||
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 Lipase_GDSL_2 domain has been found. There are 168 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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