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503  structures 7433  species 0  interactions 77902  sequences 647  architectures

Family: Abhydrolase_6 (PF12697)

Summary: Alpha/beta hydrolase family

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

This is the Wikipedia entry entitled "Alpha/beta hydrolase fold". More...

Alpha/beta hydrolase fold Edit Wikipedia article

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This tab holds annotation information from the InterPro database.

InterPro entry IPR000073

The alpha/beta hydrolase fold [ PUBMED:1409539 ] is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is an alpha/beta-sheet (rather than a barrel), containing 8 strands connected by helices [ PUBMED:1409539 ]. The enzymes are believed to have diverged from a common ancestor, preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best conserved structural features of the fold. Esterase (EST) from Pseudomonas putida is a member of the alpha/beta hydrolase fold superfamily of enzymes [ PUBMED:16321951 ].

In most of the family members the beta-strands are parallels, but some have an inversion of the first strands, which gives it an antiparallel orientation. The catalytic triad residues are presented on loops. One of these is the nucleophile elbow and is the most conserved feature of the fold. Some other members lack one or all of the catalytic residues. Some members are therefore inactive but others are involved in surface recognition. The ESTHER database [ PUBMED:14681380 ] gathers and annotates all the published information related to gene and protein sequences of this superfamily [ PUBMED:14681380 ].

This entry represents fold-1 of alpha/beta hydrolase.

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
(391)
Full
(77902)
Representative proteomes UniProt
(272967)
RP15
(8180)
RP35
(33369)
RP55
(74840)
RP75
(129847)
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
(391)
Full
(77902)
Representative proteomes UniProt
(272967)
RP15
(8180)
RP35
(33369)
RP55
(74840)
RP75
(129847)
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
(391)
Full
(77902)
Representative proteomes UniProt
(272967)
RP15
(8180)
RP35
(33369)
RP55
(74840)
RP75
(129847)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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: Jackhmmer:Q186D8_CLOD6
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 391
Number in full: 77902
Average length of the domain: 240.70 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 75.20 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.3 26.3
Trusted cut-off 26.3 26.3
Noise cut-off 26.2 26.2
Model length: 220
Family (HMM) version: 10
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 Abhydrolase_6 domain has been found. There are 503 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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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
A0A0G2KLD8 View 3D Structure Click here
A0A0N7KNQ7 View 3D Structure Click here
A0A0N7KUF3 View 3D Structure Click here
A0A0P0VKU6 View 3D Structure Click here
A0A0P0VL05 View 3D Structure Click here
A0A0P0WA76 View 3D Structure Click here
A0A0P0WLG3 View 3D Structure Click here
A0A0P0Y2E9 View 3D Structure Click here
A0A0R0F173 View 3D Structure Click here
A0A0R0FX16 View 3D Structure Click here
A0A0R0FZI3 View 3D Structure Click here
A0A0R0H3N4 View 3D Structure Click here
A0A0R0HJA9 View 3D Structure Click here
A0A0R0J288 View 3D Structure Click here
A0A0R0JZ89 View 3D Structure Click here
A0A0R0KSE4 View 3D Structure Click here
A0A0R0KSW6 View 3D Structure Click here
A0A1D6E9W6 View 3D Structure Click here
A0A1D6EBM3 View 3D Structure Click here
A0A1D6EIZ2 View 3D Structure Click here
A0A1D6EPY8 View 3D Structure Click here
A0A1D6F0J0 View 3D Structure Click here
A0A1D6GZY7 View 3D Structure Click here
A0A1D6HBN0 View 3D Structure Click here
A0A1D6I9S4 View 3D Structure Click here
A0A1D6IHR0 View 3D Structure Click here
A0A1D6JQE3 View 3D Structure Click here
A0A1D6JQE5 View 3D Structure Click here
A0A1D6K4T4 View 3D Structure Click here
A0A1D6K6X4 View 3D Structure Click here
A0A1D6KGV8 View 3D Structure Click here
A0A1D6KRT1 View 3D Structure Click here
A0A1D6LZZ6 View 3D Structure Click here
A0A1D6MEA6 View 3D Structure Click here
A0A1D6N247 View 3D Structure Click here
A0A1D6N249 View 3D Structure Click here
A0A1D6N250 View 3D Structure Click here
A0A1D6N251 View 3D Structure Click here
A0A1D6N5C2 View 3D Structure Click here
A0A1D6N6L0 View 3D Structure Click here