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271  structures 6718  species 0  interactions 48918  sequences 725  architectures

Family: Abhydrolase_3 (PF07859)

Summary: alpha/beta hydrolase fold

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

  • From a page move: This is a redirect from a page that has been moved (renamed). This page was kept as a redirect to avoid breaking links, both internal and external, that may have been made to the old page name.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

alpha/beta hydrolase fold Provide feedback

This catalytic domain is found in a very wide range of enzymes.

Literature references

  1. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, Sussman JL, Verschueren KHG, Goldman A; , Protein Eng 1992;5:197-211.: The alpha/beta hydrolase fold PUBMED:1409539 EPMC:1409539


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013094

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 the catalytic domain fold-3 of alpha/beta hydrolase.

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
(93)
Full
(48918)
Representative proteomes UniProt
(145563)
RP15
(5738)
RP35
(21138)
RP55
(42497)
RP75
(69476)
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
(93)
Full
(48918)
Representative proteomes UniProt
(145563)
RP15
(5738)
RP35
(21138)
RP55
(42497)
RP75
(69476)
Alignment:
Format:
Order:
Sequence:
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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
(93)
Full
(48918)
Representative proteomes UniProt
(145563)
RP15
(5738)
RP35
(21138)
RP55
(42497)
RP75
(69476)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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_100 (release 15.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 93
Number in full: 48918
Average length of the domain: 188.00 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 53.72 %

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: 211
Family (HMM) version: 15
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_3 domain has been found. There are 271 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
A0A0P0UYF3 View 3D Structure Click here
A0A0P0VVI4 View 3D Structure Click here
A0A0P0WTX9 View 3D Structure Click here
A0A0P0X2H6 View 3D Structure Click here
A0A0P0X9D4 View 3D Structure Click here
A0A0P0XH29 View 3D Structure Click here
A0A0P0XM40 View 3D Structure Click here
A0A0P0XNK8 View 3D Structure Click here
A0A0P0XP65 View 3D Structure Click here
A0A0P0Y6L9 View 3D Structure Click here
A0A0R0EB56 View 3D Structure Click here
A0A0R0GYY6 View 3D Structure Click here
A0A0R0H3H8 View 3D Structure Click here
A0A0R0I8Q2 View 3D Structure Click here
A0A0R0IXI2 View 3D Structure Click here
A0A0R0J647 View 3D Structure Click here
A0A0R0J647 View 3D Structure Click here
A0A0R0JSG4 View 3D Structure Click here
A0A0R0K7X4 View 3D Structure Click here
A0A0R4J5X2 View 3D Structure Click here
A0A1D6EGD3 View 3D Structure Click here
A0A1D6ERI1 View 3D Structure Click here
A0A1D6ERI3 View 3D Structure Click here
A0A1D6ERI4 View 3D Structure Click here
A0A1D6F547 View 3D Structure Click here
A0A1D6F548 View 3D Structure Click here
A0A1D6F9W9 View 3D Structure Click here
A0A1D6F9X0 View 3D Structure Click here
A0A1D6FL00 View 3D Structure Click here
A0A1D6GVU0 View 3D Structure Click here
A0A1D6HB17 View 3D Structure Click here
A0A1D6HSQ4 View 3D Structure Click here
A0A1D6HSQ9 View 3D Structure Click here
A0A1D6HSR1 View 3D Structure Click here
A0A1D6HSR3 View 3D Structure Click here
A0A1D6I1P1 View 3D Structure Click here
A0A1D6I5R5 View 3D Structure Click here
A0A1D6I5Z7 View 3D Structure Click here
A0A1D6I5Z8 View 3D Structure Click here
A0A1D6I600 View 3D Structure Click here
A0A1D6I602 View 3D Structure Click here
A0A1D6I603 View 3D Structure Click here
A0A1D6I604 View 3D Structure Click here
A0A1D6I604 View 3D Structure Click here
A0A1D6I606 View 3D Structure Click here
A0A1D6IJ70 View 3D Structure Click here
A0A1D6IJ70 View 3D Structure Click here
A0A1D6IL25 View 3D Structure Click here
A0A1D6IL28 View 3D Structure Click here
A0A1D6IL44 View 3D Structure Click here
A0A1D6ILG3 View 3D Structure Click here
A0A1D6JW98 View 3D Structure Click here
A0A1D6KLB1 View 3D Structure Click here
A0A1D6KLB5 View 3D Structure Click here
A0A1D6LVE5 View 3D Structure Click here
A0A1D6LW75 View 3D Structure Click here
A0A1D6M449 View 3D Structure Click here
A0A1D6M484 View 3D Structure Click here
A0A1D6M485 View 3D Structure Click here
A0A1D6MDL4 View 3D Structure Click here
A0A1D6ML69 View 3D Structure Click here
A0A1D6ML69 View 3D Structure Click here
A0A1D6ML72 View 3D Structure Click here
A0A1D6N7Y4 View 3D Structure Click here
A0A1D6NQU0 View 3D Structure Click here
A0A1D6Q3B7 View 3D Structure Click here
A0A2R8RW49 View 3D Structure Click here
A0A2R8RW49 View 3D Structure Click here
A2A752 View 3D Structure Click here
A2A752 View 3D Structure Click here
A2A7Z8 View 3D Structure Click here
A2A7Z8 View 3D Structure Click here
A3KPJ7 View 3D Structure Click here
A3KPJ7 View 3D Structure Click here
A4HWD4 View 3D Structure Click here
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A5PMM7 View 3D Structure Click here
B0V0X5 View 3D Structure Click here
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B1ASB3 View 3D Structure Click here
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B1AVU5 View 3D Structure Click here
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B1AVU6 View 3D Structure Click here
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B1AVU7 View 3D Structure Click here
B1AVU7 View 3D Structure Click here
B2GV54 View 3D Structure Click here
B2GV54 View 3D Structure Click here
B2RWD2 View 3D Structure Click here
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B4FFC7 View 3D Structure Click here
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B4FQ89 View 3D Structure Click here
B4FV84 View 3D Structure Click here
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B4G055 View 3D Structure Click here
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D4A340 View 3D Structure Click here
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F1Q8P9 View 3D Structure Click here
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I1JAU8 View 3D Structure Click here
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J3QPI0 View 3D Structure Click here
K7K8Y6 View 3D Structure Click here
K7KYD0 View 3D Structure Click here
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K7LE13 View 3D Structure Click here
K7LE65 View 3D Structure Click here
K7MIN9 View 3D Structure Click here
K7N568 View 3D Structure Click here
K7U051 View 3D Structure Click here
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K7W544 View 3D Structure Click here
M0R509 View 3D Structure Click here
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M0R631 View 3D Structure Click here
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M0RB39 View 3D Structure Click here
M0RB39 View 3D Structure Click here
M0RC77 View 3D Structure Click here
O06350 View 3D Structure Click here
O06832 View 3D Structure Click here
O14158 View 3D Structure Click here
O14158 View 3D Structure Click here
O53424 View 3D Structure Click here
O62460 View 3D Structure Click here
O64640 View 3D Structure Click here
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P14326 View 3D Structure Click here
P15304 View 3D Structure Click here
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P22760 View 3D Structure Click here
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P23872 View 3D Structure Click here
P54310 View 3D Structure Click here
P54310 View 3D Structure Click here
P71668 View 3D Structure Click here
P95125 View 3D Structure Click here
P96399 View 3D Structure Click here
P96402 View 3D Structure Click here
P9WK85 View 3D Structure Click here
P9WK87 View 3D Structure Click here
Q04066 View 3D Structure Click here
Q05469 View 3D Structure Click here
Q05469 View 3D Structure Click here
Q0D8F9 View 3D Structure Click here
Q0J520 View 3D Structure Click here
Q10C96 View 3D Structure Click here
Q10NU5 View 3D Structure Click here
Q18974 View 3D Structure Click here
Q19839 View 3D Structure Click here
Q19839 View 3D Structure Click here
Q2FV90 View 3D Structure Click here
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Q2G154 View 3D Structure Click here
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Q2QUR1 View 3D Structure Click here
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Q2RAT1 View 3D Structure Click here
Q4CRK1 View 3D Structure Click here
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Q4D995 View 3D Structure Click here
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Q50681 View 3D Structure Click here
Q53KT2 View 3D Structure Click here
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Q54QI3 View 3D Structure Click here
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Q63HM1 View 3D Structure Click here
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Q67J02 View 3D Structure Click here
Q67J05 View 3D Structure Click here
Q67J09 View 3D Structure Click here
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Q69J38 View 3D Structure Click here
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Q6J657 View 3D Structure Click here
Q6L545 View 3D Structure Click here
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Q6P093 View 3D Structure Click here
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Q79FE8 View 3D Structure Click here
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Q7JR83 View 3D Structure Click here
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Q8BM81 View 3D Structure Click here
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Q8BUY2 View 3D Structure Click here
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Q8GRZ3 View 3D Structure Click here
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Q8H5P5 View 3D Structure Click here
Q8H5P9 View 3D Structure Click here
Q8K4H1 View 3D Structure Click here
Q8LED9 View 3D Structure Click here
Q8RZ79 View 3D Structure Click here
Q8VYP9 View 3D Structure Click here
Q93VD4 View 3D Structure Click here
Q940G6 View 3D Structure Click here
Q94187 View 3D Structure Click here
Q94187 View 3D Structure Click here
Q94AS5 View 3D Structure Click here
Q966P1 View 3D Structure Click here
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Q99PG0 View 3D Structure Click here
Q99PG0 View 3D Structure Click here
Q9FG13 View 3D Structure Click here
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Q9HDX3 View 3D Structure Click here
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Q9LMA7 View 3D Structure Click here
Q9LT10 View 3D Structure Click here
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