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108  structures 6749  species 0  interactions 20001  sequences 143  architectures

Family: Aldolase_II (PF00596)

Summary: Class II Aldolase and Adducin N-terminal domain

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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.

Class II Aldolase and Adducin N-terminal domain Provide feedback

This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.

Literature references

  1. Dreyer MK, Schulz GE; , J Mol Biol 1993;231:549-553.: The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli. PUBMED:8515438 EPMC:8515438

  2. Dreyer MK, Schulz GE; , J Mol Biol 1996;259:458-466.: Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. PUBMED:8676381 EPMC:8676381


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001303

This entry represents the alpha/beta/alpha domain found in class II aldolases and in adducin (usually at the N terminus of adducin). Proteins containing this domain include: rhamnulose-1-phosphate aldolase ( EC ), L-fuculose phosphate aldolase ( EC ) [ PUBMED:8515438 , PUBMED:8676381 ] that is involved in the third step in fucose metabolism, L-ribulose- 5-phosphate 4-epimerase ( EC ) involved in the third step of L-arabinose catabolism, a probable sugar isomerase SgbE and the metazoan adducins, which have not been ascribed any enzymatic function but which play a role in cell membrane cytoskeleton organisation [ PUBMED:1840603 ].

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
(317)
Full
(20001)
Representative proteomes UniProt
(86318)
RP15
(2342)
RP35
(8710)
RP55
(18998)
RP75
(33217)
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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
(317)
Full
(20001)
Representative proteomes UniProt
(86318)
RP15
(2342)
RP35
(8710)
RP55
(18998)
RP75
(33217)
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
(317)
Full
(20001)
Representative proteomes UniProt
(86318)
RP15
(2342)
RP35
(8710)
RP55
(18998)
RP75
(33217)
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: MRC-LMB Genome Group
Previous IDs: Aldolase_class_II;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 317
Number in full: 20001
Average length of the domain: 183.40 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 54.50 %

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 22.2 22.2
Trusted cut-off 22.3 22.2
Noise cut-off 22.1 22.1
Model length: 186
Family (HMM) version: 23
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 Aldolase_II domain has been found. There are 108 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
A0A1D8PEI8 View 3D Structure Click here
A0A1D8PNQ3 View 3D Structure Click here
A0A2R8Q5P5 View 3D Structure Click here
A1A5X4 View 3D Structure Click here
A4I3R0 View 3D Structure Click here
B4G0F3 View 3D Structure Click here
D3ZUI1 View 3D Structure Click here
F1QTE3 View 3D Structure Click here
F1QW07 View 3D Structure Click here
I1KDU3 View 3D Structure Click here
I1LV18 View 3D Structure Click here
I1M368 View 3D Structure Click here
K7LV33 View 3D Structure Click here
P08203 View 3D Structure Click here
P0AB87 View 3D Structure Click here
P32169 View 3D Structure Click here
P35611 View 3D Structure Click here
P35612 View 3D Structure Click here
P37680 View 3D Structure Click here
P39306 View 3D Structure Click here
P47095 View 3D Structure Click here
P95075 View 3D Structure Click here
Q02645 View 3D Structure Click here
Q05764 View 3D Structure Click here
Q20952 View 3D Structure Click here
Q23261 View 3D Structure Click here
Q2R483 View 3D Structure Click here
Q46890 View 3D Structure Click here
Q54NY7 View 3D Structure Click here
Q54T47 View 3D Structure Click here
Q58813 View 3D Structure Click here
Q5AG73 View 3D Structure Click here
Q62847 View 3D Structure Click here
Q63028 View 3D Structure Click here
Q66I75 View 3D Structure Click here
Q7LKY2 View 3D Structure Click here
Q96GX9 View 3D Structure Click here
Q9FN41 View 3D Structure Click here
Q9HE08 View 3D Structure Click here
Q9P5M9 View 3D Structure Click here
Q9QYB5 View 3D Structure Click here
Q9QYB8 View 3D Structure Click here
Q9QYC0 View 3D Structure Click here
Q9U9K0 View 3D Structure Click here
Q9UEY8 View 3D Structure Click here
Q9UT22 View 3D Structure Click here
Q9VY93 View 3D Structure Click here
Q9WVQ5 View 3D Structure Click here