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46  structures 2915  species 0  interactions 5421  sequences 31  architectures

Family: Ldh_2 (PF02615)

Summary: Malate/L-lactate dehydrogenase

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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.

Malate/L-lactate dehydrogenase Provide feedback

This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyses the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyses the reactions: (S)-malate + NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively.

Literature references

  1. Jendrossek D, Kratzin HD, Steinbuchel A; , FEMS Microbiol Lett 1993;112:229-235.: The Alcaligenes eutrophus ldh structural gene encodes a novel type of lactate dehydrogenase. PUBMED:8405966 EPMC:8405966

  2. Honka E, Fabry S, Niermann T, Palm P, Hensel R; , Eur J Biochem 1990;188:623-632.: Properties and primary structure of the L-malate dehydrogenase from the extremely thermophilic archaebacterium Methanothermus fervidus. PUBMED:2110059 EPMC:2110059


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003767

The malate dehydrogenase (MDH) of some extremophilies is more similar to the L-lactate dehydrogenases (L-LDH) EC from various sources than to other MDHs [ PUBMED:8476859 ].

This family consists of bacterial and archaeal malate/L-lactate dehydrogenases and related proteins. The archaebacterial malate dehydrogenase EC , EC deviates from the eubacterial and eukaryotic enzymes having a low selectivity for the coenzyme (NAD(H) or NADP(H)) and catalyzing the reduction of oxalacetate to malate more efficiently than the reverse reaction [ PUBMED:2110059 ].

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
(322)
Full
(5421)
Representative proteomes UniProt
(28289)
RP15
(834)
RP35
(2542)
RP55
(5278)
RP75
(9353)
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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
(322)
Full
(5421)
Representative proteomes UniProt
(28289)
RP15
(834)
RP35
(2542)
RP55
(5278)
RP75
(9353)
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
(322)
Full
(5421)
Representative proteomes UniProt
(28289)
RP15
(834)
RP35
(2542)
RP55
(5278)
RP75
(9353)
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: COG2055
Previous IDs: ldh_2;
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 322
Number in full: 5421
Average length of the domain: 313 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 91.72 %

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 38.8 38.8
Trusted cut-off 39.0 38.9
Noise cut-off 38.7 38.5
Model length: 333
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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 Ldh_2 domain has been found. There are 46 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
A0A044QR19 View 3D Structure Click here
A0A077Z065 View 3D Structure Click here
A0A0D2F0U6 View 3D Structure Click here
A0A0D2GZ01 View 3D Structure Click here
A0A0H3GIN5 View 3D Structure Click here
A0A0H3GU07 View 3D Structure Click here
A0A0K0E9D2 View 3D Structure Click here
A0A0K0EMG6 View 3D Structure Click here
A0A0K0ESF4 View 3D Structure Click here
A0A0N4UMN6 View 3D Structure Click here
A0A1C1CD36 View 3D Structure Click here
A0A3P7EG46 View 3D Structure Click here
A0A3P7F3V5 View 3D Structure Click here
A0A3Q0KLL3 View 3D Structure Click here
A0A5K4EME8 View 3D Structure Click here
A8ARG3 View 3D Structure Click here
A9ALD3 View 3D Structure Click here
C0NHK3 View 3D Structure Click here
C1H1F3 View 3D Structure Click here
D7A0Y0 View 3D Structure Click here
G5EDM5 View 3D Structure Click here
G5EDW8 View 3D Structure Click here
O27273 View 3D Structure Click here
O34736 View 3D Structure Click here
P16142 View 3D Structure Click here
P30178 View 3D Structure Click here
P37672 View 3D Structure Click here
P44995 View 3D Structure Click here
P58408 View 3D Structure Click here
P58409 View 3D Structure Click here
P77555 View 3D Structure Click here
Q07251 View 3D Structure Click here
Q1QWN5 View 3D Structure Click here
Q32I77 View 3D Structure Click here
Q4KGT8 View 3D Structure Click here
Q58820 View 3D Structure Click here
Q7CVK1 View 3D Structure Click here
Q83PQ6 View 3D Structure Click here
Q8ZL83 View 3D Structure Click here
Q8ZM60 View 3D Structure Click here