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185  structures 8389  species 0  interactions 33428  sequences 197  architectures

Family: HMGL-like (PF00682)

Summary: HMGL-like

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 "Pyruvate carboxylase". More...

Pyruvate carboxylase Edit Wikipedia article

Pyruvate carboxylase is an enzyme of the ligase class that catalyzes the irreversible carboxylation of pyruvate to form oxaloacetate. The enzyme is a mitochondrial protein containing a biotin prosthetic group, requiring magnesium or manganese and acetyl CoA, and occurs in liver but not in muscle.

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.

HMGL-like Provide feedback

This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000891

Pyruvate carboxylase ( EC ) (PC), a member of the biotin-dependent enzyme family, is involved in gluconeogenesis by mediating the carboxylation of pyruvate to oxaloacetate. Biotin-dependent carboxylase enzymes perform a two step reaction. Enzyme-bound biotin is first carboxylated by bicarbonate and ATP and the carboxyl group temporarily bound to biotin is subsequently transferred to an acceptor substrate such as pyruvate [ PUBMED:11851389 ]. PC has three functional domains: a biotin carboxylase (BC) domain, a carboxyltransferase (CT) domain which perform the second part of the reaction and a biotinyl domain [ PUBMED:7780827 , PUBMED:10229653 ]. The pyruvate binding to the CT active site induces a conformational change stabilised by the interaction of conserved Asp and Tyr residues in this domain which leads to the formation of the biotin binding pocket and ensures the efficient coupling of BC and CT domain reactions [ PUBMED:23698000 ]. The mechanism by which the carboxyl group is transferred from the carboxybiotin to the pyruvate is not well understood.

The pyruvate carboxyltransferase domain is also found in other pyruvate binding enzymes and acetyl-CoA dependent enzymes suggesting that this domain can be associated with different enzymatic activities.

This domain is found towards the N-terminal region of various aldolase enzymes. This N-terminal TIM barrel domain [ PUBMED:12764229 ] interacts with the C-terminal domain. The C-terminal DmpG_comm domain ( INTERPRO ) is thought to promote heterodimerization with members of INTERPRO to form a bifunctional aldolase-dehydrogenase [ PUBMED:12764229 ].

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
(13)
Full
(33428)
Representative proteomes UniProt
(141761)
RP15
(4464)
RP35
(15810)
RP55
(32817)
RP75
(54772)
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
(13)
Full
(33428)
Representative proteomes UniProt
(141761)
RP15
(4464)
RP35
(15810)
RP55
(32817)
RP75
(54772)
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
(13)
Full
(33428)
Representative proteomes UniProt
(141761)
RP15
(4464)
RP35
(15810)
RP55
(32817)
RP75
(54772)
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_71 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 13
Number in full: 33428
Average length of the domain: 263.4 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 49.07 %

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 29.0 29.0
Trusted cut-off 29.0 29.0
Noise cut-off 28.9 28.9
Model length: 264
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 HMGL-like domain has been found. There are 185 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
A0A077YXX1 View 3D Structure Click here
A0A077ZCA7 View 3D Structure Click here
A0A077ZGE6 View 3D Structure Click here
A0A077ZGP7 View 3D Structure Click here
A0A077ZLQ4 View 3D Structure Click here
A0A0D2D9G7 View 3D Structure Click here
A0A0D2EU90 View 3D Structure Click here
A0A0D2F2G5 View 3D Structure Click here
A0A0D2GQ43 View 3D Structure Click here
A0A0D2GW69 View 3D Structure Click here
A0A0D2H0D1 View 3D Structure Click here
A0A0D2H2U9 View 3D Structure Click here
A0A0H3GJ80 View 3D Structure Click here
A0A0H3GRI1 View 3D Structure Click here
A0A0H3GU24 View 3D Structure Click here
A0A0H3H1U7 View 3D Structure Click here
A0A0K0EKD4 View 3D Structure Click here
A0A0K0EQW5 View 3D Structure Click here
A0A0N4U685 View 3D Structure Click here
A0A0R0EL79 View 3D Structure Click here
A0A0R0EM53 View 3D Structure Click here
A0A0R0FE45 View 3D Structure Click here
A0A0R0GHL3 View 3D Structure Click here
A0A0R4IFJ4 View 3D Structure Click here
A0A158Q367 View 3D Structure Click here
A0A175VP16 View 3D Structure Click here
A0A175W2T4 View 3D Structure Click here
A0A175W3F7 View 3D Structure Click here
A0A175WCZ7 View 3D Structure Click here
A0A1C1C6L5 View 3D Structure Click here
A0A1C1CBL1 View 3D Structure Click here
A0A1C1CBP9 View 3D Structure Click here
A0A1C1CHX2 View 3D Structure Click here
A0A1C1CXZ8 View 3D Structure Click here
A0A1D6EIB6 View 3D Structure Click here
A0A1D6FBC9 View 3D Structure Click here
A0A1D6IQX9 View 3D Structure Click here
A0A1D6K4Z2 View 3D Structure Click here
A0A1D6LUT4 View 3D Structure Click here
A0A1D6MHP8 View 3D Structure Click here