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52  structures 6960  species 0  interactions 17109  sequences 97  architectures

Family: GCV_T_C (PF08669)

Summary: Glycine cleavage T-protein C-terminal barrel domain

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 "Glycine cleavage system". More...

Glycine cleavage system Edit Wikipedia article

The glycine cleavage system refers to a series of metabolic processes that are triggered in response to high concentrations of the amino acid glycine. The glycine cleavage system allows excess glycine to feed into the citric acid cycle, allowing the generation of energy. The first step in this process is achieved by the glycine decarboxylase complex.

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.

Glycine cleavage T-protein C-terminal barrel domain Provide feedback

This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.

Literature references

  1. McNeil JB, Zhang F, Taylor BV, Sinclair DA, Pearlman RE, Bognar AL; , Gene 1997;186:13-20.: Cloning, and molecular characterization of the GCV1 gene encoding the glycine cleavage T-protein from Saccharomyces cerevisiae. PUBMED:9047339 EPMC:9047339


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013977

This entry represents the C-terminal beta-barrel domain of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes [ PUBMED:15609340 ]. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.

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
(260)
Full
(17109)
Representative proteomes UniProt
(75237)
RP15
(2000)
RP35
(7473)
RP55
(16891)
RP75
(28465)
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
(260)
Full
(17109)
Representative proteomes UniProt
(75237)
RP15
(2000)
RP35
(7473)
RP55
(16891)
RP75
(28465)
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
(260)
Full
(17109)
Representative proteomes UniProt
(75237)
RP15
(2000)
RP35
(7473)
RP55
(16891)
RP75
(28465)
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: Pfam-B_933 (release 4.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bashton M , Bateman A , El-Gebali S
Number in seed: 260
Number in full: 17109
Average length of the domain: 81.3 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 13.91 %

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 25.9 25.9
Trusted cut-off 25.9 25.9
Noise cut-off 25.8 25.8
Model length: 80
Family (HMM) version: 14
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 GCV_T_C domain has been found. There are 52 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
A0A044RZW5 View 3D Structure Click here
A0A044TA99 View 3D Structure Click here
A0A077Z021 View 3D Structure Click here
A0A077Z9L5 View 3D Structure Click here
A0A077ZJR1 View 3D Structure Click here
A0A0D2F101 View 3D Structure Click here
A0A0D2H930 View 3D Structure Click here
A0A0H3H2N5 View 3D Structure Click here
A0A0K0EIB0 View 3D Structure Click here
A0A0N4U7A3 View 3D Structure Click here
A0A175W6D5 View 3D Structure Click here
A0A1C1CEE3 View 3D Structure Click here
A0A1C1CRD4 View 3D Structure Click here
A0A1D8PPW9 View 3D Structure Click here
A0A3P7ELP2 View 3D Structure Click here
A0A3P7GGK7 View 3D Structure Click here
A0A3P7P3M4 View 3D Structure Click here
A0A3P7QZR5 View 3D Structure Click here
A0A486WWC6 View 3D Structure Click here
A0A5S6PSP6 View 3D Structure Click here
A0KJ03 View 3D Structure Click here
A1BI02 View 3D Structure Click here
A1S967 View 3D Structure Click here
A1WWA3 View 3D Structure Click here
A1ZAZ2 View 3D Structure Click here
A3PFH6 View 3D Structure Click here
A3QHI2 View 3D Structure Click here
A4FLG1 View 3D Structure Click here
A4ID15 View 3D Structure Click here
A4ID16 View 3D Structure Click here
A4J2F6 View 3D Structure Click here
A4SDB4 View 3D Structure Click here
A5GPL8 View 3D Structure Click here
A5GWT1 View 3D Structure Click here
A6GXW3 View 3D Structure Click here
A6L6X5 View 3D Structure Click here
A6L8T3 View 3D Structure Click here
A6TDR7 View 3D Structure Click here
A6TMY6 View 3D Structure Click here
A8APB4 View 3D Structure Click here