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146  structures 5959  species 1  interaction 11662  sequences 72  architectures

Family: Carboxyl_trans (PF01039)

Summary: Carboxyl transferase domain

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This is the Wikipedia entry entitled "Carboxyl transferase domain". More...

Carboxyl transferase domain Edit Wikipedia article

Carboxyl_trans
PDB 1pix EBI.jpg
crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme a decarboxylase
Identifiers
Symbol Carboxyl_trans
Pfam PF01039
Pfam clan CL0127
InterPro IPR000022
SCOP 1od2
SUPERFAMILY 1od2
TCDB 3.B.1

In molecular biology, proteins containing the carboxyl transferase domain include biotin-dependent carboxylases.[1][2] This domain carries out the following reaction: transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.

References[edit]

  1. ^ Toh H, Kondo H, Tanabe T (August 1993). "Molecular evolution of biotin-dependent carboxylases". Eur. J. Biochem. 215 (3): 687–96. doi:10.1111/j.1432-1033.1993.tb18080.x. PMID 8102604. 
  2. ^ Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D (September 1993). "Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli". J. Bacteriol. 175 (17): 5301–8. PMC 206582. PMID 8366018. 

This article incorporates text from the public domain Pfam and InterPro IPR000022

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.

Carboxyl transferase domain Provide feedback

All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.

Literature references

  1. Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D; , J Bacteriol 1993;175:5301-5308.: Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli. PUBMED:8366018 EPMC:8366018

  2. Toh H, Kondo H, Tanabe T; , Eur J Biochem 1993;215:687-696.: Molecular evolution of biotin-dependent carboxylases. PUBMED:8102604 EPMC:8102604

  3. Zhang H, Yang Z, Shen Y, Tong L; , Science 2003;299:2064-2067.: Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase. PUBMED:12663926 EPMC:12663926


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000022

Members in this domain include biotin dependent carboxylases [PUBMED:8102604, PUBMED:8366018]. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.

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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Pfam Clan

This family is a member of clan ClpP_crotonase (CL0127), which contains the following 10 members:

ACCA Carboxyl_trans CLP_protease ECH ECH_C MdcE Peptidase_S41 Peptidase_S49 Peptidase_S49_N SDH_sah

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(34)
Full
(11662)
Representative proteomes NCBI
(11205)
Meta
(7464)
RP15
(955)
RP35
(1849)
RP55
(2497)
RP75
(2951)
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Format an alignment

  Seed
(34)
Full
(11662)
Representative proteomes NCBI
(11205)
Meta
(7464)
RP15
(955)
RP35
(1849)
RP55
(2497)
RP75
(2951)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(34)
Full
(11662)
Representative proteomes NCBI
(11205)
Meta
(7464)
RP15
(955)
RP35
(1849)
RP55
(2497)
RP75
(2951)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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_299 (release 3.0)
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 34
Number in full: 11662
Average length of the domain: 323.30 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 68.57 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.5 19.5
Trusted cut-off 19.5 19.5
Noise cut-off 19.4 19.4
Model length: 493
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Carboxyl_trans

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 Carboxyl_trans domain has been found. There are 146 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 seqence.

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