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0  structures 195  species 0  interactions 218  sequences 5  architectures

Family: GTA_TIM (PF13547)

Summary: GTA TIM-barrel-like domain

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GTA TIM-barrel-like domain Provide feedback

This domain is found in the gene transfer agent protein. An unusual system of genetic exchange exists in the purple nonsulfur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs [1]. The genes involved in this process appear to be found widely in bacteria [2]. According to the SUPERFAMILY database this domain has a TIM barrel fold.

Literature references

  1. Lang AS, Beatty JT;, Proc Natl Acad Sci U S A. 2000;97:859-864.: Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus. PUBMED:10639170 EPMC:10639170

  2. Lang AS, Beatty JT;, Trends Microbiol. 2007;15:54-62.: Importance of widespread gene transfer agent genes in alpha-proteobacteria. PUBMED:17184993 EPMC:17184993


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025195

This domain, which appears to have a TIM barrel fold, is found in the gene transfer agent protein. An unusual system of genetic exchange exists in the purple nonsulphur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs [PUBMED:10639170]. The genes involved in this process appear to be found widely in bacteria [PUBMED:17184993].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(66)
Full
(218)
Representative proteomes NCBI
(214)
Meta
(30)
RP15
(18)
RP35
(58)
RP55
(68)
RP75
(83)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(66)
Full
(218)
Representative proteomes NCBI
(214)
Meta
(30)
RP15
(18)
RP35
(58)
RP55
(68)
RP75
(83)
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
(66)
Full
(218)
Representative proteomes NCBI
(214)
Meta
(30)
RP15
(18)
RP35
(58)
RP55
(68)
RP75
(83)
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.

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: Jackhmmer:A1B6L4
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 66
Number in full: 218
Average length of the domain: 265.80 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 25.22 %

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 27.0 27.0
Trusted cut-off 27.0 27.1
Noise cut-off 25.8 26.9
Model length: 299
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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