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0  structures 1  species 0  interactions 3  sequences 3  architectures

Family: Tox-ODYAM1 (PF15642)

Summary: Toxin in Odyssella and Amoebophilus

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Toxin in Odyssella and Amoebophilus Provide feedback

A predicted all-alpha fold toxin present in bacterial polymorphic toxin systems of the endosymbionts Odyssella and Amoebophilus [1].

Literature references

  1. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;, Biol Direct. 2012;7:18.: Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. PUBMED:22731697 EPMC:22731697


External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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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
(3)
Full
(3)
Representative proteomes NCBI
(4)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(3)
RP75
(3)
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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
(3)
Full
(3)
Representative proteomes NCBI
(4)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(3)
RP75
(3)
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
(3)
Full
(3)
Representative proteomes NCBI
(4)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(3)
RP75
(3)
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.

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

This family is new in this Pfam release.

Seed source: [1]
Previous IDs: none
Type: Family
Author: Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L, Finn RD
Number in seed: 3
Number in full: 3
Average length of the domain: 385.30 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 22.38 %

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 25.0 25.0
Trusted cut-off 665.8 665.8
Noise cut-off 23.2 21.2
Model length: 385
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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