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0  structures 22  species 0  interactions 24  sequences 1  architecture

Family: Phyto-Amp (PF15438)

Summary: Antigenic membrane protein of phytoplasma

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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.

Antigenic membrane protein of phytoplasma Provide feedback

Phyto-Amp is a family of phytopathogenic wall-less bacterial antigenic membrane proteins [1]. The bacteria are limited to the phloem and pose a major threat to agriculture worldwide. They are transmitted in a persistent, propagative manner by phloem-sucking Hemipteran insects. Phytoplasma membrane proteins are in direct contact with hosts and are assumed to be involved in determining vector specificity. Phyto-Amp is thought to be one family of proteins that mediates such specificity. The proteins appear to be encoded by circular extrachromosomal elements, at least one of which is a plasmid [2].

Literature references

  1. Barbara DJ, Morton A, Clark MF, Davies DL;, Microbiology. 2002;148:157-167.: Immunodominant membrane proteins from two phytoplasmas in the aster yellows clade (chlorante aster yellows and clover phyllody) are highly divergent in the major hydrophilic region. PUBMED:11782508 EPMC:11782508

  2. Galetto L, Bosco D, Balestrini R, Genre A, Fletcher J, Marzachi C;, PLoS One. 2011;6:e22571.: The major antigenic membrane protein of "Candidatus Phytoplasma asteris" selectively interacts with ATP synthase and actin of leafhopper vectors. PUBMED:21799902 EPMC:21799902


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
(24)
Representative proteomes NCBI
(23)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
RP75
(3)
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PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(3)
Full
(24)
Representative proteomes NCBI
(23)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
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
(24)
Representative proteomes NCBI
(23)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
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.

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

This family is new in this Pfam release.

Seed source: Jackhmmer:Q7M1T6
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 3
Number in full: 24
Average length of the domain: 179.30 aa
Average identity of full alignment: 70 %
Average coverage of the sequence by the domain: 82.31 %

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 48.6 47.8
Noise cut-off 21.5 20.4
Model length: 195
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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