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0  structures 614  species 0  interactions 1373  sequences 3  architectures

Family: SpoVAC_SpoVAEB (PF03862)

Summary: SpoVAC/SpoVAEB sporulation membrane protein

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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.

SpoVAC/SpoVAEB sporulation membrane protein Provide feedback

Members of this family are all transcribed from the spoVA operon [1]. Bacillus and Clostridium are two well studied endospore forming bacteria. Spore formation provides a resistance mechanism in response to extreme or unfavourable environmental conditions such as heat, radiation, and chemical agents or nutrient deprivation. The reverse process termed germination takes place where spores develop into growing cells in response to nutrient availability or stress reduction. Nutrient germinant receptors (GRs) and the SpoVA proteins are important players in the germination process. In B. subtilis the SpoVAC and SpoVAEB, belonging to this domain family, are predicted to be membrane proteins, with two to five membrane spanning. Biophysical and biochemical studies suggest that SpoVAC acts as a mechano-sensitive channel with properties that would allow the release of Ca-DPA (dipicolinic acid) and amino acids during germination of the spore. The release of Ca-DPA is a crucial event during spore germination. When expressed in E. coli SpoVAC provides protection against osmotic downshift. Furthermore, SpoVAC acts as channel that facilitates the efflux down the concentration gradient of osmolytes up to a mass of at least 600 Da [2]. Another conserved SpoVA protein in all spore-forming bacteria is SpoVAEb, which appears to be an integral membrane protein with no known function [3].

Literature references

  1. Tovar-Rojo F, Chander M, Setlow B, Setlow P; , J Bacteriol 2002;184:584-587.: The products of the spoVA operon are involved in dipicolinic acid uptake into developing spores of Bacillus subtilis. PUBMED:11751839 EPMC:11751839

  2. Velasquez J, Schuurman-Wolters G, Birkner JP, Abee T, Poolman B;, Mol Microbiol. 2014;92:813-823.: Bacillus subtilis spore protein SpoVAC functions as a mechanosensitive channel. PUBMED:24666282 EPMC:24666282

  3. Donnelly ML, Fimlaid KA, Shen A;, J Bacteriol. 2016;198:1694-1707.: Characterization of Clostridium difficile Spores Lacking Either SpoVAC or Dipicolinic Acid Synthetase. PUBMED:27044622 EPMC:27044622


This tab holds annotation information from the InterPro database.

InterPro entry IPR005562

Members of this family are all transcribed from the spoVA operon. These proteins are poorly characterised, but are thought to be involved in dipicolinic acid transport into the developing forespore during sporulation [PUBMED:11751839].

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, the UniProtKB sequence database, 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
(447)
Full
(1373)
Representative proteomes UniProt
(3767)
NCBI
(4098)
Meta
(19)
RP15
(315)
RP35
(982)
RP55
(1388)
RP75
(1939)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(447)
Full
(1373)
Representative proteomes UniProt
(3767)
NCBI
(4098)
Meta
(19)
RP15
(315)
RP35
(982)
RP55
(1388)
RP75
(1939)
Alignment:
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Sequence:
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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
(447)
Full
(1373)
Representative proteomes UniProt
(3767)
NCBI
(4098)
Meta
(19)
RP15
(315)
RP35
(982)
RP55
(1388)
RP75
(1939)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: DOMO:DM07026;
Previous IDs: spoVA; SpoVA;
Type: Family
Author: Finn RD, El-Gebali S
Number in seed: 447
Number in full: 1373
Average length of the domain: 113.00 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 83.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.4 25.3
Noise cut-off 24.2 23.9
Model length: 114
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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