ECF237 ECF proteins

General description: ECF237 is present in Proteobacteria (42.86%), Cyanobacteria (42.86%) Actinobacteria (11.43%), and Chloroflexi (2.86%). Members of ECF237s1 and ECF237s5 contain C-terminal extensions of variable size (~40 to ~100 amino acids), but similar enough to align well in a region of ~22aa. Instead, members of ECF237s4 contain a conserved N-terminal extension of ~220 amino acids.

Anti-σ factor: No AS factors where identified in the genetic context of members of ECF237.

Genomic context conservation: ECF237 from Proteobacteria contain from 2.4 to 6.75 “Killing trait” proteins (Pfam: RebB). These proteins, produced by Paramecium endosymbionts, are part of the R-bodies, ribbons able to kill sensitive Paramecium strains (Schrallhammer et al., 2012). Other conserved proteins in the genetic context of ECF237 include a glutamine amidotransferase (-3 of ECF237s4).

Promoter motif conservation: Promoter motifs are not conserved, indicating lack of an autoregulatory role of members of ECF237.

Summary: Members of ECF237 do not encode any putative AS factor in their genetic context. Members of subgroups from Proteobacteria encoded RebB-like proteins, part of the R-bodies of Paramecium endosymbionts. R-bodies are proteinaceous ribbon structures able to kill sensitive Paramecium strains (Schrallhammer et al., 2012).


 


Basic information

Number of representative ECFs: 92

Number of non-redundant ECFs: 131

Sequences with C-terminal extension: 24.43%

Sequences with N-terminal extension: 19.85%

Overrepresented phylum: Proteobacteria [44.57%]



Sample Neighborhood

Protein WP_063383115.1 of Assembly GCF_001625705.1 (Pseudoalteromonas luteoviolacea S4060-1)


Promoter Motif



Figures

Protein sequence length distribution

Gene neighbourhood conservation analysis


Overall Pfam domain distribution: Cumulative frequency of Pfam domains across the genetic neighborhoods. Frequency is expressed as number of Pfam domains per ECF sigma factor. Only domains present in more than 75% of the neighborhoods are shown. Genetic neighborhoods contain the proteins encoded in ±10 from the ECF coding sequence. Only the non-overlapping, highest scoring domains are considered positive. If a protein contains several copies of a domain, only one instance is further considered. In order to avoid sequence bias, only proteins from assemblies defined as "representative" or "reference" by NCBI are included (see https://www.ncbi.nlm.nih.gov/assembly/help/).
Pfam domain distribution per position: Frequency of Pfam domain architectures in the proteins encoded in ±10 (x-axis) from the ECF coding sequences. Frequency is expressed as number of times a certain domain architecture appears per ECF sigma factor. Only the highest scoring domains with no position overlap are considered in the domain architectures. Note that the order of the Pfam domains in domain architectures may differ from their name. When a protein contains several copies of a domain, only one instance is further considered. Only domain architectures present in more than 20% of the proteins encoded in any position are shown. In order to avoid sequence bias, only proteins from assemblies defined as "representative" or "reference" by NCBI are included (see https://www.ncbi.nlm.nih.gov/assembly/help/).

Related publications

Title Journal Year Authors PubMed ECF groups
Tracing the role of R-bodies in the killer trait: absence of toxicity of R-body producing recombinant E. coli on paramecia. European journal of protistology 2012 M. Schrallhammer, S. Galati, J. Altenbuchner, M. Schweikert, H. Görtz, G. Petroni PubMed: 22356923 ECF237
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