ECF131 ECF proteins

General description: Members of this group are only present in Actinobacteria (100%) and have homology to proteins from the original group ECF131 (60.71%).

Special features: Proteins encoded in -1 contain an N-terminal transmembrane helix (58.33%, at least 75% in the MSA). These proteins contain a cytoplasmic C-terminal region that could function as a new type of ASD.

Genomic context conservation: We did not find any conserved Pfam domain in the genetic context of members of this group.

Promoter motif conservation: Putative target promoter motifs contain TGTCA in -35 and CGCAC in -10 in ECF131s2 and ECF131s3, although their information content is low.

Summary: Members of ECF131 could be regulated by a new type of AS factors with C-terminal AS domain. This protein was not described for original ECF131 (Huang et al., 2015).


 


Basic information

Number of representative ECFs: 47

Number of non-redundant ECFs: 56

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 3.57%

Overrepresented order: Streptomycetales [70.21%]



Sample Neighborhood

Protein WP_058850756.1 of Assembly GCF_001482415.1 (Streptomyces silvensis)


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
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. Journal of bacteriology 2015 X. Huang, D. Pinto, G. Fritz, T. Mascher PubMed: 25986905 ECF122, ECF56, ECF118, ECF128, ECF51, ECF52, ECF132, ECF53, ECF123, ECF125, ECF54, ECF130, ECF131, ECF218, ECF294, ECF48
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