ECF54 ECF proteins

General description: Members of ECF54 are homologous to members of the original group ECF54 (100%) and are present in Actinobacteria (100%).

Genomic context conservation: Members of original ECF54 are encoded near carboxypeptidase-regulatory-like domains, subtilases and a CHAT domain protein with tetratricopeptide repeats (Huang et al., 2015). Indeed, a carboxypeptidase regulatory-like domain is present in an average of 0.61 copies per ECF always in position +1, a subtilase is found in an average of 0.68 copies per ECF in positions +2 or -1, CHAT domains are found in an average of 0.71 copies per ECF usually in positions +3 or-2, and tetratricopeptide repeats are found in an average of 1.98 per ECF usually in position +2 or -2. Given the conservation of these proteins and the lack of putative AS factor, they could take part in the regulation or response of members of ECF54, as suggested for original ECF54 (Huang et al., 2015).

Promoter motif conservation: Predicted target promoter motifs are only conserved in the largest subgroups (ECF54s2, ECF54s1, ECF54s3), with GTATCAG in -35 and CTCC in -10, in agreement with original ECF54 (Huang et al., 2015).

Summary: ECF54 preserves the characteristics of the original group ECF54 (Huang et al., 2015). Members of this group are usually encoded near subtilases, carboxypeptidase regulatory-like domains and CHAT domains, which are fused to tetratricopeptide repeats in some cases.


 


Basic information

Number of representative ECFs: 170

Number of non-redundant ECFs: 176

Sequences with C-terminal extension: 0.57%

Sequences with N-terminal extension: 6.82%

Overrepresented phylum: Actinobacteria [99.41%]



Sample Neighborhood

Protein WP_015750390.1 of Assembly GCF_000024365.1 (Nakamurella multipartita DSM 44233)


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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