ECF218 ECF proteins

General description: Members of ECF218 have homology to proteins from original ECF50 (28.48%), ECF47 (29.27%) and ECF49 (33.49%) and are present in Actinobacteria (100%).

Anti-σ factor: As members of original ECF47, ECF49 and ECF50 (Huang, Pinto, Fritz, & Mascher, 2015), members of ECF218 contain a putative AS factor with one transmembrane helix (74.33%) in position +1. This AS factor contains a RskA-like domain, but in most of the cases, there is no Pfam domain describing it. In subgroup ECF218s8, the AS factor contains a DUF4349 with two transmembrane helices.

Genomic context conservation: Genetic context conservation only extends beyond the AS factor coding sequence in ECF218s8, which contains an EPSP synthase and an aconitate hydratase.

Studied members: There is one described member of this group, Sig(MibX) from Microbispora corallina, involved in lantibiotic production (Foulston & Bibb, 2011). This protein is not included in the ECF library since its genome annotation was missing.

Promoter motif conservation: Different predicted target promoter motifs are possible depending on the subgroup. For instance, members of ECF218s41, ECF218s28 and ECF218s33 contain TGCAAG in -35 and CGACA in -10; members of ECF218s11 and ECF218s57 contain GAAAT in -35 and ACAT in -10; members of ECF218s16 and ECF218s5 contain GTAACGC in -35 and CCAAGTA in -10.

Summary: ECF218 merges original groups ECF47, ECF49 and ECF50, all present in Actinobacteria and regulated by putative AS factors with one transmembrane helix encoded in +1.


 


Basic information

Number of representative ECFs: 2804

Number of non-redundant ECFs: 3037

Sequences with C-terminal extension: 5.40%

Sequences with N-terminal extension: 1.42%

Overrepresented phylum: Actinobacteria [99.82%]



Sample Neighborhood

Protein WP_063753640.1 of Assembly GCF_000568255.1 (Kutzneria sp. 744)


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
Feed-forward regulation of microbisporicin biosynthesis in Microbispora corallina. Journal of bacteriology 2011 L. Foulston, M. Bibb PubMed: 21478362 ECF218
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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