ECF115 ECF proteins

General description: Members of ECF115 are present in Firmicutes (100%) from order Bacillales and have homology to original group ECF115 (40.3%) (Staroń et al., 2009). Members of ECF115 contain a C-terminal extension with several possible domains. This C-terminal extension is typical of ~70aa long, although in subgroup ECF115s3, where the C-terminal extension contains a SnoaL-like domain (Pfam: SnoaL_2), it extends to up to ~130 aa.

Genomic context conservation: Members of ECF115 contain a Clp protease in their genetic context (except ECF115s3). Clp proteases are in charge of the last step of the degradation of AS factors regulated by RIP (Barchinger & Ades, 2013). Genetic context conservation is not conserved beyond the Clp protease.

Anti-σ factor: no putative AS factor is present in the genetic context of members of ECF115.

Promoter motif conservation: Predicted target promoter motifs contain ATC in -35 and CGT in -10.

Summary: Members of ECF115 could be regulated by their C-terminal extension and the Clp protease encoded in their genetic neighborhood. The protease could cleave the C-terminal extension, leaving the ECF free to bind the RNAP and its target promoter. Another possibility is that the Clp protease is the target of the regulation of ECF115. Interestingly, the only subgroup with a different C-terminal extension, ECF115s3 with a SnoaL-like domain, lacks the Clp protease, indicating that only ECF115-like C-termini need the presence of the protease.


 


Basic information

Number of representative ECFs: 294

Number of non-redundant ECFs: 536

Sequences with C-terminal extension: 99.44%

Sequences with N-terminal extension: 0.56%

Overrepresented family: Bacillaceae [58.50%]



Sample Neighborhood

Protein EJW15255.1 of Assembly GCA_000293805.1 (Paenibacillus alvei DSM 29)


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
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Molecular microbiology 2009 A. Staroń, H. Sofia, S. Dietrich, L. Ulrich, H. Liesegang, T. Mascher PubMed: 19737356 ECF103, ECF21, ECF123, ECF51, ECF39, ECF281, ECF102, ECF130, ECF122, ECF291, ECF15, ECF242, ECF22, ECF285, ECF106, ECF27, ECF31, ECF240, ECF114, ECF16, ECF38, ECF41, ECF105, ECF116, ECF111, ECF03, ECF239, ECF42, ECF294, ECF17, ECF11, ECF29, ECF235, ECF293, ECF118, ECF265, ECF30, ECF23, ECF14, ECF249, ECF18, ECF115, ECF290, ECF25, ECF121, ECF02, ECF120, ECF289, ECF28, ECF243, ECF19, ECF43, ECF107, ECF12, ECF32, ECF36, ECF292, ECF286, ECF271, ECF26, ECF40, ECF56, ECF33
Regulated proteolysis: control of the Escherichia coli σ(E)-dependent cell envelope stress response. Sub-cellular biochemistry 2013 S. Barchinger, S. Ades PubMed: 23479440 ECF115
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