ECF286 ECF proteins

General description: Some members of this group are homologous to proteins from the original group ECF20 (2.2%). Members from ECF286 are present in Actinobacteria (100%).

Anti-σ factor: Proteins from ECF286 are encoded together with several soluble proteins from Asp23 family (Pfam: Asp23), which is one of the most abundant proteins of S. aureus and is related with cell envelope homeostasis (Müller et al., 2014). Deletion of Asp23 in S. aureus leads to upregulation of the cell wall stress genes (Müller et al., 2014); therefore, this protein could function as AS factor.

Genomic context conservation: Other than Asp23, the genetic context of ECF286s4 contains a conserved RibD C-terminal domain in -1 and an AFG1-like ATPase in -2.

Promoter motif conservation: Predicted target promoter motifs are conserved and contain a conserved GAC in -35 and TC in -10.

Summary: In contrast to original ECF20 (Staroń et al., 2009), members of ECF286 do not seem to be regulated by canonical AS factors. Instead, they contain several Asp23-like proteins, indicating that members of ECF286 are involved in cell envelope homeostasis as in the case of Asp23 in S. aureus (Müller et al., 2014). Provided that these Asp23 proteins function as AS factors of members of ECF286, it remains unclear why each ECF from ECF283 encodes an average of 3.33 Asp23 proteins in its genetic neighborhood.


 


Basic information

Number of representative ECFs: 456

Number of non-redundant ECFs: 410

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 3.66%

Overrepresented order: Streptomycetales [50.88%]



Sample Neighborhood

Protein AKG41942.1 of Assembly GCA_000993785.2 (Streptomyces xiamenensis)


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
Deletion of membrane-associated Asp23 leads to upregulation of cell wall stress genes in Staphylococcus aureus. Molecular microbiology 2014 M. Müller, S. Reiß, R. Schlüter, U. Mäder, A. Beyer, W. Reiß, J. Marles-Wright, R. Lewis, H. Pförtner, U. Völker, K. Riedel, M. Hecker, S. Engelmann, J. Pané-Farré PubMed: 25074408 ECF286, ECF292
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