ECF43 ECF proteins

General description: Members of this group are only present in Proteobacteria and have homology to proteins from the original group ECF43 (100%). Interestingly, this group has an ECF σ factor domain (Pfam: Sigma70_ECF) instead of the σ2 and σ4 domains that typically appear in other groups.

Special features: Proteins from ECF43 are associated with protein kinases encoded in position +1, which have been proposed to be part of the regulatory mechanism in original ECF43 (Staroń et al., 2009). These kinases contain one transmembrane helix (87.8%) and extracytoplasmic tetratricopeptide repeats. Interestingly, the first part of the σ2.2 region, which contains a DAED motif involved in core RNAP binding (Wilson & Lamont, 2006), is substituted by S/T residues in members of ECF43. It is possible that this is the phosphorylation site of the protein kinase encoded in +1, which will replace the missing negative charges.

Genomic context conservation: Other than the protein kinase, genetic contexts of members of ECF43s1 contain a conserved formamidopyrimidine-DNA glycosylase in position -1 and a transposase fused to a fatty acid desaturase.

Promoter motif conservation: The predicted target promoter motifs contain a conserved GTC in -35 and a CAG in -10.

Summary: ECF43 has a different sequence, which might impair the retrieval of more proteins of this type. Members of this group could be phosphorylated by a conserved protein kinase encoded in +1. The putative phosphorylation site could be located in an S/T rich area that substitutes the negatively-charged motif that binds to the core RNAP in σ2.2.


Basic information

Number of representative ECFs: 75

Number of non-redundant ECFs: 69

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.00%

Overrepresented class: Gammaproteobacteria [49.33%]



Sample Neighborhood

Protein KCZ99386.1 of Assembly GCA_000685315.1 (Hyphomonas polymorpha PS728)


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
Mutational analysis of an extracytoplasmic-function sigma factor to investigate its interactions with RNA polymerase and DNA. Journal of bacteriology 2006 M. Wilson, I. Lamont PubMed: 16484205 ECF43
The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Molecular microbiology 2009 A. StaroĊ„, 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
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