ECF51 ECF proteins

General description: The proteins from ECF51 could be classified against original ECF51 (97.9%), except ECF51s15, which contains ~50 amino acid N-terminal extension. Proteins from ECF51 are present in Actinobacteria (100%).

Regulation: Even though domains in position +1 are not conserved, proteins in position +1 have homology to AS factors from the original ECF classification (Staroń et al., 2009) (except in subgroup ECF51s4) and contain typically one transmembrane helix (70.73%, ~100% in the MSA). These putative AS factors were also pinpointed in the original ECF51 (Huang et al., 2015). Interestingly, members of ECF51s9 encoded a protein with a σ4 domain (80%) and with the σ2 domain (20%) in -1. These proteins might function as AAS factors since they are transmembrane proteins (100%), their σ2 domain is missing in some cases, and they contain a PknH-like extracellular domain (20%) with sensing functions. Other proteins with σ2 or σ4 domains appear in members of ECF51 with an average of 0.33 per ECF. Although these proteins are usually ECFs from different groups, some are not included in the ECF library and could be AAS factors as in the case of ECF51s9.

Genomic context conservation: Other conserved proteins encoded in the context of ECF51 are only present in ECF51s9 and ECF51s13 and include a CoA-binding protein, a formyltransferase, an AICARFT/IMPCHase bienzyme fused to an MGS-like domain, with potential functions in purine sythesis, and an ATP-grasp-domain protein.

Promoter motif conservation: The promoter motifs are conserved across subgroups with GCAACCG in -35 and GCGTGTC in -10, expanding the motifs of original ECF51 (Huang et al., 2015).

Summary: In conclussion, the AS factors of ECF51, also identified for original ECF51 (Huang et al., 2015), could be regulated, at least in ECF51s9, by partner-switching via AAS that also contain an extracytoplasmic, potentially sensing, domain. The promoter motifs are conserved and agree with original ECF51 (Huang et al., 2015).


 


Basic information

Number of representative ECFs: 774

Number of non-redundant ECFs: 761

Sequences with C-terminal extension: 1.84%

Sequences with N-terminal extension: 2.63%

Overrepresented class: Actinobacteria [99.74%]



Sample Neighborhood

Protein WP_043445886.1 of Assembly GCF_000819545.1 (Streptomyces nodosus)


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. 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
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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