ECF249 ECF proteins

General description: Proteins of ECF249 have homology to original groups ECF04 (2.63%), ECF10 (2.19%), ECF20 (0.44%) and ECF52 (0.44%) and they are present mainly in Firmicutes (41.81%), Bacteroidetes (27.68%), Acidobacteria (9.6%), Actinobacteria (4.52%), Chlorobi (4.52%), Planctomycetes (7.91%), Proteobacteria (0.56%) and Verrucomicrobia (3.39%).

Anti-σ factor: Members of ECF249 are regulated by AS factors in position +1 (except ECF249s6) and contain one (38.21%) or two (43.21%) transmembrane helices (only in ECF249s1). Putative AS factors of ECF249s14, which has homology to the original group ECF52, are fused to the ECF.

Genomic context conservation: Other conserved proteins include several cytochrome proteins, enzymes for the synthesis of tryptophan and proteins with other catalytic activities conserved in ECF249s1, and an EF-hand domain (Ca2+ binding) and a SCO1/SenC protein (required for the optimal cytochrome c oxidase activity) in ECF249s3.

Promoter motif conservation: Predicted target promoter motifs of the contain CGCAACTTT in -35 and GTT in -10.

Summary: ECF249 combines several original groups. AS factors of ECF249 contain one TM helix in most of the subgroups. Promoter motifs are conserved, which indicates that members of ECF249 are autoregulated.


 


Basic information

Number of representative ECFs: 522

Number of non-redundant ECFs: 456

Sequences with C-terminal extension: 3.29%

Sequences with N-terminal extension: 2.63%

Overrepresented phylum: Firmicutes [45.79%]



Sample Neighborhood

Protein WP_042162394.1 of Assembly GCF_000513275.1 (Paenibacillus gorillae)


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
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