ECF29 ECF proteins

General description: ECF29 has homology to original groups ECF29 (88.98%). Members of ECF29 are present in Proteobacteria (83.64%) and Bacteroidetes (16.36%).

Special features: ECF29 contains a conserved RCE/D motif in a short (~30aa) C-terminal extension that could be in charge of the modulation of its activity, either participating in sensing or repression of the ECF σ factor. Since the ECFs from ECF29 are soluble, they could sense cytoplasmic signals that could be related to ROS, disulfide or heavy metal stress.

Anti-σ factor: Proteins from ECF29 do not contain any evident putative AS factor.

Genomic context conservation: No conserved elements were found in the genetic context of members of ECF29.

Promoter motif conservation: Predicted target promoters of ECF29 usually contain GGGAACCT in -25 and CATCCAAT in -10, in agreement with original ECF29 (Rhodius et al., 2013). In subgroups ECF29s18 and ECF29s14 from Bacteroidetes, the putative target promoter motifs are TTAGAT (-35) GTTACA in -10.

Summary: ECF29 might be regulated by a short C-terminal extension with an RCE/D motif. The predicted target promoter motifs are conserved, indicating the positive autoregulation of ECFs from ECF29. Functional characterization of members of ECF29 would shed light on the function of members of ECF29.


 


Basic information

Number of representative ECFs: 638

Number of non-redundant ECFs: 753

Sequences with C-terminal extension: 4.38%

Sequences with N-terminal extension: 3.05%

Overrepresented phylum: Proteobacteria [90.28%]



Sample Neighborhood

Protein WP_045836565.1 of Assembly GCF_000384335.2 (Hyphomicrobium sp. 99)


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
Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Molecular systems biology 2013 V. Rhodius, T. Segall-Shapiro, B. Sharon, A. Ghodasara, E. Orlova, H. Tabakh, D. Burkhardt, K. Clancy, T. Peterson, C. Gross, C. Voigt PubMed: 24169405 ECF22, ECF27, ECF03, ECF21, ECF39, ECF25, ECF26, ECF42, ECF38, ECF14, ECF29, ECF33, ECF281, ECF290, ECF291
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