ECF03 ECF proteins

General description: Members of ECF03 are homologous to proteins from original ECF03 (89.41%) and are mainly present in Bacteroidetes (95.44%), but also a variety of Gram-negative organisms such as Proteobacteria (1.27%), Verrucomicrobia (2.28%), Kiritimatiellaeota (0.25%) and Chlorobi (0.25%).

Anti-σ factor: The genomic context is not conserved although it is possible to identify a putative AS factor with one TM helix (62.03%, ~100% in the MSA)in position +1. These putative AS factors of ECF03 extend their conservation also to their extracytoplasmic site.

Genomic context conservation: Proteins from ECF03s4 have extended genomic context conservation, with an NADP oxidoreductase in -1, a Maf-like protein, an elongation factor Tu fused to a LepA protein, a haloacid dehalogenase-like hydrolase, a UPF0102 protein, a glycoprotease, and an LD-carboxypeptidase. Subgroups ECF03s3 and ECF03s5 contain one or several conserved transketolases. Last, ECF03s10 contains an LTXXQ motif family protein in +2 (involved in relieving extracytoplasmic stress (Danese & Silhavy, 1998)) and a universal stress protein.

Promoter motif conservation: Predicted target promoter motifs are usually TTAAACC in -35 and a less conserved TC-containing -10, as described in previous literature (Rhodius et al., 2013).

Summary: Unlike proteins from original ECF03, new ECF03 seems to be regulated by a new type of AS factors with no registered PFAM domain. These AS factors contain a conserved extracytoplasmic domain. The reason for the lack of conserved PFAM domain in ECF03 could be due to the presence of most of the sequences from ECF03 only in Bacteroidetes, organisms where genetic studies are limited. The presence of LTXXQ-motif proteins and universal stress proteins indicates that ECF03 could be part of the cell envelope stress response as its neighboring ECF groups.


 


Basic information

Number of representative ECFs: 1280

Number of non-redundant ECFs: 1294

Sequences with C-terminal extension: 0.54%

Sequences with N-terminal extension: 2.55%

Overrepresented phylum: Bacteroidetes [93.75%]



Sample Neighborhood

Protein ALJ49182.1 of Assembly GCA_001314995.1 (Bacteroides ovatus)


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
CpxP, a stress-combative member of the Cpx regulon. Journal of bacteriology 1998 P. Danese, T. Silhavy PubMed: 9473036 ECF03, ECF111
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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