ECF290 ECF proteins

General description: Members of this group have homology members of original ECF20 (95.41%) and appear in Proteobacteria (97.64%) and Planctomycetes (2.36% of the total) from family Planctomycetaceae.

Anti-σ factor: Proteins in +1 are putative AS factors (except in ECF290s3) and harbor one transmembrane helix (42.54%, ~100% of the sequences from subgroups except for ECF290s3 in an MSA). These proteins do not appear in ECF290s3, which contains the coding sequence of flagellin instead.

Genomic context conservation: Conserved proteins encoded in the context of ECF290 include a membrane-bound heavy-metal resistance protein (+2 of ECF290s1 and ECF290s2), a diguanylate cyclase fused to a response regulator receiver domain (+3 of ECF290s2), an EF-hand (-1 of ECF290s2), a DUF983 (-2 of ECF290s2), a NUDIX domain (-3 of ECF290s2) from nucleoside diphosphate hydrolases. This genetic context, and especially the metal-resistance protein encoded in +2, is conserved in most groups from ECF290. Nevertheless, members of subgroup ECF290s3 are encoded near proteins involved in flagellum biosynthesis such as flagellin in +1, flagellar hook-associated protein 2 in +2 and FliS in +3.

Promoter motif conservation: Predicted target promoter motifs have low information content. The largest subgroups, ECF290s1 and ECF290s2, share an ACGG in -35 and CGT is conserved in several -10 elements. These motifs agree with the original group ECF20 (Staroń et al., 2009).

Summary: Members of ECF290 are associated with putative AS factors usually encoded in position +1. These putative AS factors contain one transmembrane helix and no Pfam domain. A conserved heavy metal resistance protein is encoded in +2, which points to metal detoxification as the function of members of ECF290. Subgroup ECF290s3 does not seem to encode any AS factor in its genomic context, and it contains proteins for the synthesis of the flagellum instead.


 


Basic information

Number of representative ECFs: 838

Number of non-redundant ECFs: 980

Sequences with C-terminal extension: 0.20%

Sequences with N-terminal extension: 14.29%

Overrepresented phylum: Proteobacteria [98.57%]



Sample Neighborhood

Protein ABJ04739.1 of Assembly GCA_000014825.1 (Rhodopseudomonas palustris BisA53)


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
The third pillar of metal homeostasis in Cupriavidus metallidurans CH34: preferences are controlled by extracytoplasmic function sigma factors. Metallomics : integrated biometal science 2019 C. Große, A. Poehlein, K. Blank, C. Schwarzenberger, G. Schleuder, M. Herzberg, D. Nies PubMed: 30681120 ECF18, ECF290
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