ECF293 ECF proteins

General description: Proteins from ECF293 have homology to original groups ECF101 (11.35%), ECF117 (9.46%) and ECF13 (43.98%), and are present in Proteobacteria (53.03%), Bacteroidetes (29.65%), Actinobacteria (16.88%), Verrucomicrobia (0.22%) and Spirochaetes (0.22%). Proteins from ECF293 contain an extended linker between the σ2 and σ4 domains. Most subgroups also contain three cysteines in the σ4 domain. It is unclear whether these modifications respect to the canonical ECF sequence affect the activity of members of ECF293.

Anti-σ factor: Similarly to proteins from original ECF13, ECF101 and ECF117 (Staroń et al., 2009), proteins from ECF293 encode a conserved soluble (97.92%) zinc-finger putative AS factor in position +1.

Genomic context conservation: Other conserved proteins are an ACP synthase III (-1 of ECF293s2), an acyl-CoA dehydrogenase (-1 of ECF293s8), a glycine cleavage system P-protein (+3 of ECF293s3), a DUF417 (+2 of ECF293s6), an EamA-like transporter (ECF293s2), a LysR transcriptional regulator (ECF293s2), OsmC (ECF293s8), a DUF3097 (ECF293s8), an universal stress protein (ECF293s8), an ABC transporter with a TOBE domain (ECF293s8) and a peptide methionine sulfoxide reductase (ECF293s6).

Studied members: Four members of ECF293 have been experimentally addressed - Ecf from Neisseria gonorrhoeae (ECF293s9), RpoE from Nisseria meningitidis (ECF293s9), PA3285 from Pseudomonas aeruginosa (ECF293s10) and CHU_3097 from Cytophaga hutchinsonii (ECF293s18). Ecf is overexpressed under treatment with hydrogen peroxide and is thought to participate in oxidative stress response since Ecf controls the expression of a methionine sulfoxide reductase and the genes from -4 to -1 in the locus of Ecf (Gunesekere et al., 2006). RpoE also controls the expression of its operon, which contains a methionine sulfoxide reductase (Huis in 't Veld et al., 2011). Even though this methionine sulfoxide reductase is not encoded in the proximity of Ecf in N. gonorrhoeae genome, a similar protein is encoded in the genetic context of members of ECF293s6. PA3285 from P. aeruginosa is predicted to be regulated by the FecI-like ECF PvdS (ECF05) (Chevalier et al., 2018). A short, soluble, zinc-binding anti-σ factor (MseR) has been identified for RpoE (Huis in 't Veld et al., 2011). CHU_3097 from C. hutchinsonii is released from the membrane upon induction with cellulose and upregulates proteins in charge of its degradation (!!!Wang et al., 2019!!!). An AS factor located in +1 and found in the membrane fraction has been proposed to be in charge of the shift (!!!Wang et al., 2019!!!). This AS factor does not contain any transmembrane helix when looking at the TopCons prediction.

Promoter motif conservation: Predicted target promoter motifs are not conserved among different subgroups. Indeed, Ecf from N. gonorrhoeae does not appear to be autoregulated (Gunesekere et al., 2006).

Summary: ECF293 merges three original groups (ECF13, ECF101, and ECF117) that encode a putative zinc-binding soluble AS factor in +1. Future analysis could determine if this protein is, indeed, an AS factor. ECF293 is likely involved in oxidative stress response.


Basic information

Number of representative ECFs: 1992

Number of non-redundant ECFs: 2167

Sequences with C-terminal extension: 0.05%

Sequences with N-terminal extension: 0.42%

Overrepresented phylum: Proteobacteria [63.70%]

Sample Neighborhood

Protein WP_055894407.1 of Assembly GCF_001424545.1 (Ramlibacter sp. Leaf400)

Promoter Motif


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
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

Related publications

Title Journal Year Authors PubMed ECF groups
Ecf, an alternative sigma factor from Neisseria gonorrhoeae, controls expression of msrAB, which encodes methionine sulfoxide reductase. Journal of bacteriology 2006 I. Gunesekere, C. Kahler, C. Ryan, L. Snyder, N. Saunders, J. Rood, J. Davies PubMed: 16672599 ECF293
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 ECF114, ECF31, ECF22, ECF12, ECF27, ECF122, ECF121, ECF56, ECF03, ECF21, ECF23, ECF02, ECF41, ECF15, ECF107, ECF111, ECF39, ECF19, ECF25, ECF17, ECF26, ECF118, ECF11, ECF16, ECF42, ECF38, ECF103, ECF36, ECF28, ECF51, ECF115, ECF40, ECF14, ECF29, ECF123, ECF33, ECF102, ECF105, ECF106, ECF116, ECF130, ECF18, ECF235, ECF120, ECF239, ECF240, ECF242, ECF243, ECF249, ECF265, ECF271, ECF281, ECF285, ECF286, ECF289, ECF290, ECF291, ECF292, ECF293, ECF294, ECF30, ECF32, ECF43
Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis. PloS one 2011 R. Huis in 't Veld, A. Willemsen, A. van Kampen, E. Bradley, F. Baas, Y. Pannekoek, A. van der Ende PubMed: 22194974 ECF293
Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. Biochimica et biophysica acta. Gene regulatory mechanisms 2018 S. Chevalier, E. Bouffartigues, A. Bazire, A. Tahrioui, R. Duchesne, D. Tortuel, O. Maillot, T. Clamens, N. Orange, M. Feuilloley, O. Lesouhaitier, A. Dufour, P. Cornelis PubMed: 29729420 ECF02, ECF102, ECF243, ECF293, ECF35
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