ECF242 ECF proteins

General description: Members of ECF242 do not have homology to any original group. The topology of the tree follows the taxonomy of its members. ECF242 contain proteins from Proteobacteria (44.19%) (Gammaproteobacteria from genus Alteromonas (ECF242s7), Alphaproteobacteria (ECF242s3 and ECF242s4) and Epsilonproteobacteria (ECF242s5 and ECF242s6)), and Spirochaetes from genus Leptospira (55.81%) (ECF242s1 and ECF242s2).

Anti-σ factor: All the subgroups contain a FecR-like AS factor in position +1, in some cases fused to a DUF4974 and DUF4880, as in other FecR-like AS factors. These AS factors contain one transmembrane helix (100%).

Genomic context conservation Subgroups from Proteobacteria encode at least one TonB-dependent receptor (two in ECF242s7), usually in +2, while this receptor does not appear in subgroups from Spirochaetes (ECF242s1 and ECF242s2). Other proteins conserved in the context of ECF242s1 are a thiolase, a rhodanase (in charge of detoxifying cyanide), a metalloenzyme, an ABC transporter and a DoxX protein (+2) suggesting that ECF242 might be in charge of oxidative stress response at least in ECF242s1, which explains the lack of TonB-dependent receptor.

Promoter motif conservation: Predicted target promoter motifs are not conserved, indicating lack of autoregulation of ECF242.

Summary: ECF242 is a new FecI-like group from which members of ECF242s1 might be in charge of detoxification of harmful compounds rather than functioning in metal uptake. As other FecI-like ECFs (Staroń et al., 2009), members of ECF242 do not seem autoregulated since the predicted target promoter motifs are not conserved.


 


Basic information

Number of representative ECFs: 100

Number of non-redundant ECFs: 147

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 1.36%

Overrepresented phylum: Proteobacteria [58.00%]



Sample Neighborhood

Protein AAN51703.1 of Assembly GCA_000092565.1 (Leptospira interrogans serovar Lai str. 56601)


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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