ECF240
ECF proteins

General description: ECF240 is the main group with homology to original ECF10 (82.76%). Proteins of this group are present in Bacteroidetes (99.89%). The internal clade formed by ECF240s106, ECF240s155 and ECF240s180 (family Flavobacteriae) contains a conserved ~55aa C-terminal extension. Several subgroups contain proteins with transmembrane helices (up to an average of 0.89 TMH per protein).

Anti-σ factor and regulation: Likewise original ECF10 (Staroń et al., 2009), genetic contexts of members of ECF240 encode a FecR-like AS factor in +1, a TonB-dependent outer membrane receptor in +2 (Staroń et al., 2009) and an outer-membrane carbohydrate-binding protein in +3 (Pfam: SusD_RagB: 84.20%; Pfam: SusD-like_2/3: 98.73%; Pfam: Reg_prop: 106.79%). The AS factor is fused to a DUF4974, as in the case of other FecI-like AS factors, and it contains one transmembrane helix (87.7%). In some subgroups, this putative operon is inverted in a way that the carbohydrate-binding protein is encoded -3, the TonB-dependent receptor in -2 and the AS factor in -1 (ECF240s1, ECF240s22).

Genomic context conservation: Other conserved proteins encoded in the neighborhood of members of ECF240 are a glycosyl hydrolase family 92 (-1 and +2 of ECF240s7) and a lysine exporter LysO (ECF240s4).

Promoter motif conservation: Predicted target promoter motifs are not conserved, in agreement with the lack of autoregulation associated with FecI-like groups (Staroń et al., 2009).

Summary: ECF240 maintains the characteristics of the original group ECF10 (Staroń et al., 2009). ECF240 is not autoregulated, and its function might be related to carbohydrate scavenging and degradation in Bacteroidetes, one of the most critical components of gut microbiota.


Basic information

Number of representative ECFs: 4028

Number of non-redundant ECFs: 4112

Sequences with C-terminal extension: 0.54%

Sequences with N-terminal extension: 2.55%

Overrepresented phylum: Bacteroidetes [99.73%]



Sample Neighborhood

Protein ABQ07790.1 of Assembly GCA_000016645.1 (Flavobacterium johnsoniae UW101)


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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