ECF28 ECF proteins

General description: This group has homology to the original group ECF28 (91.24%), and it is present in Proteobacteria from class Proteobacteria (99.34%) from class Gammaproteobacteria and Cyanobacteria (0.66%).

Anti-σ factor: ECFs from ECF28 are associated with putative AS factors in position +1 with a DUF3379 and one transmembrane helix (93.21%). This protein is not present in ECF28s3.

Genomic context conservation: Other conserved proteins encoded in the genetic context of members of ECF28 are a thiolase (ECF28s1 and ECF28s2), an outer membrane protein transport protein (OMPP1/FadL/TodX) (ECF28s1 and ECF28s2) involved in degradation of aromatic hydrocarbons (Pfam: Toluene_X), a 3-hydroxyacyl-CoA dehydrogenase (ECF28s2) and a von Willebrand factor type A (ECF28s1 and ECF28s2).

Promoter motif conservation: The predicted target promoter motifs are not conserved.

Summary: Likewise original ECF28 (Staroń et al., 2009), ECF28 might be regulated by a membrane-bound AS factor with a DUF3379. The conservation of the genetic context of members of ECF28 indicates that they are involved in the degradation of aromatic compounds.


 


Basic information

Number of representative ECFs: 494

Number of non-redundant ECFs: 662

Sequences with C-terminal extension: 0.30%

Sequences with N-terminal extension: 0.30%

Overrepresented phylum: Proteobacteria [99.80%]



Sample Neighborhood

Protein WP_011079873.1 of Assembly GCF_000009745.1 (Vibrio vulnificus YJ016)


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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