ECF123 ECF proteins

General description: Group ECF123 contains proteins with homology to original ECF123 (97.48%) and are present in Actinobacteria (100%). Proteins from ECF123s1 and ECF123s3 contain a C-terminal extension of 20-30 amino acids with no homology to any Pfam domain.

Special features: Position +1 has homology to AS factors from original ECF123. In this position, 73.33% of the encoded proteins contain one transmembrane helix and are most likely the proteins with homology to AS factors.

Genomic context conservation: Members of ECF123s1 and ECF123s2 encoded one or several transmembrane subunits of the succinate dehydrogenases in their genetic context and a FAD-binding domain, also present in ECF123s6.

Promoter motif conservation: The predicted target promoter motifs of ECF123 is not conserved.

Summary: Most of the members of ECF123 have a transmembrane AS factor in +1. The genomic context conservation extends further in ECF123s1, ECF123s2 with functions related to the electron transport chain, pointing out the potential regulatory role of ECF123 on oxidative stress response.


 


Basic information

Number of representative ECFs: 1057

Number of non-redundant ECFs: 994

Sequences with C-terminal extension: 29.18%

Sequences with N-terminal extension: 4.83%

Overrepresented class: Actinobacteria [99.43%]



Sample Neighborhood

Protein WP_037626721.1 of Assembly GCF_000725495.1 (Streptomyces aureus)


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
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. Journal of bacteriology 2015 X. Huang, D. Pinto, G. Fritz, T. Mascher PubMed: 25986905 ECF122, ECF56, ECF118, ECF128, ECF51, ECF52, ECF132, ECF53, ECF123, ECF125, ECF54, ECF130, ECF131, ECF218, ECF294, ECF48
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