ECF130 ECF proteins

General description: Members of this group are present in Actinobacteria (100%) mostly in genus Streptomyces and have homology to proteins from original ECF130 (73.85%).

Special features: Original ECF130 contains a putative soluble AS factor in -1 (Huang et al., 2015); nevertheless, we could not find any conserved Pfam domain in this position, proteins in this position do not align well in MSA, and none of the proteins matches any AS factor from the original library (López-García, Yagüe, Gonzalez-Quiñonez, Rioseras, & Manteca, 2018). Therefore, these proteins were not considered putative AS factors.

Genomic context conservation: We could find conserved proteins with a helix-turn-helix domain in the genetic context of members of ECF130.

Promoter motif conservation: Predicted target promoter motifs are not conserved.

Regulation: The regulation of members of ECF130 remains elusive since the putative AS factors described for members of original ECF130 (Huang et al., 2015) are not present in members of new ECF130.


 


Basic information

Number of representative ECFs: 117

Number of non-redundant ECFs: 130

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.77%

Overrepresented order: Streptomycetales [97.44%]



Sample Neighborhood

Protein WP_030184100.1 of Assembly GCF_000725565.1 (Streptomyces peucetius)


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. Staroń, 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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