ECF294 ECF proteins

General description: Members of ECF294 are present in Proteobacteria (96.15%) and Acidobacteria (3.95%). Members of this group contain a ~120aa C-terminal extension with a SnoaL-like domain (Pfam: SnoaL_2). SnoaL is a small polyketide cyclase that catalyzes closure steps of the synthesis of polyketide antibiotics in Streptomyces spp. (Sultana et al., 2004). However, it has also been observed as part of ECF σ factors from original groups ECF56 and ECF41 (Huang, Pinto, Fritz, & Mascher, 2015; Staroń et al., 2009).

Genomic context conservation: The genetic context of members of ECF294 is not conserved beyond the ECF coding sequence.

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

Summary: Members of ECF294 compose a new group of SnoaL-like C-terminal extension σ factors with no homology to any original group. As in the case of ECF56 and ECF41 from the original ECF classification (Huang et al., 2015; Staroń et al., 2009), this C-terminal extension could be regulating ECF activity given the absence of any putative AS factor in the genetic context of members of ECF294.


 


Basic information

Number of representative ECFs: 261

Number of non-redundant ECFs: 300

Sequences with C-terminal extension: 100.00%

Sequences with N-terminal extension: 0.33%

Overrepresented phylum: Proteobacteria [99.23%]



Sample Neighborhood

Protein ANT49298.1 of Assembly GCA_001686985.1 (Mesorhizobium amorphae CCNWGS0123)


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
Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. The EMBO journal 2004 A. Sultana, P. Kallio, A. Jansson, J. Wang, J. Niemi, P. Mäntsälä, G. Schneider PubMed: 15071504 ECF56, ECF294
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
Cookies help us deliver our services. By using our services, you agree to our use of cookies. Learn more