ECF38 ECF proteins

General description: Members of ECF38 share homology with members of original ECF38 (73.09%) or original ECF39 (0.34%) and are present in Actiobacteria (100%).

Anti-σ factor: As in the case of original ECF38 and ECF39 (Staroń et al., 2009), the proteins in position +1 are putative AS factors, except in ECF38s4, which is associated with YCII-related domain protein in position -1 like proteins from ECF42. These putative AS factors contain one transmembrane helix (67.46%) and no Pfam domain.

Genomic context conservation: Other domains proteins encoded in the genetic context of members of ECF38 are a HIT protein (-1 of ECF38s5 and ECF38s6), a PhoH-like protein (-2 of ECF38s5), a UPF0054 protein (ECF38s5 and ECF38s6), a transporter fused to a DUF21 (ECF38s5 and ECF38s6), a SURF1 protein (+2 of ECF38s1), a DUF3097 (ECF38s5 and ECF38s6), DnaJ (ECF38s5 and ECF38s6), a protein with a DeoR-like helix-turn-helix domain fused to the C-terminal domain of HrcA (ECF38s5 and ECF38s6), a DUF4870 (ECF38s5), a RNA methyltransferase (ECF38s5 and ECF38s6), a 50S ribosome-binding GTPase (ECF38s5), a YbaB/EbfC protein (ECF38s1), an amino acid kinase with an ACT domain (ECF38s1), a DUF5063 (ECF38s1), a semialdehyde dehydrogenase (ECF38s1), RecR (ECF38s1) and a fructose-bisphosphate aldolase class-II (ECF38s4).

Promoter motif conservation: Predicted target promoter motifs are subgroup-specific. In subgroups ECF38s1, ECF38s6 and ECF38s9 there is AACC in -35 and TC in -10. These motifs agree with original ECF39 (Rhodius et al., 2013).

Summary: Members of ECF38 are associated with AS factors in position +1 and share the same characteristics as original ECF38 (Staroń et al., 2009).


 


Basic information

Number of representative ECFs: 1690

Number of non-redundant ECFs: 1490

Sequences with C-terminal extension: 2.62%

Sequences with N-terminal extension: 17.72%

Overrepresented class: Actinobacteria [99.88%]



Sample Neighborhood

Protein WP_035288482.1 of Assembly GCF_000564855.1 (Actinokineospora spheciospongiae)


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
Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Molecular systems biology 2013 V. Rhodius, T. Segall-Shapiro, B. Sharon, A. Ghodasara, E. Orlova, H. Tabakh, D. Burkhardt, K. Clancy, T. Peterson, C. Gross, C. Voigt PubMed: 24169405 ECF22, ECF27, ECF03, ECF21, ECF39, ECF25, ECF26, ECF42, ECF38, ECF14, ECF29, ECF33, ECF281, ECF290, ECF291
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