ECF22 ECF proteins

General description: ECF22 has homology to original ECF22 (88.1%). Proteins from this group are present in Bacteroidetes (78.81%), Proteobacteria (18.14%), Verrucomicrobia (1.19%), Planctomycetes (1.02%) and Acidobacteria (0.68%).

Anti-σ factor: Putative AS factors of ECF22 are encoded in +1 and usually contain DUF2207 and four (48.06%) TM helices.

Genomic context conservation: Other proteins conserved in the genetic context of members of ECF22 are an alpha/beta hydrolase (-1 of ECF22s16 and ECF22s4), σ-54 factor (ECF22s8) and two proteins from ABC transporters (-2 and -3 of ECF22s22).

Promoter motif conservation: Promoter motifs are conserved and contain TGTGATTTT in -35 and GCGAAT(C/A)AT in -10, in agreement with original ECF22 (Rhodius et al., 2013) and expanding these motifs.

Summary: ECF22 could be regulated by 4-transmembrane helix AS factors located in +1. This expands the knowledge of original ECF22, where putative AS factors were not identified (Staroń et al., 2009). This group seems to be autoregulated since the promoter motifs are conserved.


 


Basic information

Number of representative ECFs: 1921

Number of non-redundant ECFs: 1950

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.77%

Overrepresented phylum: Bacteroidetes [79.85%]



Sample Neighborhood

Protein WP_026293195.1 of Assembly GCF_000378125.1 (Rudaea cellulosilytica DSM 22992)


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
Cookies help us deliver our services. By using our services, you agree to our use of cookies. Learn more