ECF21 ECF proteins

General description: ECF21 has homology to original ECF21 (62.35%). Proteins in the base of ECF21’s clade are present in Bacteroidetes (99.62%). Subgroups ECF21s12 and ECF21s29 are fused to the putative AS factors with an outer membrane beta-barrel, which are encoded in +1 for the rest of the subgroups.

Anti-σ factor: Members of ECF21 are mainly regulated by AS factors with one inner membrane transmembrane helix (71.31%) located in position +1 (except ECF21s12). These putative AS factors contain an outer-membrane beta-barrel in most of the cases, although, in some subgroups ECF21s9, ECF21s16, and ECF21s28, the AS factor and the outer membrane beta-barrel are decoupled and located in different proteins encoded in +1 and +2, respectively.

Genomic context conservation: The conservation of the genetic neighborhood is extensive in some subgroups and involves a protein from the radical SAM superfamily (ECF21s35 and +1 of ECF21s12), an oxidoreductase (ECF21s28, +2 of ECF21s12), a DUF4840 (-1 of ECF21s10), a polyprenyl synthetase (ECF21s1 and -1 of ECF21s26), a DNA primase (+3 of ECF21s26), a response regulator with a LuxR repressor (ECF21s1 and +4 of ECF21s26), a NAD synthase (ECF21s1 and +5 of ECF21s26), a RecA protein (-1 of ECF21s3 and ECF21s6), a FKBP-type peptidyl-prolyl cis-trans isomerase (+2 of ECF21s35), an adenylosuccinate lyase (ECF21s28), a thiolase (ECF21s13), two fumarase C (ECF21s16), a coenzyme A transferase (ECF21s6 and ECF21s3), a thioesterase (ECF21s3), a rhodanase (ECF21s3), an acyltransferase (ECF21s3), a GldH lipoprotein (ECF21s3), a haloacid dehalogenase (ECF21s32), a M42 glutamyl aminopeptidase (ECF21s35), an uracil phosphoribosyltransferase (ECF21s35), a phosphoribosyl transferase (ECF21s35) and a sodium/calcium exchanger (ECF21s35).

Promoter motif conservation: The most common predicted target promoter motif is GCAACC in -35 and CGTCT in -10, in agreement with original ECF21 (Rhodius et al., 2013).

Summary: ECF21 might be regulated by AS factors encoded in +1. These AS factors contain one transmembrane helix and, in some cases, are fused to an outer membrane beta-barrel. In other instances, the outer membrane beta-barrel is encoded in the +2. No members of ECF21 have been functionally addressed.


 


Basic information

Number of representative ECFs: 2391

Number of non-redundant ECFs: 2473

Sequences with C-terminal extension: 3.60%

Sequences with N-terminal extension: 0.77%

Overrepresented phylum: Bacteroidetes [99.75%]



Sample Neighborhood

Protein WP_022829830.1 of Assembly GCF_000333295.1 (Cytophagales bacterium B6)


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
The extracytoplasmic function sigma factor EcfO protects Bacteroides fragilis against oxidative stress. Journal of bacteriology 2012 I. Ndamukong, J. Gee, C. Smith PubMed: 23104808 ECF21
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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