ECF289 ECF proteins

General description: Members of ECF289 are homologous to proteins from the original group ECF20 (42.27%) and are present in Proteobacteria (100%).

Anti-σ factor: Members of ECF289 encode a putative AS factor in position +1. This putative AS factor contains a von Willebrand domain fused to a DUF3520 in C-terminal and harbors one transmembrane helix (87.34%). In ECF289s6 the N-terminal domain ASD is truncated even though the rest of the protein is similar other putative AS factors from ECF289.

Genomic context conservation: Other conserved domains found in the genetic context of members of ECF289 are a trimethylamine methyltransferase (ECF289s1) and an aldehyde dehydrogenase (ECF289s4).

Promoter motif conservation: Predicted target promoter motifs are conserved and contain CCCAAGGA in -35 and CGTCTxA in -10. In subgroups ECF289s2 and ECF289s4 the up-element (AAAATTT) is more conserved than the -10 element. The overall conservation of the predicted binding motifs indicates that members of ECF289 self-regulate their transcription.

Summary: ECF289 is regulated by putative AS factors encoded in +1 with a DUF3520 fused to a von Willebrand domain. These AS factors are bound to the membrane by a single transmembrane helix. Original ECF20 was found close to von Willebrand factors, but they were not identified as AS factors (Staroń et al., 2009). New experiments will determine if these proteins are functioning as AS factors.


 


Basic information

Number of representative ECFs: 344

Number of non-redundant ECFs: 343

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.29%

Overrepresented class: Alphaproteobacteria [95.64%]



Sample Neighborhood

Protein ADV12507.1 of Assembly GCA_000185905.1 (Mesorhizobium ciceri biovar biserrulae WSM1271)


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. StaroĊ„, 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
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