ECF285 ECF proteins

General description: Members of ECF285 are present in Proteobacteria (100%).

Anti-σ factor: Members of ECF285 encode 2-transmembrane helix proteins (67.39%) with a DUF2892 in -1. These proteins could be a new type of AS factor with no homology to AS factors from the original library (Staroń et al., 2009).

Genomic context conservation: Genetic context conservation extends to a DUF692 (+2 of ECF285s5), a putative DNA-binding domain (Pfam: DUF2093) (+3 of ECF285s5), a RNA 2'-O ribose methyltransferase (ECF285s5), a PBP (Pfam: PBP_like_2) that might bind to phosphatidylethanolamine and have a role in membrane signal transduction (Banfield, Barker, Perry, & Brady, 1998) (ECF285s5), an exonuclease (Pfam: RNase_T) (ECF285s5), the periplasmic component of an ABC transporter (ECF285s5) and a PhoU, mainly as part of the putative AS factor in position -1, but also possibly involved in phosphate uptake (ECF285s5).

Promoter motif conservation: Predicted target promoter motifs of members of ECF285 contain AA in -35 and CCTCT in -10.

Summary: members of ECF285 might be regulated by a new type of single-transmembrane helix-containing AS factors encoded in position -1.


 


Basic information

Number of representative ECFs: 214

Number of non-redundant ECFs: 217

Sequences with C-terminal extension: 0.46%

Sequences with N-terminal extension: 1.84%

Overrepresented class: Betaproteobacteria [43.93%]



Sample Neighborhood

Protein WP_057948205.1 of Assembly GCF_001442515.1 (Lysobacter enzymogenes)


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
Function from structure? The crystal structure of human phosphatidylethanolamine-binding protein suggests a role in membrane signal transduction. Structure (London, England : 1993) 1998 M. Banfield, J. Barker, A. Perry, R. Brady PubMed: 9782050 ECF285
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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