ECF103 ECF proteins

General description: Proteins from ECF103 have homology to original ECF103 (83.78%) and are present in Firmicutes (100%).

Anti-σ factor: Proteins from ECF103 encode AS factors with one transmembrane helix (84%) in position +1.

Genomic context conservation: Other conserved genes in the genetic context of members of ECF103 include proteins from ABC transporters (+2 and +3 of ECF103s3).

Promoter motif conservation: Putative target promoter motifs are only conserved in the largest subgroups and contain TGTCACAA in -35 and a less conserved TCT in -10.

Summary: ECF103 is regulated by AS factors with one transmembrane helix and either a zinc-binding domain or a DUF4179 (ECF103s2). In agreement with original ECF103 (Staroń et al., 2009), members of ECF103 might be involved in the expression of ABC transporters.


 


Basic information

Number of representative ECFs: 181

Number of non-redundant ECFs: 296

Sequences with C-terminal extension: 0.34%

Sequences with N-terminal extension: 0.68%

Overrepresented class: Bacilli [85.64%]



Sample Neighborhood

Protein KFN08161.1 of Assembly GCA_000746875.1 (Paenibacillus macerans)


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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