ECF105 ECF proteins

General description: Members of ECF105 are homologous to proteins from the original ECF105 (12.33%) and are present in Firmicutes from order Bacillales (100%).

Anti-σ factors: Likewise the original group ECF105 (Staroń et al., 2009), proteins from ECF105 are regulated by TM-bound ZAS factors encoded in position encoded in +1. These AS factor contain a single transmembrane helix (85.11%).

Genomic context conservation: The multiple transmembrane proteins encoded in positions +2 and +3 in original ECF105 (Staroń et al., 2009) were also found in new ECF105 (usually 9 (34.04%) and 3 (57.46%) transmembrane helices, respectively). Other proteins conserved in the genetic context of members of ECF105 are some enzymes in ECF105s1 involved in translation and amino acid metabolism: acetokinase, pyrroline-5-carboxylate reductase, tRNA synthetase class II and 3-hydroxyacyl-CoA dehydrogenase.

Promoter motif conservation: Predicted target promoter motifs are conserved. Two -35 elements contain TG(A/T)AGGG and the -10 element has CGTCTAT. The predicted target promoter motif expands the knowledge over members of original ECF105 (Staroń et al., 2009), which lacks a conserved target promoter motif.

Summary: ECF105 expands the number of proteins (from 4 in original ECF105 (Staroń et al., 2009) to 312 in new ECF105), predicts a target promoter motif but keeps the same genetic neighborhood as original group ECF105.


 


Basic information

Number of representative ECFs: 382

Number of non-redundant ECFs: 527

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 3.42%

Overrepresented class: Bacilli [67.80%]



Sample Neighborhood

Protein SDL63637.1 of Assembly GCA_900102965.1 (Paenibacillus jilunlii)


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
Adhesion to cellulose of the Gram-positive bacterium Ruminococcus albus involves type IV pili. Microbiology (Reading, England) 2002 H. Rakotoarivonina, G. Jubelin, M. Hebraud, B. Gaillard-Martinie, E. Forano, P. Mosoni PubMed: 12055307 ECF105
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
Type IV pili in Gram-positive bacteria. Microbiology and molecular biology reviews : MMBR 2013 S. Melville, L. Craig PubMed: 24006467 ECF31, ECF105
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