ECF288 ECF proteins

General description: Members of ECF288 appear in Firmicutes (100%) and contain a C-terminal extension of ~100 amino acids. Interestingly, both σ4 domain and the C-terminal extension of members of ECF288 contain multiple cysteine residues, which indicates that disulfide-bridge formation could be in charge of the modulation of their activity, as in the case of SigK from M. tuberculosis (Shukla et al., 2014) (ECF19s2) and CorE2 from M. xanthus (Marcos-Torres et al., 2016; Torres et al., 2018) (ECF238s15).

Anti-σ factor: No putative AS factors were found in the genetic context of members of ECF288. Nevertheless, there is a soluble conserved DUF2461-containing protein in +1, which might be part of the regulatory mechanism of ECF288.

Promoter motif conservation: Predicted target promoter motifs are highly conserved, with TGTCACA in -35 and TGTCTAAT in -10.

Summary: In conclusion, proteins ECF288 contains C-rich C-terminal extensions that could be in charge of their activation or inactivation as in the case of CorE2 from M. xanthus (Marcos-Torres et al., 2016; Torres et al., 2018) (ECF238s15) and SigK from M. tuberculosis (Shukla et al., 2014) (ECF19s2).


 


Basic information

Number of representative ECFs: 73

Number of non-redundant ECFs: 74

Sequences with C-terminal extension: 100.00%

Sequences with N-terminal extension: 0.00%

Overrepresented class: Clostridia [76.71%]



Sample Neighborhood

Protein WP_028528740.1 of Assembly GCF_000425525.1 (Ruminococcus gauvreauii DSM 19829)


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
Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA σ-anti-σ complex. Acta crystallographica. Section D, Biological crystallography 2014 J. Shukla, R. Gupta, K. Thakur, R. Gokhale, B. Gopal PubMed: 24699647 ECF57, ECF19, ECF18, ECF288
In depth analysis of the mechanism of action of metal-dependent sigma factors: characterization of CorE2 from Myxococcus xanthus. Nucleic acids research 2016 F. Marcos-Torres, J. Pérez, N. Gómez-Santos, A. Moraleda-Muñoz, J. Muñoz-Dorado PubMed: 26951374 ECF238, ECF287, ECF288
The complex global response to copper in the multicellular bacterium Myxococcus xanthus. Metallomics : integrated biometal science 2018 J. Pérez, J. Muñoz-Dorado, A. Moraleda-Muñoz PubMed: 29961779 ECF238, ECF287, ECF288
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