ECF125 ECF proteins

General description: Proteins from ECF125 have homology to original ECF125 (100%) and are present in Actinobacteria.

Special features: Members of ECF125 are associated with a soluble glyoxalase/bleomycin resistance protein/dioxygenase encoded in +1. This protein could work as an AS factor due to its homology to AS factors in the original classification and to AS factors of group ECF121.

Genomic context conservation: Other than position +1, conserved proteins encoded in the genetic context of members of ECF125 include a TetR represor, a protein from the major facilitator superfamily (ECF125s4), an aminopeptidase I zinc metalloprotease M18 (ECF125s2), an enoyl-CoA hydratase/isomerase (ECF125s2), a CobB/CobQ-like glutamine amidotransferase (ECF125s2), a creatinine amidohydrolase (ECF125s1), an aminotransferase class-III (ECF125s1), a GMC oxidoreductase (ECF125s1), a FMN-dependent dehydrogenase (ECF125s1), a radical SAM with an iron-sulfur cluster (ECF125s1), an amidinotransferase (ECF125s1) and a pyridine nucleotide-disulphide oxidoreductase (ECF125s1).

Promoter motif conservation: The predicted target promoter motifs contain AAAA in -35 and CGTCGGA in -10.

Summary: In conclusion, ECF125 is associated with soluble glyoxalase/bleomycin resistance dioxygenases encoded in position +1 as in original ECF125 (Huang et al., 2015). These proteins could function as AS factors of ECF125.


 


Basic information

Number of representative ECFs: 237

Number of non-redundant ECFs: 245

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.41%

Overrepresented class: Actinobacteria [99.58%]



Sample Neighborhood

Protein WP_057167004.1 of Assembly GCF_001428895.1 (Mycobacterium sp. Root265)


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
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. Journal of bacteriology 2015 X. Huang, D. Pinto, G. Fritz, T. Mascher PubMed: 25986905 ECF122, ECF56, ECF118, ECF128, ECF51, ECF52, ECF132, ECF53, ECF123, ECF125, ECF54, ECF130, ECF131, ECF218, ECF294, ECF48
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