ECF239 ECF proteins

General description: This is a FecI-like group whose proteins have homology to the original group ECF10 (95.18%), although this is not the largest ECF10-like group. The proteins in ECF239 are mainly present in Bacteroidetes (99.22%) mostly from family Flavobacteriaceae.

Regulation and function: The genetic context of members of ECF239 follow the rule of FecI-like ECFs, with a FecR-like single TM helix AS factor in +1 and an outer-membrane TonB-dependent receptor in +2 (Staroń et al., 2009). The FecR-like AS factor is fused to a DUF4974 domain (except ECF239s9), as in other FecR-like proteins, and contain one TM helix (96.88%). The TonB-dependent receptor might be fused to a carboxypeptidase regulatory-like domain (Pfam: CarbopepD_reg_2) of unknown function, and it is predicted to be a β-barrel outer membrane protein. In the FecI system of E. coli, this outer-membrane protein is FecA, a TonB-dependent transporter of ferric citrate across the outer membrane (reviewed in (Braun & Mahren, 2005)). Members of original ECF10 are suggested to transport carbohydrates across the membrane since their genetic neighborhood contains an outer membrane protein homolog of the polysaccharide-binding proteins SusC and SusD (Staroń et al., 2009). Nevertheless, despite being part of original ECF10, members of ECF239 lack of this carbohydrate binding protein.

Genomic context conservation: Other conserved proteins are only present in ECF239s3 and include an SRP54-type protein (-2), a tetrahydrofolate dehydrogenase/cyclohydrolase (-3), an amidinotransferase, a glyoxalase/bleomycin resistance protein/dioxygenase superfamily and an arginyl tRNA synthetase.

Promoter motif conservation: Predicted target promoter motifs often (6/9) contain a conserved (A|G)ACA in -35 and a TAC in -10. It is possible that members of ECF239 are autoregulated, a new feature for a FecI-like group (Staroń et al., 2009).

Summary: ECF239 contains sequences with homology to the original group ECF10. However, unlike original ECF10 (Staroń et al., 2009), AS factors from ECF239 do not contain a carbohydrate-binding domain in their genetic context and contain conserved target promoter motifs, indicating autoregulation.


 


Basic information

Number of representative ECFs: 296

Number of non-redundant ECFs: 311

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.00%

Overrepresented class: Flavobacteriia [93.58%]



Sample Neighborhood

Protein WP_034044300.1 of Assembly GCF_000789235.1 (Flaviramulus ichthyoenteri Th78)


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
Transmembrane transcriptional control (surface signalling) of the Escherichia coli Fec type. FEMS microbiology reviews 2004 V. Braun, S. Mahren PubMed: 16102597 ECF239, ECF243
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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