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.
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%]
|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. Staroń, 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|