ECF35 ECF proteins

General description: Members of ECF35 have homology to members of the original group ECF35 (6.13%) and are present in Proteobacteria (100%).

Anti-σ factor: Members of ECF35 might be regulated by a putative AS factor encoded in position +1. This AS factor contains one transmembrane helix (67.68%, ~100% when looking at an MSA) and periplasmic tetratricopeptide repeats in some cases. Members of subgroups ECF35s17, ECF35s12, ECF35s1, ECF35s6, ECF35s14, ECF35s20 and ECF35s4 contain an average of ~1 protein with a DUF3520 in their genetic context, usually in positions -1 of -2. These proteins were identified as putative AS factors in groups ECF226 and ECF289, where they are fused to von Willebrand factors. Nevertheless, DUF3520-containing proteins do not bear any transmembrane helix when associated with members of ECF35.

Genomic context conservation: Other conserved domains include a UPF0029 (+2 of ECF35s2), the C-terminal domain of a TonB protein (-1 of ECF35s13), a diguanylate cyclase with an EAL and a GAF domain (-1 of ECF35s2), an oligopeptide/dipeptide ABC transporter (ECF35s11), a protein with a transglycosylase SLT domain (ECF35s7) and an AIR carboxylase (ECF35s7).

Studied members: A characterized member of ECF35 is SbrI from Pseudomonas aeruginosa (ECF35s1). SbrI is involved in cell envelope integrity in the control of swarming motility and biofilm formation. It is inhibited by the AS factor SbrR, encoded in +1 in the same operon (see review (Chevalier et al., 2018)).

Promoter motif conservation: Predicted target promoter motifs are subgroup-dependent. Subgroups ECF35s2 and ECF35s5 contain ACCC in -35 and CGT in -10, whereas subgroups ECF35s1 and ECF35s6 contain TAACCCG in -35 and CGTCT in -10. Indeed, this last motif agrees with the binding promoter motif of SbrI (Aires, Köhler, Nikaido, & Plésiat, 1999).

Summary: ECF35 is regulated by one-transmembrane helix AS factors encoded in +1. Members of this group might be involved in the control of swarming motility, biofilm formation and cell envelope integrity as in the case of SbrI from P. aeruginosa (ECF35s1).


 


Basic information

Number of representative ECFs: 835

Number of non-redundant ECFs: 1027

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 3.60%

Overrepresented phylum: Proteobacteria [99.88%]



Sample Neighborhood

Protein KFL37610.1 of Assembly GCA_000743535.1 (Arenimonas donghaensis DSM 18148 = HO3-R19)


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
Involvement of an active efflux system in the natural resistance of Pseudomonas aeruginosa to aminoglycosides. Antimicrobial agents and chemotherapy 1999 J. Aires, T. Köhler, H. Nikaido, P. Plésiat PubMed: 10543738 ECF35
Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. Biochimica et biophysica acta. Gene regulatory mechanisms 2018 S. Chevalier, E. Bouffartigues, A. Bazire, A. Tahrioui, R. Duchesne, D. Tortuel, O. Maillot, T. Clamens, N. Orange, M. Feuilloley, O. Lesouhaitier, A. Dufour, P. Cornelis PubMed: 29729420 ECF02, ECF102, ECF243, ECF293, ECF35
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