ECF120 ECF proteins

General description: A percentage of 20.53% of the proteins from new ECF120 has homology to original ECF120. Proteins from ECF120 belong to Bacteroidetes of the orders Bacteroidales, Chitonophagales, Cytophagales, and Flavobacteriales.

Anti-σ factor: Proteins from ECF120 contain an AS factor with one TM helix in position +1 (71.22%). This AS factor usually contains either a putative zinc-finger domain or a DUF3379.

Genetic context conservation: The most conserved domain in the genetic context is DUF4252, which appears in positions +2 and +3, in some cases together with a putative auto-transporter adhesin head GIN domain (PFAM: DUF2807, with structural similarity to pectinases), in position +2 of ECF120s13, and in positions +2, -1 and -2 of ECF120s12. These proteins are soluble and might be part of the signaling mechanisms of ECF120. Members of Flavobacteriales encode a peptidase in position -1 (ECF120s2, ECF120s24, ECF120s4ECF120s6). Other proteins conserved are an outer membrane beta-barrel protein (+2 of ECF120s9, ECF120s7), a protein contain a 4Fe-4S dicluster domain (-1 of ECF120s15), a protein with a Cys-rich domain (-2 of ECF120s15), an amino acid kinase (-1 of ECF120s3), the pyridoxal binding domain of a pyridoxal-dependent decarboxylase (-2 of ECF120s3), a shikimate kinase (ECF120s1 and ECF120s3), a DUF45 (ECF120s3), an Holliday junction DNA helicase ruvB (ECF120s11),  a pyruvate ferredoxin/flavodoxin oxidoreductase (ECF120s13), the TPP binding domain of a thiamine pyrophosphate enzyme (ECF120s13), a putative porin (ECF120s13), a pyruvate flavodoxin/ferredoxin oxidoreductase (ECF120s13), an Adenylosuccinate lyase (ECF120s6) and a periplasmic binding protein (ECF120s4 and ECF120s6).

Studied members: One characterized member of ECF120 is PG0985 from P. gingivalis (ECF120s16). This ECF and the protein coded in +1 (inner membrane protein) and +2 (outer membrane protein with a DUF4252) are highly abundant under heme excess (Veith, Luong, Tan, Dashper, & Reynolds, 2018). Under these conditions, the PG0985 induces the expression of heme efflux pumps (Veith et al., 2018).

Promoter motif conservation: The promoter motifs are conserved and involved TGTAACAAA in -35 and TCGTCAT in -10, which suggest that they autoregulate their expression.

Summary: Given the conservation of the large amount of sensing and transport systems in the genetic context of ECF120 and the function of the only described member of this group, it is likely that ECF120 is in charge of sensing and transporting of heme and/or other metal-containing compounds, potentially from the host organisms if the bacteria is a pathogen or a commensal of mammals. ECF120 inherits the disposal of the genetic context of original ECF120 in some subgroups (Staroń et al., 2009), but extends it to other possibilities. Given the conservation of the promoter motifs, it is likely that members of ECF120 are self-regulated.


 


Basic information

Number of representative ECFs: 1015

Number of non-redundant ECFs: 1018

Sequences with C-terminal extension: 1.57%

Sequences with N-terminal extension: 0.00%

Overrepresented phylum: Bacteroidetes [99.90%]



Sample Neighborhood

Protein EGV43992.1 of Assembly GCA_000224335.2 (Bizionia argentinensis JUB59)


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
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
Outer Membrane Vesicle Proteome of Porphyromonas gingivalis Is Differentially Modulated Relative to the Outer Membrane in Response to Heme Availability. Journal of proteome research 2018 P. Veith, C. Luong, K. Tan, S. Dashper, E. Reynolds PubMed: 29766714 ECF120
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