General description: Members of ECF03 are homologous to proteins from original ECF03 (89.41%) and are mainly present in Bacteroidetes (95.44%), but also a variety of Gram-negative organisms such as Proteobacteria (1.27%), Verrucomicrobia (2.28%), Kiritimatiellaeota (0.25%) and Chlorobi (0.25%).
Anti-σ factor: The genomic context is not conserved although it is possible to identify a putative AS factor with one TM helix (62.03%, ~100% in the MSA)in position +1. These putative AS factors of ECF03 extend their conservation also to their extracytoplasmic site.
Genomic context conservation: Proteins from ECF03s4 have extended genomic context conservation, with an NADP oxidoreductase in -1, a Maf-like protein, an elongation factor Tu fused to a LepA protein, a haloacid dehalogenase-like hydrolase, a UPF0102 protein, a glycoprotease, and an LD-carboxypeptidase. Subgroups ECF03s3 and ECF03s5 contain one or several conserved transketolases. Last, ECF03s10 contains an LTXXQ motif family protein in +2 (involved in relieving extracytoplasmic stress (Danese & Silhavy, 1998)) and a universal stress protein.
Promoter motif conservation: Predicted target promoter motifs are usually TTAAACC in -35 and a less conserved TC-containing -10, as described in previous literature (Rhodius et al., 2013).
Summary: Unlike proteins from original ECF03, new ECF03 seems to be regulated by a new type of AS factors with no registered PFAM domain. These AS factors contain a conserved extracytoplasmic domain. The reason for the lack of conserved PFAM domain in ECF03 could be due to the presence of most of the sequences from ECF03 only in Bacteroidetes, organisms where genetic studies are limited. The presence of LTXXQ-motif proteins and universal stress proteins indicates that ECF03 could be part of the cell envelope stress response as its neighboring ECF groups.
Number of representative ECFs: 1280
Number of non-redundant ECFs: 1294
Sequences with C-terminal extension: 0.54%
Sequences with N-terminal extension: 2.55%
Overrepresented phylum: Bacteroidetes [93.75%]
|CpxP, a stress-combative member of the Cpx regulon.||Journal of bacteriology||1998||P. Danese, T. Silhavy||PubMed: 9473036||ECF03, ECF111|
|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|
|Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters.||Molecular systems biology||2013||V. Rhodius, T. Segall-Shapiro, B. Sharon, A. Ghodasara, E. Orlova, H. Tabakh, D. Burkhardt, K. Clancy, T. Peterson, C. Gross, C. Voigt||PubMed: 24169405||ECF22, ECF27, ECF03, ECF21, ECF39, ECF25, ECF26, ECF42, ECF38, ECF14, ECF29, ECF33, ECF281, ECF290, ECF291|