ECF33 ECF proteins

General description: Members of ECF33 are present in Proteobacteria (100%) and have homology against original ECF33 (44.11%).

Anti-σ factor: Members of ECF33 might be regulated by putative AS factors encoded in +1 with one transmembrane helix (73.64%) and a zinc finger.

Genomic context conservation: Other than this protein, conserved domains in the genetic context of members of ECF33 include a subtilase (+2 of ECF33s3 and ECF33s2) and a binding-protein-dependent transport system inner membrane component (ECF33s3), which is usually present in the periplasmic transporters of ABC transport systems.

Studied members: One described member of ECF33, EcfQ from Bradyrhizobium japonicum (ECF33s1), is responsible for singlet oxygen resistance (Masloboeva et al., 2012).

Promoter motif conservation: The target -35 element is extensively conserved (TGAACCTTT), and the -10 element varies amongst subgroups, although an AC is usually conserved. This promoter matches previous work on original ECF33 (Rhodius et al., 2013) and agrees with experimentally described target promoter of EcfQ (Masloboeva et al., 2012).

Summary: ECF33 might be regulated by zinc-finger AS factors located in position +1 with one TM helix (73.64%). Members of this group could be responsible for singlet oxygen resistance, as described for EcfQ of B. japonicum (Masloboeva et al., 2012). The conservation of the target promoter elements indicates that members of ECF33 usually are self-regulated.


 


Basic information

Number of representative ECFs: 512

Number of non-redundant ECFs: 492

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 1.63%

Overrepresented phylum: Proteobacteria [99.61%]



Sample Neighborhood

Protein ABE64409.1 of Assembly GCA_000013885.1 (Nitrobacter hamburgensis X14)


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
Reactive oxygen species-inducible ECF σ factors of Bradyrhizobium japonicum. PloS one 2012 N. Masloboeva, L. Reutimann, P. Stiefel, R. Follador, N. Leimer, H. Hennecke, S. Mesa, H. Fischer PubMed: 22916258 ECF16, 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
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