ECF122 ECF proteins

General description: Members of ECF122 are homologous to proteins from the original ECF122 (94.99%) and are present in Actinobacteria (100%).

Genetic context conservation: There are no putative AS factors present for members of ECF122. Instead, all subgroups of ECF122 contain a conserved 6-O-methylguanine DNA methyltransferase involved in DNA repair encoded in position +1 (an average of 1.26 ribonuclease-like domains and 1.41 DNA binding domains per ECF). Whereas this is the only conserved function in the context of proteins from subgroups ECF122s1, ECF122s2, and ECF122s3, proteins from the outermost subgroup, ECF122s4, are also associated with a glycerophosphoryl diester phosphodiesterase (-1), an histidine kinase-like ATPase domain also known as GHKL domain from Gyrase, Hsp90, Histidine Kinase, MutL since they share a structurally related ATPase domain (Staroń et al., 2009) (-2), one or two copies of the glycosyltransferase family 2 domain involved in transferring sugar from/to a variety of substracts (-4), three repeats of the glycosyltransferase domain from family 87 involved in the synthesis of glycolipids in mycobacteria (Wilson & Lamont, 2006) and proteins containing the domain UPF0016 suggested to function as calcium transporters (Huang, Pinto, Fritz, & Mascher, 2015).

Promoter motif conservation: The predicted target promoter motifs share the pattern CTCAC in -35  and CGTCTAC in -10 in ECF122s1, ECF122s2, and ECF122s3, whereas the promoter motif of ECF122s4 is not conserved. The information content of these motifs is reduced.

Summary: All in all, the proteins from ECF122 seem to be involved in DNA damage repair. Moreover, genetic neighborhoods of subgroup ECF122s4 contains conserved proteins related to glycolipid metabolism. A possible reason is that members of ECF122s4 evolved in a different range of bacteria that the rest of the members of ECF122. Supporting this notion, members of ECF122s4 appear only in families Intrasporangiaceae (90%) and Nocardioidaceae (10%), whereas remaining subgroups have a different family composition (at least six families in a subgroup).


 


Basic information

Number of representative ECFs: 495

Number of non-redundant ECFs: 559

Sequences with C-terminal extension: 0.18%

Sequences with N-terminal extension: 0.36%

Overrepresented order: Corynebacteriales [52.32%]



Sample Neighborhood

Protein WP_057168614.1 of Assembly GCF_001428895.1 (Mycobacterium sp. Root265)


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
GHKL, an emergent ATPase/kinase superfamily. Trends in biochemical sciences 2000 R. Dutta, M. Inouye PubMed: 10637609 ECF122
PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of phosphatidylinositol mannoside in mycobacteria. The Journal of biological chemistry 2006 Y. Morita, C. Sena, R. Waller, K. Kurokawa, M. Sernee, F. Nakatani, R. Haites, H. Billman-Jacobe, M. McConville, Y. Maeda, T. Kinoshita PubMed: 16803893 ECF122
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
Molecular evolution of a novel family of putative calcium transporters. PloS one 2014 D. Demaegd, A. Colinet, A. Deschamps, P. Morsomme PubMed: 24955841 ECF122
Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum. Journal of bacteriology 2015 X. Huang, D. Pinto, G. Fritz, T. Mascher PubMed: 25986905 ECF122, ECF56, ECF118, ECF128, ECF51, ECF52, ECF132, ECF53, ECF123, ECF125, ECF54, ECF130, ECF131, ECF218, ECF294, ECF48
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