ECF265

ECF265s1 54 ECF265s2 59 ECF265s3 75 ECF265s4 77 ECF265s5 55 ECF265s6 72 ECF265s7 29 ECF265s8 65 ECF265s9 37 ECF265s10 22 ECF265s11 24 ECF265s12 36 ECF265s13 31 ECF265s14 35 ECF265s15 36 ECF265s16 35 ECF265s17 28 ECF265s18 18 ECF265s19 23 ECF265s20 26 ECF265s21 19 ECF265s22 21 ECF265s23 12 ECF265s24 21 ECF265s25 25 ECF265s26 16 ECF265s27 20 ECF265s28 2 ECF265s29 15 ECF265s30 17 ECF265s31 17 ECF265s32 20 ECF265s33 17 ECF265s34 15 ECF265s35 18 ECF265s36 17 ECF265s37 13 ECF265s38 8 ECF265s39 15 ECF265s40 13 ECF265s41 16 ECF265s42 15 ECF265s43 10 ECF265s44 13 ECF265s45 12 ECF265s46 1 ECF265s47 9 ECF265s48 12 ECF265s49 10 ECF265s50 13 ECF265s51 8 ECF265s52 12 ECF265s53 10 ECF265s54 13 ECF265s55 5 ECF265s56 11

ECF proteins

General description: Proteins from ECF265 have homology to proteins from original ECF30 (46.6%), ECF55 (5.84%) and ECF112 (0.51%), and are present in Firmicutes (95.80%) and Actinobacteria (3.50%).

Regulation: Members of ECF265 are associated with AS factors with one transmembrane helix (51.87%) in +1. In the case of ECF265s4 and ECF265s7, which appear primarily in the Bacillus genus, there is no apparent AS factor in their genetic context. In these groups, ECFs share the genetic neighborhood with a transcriptional repressor from PadR family (+1) and a cell cycle protein (+2) involved in peptidoglycan synthesis such as FtsW, RodA or SpoVE (Pfam: PadR and FTSW_RODA_SPOVE) in +1 and +2, respectively. PadR is involved in negative regulation of the phenolic acid metabolism and RodA is a peptidoglycan glycosyltransferase involved in peptidoglycan biosynthesis. It is possible that in these two subgroups the AS factor is substituted by transcriptional control.

Genomic context conservation: Apart from the proteins mentioned above, the only conserved element in the genomic neighborhood of members of ECF265 are the inner-membrane component of an ABC transporter (Pfam: BPD_transp_1) (ECF265s24).

Promoter motif conservation: Promoter motifs are subgroup-dependent conserved and usually contain AAC in -35 and CGTC in -10; in agreement with the prediction for original ECF30 (Staroń et al., 2009).

Summary: In summary, ECF265 seems to be regulated by putative AS factors encoded in +1 with diverse unknown domains, in contrast to original ECF30 (Staroń & Mascher, 2010). Two subgroups, ECF265s4 and ECF265s7, seem to be regulated by a PadR transcriptional repressor encoded in +1 and involved in phenolic acid metabolism. Since RodA is encoded in position +2 in ECF265s4 and ECF265s7, proteins from these subgroups might be involved in peptidoglycan biosynthesis.

Basic information

Number of representative ECFs: 1328

Number of non-redundant ECFs: 1781

Sequences with C-terminal extension: 0.11%

Sequences with N-terminal extension: 1.80%

Overrepresented phylum: Firmicutes [97.36%]

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Sample Neighborhood

Protein EOS21727.1 of Assembly GCA_000403215.2 (Lachnospiraceae bacterium A4)

Promoter Motif

MSA Viewer

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	ECF114, ECF31, ECF22, ECF12, ECF27, ECF122, ECF121, ECF56, ECF03, ECF21, ECF23, ECF02, ECF41, ECF15, ECF107, ECF111, ECF39, ECF19, ECF25, ECF17, ECF26, ECF118, ECF11, ECF16, ECF42, ECF38, ECF103, ECF36, ECF28, ECF51, ECF115, ECF40, ECF14, ECF29, ECF123, ECF33, ECF102, ECF105, ECF106, ECF116, ECF130, ECF18, ECF235, ECF120, ECF239, ECF240, ECF242, ECF243, ECF249, ECF265, ECF271, ECF281, ECF285, ECF286, ECF289, ECF290, ECF291, ECF292, ECF293, ECF294, ECF30, ECF32, ECF43
General stress response in α-proteobacteria: PhyR and beyond.	Molecular microbiology	2010	A. Staroń, T. Mascher	PubMed: 20979331	ECF265