ECF22

ECF22s1 360 ECF22s2 140 ECF22s3 110 ECF22s4 89 ECF22s5 109 ECF22s6 85 ECF22s7 74 ECF22s8 74 ECF22s9 61 ECF22s10 61 ECF22s11 58 ECF22s12 30 ECF22s13 36 ECF22s14 36 ECF22s15 36 ECF22s16 27 ECF22s17 34 ECF22s18 30 ECF22s19 26 ECF22s20 26 ECF22s21 20 ECF22s22 22 ECF22s23 22 ECF22s24 15 ECF22s25 17 ECF22s26 19 ECF22s27 22 ECF22s28 20 ECF22s29 18 ECF22s30 22 ECF22s31 16 ECF22s32 16 ECF22s33 4 ECF22s34 21 ECF22s35 16 ECF22s36 15 ECF22s37 11 ECF22s38 13 ECF22s39 14 ECF22s40 12 ECF22s41 21 ECF22s42 10 ECF22s43 4 ECF22s44 15 ECF22s45 12 ECF22s46 10 ECF22s47 12

ECF proteins

General description: ECF22 has homology to original ECF22 (88.1%). Proteins from this group are present in Bacteroidetes (78.81%), Proteobacteria (18.14%), Verrucomicrobia (1.19%), Planctomycetes (1.02%) and Acidobacteria (0.68%).

Anti-σ factor: Putative AS factors of ECF22 are encoded in +1 and usually contain DUF2207 and four (48.06%) TM helices.

Genomic context conservation: Other proteins conserved in the genetic context of members of ECF22 are an alpha/beta hydrolase (-1 of ECF22s16 and ECF22s4), σ-54 factor (ECF22s8) and two proteins from ABC transporters (-2 and -3 of ECF22s22).

Promoter motif conservation: Promoter motifs are conserved and contain TGTGATTTT in -35 and GCGAAT(C/A)AT in -10, in agreement with original ECF22 (Rhodius et al., 2013) and expanding these motifs.

Summary: ECF22 could be regulated by 4-transmembrane helix AS factors located in +1. This expands the knowledge of original ECF22, where putative AS factors were not identified (Staroń et al., 2009). This group seems to be autoregulated since the promoter motifs are conserved.

Basic information

Number of representative ECFs: 1921

Number of non-redundant ECFs: 1950

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.77%

Overrepresented phylum: Bacteroidetes [79.85%]

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Sample Neighborhood

Protein WP_026293195.1 of Assembly GCF_000378125.1 (Rudaea cellulosilytica DSM 22992)

Promoter Motif

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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
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