ECF23

ECF23s1 106 ECF23s2 20 ECF23s3 25 ECF23s4 14 ECF23s5 55 ECF23s6 27 ECF23s7 38 ECF23s8 22 ECF23s9 26 ECF23s10 32 ECF23s11 28 ECF23s12 3 ECF23s13 1 ECF23s14 3 ECF23s15 7 ECF23s16 5 ECF23s17 11 ECF23s18 17 ECF23s19 16 ECF23s20 14 ECF23s21 9 ECF23s22 0 ECF23s23 11 ECF23s24 12 ECF23s25 8 ECF23s26 8 ECF23s27 3 ECF23s28 13 ECF23s29 9 ECF23s30 5 ECF23s31 11 ECF23s32 8 ECF23s33 0 ECF23s34 8 ECF23s35 10 ECF23s36 16

ECF proteins

General description: Members of ECF23 are homologous to original ECF23 (55.79%) and are present in Firmicutes (100%).

Anti-σ factor: Members of this group contain an AS factor encoded in position +1 with a DUF4179 in most of the cases. Proteins encoded in this position contain one transmembrane helix (88.7%). The genetic context conservation does not extend beyond the AS factor.

Promoter motif conservation: The only conserved predicted target promoter is TGATAG in -35 and CGTATTA in -10, although it is only evident in ECF23s3, ECF23s9, ECF23s6, and ECF23s7.

Summary: Members of ECF23 are regulated by single transmembrane AS factors encoded in +1 that contain a DUF4179. The genetic context conservation does not extend beyond the AS factor.

Basic information

Number of representative ECFs: 601

Number of non-redundant ECFs: 1149

Sequences with C-terminal extension: 0.26%

Sequences with N-terminal extension: 0.17%

Overrepresented class: Clostridia [51.25%]

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Sample Neighborhood

Protein WP_040436389.1 of Assembly GCF_000401215.1 (Clostridium sartagoforme AAU1)

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