ECF31 ECF proteins

General description: Members of ECF31 have homology to proteins from original ECF31 (91.1%) and are exclusively present in Firmicutes.

Anti-σ factor: Members of ECF31 might be regulated by putative AS factors encoded in +1. These AS factors contain two transmembrane helices (84.35%) with a DUF3545 and a DUF2207 that covers the total length of the sequence. Members of ECF31s5 (12.5%) contain a cytoplasmic zinc-finger in their putative AS factor. Proteins encoded in +2 are conserved and contain two transmembrane helices. Among the domains that these proteins contain we could find a virulence factor BrkB domain or a MAP17 domain, known to interact with PDZ domains (Kocher, Comella, Tognazzi, & Brown, 1998).

Genomic context conservation: Other than the AS factor, members of ECF31 contain several genes that encode proteins from ABC transporters (positions +3 and +4 in ECF31s1 and ECF31s2) and the N-terminal domain of a phospholipase D-nuclease (Pfam: PLDc_N) (position +5 in ECF31s1 and ECF31s2) in their genetic context. Other domains conserved in the genetic context of members of ECF31 included the C subunit of Glu-tRNAGln amidotransferase (+7 of ECF31s2), an amidase (+8 of ECF31s2), GatB (+9 of ECF31s2), a protein with an acetyltransferase (GNAT) domain (+10 of ECF31s2), a metallo-beta-lactamase (-2 of ECF31s2), a thioredoxin (-3 of ECF31s2), a SNARE-associated Golgi protein (-4 of ECF31s2).

Studied members: Characterized members of ECF31 include SigY from Bacillus subtilis (ECF31s1). SigY’s activity is dependent on YxlC, the putative AS factor encoded in +1, and YxlD encoded in +2 (Cao et al., 2003; Tojo et al., 2003; Yoshimura, Asai, Sadaie, & Yoshikawa, 2004). SigY is induced under nitrogen starvation (Tojo et al., 2003) and it is needed for maintaining the SPβ prophage, which encodes sublacin and its resistance cassette (Mendez, Gutierrez, Reyes, & Márquez-Magaña, 2012). When active, SigY induces only its expression and the one protein of unknown function YbgB (Cao et al., 2003). Homologs of YxlD are conserved across ECF31.

Promoter motif conservation: Promoter motifs are conserved and contain TGAAC in -35 and CGT in -10, in agreement with original ECF31 (Staroń et al., 2009).

Summary: Members of ECF31 might be regulated by AS factors with two transmembrane helices encoded in +1. The function of members of ECF31 might be related to the presence of conserved transmembrane proteins in +2, as in the case of SigY from B. subtilis (Cao et al., 2003; Tojo et al., 2003; Yoshimura et al., 2004). Other proteins that could participate in ECF31 activity are ABC transporters and phospholipase D-nuclease, encoded in their genetic context.


 


Basic information

Number of representative ECFs: 291

Number of non-redundant ECFs: 326

Sequences with C-terminal extension: 0.00%

Sequences with N-terminal extension: 0.92%

Overrepresented class: Bacilli [89.00%]



Sample Neighborhood

Protein WP_057989799.1 of Assembly GCF_001439635.1 (Bacillus cecembensis)


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
Identification and partial characterization of PDZK1: a novel protein containing PDZ interaction domains. Laboratory investigation; a journal of technical methods and pathology 1998 O. Kocher, N. Comella, K. Tognazzi, L. Brown PubMed: 9461128 ECF31
Regulation of the Bacillus subtilis extracytoplasmic function protein sigma(Y) and its target promoters. Journal of bacteriology 2003 M. Cao, L. Salzberg, C. Tsai, T. Mascher, C. Bonilla, T. Wang, R. Ye, L. Márquez-Magaña, J. Helmann PubMed: 12897008 ECF31
Organization and expression of the Bacillus subtilis sigY operon. Journal of biochemistry 2003 S. Tojo, M. Matsunaga, T. Matsumoto, C. Kang, H. Yamaguchi, K. Asai, Y. Sadaie, K. Yoshida, Y. Fujita PubMed: 14769884 ECF31
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
The extracytoplasmic function sigma factor SigY is important for efficient maintenance of the Spβ prophage that encodes sublancin in Bacillus subtilis. DNA and cell biology 2012 R. Mendez, A. Gutierrez, J. Reyes, L. Márquez-Magaña PubMed: 22400495 ECF31
Type IV pili in Gram-positive bacteria. Microbiology and molecular biology reviews : MMBR 2013 S. Melville, L. Craig PubMed: 24006467 ECF31, ECF105
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