Family Search for PF04025 (RemA-like)

PF04025 hits 7 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

D9S306 Putative regulatory protein Toce_1021 from Thermosediminibacter oceani (strain ATCC BAA-1034 / DSM 16646 / JW/IW-1228P)
Aligns to 5:77 / 89 (82.0%), covers 100.0% of PF04025, 133.0 bits

• Linkage-disequilibrium mapping narrows the Fukuyama-type congenital muscular dystrophy (FCMD) candidate region to <100 kb.
  Toda, American journal of human genetics 1996

CPF_2002 hypothetical protein from Clostridium perfringens ATCC 13124
Aligns to 5:77 / 89 (82.0%), covers 100.0% of PF04025, 130.8 bits

• Putative function of hypothetical proteins expressed by Clostridium perfringens type A strains and their protective efficacy in mouse model
  Alam, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 (PubMed)
  • “...proteins CPF_2500, CPF_1441, CPF_0876, CPF_0093, CPF_2002, CPF_2314, CPF_1179, CPF_1132, CPF_2853, CPF_0552, CPF_2032, CPF_0438, CPF_1440, CPF_2918, CPF_0656,...”
  • “...of three relatively conserved hypothetical proteins (CPF_0876, CPF_2002; and CPF_2032) showing phylogenetic relationship of homologs in strains of Clostridium...”

Csac_2087 hypothetical protein from Caldicellulosiruptor saccharolyticus DSM 8903
Aligns to 9:81 / 101 (72.3%), covers 98.6% of PF04025, 130.2 bits

• Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting
  Andrews, Analytical and bioanalytical chemistry 2010
  • “...Putative, probable SP0561-like 7.7 5 0.07995 KAD Adenylate kinase 24.0 5 0.02640 Y2087 UPF0296 protein Csac_2087 11.2 4 0.04496 A4XG97 Hemerythrin-like metal-binding protein 16.6 4 0.03291 A4XJT0 Putative, probable YhbY-like protein 10.8 4 0.04780 A4XH18 Glutamate synthase 41.3 4 0.01248 There was a reduction in the...”

REMA_BACSU / Q7WY72 Extracellular matrix regulatory protein A; Regulator of extracellular matrix A from Bacillus subtilis (strain 168) (see 3 papers)
NP_570902 essential sporulation DNA binding protein; regulator of biofilm formation from Bacillus subtilis subsp. subtilis str. 168
Aligns to 5:77 / 89 (82.0%), covers 100.0% of PF04025, 126.8 bits

• function: Regulates the biosynthesis of the extracellular matrix and the biofilm formation (PubMed:19363116, PubMed:23646920). Activates the transcription of the matrix biosynthesis operons eps and tapA-sipW- tasA. Also activates expression of the opuA operon, involved in osmoprotection. Acts by binding specifically to the promoter region of the target genes (PubMed:23646920). Acts in parallel to the pathway that governs SinR derepression (PubMed:19363116, PubMed:23646920). Required for endosporulation (PubMed:23396918).
  disruption phenotype: Mutation impairs pellicle formation, complex colony architecture and motility inhibition in a sinR mutant background (PubMed:19363116). Mutant is defective in biofilm formation and also shows a delay in spore formation during biofilm formation (PubMed:23396918).
• RemA (YlzA) and RemB (YaaB) regulate extracellular matrix operon expression and biofilm formation in Bacillus subtilis.
  Winkelman, Journal of bacteriology 2009
  • GeneRIF: Required for transcription of the eps and tapA operons. Mutation of remA(ylzA) results in loss of expression of the genes required for extracellular matrix formation and motility inhibition. As a result, remA mutants cannot form biofilms and are constitutively motile.
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
  Amemiya, Transcription 2021 (secret)

GK1166 hypothetical protein from Geobacillus kaustophilus HTA426
Aligns to 5:77 / 87 (83.9%), covers 100.0% of PF04025, 126.5 bits

• The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases
  Chow, PloS one 2012
  • “...Krauss acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) in frame of the research training group GK1166 Biocatalysis in non-conventional media: (BioNoCo; www.bionoco.rwth-aachen.de ). J. Pietruszka thanks the BMBF for funding the project ExpresSys: in the framework of the funding measure GenoMik ( http://genomik-transfer.de/en/index_en.php?section=home ). The funders...”

ssl2874 unknown protein from Synechocystis sp. PCC 6803
Aligns to 5:77 / 89 (82.0%), covers 100.0% of PF04025, 126.0 bits

• Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
  Riediger, The Plant cell 2021
  • “...DUF820 featuring a restriction endonuclease domain ssl2064 10 7 4, 7 75 0.64 2.22 DUF4160 ssl2874 10 6 4, 6, 11 89 0.9 2.42 RemA homolog; KEGG K09777 sll0319 11 8 3, 8 297 0.57 1.55 DUF3747, periplasmic protein slr0287 12 9 5, 9 118 0.9...”
  • “...four proteins might interact with nucleic acids but less so with RNA. These proteins were Ssl2874, a homolog of RemA, an essential regulator of biofilm formation in Bacillus subtilis ( Winkelman et al., 2009 , 2013 ); Sll0639, a DHH phosphoesterase domain-containing protein with similarities to...”

REMB_BACSU / P37525 Extracellular matrix regulatory protein B; Regulator of the extracellular matrix B from Bacillus subtilis (strain 168) (see paper)
Aligns to 2:73 / 81 (88.9%), covers 97.3% of PF04025, 30.2 bits

• function: Regulates the biosynthesis of the extracellular matrix and the biofilm formation. May act as an enhancer of biofilm gene expression. Acts in parallel to the pathway that governs SinR derepression.
  disruption phenotype: Mutation impairs pellicle formation, complex colony architecture and motility inhibition in a sinR mutant background.

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