Fig. 4
From: Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria
PmoD subfamilies and their connections to copper homeostasis. a Genomes present in the JGI/IMG database were analyzed for the presence of genes with a proposed relationship to the methanotroph copper homeostasis, including csp1/2 (TIGR04401), copper membrane monooxygenases (CuMMOs) via a/pmoB (PF04744/TIGR03079), Mbn via mbnB (TIGR04159), pmoD (the dataset in this paper), csp3/DUF326 (PF03860), mopE/corA (via BLAST, no profile HMM available), and sMMO via mmoD (TIGR04550, absent in non-sMMO soluble diiron monooxygenase enzymes). The strongest reciprocal relationship is observed between PmoDs and pMMO components. b A sequence similarity network (SSN) for PmoD homologs was constructed using the EFI/EST network generation tool and an E-value cutoff of 21, colored by AOB/MOB distribution among PmoD homologs. c SSN colored by core cysteine-containing sequence motifs among PmoD homologs. The Cx7MxHxnC motif (pink) corresponds to the PmoDMet49242_1452 CuA site ligand set and is also present in AmoEs. d SSN colored by proximity to copper-related genes, including amoCAB/pmoCAB operons (pmo operons), lone amoC/pmoC genes (pmoC), copCD pairs or lone copC genes, pCuAC genes, genes encoding multicopper oxidases, and genes encoding additional pmoD homologs. e Optical spectra of representative classes of copper-loaded PmoD homologs denoted by locus tag and metal binding motif
