REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
monoclonal mouse anti-polyhis-peroxidase antibody	Sigma	A7058; RRID: AB_258326
monoclonal mouse anti-his antibody	Bio-Rad	AD1.1.10
monoclonal mouse anti-MBP probe antibody	Santa Cruz Biotechnology	sc-13564; RRID: AB_675707
sheep anti-mouse antibody-horseradish peroxidase	Merck	NXA931V
Bacterial and virus strains
Escherichia coli K-12 MG1655	Yale Culture Collection	N/A
Escherichia coli K-12 MG1655 derivatives	See Table S2	N/A
Escherichia coli K-12 BW25113	Datsenko et al., 200061	N/A
Escherichia coli K-12 BW25113 derivatives	Baba et al., 200652	N/A
Escherichia coli BTH101	BACTH System Kit	N/A
Chemicals, peptides, and recombinant proteins
RtcB ligase	New England Biolabs	M0458S
RQ1 RNase-free DNase	Promega	M6101
SuperScript III Reverse Transcriptase	ThermoFisher Scientific	18080044
Power SYBR Green PCR Master Mix	Applied Biosystems	4367660
Pierce Premium Grade dithiobis(succinimidyl propionate)	ThermoFisher Scientific	PG82081
native PAGE sample buffer	ThermoFisher Scientific	BN2003
Critical commercial assays
Bacterial Adenylate Cyclase Two-Hybrid System Kit	Euromedex	EUK001
RNeasy Protect Bacteria mini kit	Qiagen	76506/74104
Monolith Protein Labelling Kit RED-NHS 2nd Generation (Amine Reactive)	NanoTemper Technologies	MO-L011
Westar Supernova HRP Detection Substrate	Cyanagen	K1-0068
Deposited data
Escherichia coli K-12 MG1655 genome	NCBI Reference Sequence	NC_000913
Transcriptome profile of Escherichia coli K-12 MG1655	This study	GSE165118
Oligonucleotides
qPCR primers for rtcB F: 5’-ACGTGATAAAGGTGCCTGGG-3’ R: 5’-CACACCTGGTCCGACTCATC-3’	Engl et al., 201615	N/A
qPCR primers for rtcA F: 5’-GACCAACTGGTGCTACCGAT-3’ R: 5’-GCGTTACGCCATCTGTTTCT-3’	Engl et al., 201615	N/A
qPCR primers for rtcR F: 5’-GGTCATCGATCGACTGGAAT-3’ R: 5’-TCAATCTCAACGCTCACCAC-3’	This study	N/A
qPCR primers for ssrA F: 5’-AGTCGCAAACGACGAAAACT-3’ R: 5’-GCGATCTCTTTTGGGTTTGA-3’	This study	N/A
adapter for RtcB-mediated ligation 5’-NNNNTGGAATTGTCGGGTGCCAAGG-3’	This study	N/A
tRNAGlu[UUC] 35-mer 5’-ACUCCGAUAUCACGCUUUCACCGUG AUAUCGGAGU-3’	This study	N/A
tRNAGlu[UUC] 17-mer 5’-ACUCCGAUAUCACGCUU-3’	This study	N/A
Recombinant DNA
Plasmid vectors and derivatives	See Table S1	N/A
Software and algorithms
FIJI/ImageJ	Schindelin et al., 201279	https://imagej.net/software/fiji/
progressiveMauve	Darling et al., 201064	https://darlinglab.org/mauve/user-guide/progressivemauve.html
FASTQC	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Trimmomatic	Bolger et al., 201465	http://www.usadellab.org/cms/?page=trimmomatic
Bowtie 2	Langmead and Salzberg, 201266	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
HTSeq	Anders et al., 201567	https://htseq.readthedocs.io/en/master/
DESeq2 R/Bioconductor package	Love et al., 201468	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
FASTX toolkit	Hannon Lab	http://hannonlab.cshl.edu/fastx_toolkit/
SAM tools	Li et al., 200969	http://www.htslib.org/
Integrative Genomics Viewer (IGV)	Thorvaldsdóttir et al., 201370	https://software.broadinstitute.org/software/igv/
PANTHER Classification System for GO	Mi et al., 201371	http://geneontology.org/
KEGG Automatic Annotation Server (KAAS)	Moriya et al., 200773	http://www.genome.jp/kegg/kaas/
BioVenn	Hulsen et al., 200874	https://www.biovenn.nl/
Weblogo	Crooks et al., 200475	https://weblogo.berkeley.edu/logo.cgi
Iterative Threading ASSEmbly Refinement (I-TASSER)	Yang et al., 201576	https://zhanggroup.org/I-TASSER/
UCSF Chimera	Pettersen et al., 200477	https://www.cgl.ucsf.edu/chimera/
Cysteine Oxidation Prediction Algorithm (COPA)	Sanchez et al., 200878	N/A
Missense3D	Ittisoponpisan et al., 201979	http://missense3d.bc.ic.ac.uk/
DUET	Pires et al., 201480	http://structure.bioc.cam.ac.uk/duet
GraphPad Prism 6	Dotmatics	https://www.graphpad.com/dl/96314/10B92408/