T-box Riboswitch Annotation Database - TBDB - 0H9UAQWR from

T-box riboswitch 0H9UAQWR

Putative GLY (GCC) T-box riboswitch from Paenibacillus durus

Source information

TBDB ID	0H9UAQWR
Host organism	Paenibacillus durus
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP009288.1:4429845-4429301
Downstream protein description	glycine--tRNA ligase alpha subunit
Downstream protein ID	GenBank: AIQ13951.1
T-box riboswitch length
Specifier loop sequence	CGGCA
T-box 5'-UGGN-3' sequence	UGGA
Predicted specifier	GGC
Predicted tRNA family	GLY (GCC)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence 0H9UAQWR GCACGCATGTAGAACGGGAAAGTAGTGAACGATTGCTTGGCATAGCGAGCCGGGGATGGTGAGAGCCCGGTAAAGCAGCGCTCATGAAACGGCACCCGGGAGTGCGGAGGCGGCAGCATGAAAAGTGGATTTCGTCAGCACCGGCAGCAGTCAGTGAAGAACGGAATCAAGTAGGGTGGAACCGCGGGAGAACATGATTGCTCTCGTCCCTATGTCTGAATTTCAGGCATGGGGGCGGGAGTTTTTT

Predicted secondary structures

T-box riboswitch 0H9UAQWR Antiterminator ......((......((((......((((.(.......(..........((((((...........))))))..).....).)))).........))))...))........................(((((((...........................)))))))....((((.......(((((((..((....)))))))))))))....................................

T-box riboswitch 0H9UAQWR Terminator ......((......((((......((((.(.......(..........((((((...........))))))..).....).)))).........))))...))........................(((((((...........................)))))))................................(((((((((((((((((((...)))))))))))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: GGC
Top predicted tRNA family: GLY (GCC)

Best tRNA match for top specifier >GLY (GCC) tRNA from Paenibacillus durus
GCGGACGTGGCTCAGCGGTAGAGCATCGCCTTGCCAAGGCGAGGGTCGCGGGTTCGATTCCCGTCGTCCGCTCCA

Predicted tRNA structure (((((((..((((.......)))).(((((.......))))).....(((((.......))))))))))))....

Alternative specifier 1

Alternative 1 for predicted specifier: -
Alternative 1 for predicted tRNA family: -

Best tRNA match for alternative specifier 1 >TBDB tRNA pairing failed
tRNAscan-SE failed to find tRNA in host organism with anticodon matching predicted T-box specifier.

Predicted tRNA structure No tRNA structure predicted.

Alternative specifier 2

Alternative 2 for predicted specifier: -
Alternative 2 for predicted tRNA family: -

Best tRNA match for alternative specifier 2 >TBDB tRNA pairing failed
tRNAscan-SE failed to find tRNA in host organism with anticodon matching predicted T-box specifier.

Predicted tRNA structure No tRNA structure predicted.

Minimum Free Energy (MFE) Calculations

Folding MFE predictions

Antiterminator	ΔG° (kcal/mol)	-11.7
Terminator	ΔG° (kcal/mol	-33.2
	ΔΔG° (kcal/mol)

*Calculations performed using Vienna RNAeval at 37°C. More information available on methods avaialble on BioRXIV.

INFERNAL T-box riboswitch prediction output

Infernal prediction values

E-Value
Score	66.8
Bias	0.2
CM Accuracy	0.92

*More information about the meaning of these values can be found here.

T-box riboswitch structure prediction from input sequence

Feature	Length	Locus
Stem I		[106,202]
Stem II region
Stem III
Specifier region	-	[189,191]
T-box UGGN locus	-	[276,279]
Antiterminator		[272,310]
Terminator		[300,346]
All stems	-	[[106, 202], [227, 267], [272, 310]]

Input source sequence >CP009288.1:4429845-4429301
CGAAATCCGAATTTTCCGTTAATATAGGAGCAGTCTCTTCTTGTTGGAGTATGCCTGATTAAAGGCAAATAACGAGAGGATCGCCGCTGGCTGAAGTCGGCACGCATGTAGAACGGGAAAGTAGTGAACGATTGCTTGGCATAGCGAGCCGGGGATGGTGAGAGCCCGGTAAAGCAGCGCTCATGAAACGGCACCCGGGAGTGCGGAGGCGGCAGCATGAAAAGTGGATTTCGTCAGCACCGGCAGCAGTCAGTGAAGAACGGAATCAAGTAGGGTGGAACCGCGGGAGAACATGATTGCTCTCGTCCCTATGTCTGAATTTCAGGCATGGGGGCGGGAGTTTTTTGGTCTGGAACGAAAGAACATTTCTTCTTCATTCCGGAATATATAAACACCGCCTCCATCGCAATAGCGCTTTGCCGGGTTTATTCTCTCAGGCTCAAAGCCTGCAGCGAAATCCGGCTGCTCTCAAACTTAAGCGAAGGAGTCGGTAACATGAATTTTCAGCAGATGATTTTGACGCTGCAAGAGTTCTGGTCGAAGCA

INFERNAL output sequence >Infernal-CP009288.1:4429845-4429301
GCACGCAUGUAGAACGGG-AAAGUAGUGAACGAUUGCUUGGCAUAGCGAGCCGGGGAU-GGUGAGAgCCCGGUAAAGCAGCGCUCAUGAAAcGGCACCCGGGAGUGC*[ 3]**[ 5]*-CA----GCAUGAAAAGUGGAUUUCGUCAgcaccggcagcagucagugAAGAACGGAAUCAAGUAGGGUGGAACCGCGGGAga-ACAugauugcUCUCGUCCCUAUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP009288.1:4429845-4429301
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>----->>>>>>----.---->>>>--->>,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,<<<<<<<___..................._____>>>>>>>,,,,<<<<-------<<<<<_..____......._>>>>>>>>>:::