T-box Riboswitch Annotation Database - TBDB - O6DRYECQ from

T-box riboswitch O6DRYECQ

Putative MET (CAU) T-box riboswitch from Clostridium tyrobutyricum

Source information

TBDB ID	O6DRYECQ
Host organism	Clostridium tyrobutyricum
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP038158.1:3039898-3039487
Downstream protein description	Methionine-tRNA ligase
Downstream protein ID	GenBank: QCH29425.1
T-box riboswitch length
Specifier loop sequence	UAUGG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AUG
Predicted tRNA family	MET (CAU)
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 O6DRYECQ AAAAATGCAATGAAGGAAAGAGTAATAAATCAAGGGTTCAGGAGAGAGTCAGTGCATGGTGAAAACTGATGAGATATTGATTTATGAATATGGCTCTGGAGCATATTATCTGAAGATATATTAGGGTAATCCGGATTTACAGGCGTTATACTGTATAGTGATTTAAATTACTTAGTGAGATTTTTACTGTGAGGTAAAAATGAAATAGAGTGGTAAAGTGTTATTGTATGCCTCTATATGGATATGTTATATCTATATAGAGGTTTTTT

Predicted secondary structures

T-box riboswitch O6DRYECQ Antiterminator ......((......(((.......((((((......(((........((((((...........)))))))))......)))))).........)))...))..(((((((............))))))).((..........))..................................(((((((........))))))).....((((.......((((......))))))))..................................

T-box riboswitch O6DRYECQ Terminator ......((......(((.......((((((......(((........((((((...........)))))))))......)))))).........)))...))..(((((((............))))))).((..........))..................................(((((((........))))))).............................(((((((((((((((...)))))))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AUG
Top predicted tRNA family: MET (CAU)

Best tRNA match for top specifier >MET (CAU) tRNA from Clostridium tyrobutyricum
CGCGGGGTGGAGCAGTTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGCAGGTTCAAATCCTGCCTCCGCAACCA

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)	-1.4
Terminator	ΔG° (kcal/mol	-18.9
	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	92.8
Bias	19.2
CM Accuracy	0.95

*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		[46,141]
Stem II region
Stem III
Specifier region	-	[128,130]
T-box UGGN locus	-	[250,253]
Antiterminator		[246,274]
Terminator		[270,308]
All stems	-	[[46, 141], [144, 169], [171, 184], [219, 240], [246, 274]]

Input source sequence >CP038158.1:3039898-3039487
ATATTGACAGACTGAAATATATAATTTATTATGTTACTGAAAAATGCAATGAAGGAAAGAGTAATAAATCAAGGGTTCAGGAGAGAGTCAGTGCATGGTGAAAACTGATGAGATATTGATTTATGAATATGGCTCTGGAGCATATTATCTGAAGATATATTAGGGTAATCCGGATTTACAGGCGTTATACTGTATAGTGATTTAAATTACTTAGTGAGATTTTTACTGTGAGGTAAAAATGAAATAGAGTGGTAAAGTGTTATTGTATGCCTCTATATGGATATGTTATATCTATATAGAGGTTTTTTATTGTCAGTATTATAAAAATAATCCATTAAACAAATGTAAAAGGAAAGGAAGTAATGGAAGTGAATAAAAAAACTTATTATATTACAACACCAATTTATTATCC

INFERNAL output sequence >Infernal-CP038158.1:3039898-3039487
AAAAAUGCAAUGAAGGAA-AGAGUAAUAAAUCA-AGGGUUCAGGAGAGAGUCAGUGCAUGGUGAAAACUGAUGAGAUAuUGAUUUAUGAAUAUGGCUCUGGAGCAUAUUAUCUGAA-GAUAUAUUAGGGUAAUCCGGAUUUacAGGCGUUAUacuguauagugauuuAAAUUACUUAGUGAGAUUUUUACUGUGAGGUAAAAAUgAAAUAGAGUGGUAAAGUGUU-AUUG-UAUGCCUCUAUA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP038158.1:3039898-3039487
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<____..__>>>,,,,...............,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>.,,,,<<<<-------<<<<<______>>>>>>>>>:::