T-box Riboswitch Annotation Database - TBDB - HKSRLLT from

T-box riboswitch HKSRLLT

Putative LEU (AAG) T-box riboswitch from Listeria grayi DSM 20601

Source information

TBDB ID	HKSRLLT
Host organism	Listeria grayi DSM 20601
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	ACCR02000005.1:996802-996557
Downstream protein description	leucine--tRNA ligase
Downstream protein ID	GenBank: EFI83829.1
T-box riboswitch length
Specifier loop sequence	ACUUG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	CUU
Predicted tRNA family	LEU (AAG)
Found cognate tRNA	False
Alternative specifiers	UUG
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence HKSRLLT AAATTGGCGTTGAAGAGGAGTAGTAATCTTATAAGTGGATGAGAAGAGAGTCAGCGGGTGGTGCAAGCTGAACATCGACTAAGATGAACTTGCCTTGGAGCTGGGCATTGCCCCGTTTTCCGCGTTAAGGAAAAATAAGTTGAGTGGTAAAACACTAATGTGGGTGGTACCGCGGGAGATGTCTCTCGTCCCATGGCCGAAGGAAGGCTATGAGATGGAGGGCTTTTTTT

Predicted secondary structures

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

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

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CUU
Top predicted tRNA family: LEU (AAG)

Best tRNA match for top specifier >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 1

Alternative 1 for predicted specifier: UUG
Alternative 1 for predicted tRNA family: LEU (CAA)

Best tRNA match for alternative specifier 1 >LEU (CAA) tRNA from Listeria grayi DSM 20601
GCCGGCGTGGCGGAATTGGCAGACGCGCTGGACTCAAAATCCAGTGCCCGTTAAGGGCGTGCCGGTTCGACCCCGGCCGCCGGTACCA

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

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)	-12.6
Terminator	ΔG° (kcal/mol	-20.0
	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	113.4
Bias	0.0
CM Accuracy	0.94

*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		[7,101]
Stem II region
Stem III
Specifier region	-	[88,90]
T-box UGGN locus	-	[165,168]
Antiterminator		[161,193]
Terminator		[182,230]
All stems	-	[[7, 101], [104, 112], [114, 124], [143, 156], [161, 193]]

Input source sequence >ACCR02000005.1:996802-996557
AAATTGGCGTTGAAGAGGAGTAGTAATCTTATAAGTGGATGAGAAGAGAGTCAGCGGGTGGTGCAAGCTGAACATCGACTAAGATGAACTTGCCTTGGAGCTGGGCATTGCCCCGTTTTCCGCGTTAAGGAAAAATAAGTTGAGTGGTAAAACACTAATGTGGGTGGTACCGCGGGAGATGTCTCTCGTCCCATGGCCGAAGGAAGGCTATGAGATGGAGGGCTTTTTTTATGCAGAAAATGAAAG

INFERNAL output sequence >Infernal-ACCR02000005.1:996802-996557
AAAUUGGCGUUGAAGAGGAGUAGUAAUCUUAUAAGUGGAUGAGAAGAGAGUCAGCGGGUGGUGCAAGCUGAACAUCGA-CUAAGAUGAA-CUUGCCUUGGAGCUGGGCA*[ 1]*UGCCCCGUUUU-CCGCGUUA-AGGAAAAAUAAGUUGAGUGGUA--------AAACACUAAUGUGGGUGGUACCGCGGGAgAUGUcUCUCGUCCCAUGG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-ACCR02000005.1:996802-996557
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<~~~~~~>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_.____._>>>>>>>>>:::