T-box Riboswitch Annotation Database - TBDB - 5VA4MQ8 from

T-box riboswitch 5VA4MQ8

Putative TRP (CCA) T-box riboswitch from Lactobacillus rennini DSM 20253

Source information

TBDB ID	5VA4MQ8
Host organism	Lactobacillus rennini DSM 20253
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	AYYI01000017.1:11910-12164
Downstream protein description	tryptophanyl-tRNA synthetase II
Downstream protein ID	GenBank: KRM99276.1
T-box riboswitch length
Specifier loop sequence	GUGGG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	UGG
Predicted tRNA family	TRP (CCA)
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 5VA4MQ8 GGCAACACGTTGAAAGGGAAAGTAACTGCCAGCAACCAGTTTTCAGCGAGCCGTTGGTAGGTGTGAAACGGCACTGTCTGCAGTGAGTGGGCCCTTGAGTGCAATGATGAAAATTAGTAATGATTGCGGTGGTTGCGCCTTAAGCAAAAGTGGTGTCGAAAAACGGCACAATTTAGGTGGTACCACGACATTTGGCGTCCTATTGATAGCAATATCAATAGGACCTTTTTT

Predicted secondary structures

T-box riboswitch 5VA4MQ8 Antiterminator ......((......((((......(((((........(((.........((((((...........)))))))))....))))).......))))...)).((((.((...........)).)))).(((......))).............((((((.....))))))....((((.......(((.(....).))))))).............................

T-box riboswitch 5VA4MQ8 Terminator ......((......((((......(((((........(((.........((((((...........)))))))))....))))).......))))...)).((((.((...........)).)))).(((......))).............((((((.....))))))...........................((((((((((((....)))))))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UGG
Top predicted tRNA family: TRP (CCA)

Best tRNA match for top specifier >TRP (CCA) tRNA from Lactobacillus rennini DSM 20253
AGGGATATAGTTCAATGGTAGAATAGCGGTCTCCAAAACCGTAGATGTGGGTTCAACTCCTACTATCCCTGCCA

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)	-5.2
Terminator	ΔG° (kcal/mol	-16.9
	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	116.9
Bias	0.0
CM Accuracy	0.96

*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		[7,100]
Stem II region
Stem III
Specifier region	-	[87,89]
T-box UGGN locus	-	[178,181]
Antiterminator		[174,202]
Terminator		[197,231]
All stems	-	[[7, 100], [102, 126], [128, 139], [153, 169], [174, 202]]

Input source sequence >AYYI01000017.1:11910-12164
GGCAACACGTTGAAAGGGAAAGTAACTGCCAGCAACCAGTTTTCAGCGAGCCGTTGGTAGGTGTGAAACGGCACTGTCTGCAGTGAGTGGGCCCTTGAGTGCAATGATGAAAATTAGTAATGATTGCGGTGGTTGCGCCTTAAGCAAAAGTGGTGTCGAAAAACGGCACAATTTAGGTGGTACCACGACATTTGGCGTCCTATTGATAGCAATATCAATAGGACCTTTTTT

INFERNAL output sequence >Infernal-AYYI01000017.1:11910-12164
GGCAACACGUUGAAAGGG-AAAGUAACUGCCAGCAACCAGUUUuCAGCGAGCCGUUGGUAGGUGUGAAACGGCACUGU--CUGCAGUGAG-UGGGCCCUUGAGU-GCAAUGAUGAA--AAUUAGUAAUGAUUGCGGUGGUUGCGCCUUA------AGCAAAAGUGGUGUCGA-----AAAACGGCACAAUUUAGGUGGUACCACGAC-AUU-UGGCGUCCUAUUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AYYI01000017.1:11910-12164
::::::<<------<<<<-------<<<<<<-------<<<--.------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::