T-box Riboswitch Annotation Database - TBDB - YYLA93A2 from - Lactobacillus apodemi DSM 16634 = JCM 16172

T-box riboswitch YYLA93A2

Putative VAL (UAC) T-box riboswitch from Lactobacillus apodemi DSM 16634 = JCM 16172

Source information

TBDB ID	YYLA93A2
Host organism	Lactobacillus apodemi DSM 16634 = JCM 16172
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	AZFT01000053.1:867549-867291
Downstream protein description	valyl-tRNA synthetase
Downstream protein ID	GenBank: KRL84170.1
T-box riboswitch length
Specifier loop sequence	AGUAG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	GUA
Predicted tRNA family	VAL (UAC)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Full

Genomic Context

Error loading NCBI Genome Browser - Cookies disabled To use the NCBI genome browser for visualizing genetic context of T-box riboswitch sequences, please enable cookies on your web browser.

Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence YYLA93A2 TTATAAGCTTTGAACAAGAGGATTTGACCAGGGACTGTTTTTAGAGAGAAGCGGGTCGGTGCAACGCTTTAGCAGTTGGTCAAAGAGTAGCTTGGGAGCTGTCCTACTGAAATTTTTAGTAAGTAAGACCGGATATCTATTCGTTAACGCAGATCAAAGAGGGGATAAAAGCCCAATTTAGGTGGTACCACGGCACTGTCGTCCTAAGCGGATGGCAGTGCTTTTTT

Predicted secondary structures

T-box riboswitch YYLA93A2 Antiterminator ......((......((((....((((((........(((........((((((...........))))))))).....))))))......))))...))..((.((((.............)))).)).(((........)))..................(((.(...).)))....((((.......(((((...))))))))).....................

T-box riboswitch YYLA93A2 Terminator ......((......((((....((((((........(((........((((((...........))))))))).....))))))......))))...))..((.((((.............)))).)).(((........)))..................(((.(...).)))..................((((((((((((.....))))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: GUA
Top predicted tRNA family: VAL (UAC)

Best tRNA match for top specifier >VAL (UAC) tRNA from Lactobacillus apodemi DSM 16634 = JCM 16172
GGAGGATTAGCTCAGTTGGGAGAGCGTCTGCCTTACAAGCAGAGGGTCACAGGTTCGAGCCCTGTATCCTCCACCA

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)	-5.1
Terminator	ΔG° (kcal/mol	-21.1
	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	115.1
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		[7,99]
Stem II region
Stem III
Specifier region	-	[86,88]
T-box UGGN locus	-	[183,186]
Antiterminator		[179,206]
Terminator		[193,227]
All stems	-	[[7, 99], [102, 128], [130, 143], [162, 174], [179, 206]]

Input source sequence >AZFT01000053.1:867549-867291
TTATAAGCTTTGAACAAGAGGATTTGACCAGGGACTGTTTTTAGAGAGAAGCGGGTCGGTGCAACGCTTTAGCAGTTGGTCAAAGAGTAGCTTGGGAGCTGTCCTACTGAAATTTTTAGTAAGTAAGACCGGATATCTATTCGTTAACGCAGATCAAAGAGGGGATAAAAGCCCAATTTAGGTGGTACCACGGCACTGTCGTCCTAAGCGGATGGCAGTGCTTTTTT

INFERNAL output sequence >Infernal-AZFT01000053.1:867549-867291
UUAUAAGCUUUGAACAAG---AGGAUUUGACCAGgGACUGUUUUUAGAGAGAAGCGGGUCGGUGCAACGCUUUAGCAGUUGGUCAAAGA--GUAGCUUGGGAGCUGUCCUACUGAAAUUUUUAGUAAGUAAGACCGGAUAUcuAUUCGUUA-ACGCAGAUCAAAGAGGGGAU---------AAAAGCCCAAUUUAGGUGGUACCACGGC--ACU-GUCGUCCUAAGC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AZFT01000053.1:867549-867291
::::::<<------<<<<-------<<<<<<---.----<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<____..__>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::