T-box Riboswitch Annotation Database - TBDB - UBQHEC8I from - Lactobacillus farraginis DSM 18382 = JCM 14108

T-box riboswitch UBQHEC8I

Putative VAL (UAC) T-box riboswitch from Lactobacillus farraginis DSM 18382 = JCM 14108

Source information

TBDB ID	UBQHEC8I
Host organism	Lactobacillus farraginis DSM 18382 = JCM 14108
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	BAKI01000009.1:68924-69218
Downstream protein description	2-dehydropantoate 2-reductase
Downstream protein ID	DDBJ: GAF36309.1
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	AGU
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence UBQHEC8I AAGAATGCAATGAAGAGGAGAGTAGTTTCGGCAAGTCATTTCAGGGAGTCCTGGTAAGTGAGAAGGGATAATGATTACCGAAACGAAAGTAGCCTTTGAGCAGTAAATGCGAAGTAATGAGTATTTACGGCGCGCACGCCTTAAAGTGCCGGTGTATCGCTGAGTAAAATTGGCCGTACATGACGAGGTAATTTGTGTAAGCAGATTATAAATTAAGGTGGTACCGTGCTTAAAGCGCCCTTGATCTTTACTATAAAAAGATCAGGGGCGCTTTTTT

Predicted secondary structures

T-box riboswitch UBQHEC8I Antiterminator ......((......((((......((((((......(((........(((((...........).)))).))).....))))))........))))...))..(((((((..........))))))).(((......)))...............................................(((((((........))))))).....((((.......(((((...)))))))))...................................

T-box riboswitch UBQHEC8I 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 farraginis DSM 18382 = JCM 14108
GGAGGATTAGCTCAGCTGGGAGAGCATCTGCCTTACAAGCAGGAGGTCACAGGTTCGATCCCTGTATCCTCCACCA

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

Alternative specifier 1

Alternative 1 for predicted specifier: AGU
Alternative 1 for predicted tRNA family: SER (ACU)

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)	-5.4
Terminator	ΔG° (kcal/mol	-25.9
	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	119.1
Bias	0.1
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		[7,101]
Stem II region
Stem III
Specifier region	-	[88,90]
T-box UGGN locus	-	[219,222]
Antiterminator		[215,242]
Terminator		[235,277]
All stems	-	[[7, 101], [104, 127], [129, 140], [188, 209], [215, 242]]

Input source sequence >BAKI01000009.1:68924-69218
AAGAATGCAATGAAGAGGAGAGTAGTTTCGGCAAGTCATTTCAGGGAGTCCTGGTAAGTGAGAAGGGATAATGATTACCGAAACGAAAGTAGCCTTTGAGCAGTAAATGCGAAGTAATGAGTATTTACGGCGCGCACGCCTTAAAGTGCCGGTGTATCGCTGAGTAAAATTGGCCGTACATGACGAGGTAATTTGTGTAAGCAGATTATAAATTAAGGTGGTACCGTGCTTAAAGCGCCCTTGATCTTTACTATAAAAAGATCAGGGGCGCTTTTTT

INFERNAL output sequence >Infernal-BAKI01000009.1:68924-69218
AAGAAUGCAAUGAAGAGG-AGAGUAGUUUCGGC-AAGUCAUUUCAGGGAGUCC-UGGUAAGUGAGAAGGGAUaAUGAUUACCGAAACGAAAGUAGCCUUUGAGCAGUAAAUGCGAA---GUAAUGAGUAUUUACGGCGCGCACGCCUUAAagugccgguguaucgcugaguaaaauugGCCGUACAUGACGAGGUAAUUUGUGUAAGCAGAUUAUAAAuUAAGGUGGUACCGUGCU--UAA-AGCGCCCUUGAU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-BAKI01000009.1:68924-69218
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>.>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,............................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,.,<<<<-------<<<<<______>>>>>>>>>:::