T-box Riboswitch Annotation Database - TBDB - S6VDOJ from

T-box riboswitch S6VDOJ

Putative VAL (UAC) T-box riboswitch from Lachnoclostridium sp. An131

Source information

TBDB ID	S6VDOJ
Host organism	Lachnoclostridium sp. An131
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	NFLI01000018.1:75615-75339
Downstream protein description	valine--tRNA ligase
Downstream protein ID	GenBank: OUQ24278.1
T-box riboswitch length
Specifier loop sequence	GGUAG
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

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence S6VDOJ GAAAAGGCATGGAAGAAGAGGAGTACGCAGGCAGGCGTCACACAGAGAGGGCGGCCCATGGCTGAAAGGCTGCCGGGGAAGAGTCGTTTGCGGAAGGTAGCTTTGGAGCCGGGACGGTGAAAGAGGAGTAGCCGTTCACGCCTGACCAGCGTTAACGGGTAAAGAGATACGCGGGTTCGTCCGCGTATGAAGTAAGGTGGTACCGCGTGCTGACTGACGCCCTTTCGACAGAAGGGGCGTCTTTATTTTT

Predicted secondary structures

T-box riboswitch S6VDOJ Antiterminator ......((......((((.......((((((......((...........((((((...........))))))....)).......))))))........))))...))..(((((((............))))))).(((.......)))...............(((((((........))))))).....((((.......((((........))))))))..........................

T-box riboswitch S6VDOJ 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 Lachnoclostridium sp. An131
GGGATCTTAGCTCAGCTGGGAGAGCATCTGCCTTACAAGCAGAGGGTCATAGGTTCGAGCCCTATAGGTCCCACCA

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)	-5.3
Terminator	ΔG° (kcal/mol	-20.9
	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	103.7
Bias	1.0
CM Accuracy	0.89

*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		[7,109]
Stem II region
Stem III
Specifier region	-	[96,98]
T-box UGGN locus	-	[198,201]
Antiterminator		[194,224]
Terminator		[216,250]
All stems	-	[[7, 109], [112, 137], [139, 151], [167, 188], [194, 224]]

Input source sequence >NFLI01000018.1:75615-75339
GAAAAGGCATGGAAGAAGAGGAGTACGCAGGCAGGCGTCACACAGAGAGGGCGGCCCATGGCTGAAAGGCTGCCGGGGAAGAGTCGTTTGCGGAAGGTAGCTTTGGAGCCGGGACGGTGAAAGAGGAGTAGCCGTTCACGCCTGACCAGCGTTAACGGGTAAAGAGATACGCGGGTTCGTCCGCGTATGAAGTAAGGTGGTACCGCGTGCTGACTGACGCCCTTTCGACAGAAGGGGCGTCTTTATTTTT

INFERNAL output sequence >Infernal-NFLI01000018.1:75615-75339
GAAAAGGCAUGGAAGAAGAGGAGUACGCAGGCA-GGCGUCACACAGAGAggGCGGCCCAUGGCUGAAAGGCUGCcggGGAAGAguCGUUUGCGGAAGGUAGCUUUGGAGCCGGGACGGUGAA-AGAGGAGUAGCCGUUCACGCCUGAcCAGCGUUA----ACGGGUAAAGAGAUACGCGGGUUCGUCCGCGUAUgAAGUAAGGUGGUACCGCGUGCUGACUGACGCCCUUUCG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-NFLI01000018.1:75615-75339
::::::<<------<<<<-------<<<<<<-------<<<--------..<<<<<<___________>>>>>>...>>>---..-->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<____.__>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>.,,,,<<<<-------<<<<<______>>>>>>>>>:::