T-box Riboswitch Annotation Database - TBDB - 8F4TEOJH from

T-box riboswitch 8F4TEOJH

Putative LEU (GAG) T-box riboswitch from Caldibacillus debilis

Source information

TBDB ID	8F4TEOJH
Host organism	Caldibacillus debilis
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	LQYT01000092.1:122-401
Downstream protein description	Leucyl-tRNA synthetase
Downstream protein ID	GenBank: KYD12455.1
T-box riboswitch length
Specifier loop sequence	ACUCG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	CUC
Predicted tRNA family	LEU (GAG)
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 8F4TEOJH CCAAAGGCTGTGAAAAGGAGCAGTAGCAGGCGGATTCCCGTCACAGAGAGCCGGCGGTCGGTGCAAGCCGGACGGTTACGCTTGCGAACTCGCCTTGGAGCCGCAAATGCGAAGGGAAGTAGCATTTGCCGCATCCCTGCGTTACGGGCAATGAAGGGAACGCCGTCCCTGAATATTCAGGAGGCGTTAATTTGGGTGGTACCGCGGGAGATTCGCCTCCCGTCCCAAGGTTATTGGGACGGGAGGTTTTTGTTTTT

Predicted secondary structures

T-box riboswitch 8F4TEOJH Antiterminator ......((......((((.......((((((.......(((.........(((((...........)))))))).....)))))).......))))...))..(((((((...........))))))).(((......))).................((((((..................))))))....((((.......(((((((......)))))))))))..............................

T-box riboswitch 8F4TEOJH Terminator ......((......((((.......((((((.......(((.........(((((...........)))))))).....)))))).......))))...))..(((((((...........))))))).(((......))).................((((((..................))))))...........................(((((((((((((.....)))))))))))))...........

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CUC
Top predicted tRNA family: LEU (GAG)

Best tRNA match for top specifier >LEU (GAG) tRNA from Caldibacillus debilis
GCGGTCGTGGCGGAATGGCAGACGCGCTAGGTTGAGGGCCTAGTGGTGGCAACACCGTGGAGGTTCAAGTCCTCTCGGCCGCACCA

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)	-16.0
Terminator	ΔG° (kcal/mol	-27.6
	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	130.8
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	-	[197,200]
Antiterminator		[193,227]
Terminator		[216,257]
All stems	-	[[7, 101], [104, 128], [130, 141], [159, 188], [193, 227]]

Input source sequence >LQYT01000092.1:122-401
CCAAAGGCTGTGAAAAGGAGCAGTAGCAGGCGGATTCCCGTCACAGAGAGCCGGCGGTCGGTGCAAGCCGGACGGTTACGCTTGCGAACTCGCCTTGGAGCCGCAAATGCGAAGGGAAGTAGCATTTGCCGCATCCCTGCGTTACGGGCAATGAAGGGAACGCCGTCCCTGAATATTCAGGAGGCGTTAATTTGGGTGGTACCGCGGGAGATTCGCCTCCCGTCCCAAGGTTATTGGGACGGGAGGTTTTTGTTTTT

INFERNAL output sequence >Infernal-LQYT01000092.1:122-401
CCAAAGGCUGUGAAAAGGAGCAGUAGCAGGCGGAUUCCCGUCACAGAGAGCCGGCGGUCGGUGCAAGCCGG-ACGGUUACGCUUGCGAA-CUCGCCUUGGAGCCGCAAAUGCGAA--GGGAAGUAGCAUUUGCCGCAUCCCUGCGUUA--CGGGCAAUGAAGGGAACGCCGUCCcugaauauUCAGGAGGCGUUAAUUUGGGUGGUACCGCGGGAgAUUCgccUCCCGUCCCAAGG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-LQYT01000092.1:122-401
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<___........_____>>>>>>>,,,,<<<<-------<<<<<_.____..._>>>>>>>>>:::