T-box Riboswitch Annotation Database - TBDB - STJAPP6B from

T-box riboswitch STJAPP6B

Putative GLY (GCC) T-box riboswitch from Thermincola potens JR

Source information

TBDB ID	STJAPP6B
Host organism	Thermincola potens JR
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP002028.1:2477805-2477546
Downstream protein description	glycyl-tRNA synthetase, alpha subunit
Downstream protein ID	GenBank: ADG83243.1
T-box riboswitch length
Specifier loop sequence	AGGCG
T-box 5'-UGGN-3' sequence	UGGA
Predicted specifier	GGC
Predicted tRNA family	GLY (GCC)
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 STJAPP6B TGTTGCGTGATGAGGGAGAAAGTAGCCGTATGTTTACTGCCAAGAGAGCCGGTGGTGGTGGAAATCCGGCCAGAGGCATACGGGGAAAGGCGCTCCTGAACGGCAGGAGGAAAGGGCCCTGGCCTGAGTAAAGCCTGCAGAAAAGAAAGTGGGTCAATGTTTTTTTGGCCAAGCAGGGTGGAACCGCGGGAAATTCCTCTCGTCCCTGGCAATTTGCCGGGGATGGGAGGTTTTTTT

Predicted secondary structures

T-box riboswitch STJAPP6B Antiterminator ......((......((((.......(((((......(((........(((((.............)))))))).....))))).........))))...))..(.((.(.......).)).)...(........)................((((((.......))))))....((((.......((((((......))))))))))..............................

T-box riboswitch STJAPP6B Terminator ......((......((((.......(((((......(((........(((((.............)))))))).....))))).........))))...))..(.((.(.......).)).)...(........)................((((((.......)))))).........................((((((((((((((((...)))))))))))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: GGC
Top predicted tRNA family: GLY (GCC)

Best tRNA match for top specifier >GLY (GCC) tRNA from Thermincola potens JR
GCGGAAGTGGCTCAGTGGTAGAGCATCGCCTTGCCAAGGCGAGGGTCGCGGGTTCGAATCCCGTCTTCCGCTCCA

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)	-9.8
Terminator	ΔG° (kcal/mol	-30.3
	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	89.2
Bias	0.0
CM Accuracy	0.86

*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	-	[179,182]
Antiterminator		[175,207]
Terminator		[196,237]
All stems	-	[[7, 101], [104, 122], [125, 136], [152, 170], [175, 207]]

Input source sequence >CP002028.1:2477805-2477546
TGTTGCGTGATGAGGGAGAAAGTAGCCGTATGTTTACTGCCAAGAGAGCCGGTGGTGGTGGAAATCCGGCCAGAGGCATACGGGGAAAGGCGCTCCTGAACGGCAGGAGGAAAGGGCCCTGGCCTGAGTAAAGCCTGCAGAAAAGAAAGTGGGTCAATGTTTTTTTGGCCAAGCAGGGTGGAACCGCGGGAAATTCCTCTCGTCCCTGGCAATTTGCCGGGGATGGGAGGTTTTTTTAATTGGCAATTGATAGTTGACAA

INFERNAL output sequence >Infernal-CP002028.1:2477805-2477546
UGUUGCGUGAUGAGGGAG-AAAGUAGCCGUAUG-UUUACUGCCAAGAGAGCCGGUGGU-GGUGGAAaUCCGGCCAGAGGCAUACGGGGAAAGGCGCUCCUGAACGG-CAGGAGGAA------AGGGCCCUGGCCUGAGUAAAGCCUG----CAGAAAAGAAAGUGGGUCAAU---GUUUUUUUGGCCAAGCAGGGUGGAACCGCGGGAAAUUccUCUCGUCCCUGGC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP002028.1:2477805-2477546
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_____.._>>>>>>>>>:::