T-box Riboswitch Annotation Database - TBDB - J4VCYTXV from

T-box riboswitch J4VCYTXV

Putative GLY (GCC) T-box riboswitch from Tetragenococcus koreensis

Source information

TBDB ID	J4VCYTXV
Host organism	Tetragenococcus koreensis
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP027786.1:1033053-1032701
Downstream protein description	glycine--tRNA ligase subunit alpha
Downstream protein ID	GenBank: AYW45319.1
T-box riboswitch length
Specifier loop sequence	AGGCA
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 J4VCYTXV AATCGTGCGATGATCATTTAAAGGAAAAGAACAACTTCTCTTAGCGAGTTTGGGAAAGTGTGAGCCAGACAGAAGAACTTTGACCACAGGCAATTGTGAGCACAATTAAAAAGCTGCCGATAATTGGATCGGAAGTAGGGTGGAACCGCGAAATTATTCGTCCCTATATCTATGCAAAGGATGTATAGATATAGGGACTTTTTT

Predicted secondary structures

T-box riboswitch J4VCYTXV Antiterminator ......((......((.(.......(((........(((........((((((...........))))))))).....)))...........).))...))...............(((((......)))))....((((.......(((((....))))))))).......................................

T-box riboswitch J4VCYTXV 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 Tetragenococcus koreensis
GCGGAAATAGCTCAGCGGTAGAGCACCACCTTGCCAAGGTGGGGGTCGCGGGTTCGAATCCCGTTTTCCGCTCCA

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)	-6.7
Terminator	ΔG° (kcal/mol	-26.6
	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	50.5
Bias	0.0
CM Accuracy	0.88

*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		[80,174]
Stem II region
Stem III
Specifier region	-	[161,163]
T-box UGGN locus	-	[214,217]
Antiterminator		[210,238]
Terminator		[233,277]
All stems	-	[[80, 174], [190, 205], [210, 238]]

Input source sequence >CP027786.1:1033053-1032701
ATTGAAGTATTTCAGAAAATTTCACTTTTTATTTGACAAATGACTACTTTTACTACTATGATAGTAGTAATTAAATCGTGCGATGATCATTTAAAGGAAAAGAACAACTTCTCTTAGCGAGTTTGGGAAAGTGTGAGCCAGACAGAAGAACTTTGACCACAGGCAATTGTGAGCACAATTAAAAAGCTGCCGATAATTGGATCGGAAGTAGGGTGGAACCGCGAAATTATTCGTCCCTATATCTATGCAAAGGATGTATAGATATAGGGACTTTTTTATCGCAAATTTGAGAGGAGCAAAAAAATGGCAAAAAAAATTACTTTACAAGAAATGATTTTACGCTTGCAGAAATA

INFERNAL output sequence >Infernal-CP027786.1:1033053-1032701
AAUCGUGCGAUGAUCAUUUAAAGGAAAAGAACA--ACUUCUCUUAGCGAGUUUGGGAA-AGUGUGAgCCAGACAGAAGAAC---UUUGACCacaGGCAAUUGUGAGCAC*[ 2]*UUA--------AAAAGCUGCCGAUAA------UUGGAUCGGAAGUAGGGUGGAACCGCGAA-AUUA-UUCGUCCCUAUA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP027786.1:1033053-1032701
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>----->>>>>>----...---->>>>--->>,,~~~~~~,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::