T-box Riboswitch Annotation Database - TBDB - RMB1LX9O from

T-box riboswitch RMB1LX9O

Putative ILE (GAU) T-box riboswitch from Staphylococcus aureus RF122

Source information

TBDB ID	RMB1LX9O
Host organism	Staphylococcus aureus RF122
Model used	Class I
Predicted regulation	Unknown
T-box riboswitch genomic accession	AJ938182.1:1138087-1138309
Downstream protein description	isoleucyl-tRNA synthetase
Downstream protein ID	ENA: CAI80746.1
T-box riboswitch length
Specifier loop sequence	UAUCA
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AUC
Predicted tRNA family	ILE (GAU)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Partial

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence RMB1LX9O AAATAAAGACAGACGCGTAATATACATTTAACTTTTCACAGCGAATTAGGTCATGGTGAGAGCCTAGTAAAAGCATGTATGTTATATCACTGGCTTTTTAATATTTAAATAATGTAATGAGAGAACTCTAAGTTGAGTTAATAAGGGTGGTACCGCGAGCAATCGTCCCTTTTAATTTAACTTAGAGTTTTTT

Predicted secondary structures

T-box riboswitch RMB1LX9O Antiterminator ......((.(((.......((((((........(((........((((((............))))))))).....)))))).......))).))............................(((((......)))))....((((.......((((....)))))))).......................

T-box riboswitch RMB1LX9O Terminator Error: TBDB structure refinement failed to predict a terminator structure for this T-box

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AUC
Top predicted tRNA family: ILE (GAU)

Best tRNA match for top specifier >ILE (GAU) tRNA from Staphylococcus aureus RF122
GGGCCTATAGCTCAGCTGGTTAGAGCGCACGCCTGATAAGCGTGAGGTCGGTGGTTCGAGTCCACTTAGGCCCACCA

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)	-6.1
Terminator	ΔG° (kcal/mol	-3.2
	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	70.1
Bias	0.2
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		[7,95]
Stem II region
Stem III
Specifier region	-	[85,87]
T-box UGGN locus	-	[148,151]
Antiterminator		[144,170]
Terminator		[155,193]
All stems	-	[[7, 95], [124, 139], [144, 170]]

Input source sequence >AJ938182.1:1138087-1138309
AAATAAAGACAGACGCGTAATATACATTTAACTTTTCACAGCGAATTAGGTCATGGTGAGAGCCTAGTAAAAGCATGTATGTTATATCACTGGCTTTTTAATATTTAAATAATGTAATGAGAGAACTCTAAGTTGAGTTAATAAGGGTGGTACCGCGAGCAATCGTCCCTTTTAATTTAACTTAGAGTTTTTTAAATTTTTAAGGAGTGAAAAAAATGGATTA

INFERNAL output sequence >Infernal-AJ938182.1:1138087-1138309
AAAUAAAG------ACAGACGCGUAAUAUACAUUuAACUUUUCACAGCGAAUUAGGUCAUGGUGAGAgCCUAGUAAAAGCAUGUAUGUUAU-AUCACUGG---CUUU*[ 4]**[ 3]*UUAAAUAAUGUAAUGAGAGAACUCUA------AGUUGAGUUAAUAAGGGUGGUACCGCGA--GCAA--UCGUCCCUUUU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AJ938182.1:1138087-1138309
::::::<<------<<<<-------<<<<<<---.----<<<--------<<<<<<___________.>>>>>>>>>----->>>>>>-------->>>>--->>,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::