T-box Riboswitch Annotation Database - TBDB - Q1OWWVR2 from

T-box riboswitch Q1OWWVR2

Putative PHE (GAA) T-box riboswitch from Halothermothrix orenii H 168

Source information

TBDB ID	Q1OWWVR2
Host organism	Halothermothrix orenii H 168
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP001098.1:611920-612199
Downstream protein description	phenylalanyl-tRNA synthetase, alpha subunit
Downstream protein ID	GenBank: ACL69320.1
T-box riboswitch length
Specifier loop sequence	GUUCC
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	UUC
Predicted tRNA family	PHE (GAA)
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 Q1OWWVR2 ATAAAGGCTATGAAAGAGAGAGTAGTTATCTGAAACCTTTTCAGGGAGAGGTTGTCGTAGACTGGAAGCAACCTTAAGGTGATAGATAATGAAGTTCCCTCTGGAGCTGTGGGCTGAACCTTTAGTAGGCCTTACCGGGAAGCATTTTATTCCCTGCTTTCCGTTATTTAAATAAGTGATCTGTTTTTAGCAGATAATTAGGGTGGTACCACGAATCTCTCGTCCCTTGGGATGAGAGATTTTTT

Predicted secondary structures

T-box riboswitch Q1OWWVR2 Antiterminator ......((......((((......((((((......(((..........((((((............))))))..)))......))))))........))))...))..((((((............)))).)).(((......................)))...............(((((((...)))))))....((((.......((((.....))))))))..................

T-box riboswitch Q1OWWVR2 Terminator ......((......((((......((((((......(((..........((((((............))))))..)))......))))))........))))...))..((((((............)))).)).(((......................)))...............(((((((...)))))))....................((((((((((....))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UUC
Top predicted tRNA family: PHE (GAA)

Best tRNA match for top specifier >PHE (GAA) tRNA from Halothermothrix orenii H 168
GGTGAGATAGCTCAGTTGGTAGAGCAGAGGACTGAAAATCCTCGTGTCGGCAGTTCGATTCTGCCTCTCACCACCA

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)	-5.0
Terminator	ΔG° (kcal/mol	-15.4
	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	116.1
Bias	0.0
CM Accuracy	0.9

*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		[7,107]
Stem II region
Stem III
Specifier region	-	[94,96]
T-box UGGN locus	-	[204,207]
Antiterminator		[200,227]
Terminator		[216,245]
All stems	-	[[7, 107], [110, 134], [136, 163], [179, 195], [200, 227]]

Input source sequence >CP001098.1:611920-612199
ATAAAGGCTATGAAAGAGAGAGTAGTTATCTGAAACCTTTTCAGGGAGAGGTTGTCGTAGACTGGAAGCAACCTTAAGGTGATAGATAATGAAGTTCCCTCTGGAGCTGTGGGCTGAACCTTTAGTAGGCCTTACCGGGAAGCATTTTATTCCCTGCTTTCCGTTATTTAAATAAGTGATCTGTTTTTAGCAGATAATTAGGGTGGTACCACGAATCTCTCGTCCCTTGGGATGAGAGATTTTTTAATGTTTACAGGTATTTAAAGACATAGAAAAGAAG

INFERNAL output sequence >Infernal-CP001098.1:611920-612199
AUAAAGGCUAUGAAAGAG-AGAGUAGUUAUCUG-AAACCUUUUCAGGGAgaGGUUGUCGUAgACUGGAAGCAACCuuAAGGUGaUAGAUAAUGAAGUUCCCUCUGGAGCUGUG-GGCUGAA-CCUUUAGUAGGCCUUACCGGGA*[20]*CCGUUA----UUUAAAUAAGUGAUCUGUU-----UUUAGCAGAUAAUUAGGGUGGUACCACGAA--UCU-CUCGUCCCUUGG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP001098.1:611920-612199
::::::<<------<<<<-------<<<<<<-------<<<--------..<<<<<<____._______>>>>>>..>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<__~~~~~~>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::