T-box Riboswitch Annotation Database - TBDB - XXPD2UQV from

T-box riboswitch XXPD2UQV

Putative TYR (GUA) T-box riboswitch from Eubacterium hallii CAG:12

Source information

TBDB ID	XXPD2UQV
Host organism	Eubacterium hallii CAG:12
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	FR883579.1:1122-1485
Downstream protein description	tyrosine--tRNA ligase
Downstream protein ID	ENA: CDB18078.1
T-box riboswitch length
Specifier loop sequence	AUACA
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	UAC
Predicted tRNA family	TYR (GUA)
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 XXPD2UQV AGAAAGACGAAGACGGAAACAAGTAGCTTTTATTCATGCATTCCAGAGAGTGATCGGCTGGTGGGAGGTCATATGGCAGATAGTAAGTGAATACATTCCTGAGTTGTACACCGAATGAGACAGATATTTATCATGTTAAGCGTGAGTAGATTTTAGAAATTGCTGAATGTGATGGAACAGGTAAGATTTGTTTTTAGTAGGCTGTGACGGAGCGGCGGCCGTTATCCGCAGAGGCGTTGTTTGACGCTCATTTGAGGCAGAGCATTTACTCTGCGAAAAAAGGTGGTACCACGAAGTTATATCTCGTCCTTTTATTAGGACGGGATTTTTTT

Predicted secondary structures

T-box riboswitch XXPD2UQV Antiterminator ......((......((((.......((((.(.......(((........((((((...........))))))))).......).)))).......))))...))..((((.(........................................................................................).)))).(((........)))...................................((((((......)))))).....((((.......((((.((...)).)))))))).....................

T-box riboswitch XXPD2UQV Terminator ......((......((((.......((((.(.......(((........((((((...........))))))))).......).)))).......))))...))..((((.(........................................................................................).)))).(((........)))...................................((((((......))))))...........................(((((((((......))))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UAC
Top predicted tRNA family: TYR (GUA)

Best tRNA match for top specifier >TYR (GUA) tRNA from Eubacterium hallii CAG:12
GGGTGGATTCCCGAGTGGCCAAAGGGGACAGACTGTAAATCTGCTGCAAATTGCTTCGGTGGTTCGAATCCACCTCCGCCCACCA

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)	-3.6
Terminator	ΔG° (kcal/mol	-14.0
	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	104.2
Bias	0.1
CM Accuracy	0.93

*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		[7,104]
Stem II region
Stem III
Specifier region	-	[91,93]
T-box UGGN locus	-	[284,287]
Antiterminator		[280,311]
Terminator		[302,332]
All stems	-	[[7, 104], [107, 206], [208, 221], [257, 274], [280, 311]]

Input source sequence >FR883579.1:1122-1485
AGAAAGACGAAGACGGAAACAAGTAGCTTTTATTCATGCATTCCAGAGAGTGATCGGCTGGTGGGAGGTCATATGGCAGATAGTAAGTGAATACATTCCTGAGTTGTACACCGAATGAGACAGATATTTATCATGTTAAGCGTGAGTAGATTTTAGAAATTGCTGAATGTGATGGAACAGGTAAGATTTGTTTTTAGTAGGCTGTGACGGAGCGGCGGCCGTTATCCGCAGAGGCGTTGTTTGACGCTCATTTGAGGCAGAGCATTTACTCTGCGAAAAAAGGTGGTACCACGAAGTTATATCTCGTCCTTTTATTAGGACGGGATTTTTTT

INFERNAL output sequence >Infernal-FR883579.1:1122-1485
AGAAAGACGAAGACGGAAACAAGUAGCUUUUAUUCAUGCAUUCCAGAGAGUGAUCGGCUGGUGGGAGGUCAUAUGGCAgaUAGUAAGUGAA-UACAUUCCUGAGUUGUACACCGAAUGagacagauauuuaucauguuaagcgugaguagauuuuagaaauugcugaaugugauggaacagguaagauuugUUUUUAGUAGGCUGUGACGGAGCGgcGGCCGUUAUccgcagaggcguuguuUGACGCUCAUUUGAGGCAGAGC----AUUUACUCUGCgAAAAAAGGUGGUACCACGAAGu-UAUaUCUCGUCCUUUUA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-FR883579.1:1122-1485
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>---..-->>>>>>-------->>>>--->>,,<<<<<<<____........................................................................._________>>>>>>>,<<<____..__>>>,,,,................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>.,,,,<<<<-------<<<<<_.____._>>>>>>>>>:::