T-box Riboswitch Annotation Database - TBDB - XQ5YYXZ5 from

T-box riboswitch XQ5YYXZ5

Putative VAL (AAC) T-box riboswitch from Spiroplasma culicicola AES-1

Source information

TBDB ID	XQ5YYXZ5
Host organism	Spiroplasma culicicola AES-1
Model used	Class I
Predicted regulation	Unknown
T-box riboswitch genomic accession	CP006681.1:653130-652791
Downstream protein description	valyl-tRNA synthetase
Downstream protein ID	GenBank: AHI52930.1
T-box riboswitch length
Specifier loop sequence	GGUUG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	GUU
Predicted tRNA family	VAL (AAC)
Found cognate tRNA	False
Alternative specifiers	None
Metagenome	False
Structural predictions	Partial

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence XQ5YYXZ5 TTGAAAGTTATAAGGAGTAAAAAACATTTATCTTTTCAGAGAGTTAGTGGCTGGTGTGAACTAATAAGATAGGTTTTTGAAGGTTGTATAACTATAACAACTTTAGATAAATGAGGCGAGCTTATAAAAATATAAGCTAAACAGGATGGTACCGCGGATTTAATATGCAATTCGTTCCTATTTTT

Predicted secondary structures

T-box riboswitch XQ5YYXZ5 Antiterminator ......((((((.......((((((......(((........((((((...........)))))))))....))))))........))))))..........................(((((((......)))))))....((((.......(((((((........)))))))))))......

T-box riboswitch XQ5YYXZ5 Terminator Error: TBDB structure refinement failed to predict a terminator structure for this T-box

Specifier and tRNA predictions

Top specifier

Top predicted specifier: GUU
Top predicted tRNA family: VAL (AAC)

Best tRNA match for top specifier >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 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	-4.4
	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	91.9
Bias	7.7
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		[65,150]
Stem II region
Stem III
Specifier region	-	[140,142]
T-box UGGN locus	-	[205,208]
Antiterminator		[201,237]
Terminator		[212,243]
All stems	-	[[65, 150], [177, 196], [201, 237]]

Input source sequence >CP006681.1:653130-652791
TTTACACAACCAATAAGCAATTTTTATTCTTTTGGTATTATTTTGAGATATAATTTTATTGAAAGTTATAAGGAGTAAAAAACATTTATCTTTTCAGAGAGTTAGTGGCTGGTGTGAACTAATAAGATAGGTTTTTGAAGGTTGTATAACTATAACAACTTTAGATAAATGAGGCGAGCTTATAAAAATATAAGCTAAACAGGATGGTACCGCGGATTTAATATGCAATTCGTTCCTATTTTTATAATTAAAAATAGGAACGAATTCTTTTATTTGAAAGGAAATAAATTATGAAAAAAGAATTAGCAAAAAAATATGATCATTTAGATATTGAAAATGA

INFERNAL output sequence >Infernal-CP006681.1:653130-652791
UUGAAAGU------UAUAAGGAGUAAAAAACAU-UUAUCUUUUCAGAGAGUUAGUGGCUGGUGUGAACUAAUAAGAUA-GGUUUUUGAAGGUUGUAUA---ACUA*[ 2]**[ 6]*UUA---GAUAAAUGAGGCGAGCUUAUA--AAAAUAUAAGCUAAACAGGAUGGUACCGCGGAUu-UAAuaugcaAUUCGUUCCUAUU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP006681.1:653130-652791
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_.____......_>>>>>>>>>:::