T-box Riboswitch Annotation Database - TBDB - 4APV6CYY from

T-box riboswitch 4APV6CYY

Putative PHE (GAA) T-box riboswitch from Fusibacter sp. 3D3

Source information

TBDB ID	4APV6CYY
Host organism	Fusibacter sp. 3D3
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	BDHH01000029.1:44262-44007
Downstream protein description	phenylalanyl-tRNA synthetase alpha chain
Downstream protein ID	DDBJ: GAU79773.1
T-box riboswitch length
Specifier loop sequence	GUUCA
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 4APV6CYY AAAAAATCTATGATGGAGAGAGTAGATGTTTGCGGAAATTAGAGAGGAAAACGGCTGGTGAAAGTTTTCATTCCAATACATTGAAGTTCACTCTGGAGATGCACTTTTGAATTAAGTAGAAAGTGACGTTTGCTGCGTTAAGGCCATAAGTGAATTACTTATGTAATTAATTTGGGTGGTACCGCGGAATAACCTTCGTCCCATGATTGGGAGAGGGTTTTTTTTATTGT

Predicted secondary structures

T-box riboswitch 4APV6CYY Antiterminator ......((......((((......(((((.......(((.......((((((...........))))))))).....)))))........))))...))..(((((((..........))))))).(((.....)))...............((((((....))))))....((((.......(((((......)))))))))...........................

T-box riboswitch 4APV6CYY 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 Fusibacter sp. 3D3
GCCCGGATAGCTCAGTCGGTAGAGCAGGGGACTGAAAATCCCCGTGTCGGTGGTTCGATTCCGCCTCCGGGCACCA

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)	-6.5
Terminator	ΔG° (kcal/mol	-14.5
	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	138.6
Bias	0.2
CM Accuracy	0.95

*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		[7,99]
Stem II region
Stem III
Specifier region	-	[86,88]
T-box UGGN locus	-	[177,180]
Antiterminator		[173,203]
Terminator		[193,230]
All stems	-	[[7, 99], [102, 125], [127, 137], [153, 168], [173, 203]]

Input source sequence >BDHH01000029.1:44262-44007
AAAAAATCTATGATGGAGAGAGTAGATGTTTGCGGAAATTAGAGAGGAAAACGGCTGGTGAAAGTTTTCATTCCAATACATTGAAGTTCACTCTGGAGATGCACTTTTGAATTAAGTAGAAAGTGACGTTTGCTGCGTTAAGGCCATAAGTGAATTACTTATGTAATTAATTTGGGTGGTACCGCGGAATAACCTTCGTCCCATGATTGGGAGAGGGTTTTTTTTATTGTCATTTTT

INFERNAL output sequence >Infernal-BDHH01000029.1:44262-44007
AAAAAAUCUAUGAUGGAG-AGAGUAGAUGUUUG-CGGAAAUUAGAGAG-GAAAACGGCUGGUGAAAGUUUUCAUUCCA-AUACAUUGAAGUUCACUCUGGAGAUGCACUUUUGAA---UUAAGUAGAAAGUGACGUUUG-CUGCGUUA----AGGCCAUAAGUGAAUUACU------UAUGUAAUUAAUUUGGGUGGUACCGCGGAA-UAAcCUUCGUCCCAUGA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-BDHH01000029.1:44262-44007
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_____._>>>>>>>>>:::