T-box Riboswitch Annotation Database - TBDB - VDUYSI4X from

T-box riboswitch VDUYSI4X

Putative PHE (GAA) T-box riboswitch from Desulfosporosinus acidiphilus SJ4

Source information

TBDB ID	VDUYSI4X
Host organism	Desulfosporosinus acidiphilus SJ4
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP003639.1:141886-142382
Downstream protein description	phenylalanyl-tRNA synthetase, alpha subunit
Downstream protein ID	GenBank: AFM39237.1
T-box riboswitch length
Specifier loop sequence	GUUCG
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 VDUYSI4X ATATAAGCGATGATTGGGTAAAAAGGATGCTTTTCTTCACAGGGAGGCAGGCCGAAGACTGTAAGCCTGCTAAGAAAATATCCTCCTCTTAGAGTAAGAGGTTAAAGTTCGCCTAGGAGTGGCCTTCTGATCTGTAGGAAGGTACGGTTTCCTCCGTTATCAGGAACATGAGTGTGGCAGAAAAAGCCAAACCAGGGTGGTACCGCGAGAATGACGCTCGTCCCTATTAGGGGATTGGGCGTTTTT

Predicted secondary structures

T-box riboswitch VDUYSI4X Antiterminator ......((......((((...........................(................................................)................))))...)).(((((((........))))))).(((......)))..................((((.......))))....((((.......(((((.......))))))))).....................

T-box riboswitch VDUYSI4X 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 Desulfosporosinus acidiphilus SJ4
GCCTCGGTAGCTCAGTCGGTAGAGCAGAGGACTGAAAATCCTCGTGTCGGCGGTTCGATTCCGTCCTGAGGCACCA

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)	-8.5
Terminator	ΔG° (kcal/mol	-15.5
	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	77.5
Bias	0.0
CM Accuracy	0.85

*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		[60,173]
Stem II region
Stem III
Specifier region	-	[160,162]
T-box UGGN locus	-	[251,254]
Antiterminator		[247,278]
Terminator		[268,299]
All stems	-	[[60, 173], [175, 196], [198, 209], [228, 242], [247, 278]]

Input source sequence >CP003639.1:141886-142382
TTTCCAAGGATGCTATGCTATAATAACGTGAGAAAATGTTGATGGATTATAAAATATAAGCGATGATTGGGTAAAAAGGATGCTTTTCTTCACAGGGAGGCAGGCCGAAGACTGTAAGCCTGCTAAGAAAATATCCTCCTCTTAGAGTAAGAGGTTAAAGTTCGCCTAGGAGTGGCCTTCTGATCTGTAGGAAGGTACGGTTTCCTCCGTTATCAGGAACATGAGTGTGGCAGAAAAAGCCAAACCAGGGTGGTACCGCGAGAATGACGCTCGTCCCTATTAGGGGATTGGGCGTTTTTATTATTTCGCATACTTCTGCAGTGTGCATTGGTCGAGTGTCTCTGATGCCAAACAAGTGCATACTCTCCACTGGAGACCTTCGGGATGGCGAGAAATGGATAAGGTTGTAGTATCGACAGATTCAGGAAGTTTGAGAATTCGGAAGGGATGGTTGACTTGAAGAAAGAAATACTTCGCATTGGAGAAGAGGCTTTGCG

INFERNAL output sequence >Infernal-CP003639.1:141886-142382
AUAUAAGCGAUGAUUGGGuaAAAAGGA------UGCUUUUCUUCACAGGGAG*[48]*U------AAGAGGUUAAAGUUCGCCUAGGAGU-GGCCUUCUGAU-----CUGUAGGAAGGUACGGUUUCCUCCGUUA-UCAGGAACAUGAGUGUGGCAGA----A---AAAGCCAAACCAGGGUGGUACCGCGAGAAUGAcGCUCGUCCCUAUU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP003639.1:141886-142382
::::::<<------<<<<..-------<<<<<<-------<<<--------<~~~~~~>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_____._>>>>>>>>>:::