T-box Riboswitch Annotation Database - TBDB - JADHFXY7 from

T-box riboswitch JADHFXY7

Putative PHE (GAA) T-box riboswitch from Clostridium cellulovorans 743B

Source information

TBDB ID	JADHFXY7
Host organism	Clostridium cellulovorans 743B
Model used	Class I
Predicted regulation	Unknown
T-box riboswitch genomic accession	CP002160.1:2571162-2570898
Downstream protein description	phenylalanyl-tRNA synthetase, alpha subunit
Downstream protein ID	GenBank: ADL51900.1
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	Partial

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence JADHFXY7 AAAGATGCTAAGATAGAGAGAGTAAATTTAATCAATTATTTAGAGAGAGAAGATTACCAGCTGCAAGTCTTCTTATAAGCGATTATTTTGAAGTTCACTCTGGAGCACCTGTAATGAACTAACAGTAATTACAGGCGGAGAAACACCGTTACGTATATGAGAGAACATAAACTTTATGTTAATTAGGGTGGTACCACGGAAATTTCGTCCCTAAATAGCATAGGTTTTTTTATTTTTT

Predicted secondary structures

T-box riboswitch JADHFXY7 Antiterminator ......((......((((......((..((.........(........((((((............))))))..)........))..))........))))...))..(((((((............))))))).(((.......)))...............(((((((...)))))))....((((.......(((((...)))))))))..........................

T-box riboswitch JADHFXY7 Terminator Error: TBDB structure refinement failed to predict a terminator structure for this T-box

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 Clostridium cellulovorans 743B
GGCTCGATAGCTCAGTCGGTAGAGCAGAGGACTGAAAATCCTCGTGTCCCTGGTTCGATTCCTGGTCGAGCCACCA

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)	-5.3
Terminator	ΔG° (kcal/mol	-3.6
	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	130.5
Bias	1.4
CM Accuracy	0.92

*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		[7,106]
Stem II region
Stem III
Specifier region	-	[93,95]
T-box UGGN locus	-	[189,192]
Antiterminator		[185,212]
Terminator		[196,238]
All stems	-	[[7, 106], [109, 134], [136, 148], [164, 180], [185, 212]]

Input source sequence >CP002160.1:2571162-2570898
AAAGATGCTAAGATAGAGAGAGTAAATTTAATCAATTATTTAGAGAGAGAAGATTACCAGCTGCAAGTCTTCTTATAAGCGATTATTTTGAAGTTCACTCTGGAGCACCTGTAATGAACTAACAGTAATTACAGGCGGAGAAACACCGTTACGTATATGAGAGAACATAAACTTTATGTTAATTAGGGTGGTACCACGGAAATTTCGTCCCTAAATAGCATAGGTTTTTTTATTTTTTGTATATGTATGTTAAAGCTTTATATAG

INFERNAL output sequence >Infernal-CP002160.1:2571162-2570898
AAAGAUGCUAAGAUAGAG-AGAGUAAAUUUAAUCAAUUAUUUAGAGAGAGAAGAUUACCaGCUGCAAGUCUUCuuAUAAG-cgAUUAUUUUGAAGUUCACUCUGGAGCACCUGUAAUGAA-CUAACAGUAAUUACAGGCGGAGAAaCACCGUUA----CGUAUAUGAGAGAACAUAA-----ACUUUAUGUUAAUUAGGGUGGUACCACGGA--AAU-UUCGUCCCUAAA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP002160.1:2571162-2570898
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<____._______>>>>>>..>>>---..-->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<____.__>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::