T-box Riboswitch Annotation Database - TBDB - 1JIJOXHC from

T-box riboswitch 1JIJOXHC

Putative MET (CAU) T-box riboswitch from Peptoniphilus lacrimalis 315-B

Source information

TBDB ID	1JIJOXHC
Host organism	Peptoniphilus lacrimalis 315-B
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	ADDO01000041.1:33250-33529
Downstream protein description	ABC transporter, ATP-binding protein
Downstream protein ID	GenBank: EFA90114.1
T-box riboswitch length
Specifier loop sequence	CAUGG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AUG
Predicted tRNA family	MET (CAU)
Found cognate tRNA	True
Alternative specifiers	CAU,UGG
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence 1JIJOXHC ATAAACTTGATAAAGAGAAGAGTAGTTAAGTCTTTGGGATTAAAGAGAGCTTCGTTTTGGTGAAAGAAGATAAACAAAACTTAATGAACATGGCCTCTTTGAAGGAAGGTTCGATAATTAGAGCCTGACGGGAACTCCCGTTATAGAGTCAGGGTATGATTGTACCTAGTGAGTTTATATGCGTGAGCATATATTAAATAAAGGTGGTAACACGAGCTTTCGTCCTTTTAGGATGGAAGCTCTTTTTTT

Predicted secondary structures

T-box riboswitch 1JIJOXHC Antiterminator ......((......(((.......((((((.........(........(((((............)))).)).......)))))).........))).....))..((((((........))))))..(((......)))...................................(((((........))))).......((((.......((((....))))))))......................

T-box riboswitch 1JIJOXHC Terminator ......((......(((.......((((((.........(........(((((............)))).)).......)))))).........))).....))..((((((........))))))..(((......)))...................................(((((........)))))....................(((((((((((((...))))))))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AUG
Top predicted tRNA family: MET (CAU)

Best tRNA match for top specifier >MET (CAU) tRNA from Peptoniphilus lacrimalis 315-B
CGCGGGATGGAGCAGTCTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTAGGTTCAAATCCTGCTCCCGCTACCA

Predicted tRNA structure .((((((..((((.........)))).(((((.......))))).....(((((.......))))))))))).....

Alternative specifier 1

Alternative 1 for predicted specifier: CAU
Alternative 1 for predicted tRNA family: HIS (AUG)

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: UGG
Alternative 2 for predicted tRNA family: HIS (CCA)

Best tRNA match for alternative specifier 2 >HIS (CCA) tRNA from Peptoniphilus lacrimalis 315-B
AGGGGTATAGTTCAGTTGGTAGAACACTAGTCTCCAAAACTAGGTGTCGTGGGTTCGAGTCCTGCTACCCCTGCCA

Predicted tRNA structure (((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))....

Minimum Free Energy (MFE) Calculations

Folding MFE predictions

Antiterminator	ΔG° (kcal/mol)	-2.7
Terminator	ΔG° (kcal/mol	-19.8
	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	104.0
Bias	2.4
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		[7,104]
Stem II region
Stem III
Specifier region	-	[89,91]
T-box UGGN locus	-	[205,208]
Antiterminator		[201,227]
Terminator		[214,249]
All stems	-	[[7, 104], [106, 127], [129, 140], [174, 195], [201, 227]]

Input source sequence >ADDO01000041.1:33250-33529
ATAAACTTGATAAAGAGAAGAGTAGTTAAGTCTTTGGGATTAAAGAGAGCTTCGTTTTGGTGAAAGAAGATAAACAAAACTTAATGAACATGGCCTCTTTGAAGGAAGGTTCGATAATTAGAGCCTGACGGGAACTCCCGTTATAGAGTCAGGGTATGATTGTACCTAGTGAGTTTATATGCGTGAGCATATATTAAATAAAGGTGGTAACACGAGCTTTCGTCCTTTTAGGATGGAAGCTCTTTTTTTATTCATGGAGGAAAAAAATGATAGAGGTAAA

INFERNAL output sequence >Infernal-ADDO01000041.1:33250-33529
AUAAACUUGAUAAAGAGA-AGAGUAGUUAAGUCUUUGGGAUUAAAGAGAG-CUUCGUUUuGGUGAAAGAAGAUAAACAAAACUUAAUGAACAUGGCCUCuuUGAAG-GAAGGUUCGAU-----AAUUAGAGCCUGACGGGAACUCCCGUUAUagagucaggguaugAUUGUACCUAGUGAGUUUAUAUGCGUGAGCAUAUAUUAAAuAAAGGUGGUAACACGAG---CU-UUCGUCCUUUUA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-ADDO01000041.1:33250-33529
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<____._______>>>>>>>>>----->>>>>>-------->>>>..--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,..............,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,.,<<<<-------<<<<<______>>>>>>>>>:::