T-box Riboswitch Annotation Database - TBDB - COSO6POR from - Thermosediminibacter oceani DSM 16646

T-box riboswitch COSO6POR

Putative LEU (GAG) T-box riboswitch from Thermosediminibacter oceani DSM 16646

Source information

TBDB ID	COSO6POR
Host organism	Thermosediminibacter oceani DSM 16646
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP002131.1:758518-758804
Downstream protein description	leucyl-tRNA synthetase
Downstream protein ID	GenBank: ADL07538.1
T-box riboswitch length
Specifier loop sequence	CUCGC
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	CUC
Predicted tRNA family	LEU (GAG)
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 COSO6POR TTAATAGAGGGCATCAAGGAGTAGTAGGGGAGGTAGTCCTTTCAGAGACCGGAGGCTTGGTGGGAATCCGGAGGACGAAACCTCGAACTCGCCTTGGTAACCTTGCCGGCAGGCGTTAAAATGCGAAGAGCGGGCATTCTGCCAATTAGGGTGGTACCGCGAGAAAGAGGCTTCTCGTCCCTAAATCGACGAGAGGCCTTTTATTTTT

Predicted secondary structures

T-box riboswitch COSO6POR Antiterminator ......(.......((((........((((.......(((........(((((.............))))))))......))))........))))....)...............................((((...))))....((((.......(((((((......)))))))))))..........................

T-box riboswitch COSO6POR Terminator ......(.......((((........((((.......(((........(((((.............))))))))......))))........))))....)...............................((((...)))).........................(((((((((((........)))))))))))..........

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CUC
Top predicted tRNA family: LEU (GAG)

Best tRNA match for top specifier >LEU (GAG) tRNA from Thermosediminibacter oceani DSM 16646
GCAGGGATGGTGGAACTGGCAGACACGCTACTTTGAGGGGGTAGTGGAGATTTGCTCCGTGCGGGTTCAAATCCCGCTCCCTGCACCA

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)	-11.6
Terminator	ΔG° (kcal/mol	-19.9
	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	75.8
Bias	0.0
CM Accuracy	0.86

*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		[8,102]
Stem II region
Stem III
Specifier region	-	[89,91]
T-box UGGN locus	-	[153,156]
Antiterminator		[149,183]
Terminator		[170,209]
All stems	-	[[8, 102], [134, 144], [149, 183]]

Input source sequence >CP002131.1:758518-758804
ATTAATAGAGGGCATCAAGGAGTAGTAGGGGAGGTAGTCCTTTCAGAGACCGGAGGCTTGGTGGGAATCCGGAGGACGAAACCTCGAACTCGCCTTGGTAACCTTGCCGGCAGGCGTTAAAATGCGAAGAGCGGGCATTCTGCCAATTAGGGTGGTACCGCGAGAAAGAGGCTTCTCGTCCCTAAATCGACGAGAGGCCTTTTATTTTTATAATTTTAACGAAAGGAGGCATTGGGCATGAGTCATTACGATTTTAAGACTGTAGAACTCAAATGGCAGAAAAGGTG

INFERNAL output sequence >Infernal-CP002131.1:758518-758804
UUAAUAGAGGGCAUCAAGgAGUAGUAGGGGAGGU--AGUCCUUUCAGAGACCGGAGGCUUGGUGGGAAUCCGGAGGACG-AAACCUCGAA-CUCGcCUUGGUAACCU*[ 9]*----------GCGUUA--AAAUGCGAAGAGCGGGCA*[ 3]*UGCCAAUUAGGGUGGUACCGCGAGAAAGAggcuUCUCGUCCCUAAA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP002131.1:758518-758804
::::::<<------<<<<.-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>--------.>>>>--->>,,~~~~~~,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<~~~~~~>>>>,,,,<<<<-------<<<<<_____...._>>>>>>>>>:::