T-box Riboswitch Annotation Database - TBDB - 4YFFUGFC from - Mycobacterium chelonae subsp. gwanakae

T-box riboswitch 4YFFUGFC

Putative ILE (GAU) T-box riboswitch from Mycobacterium chelonae subsp. gwanakae

Source information

TBDB ID	4YFFUGFC
Host organism	Mycobacterium chelonae subsp. gwanakae
Model used	Class II
Predicted regulation	Translational
T-box riboswitch genomic accession	NZ_CP031516.1:2730584-2730368
Downstream protein description	isoleucine--tRNA ligase
Downstream protein ID	RefSeq: WP_070941052.1
T-box riboswitch length
Specifier loop sequence	GAUCU
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AUC
Predicted tRNA family	ILE (GAU)
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 4YFFUGFC CTACAGACATCGATCCGGCCATCACCGGGGAGTCTCCGGAAGAAAGGATCCGTGCGCAGCACGGATCACCGAGTAGAACCGGACGGGTAGGCCCGTCACAGCCTGTGTGAGAGGCCCCGGGTAAGTAGGGGCAAGCGGGGTGGTACCGCGGAGGTACGCCGACGGCGTCCCATCGTCCCCGTGCCGGCGAGCACAGGGAGATGTACCGACTATGCCT

Predicted secondary structures

T-box riboswitch 4YFFUGFC Antisequestrator ....((((.....(((((......)))))..)))).(((....(.((.....................))...)....)))((((((....))))))................(((((.........)))))..((((((.......((((.((.(((((...))))).)).))))))))))...............................

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AUC
Top predicted tRNA family: ILE (GAU)

Best tRNA match for top specifier >ILE (GAU) tRNA from [Mycobacterium] chelonae subsp. gwanakae
GGGGCTATAGCTCAGGTGGTTAGAGCGCTTCGCTGATAACGAAGAGGTCGGAGGTTCGAGTCCTCCTAGCCCCACCA

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

Antisequestrator	ΔG° (kcal/mol)	-24.4
Sequestrator	ΔG° (kcal/mol	0.0
	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	143.7
Bias	2.8
CM Accuracy	0.87

*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		[5,35]
Stem II region
Stem III
Specifier region	-	[20,22]
T-box UGGN locus	-	[141,144]
Antisequestrator		[135,182]
Sequestrator		[147,213]
All stems	-	[[5, 35], [37, 81], [82, 97], [114, 132], [135, 182]]

Input source sequence >NZ_CP031516.1:2730584-2730368
CTACAGACATCGATCCGGCCATCACCGGGGAGTCTCCGGAAGAAAGGATCCGTGCGCAGCACGGATCACCGAGTAGAACCGGACGGGTAGGCCCGTCACAGCCTGTGTGAGAGGCCCCGGGTAAGTAGGGGCAAGCGGGGTGGTACCGCGGAGGTACGCCGACGGCGTCCCATCGTCCCCGTGCCGGCGAGCACAGGGAGATGTACCGACTATGCCT

INFERNAL output sequence >Infernal-NZ_CP031516.1:2730584-2730368
CUACAGACAUCGAUCCGGCCAUCACCGGGGAGUCUCCGGAAGAAAGGAUCCGUGCGCAGca-CGGAUCACCGAGUAGAACCGGACGGGUAGGCCCGUCACAGCCU--GUGUGAGAGGCCCCGGGUA----------AGUAGGGGCAAGCGGGGUGGUACCGCGGAGGUACGCCGAC-GGCGUCCCAUCGUCCCCGUGCCGGCGAGCACAGGGAGAUGUACCG--------ACUAU

INFERNAL output structure - (Antisequestrator) >Infernal-Structure-NZ_CP031516.1:2730584-2730368
::::<<<<-----<<<<<______>>>>>-->>>>,<<<----<<<<<<__________..______>>>>-->>---->>><<<<<<____>>>>>>,,,,,,,,,,,,,,,,,,<<<<<___________________>>>>>,,<<<<<<-------<<<<<<__________________>>>>>>>>>>>>:::::::::::::::::::::::::::::::::::::::