T-box Riboswitch Annotation Database - TBDB - ZINGOUL4 from - Corynebacterium argentoratense DSM 44202

T-box riboswitch ZINGOUL4

Putative ILE (GAU) T-box riboswitch from Corynebacterium argentoratense DSM 44202

Source information

TBDB ID	ZINGOUL4
Host organism	Corynebacterium argentoratense DSM 44202
Model used	Class II
Predicted regulation	Unknown
T-box riboswitch genomic accession	CP006365.1:1368457-1368137
Downstream protein description	isoleucyl-tRNA synthase
Downstream protein ID	GenBank: AGU15447.1
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 ZINGOUL4 TTTTGTGCATTGATCCGGCTATCACCGGGGAGCACCCGGAAGAACAGTCACGAGACTCAGTAGAACCGGGCGGGTGGGACCGACATCTCCTTTAGAAACAAGTGGCTCGTCTCTTTTTGGGCGAGCAAGCAGGGTGGTACCGCGTGCACAGTCACGTCCCTGCACCCGAAGAAACAATGTTTTTAAAGGAGTTAACA

Predicted secondary structures

T-box riboswitch ZINGOUL4 Antiterminator ....((((.....(((((......)))))..)))).(((....((((((....))))..))....)))(.(((......))).)....................(((((............)))))..((((((.......(((((......)))))))))))..................................

T-box riboswitch ZINGOUL4 Terminator ....((((.....(((((......)))))..)))).(((....((((((....))))..))....)))(.(((......))).)....................(((((............)))))...............(((.(..(......)..).)))....(((.(.....).))).............

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 Corynebacterium argentoratense DSM 44202
GGGCCTATAGCTCAGTCGGTTAGAGCGCATCGCTGATAACGATGAGGTCGCAAGTTCGATTCTTGCTAGGCCCACCA

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)	-16.2
Terminator	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	143.3
Bias	0.0
CM Accuracy	0.97

*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		[79,109]
Stem II region
Stem III
Specifier region	-	[94,96]
T-box UGGN locus	-	[208,212]
Antiterminator		[203,237]
Terminator		[213,271]
All stems	-	[[79, 109], [111, 142], [143, 158], [179, 200], [203, 237]]

Input source sequence >CP006365.1:1368457-1368137
ACCGTTAAAAGCTGACAAAAGCACCGGCCCGTGGATTGCTGCCACGGGCCGGTGCATTTTTGTGTGCTAGTATCTTTTGTGCATTGATCCGGCTATCACCGGGGAGCACCCGGAAGAACAGTCACGAGACTCAGTAGAACCGGGCGGGTGGGACCGACATCTCCTTTAGAAACAAGTGGCTCGTCTCTTTTTGGGCGAGCAAGCAGGGTGGTACCGCGTGCACAGTCACGTCCCTGCACCCGAAGAAACAATGTTTTTAAAGGAGTTAACAGTGGCGATTTACCCACGCGTCGATATGACCGGTGGTTCGGCTAAGTTCCC

INFERNAL output sequence >Infernal-CP006365.1:1368457-1368137
UUUUGUGCAUUGAUCCGGCUAUCACCGGGGAGCACCCGGAAGAACAGUCAC------------GAGACUCAGUAGAACCGGGCGGGUGGGACCGACAUCUCCUuuAGAAACAAGUGGCUCGUCUCUUU-------UUGGGCGAGCAAGCAGGGUGGUACCGCGUGCACAG--------------UCACGUC--CCUGCACCCGAAGAAACAAUGUUUUUAAAGGAGUUAACA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP006365.1:1368457-1368137
::::<<<<-----<<<<<______>>>>>-->>>>,<<<----<<<<<<________________>>>>-->>---->>><<<<<<____>>>>>>,,,,,,,..,,,,,,,,,,,<<<<<___________________>>>>>,,<<<<<<-------<<<<<<__________________>>>>>>>-->>>>>::::::::::::::::::::::::::::::::::