T-box Riboswitch Annotation Database - TBDB - INUQVCBR from

T-box riboswitch INUQVCBR

Putative LEU (GAG) T-box riboswitch from Dialister invisus CAG:218

Source information

TBDB ID	INUQVCBR
Host organism	Dialister invisus CAG:218
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	HF996442.1:125539-125294
Downstream protein description	putative branched-chain amino acid ABC transporter periplasmic amino acid-binding protein
Downstream protein ID	ENA: CCZ54087.1
T-box riboswitch length
Specifier loop sequence	ACUCU
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	CUC
Predicted tRNA family	LEU (GAG)
Found cognate tRNA	True
Alternative specifiers	ACU,UCU
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence INUQVCBR TGAAAAGCGATGAACGGAAAAAAGTCATGTTTCTGAGATAACAGAGAGCCGGTGGCAGGTGGAAACCGGTATGAAGGATATGTCGAACTCTTCCGCAAGCTCCTCGTTGAATCAAGTAGATGGAGGCGTCATCCACGTTACGGACAGGAGCCATAAGTATAATGCAGGGTGGTACCGCGATGAATTCGCCCCTGTCCGATTTATTCGGGCAGGGTTTTATATT

Predicted secondary structures

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

T-box riboswitch INUQVCBR 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 Dialister invisus CAG:218
GCGGCTGTGGCGGAATGGCAGACGCGCTACTTTGAGGGGGTAGTGATCCTTGATCGTGTGAGTTCAAGTCTCACCAGCCGCACCA

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

Alternative specifier 1

Alternative 1 for predicted specifier: ACU
Alternative 1 for predicted tRNA family: THR (AGU)

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: UCU
Alternative 2 for predicted tRNA family: THR (AGA)

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)	-8.0
Terminator	ΔG° (kcal/mol	-19.4
	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	95.4
Bias	0.0
CM Accuracy	0.93

*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		[7,100]
Stem II region
Stem III
Specifier region	-	[87,89]
T-box UGGN locus	-	[170,173]
Antiterminator		[166,193]
Terminator		[190,223]
All stems	-	[[7, 100], [103, 125], [127, 137], [153, 160], [166, 193]]

Input source sequence >HF996442.1:125539-125294
TGAAAAGCGATGAACGGAAAAAAGTCATGTTTCTGAGATAACAGAGAGCCGGTGGCAGGTGGAAACCGGTATGAAGGATATGTCGAACTCTTCCGCAAGCTCCTCGTTGAATCAAGTAGATGGAGGCGTCATCCACGTTACGGACAGGAGCCATAAGTATAATGCAGGGTGGTACCGCGATGAATTCGCCCCTGTCCGATTTATTCGGGCAGGGTTTTATATTACCCGGAGGCAGAGTGATAAATG

INFERNAL output sequence >Infernal-HF996442.1:125539-125294
UGAAAAGCGAUGAACGGAAAAA--AGUCAUGUUUCUGAGAUAACAGAGAGCCGGUGGCAGGUGGAAACCGGUAUGAAGGAUAUGUCGAA-CUCUUCCGCAAGCUCCU-CGUUGAA---UCAAGUAGAUGGAGGCGUCAU-CCACGUUA----CGGACAGGAGCCAUA*[ 2]*UAUAAUgCAGGGUGGUACCGCGAU--GAA-UUCGCCCCUGUC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-HF996442.1:125539-125294
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<~~~~~~>>>,,,.,<<<<-------<<<<<______>>>>>>>>>:::