T-box Riboswitch Annotation Database - TBDB - 0LIX2BFA from

T-box riboswitch 0LIX2BFA

Putative HIS (GUG) T-box riboswitch from Enterococcus sp. RIT-PI-f

Source information

TBDB ID	0LIX2BFA
Host organism	Enterococcus sp. RIT-PI-f
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	LHOX01000015.1:260301-260721
Downstream protein description	amino acid ABC transporter permease
Downstream protein ID	GenBank: KPG70543.1
T-box riboswitch length
Specifier loop sequence	ACACA
T-box 5'-UGGN-3' sequence	UGGA
Predicted specifier	CAC
Predicted tRNA family	HIS (GUG)
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 0LIX2BFA AAATAGACATCGAAAAGAAGAGTAGCAAGACTTGTTGTTCAAAGAGAATCTCTGGTTGGTGCAAAGAGATAGCACAGGGTTGTGAAACACATCTTGGAGTCGTTTTTCCGAAGAAGAAGTAGGAAAGACCGGGTATGCCCGTTAGCGCTGCAGTCATTGATTGATGACTTTCTAAGATCAGTTTGCCGTGAGGCACTGATAAACAAAGGTGGAACCGCGTTGATAACGTCCTTTAGCTGTAATGGCTAGAGGACGTTTTTTTATTTTCCGACCGGATGCCTTTTTACTATTGGGAAGCCATAGACTGCTTGAGGTTTTTTCTGAGAGGAAAAAACAAATTGAGGTGGAACCACGTGTAGCGCGTCCTCTGGCATAAGCCGGAGTACGCGTTTTTT

Predicted secondary structures

T-box riboswitch 0LIX2BFA Antiterminator ......((......((((......((((........(((........((((((...........)))))))))......))))........))))...))..(((((((............))))))).(((......)))............................................................................................................................................................................(((((((........))))))).....((((.......(((((...)))))))))...........................

T-box riboswitch 0LIX2BFA Terminator ......((......((((......((((........(((........((((((...........)))))))))......))))........))))...))..(((((((............))))))).(((......)))............................................................................................................................................................................(((((((........)))))))........................(((((.(((((((....))))))).)))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CAC
Top predicted tRNA family: HIS (GUG)

Best tRNA match for top specifier >HIS (GUG) tRNA from Enterococcus sp. RIT-PI-f
GCGGGTGTGGCGAAGTGGTTAACGCACCGGATTGTGGCTCCGGCATTCGTGGGTTCGATTCCCATCATTCGCCCCA

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)	-7.0
Terminator	ΔG° (kcal/mol	-20.9
	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	127.8
Bias	0.0
CM Accuracy	0.98

*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	-	[345,348]
Antiterminator		[341,368]
Terminator		[360,395]
All stems	-	[[7, 100], [103, 128], [130, 141], [314, 335], [341, 368]]

Input source sequence >LHOX01000015.1:260301-260721
AAATAGACATCGAAAAGAAGAGTAGCAAGACTTGTTGTTCAAAGAGAATCTCTGGTTGGTGCAAAGAGATAGCACAGGGTTGTGAAACACATCTTGGAGTCGTTTTTCCGAAGAAGAAGTAGGAAAGACCGGGTATGCCCGTTAGCGCTGCAGTCATTGATTGATGACTTTCTAAGATCAGTTTGCCGTGAGGCACTGATAAACAAAGGTGGAACCGCGTTGATAACGTCCTTTAGCTGTAATGGCTAGAGGACGTTTTTTTATTTTCCGACCGGATGCCTTTTTACTATTGGGAAGCCATAGACTGCTTGAGGTTTTTTCTGAGAGGAAAAAACAAATTGAGGTGGAACCACGTGTAGCGCGTCCTCTGGCATAAGCCGGAGTACGCGTTTTTT

INFERNAL output sequence >Infernal-LHOX01000015.1:260301-260721
AAAUAGACAUCGAAAAGA-AGAGUAGCAAGACU-UGUUGUUCAAAGAGAAUCUCUGGUUGGUGCAAAGAGAUAGCACAgGG--UUGUGAAACACAUCUUGGAGUCGUUUUUCCGAA-GAAGAAGUAGGAAAGACCGGGUAUGCCCGUUAGcgcugcagucauugauugaugacuuucuaagaucaguuugccgugaggcacugauaaacaaagguggaaccgcguugauaacguccuuuagcuguaauggcuagaggacguuuuuuuauuuuccgaccggaugccuuuuuacuauugggaagcCAUAGACUGCUUGAGGUUUUUUCUGAGAGGAAAAAACAAAuUGAGGUGGAACCACGUG--UAG-CGCGUCCUCUGG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-LHOX01000015.1:260301-260721
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