T-box Riboswitch Annotation Database - TBDB - GLNDNLU from

T-box riboswitch GLNDNLU

Putative ASN (GUU) T-box riboswitch from Ruminococcus albus 7 = DSM 20455

Source information

TBDB ID	GLNDNLU
Host organism	Ruminococcus albus 7 = DSM 20455
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP002403.1:2974253-2974553
Downstream protein description	asparaginyl-tRNA synthetase
Downstream protein ID	GenBank: ADU23116.1
T-box riboswitch length
Specifier loop sequence	UAACA
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AAC
Predicted tRNA family	ASN (GUU)
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 GLNDNLU TGAAACGCTATGACCGGGAGAAGTAACTCTGGTATTCACTCACAGAGAGCGCGGGAGAGGTGTGAGCCGCGCAGCAGAGCCTTTGTGAATAACACCCGTGAGCGGCAGACCCAACGGCATTCTGCCAAGTAGGAAAGACGTGTTCCTCACGTTATGAGGATAAGAGTGACAACGCTCGGATACTTTTTTTAAGCTTTTGAGCGCTTGTAAATTCAGGTGGTACCGCGAAGTCTATGGCTTTCGTCCTGTTATCGGGACGGGAGCCTTTTTT

Predicted secondary structures

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

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

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AAC
Top predicted tRNA family: ASN (GUU)

Best tRNA match for top specifier >ASN (GUU) tRNA from Ruminococcus albus 7 = DSM 20455
GCCTCCTTAGCTCAGTCGGTAGAGCATGCGGCTGTTAACCGCAGGGTCGTTGGTTCGAGTCCAACAGGTGGCG

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)	-8.1
Terminator	ΔG° (kcal/mol	-23.1
	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	104.9
Bias	0.0
CM Accuracy	0.85

*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		[7,103]
Stem II region
Stem III
Specifier region	-	[90,92]
T-box UGGN locus	-	[218,221]
Antiterminator		[214,248]
Terminator		[236,271]
All stems	-	[[7, 103], [106, 137], [139, 151], [196, 209], [214, 248]]

Input source sequence >CP002403.1:2974253-2974553
TGAAACGCTATGACCGGGAGAAGTAACTCTGGTATTCACTCACAGAGAGCGCGGGAGAGGTGTGAGCCGCGCAGCAGAGCCTTTGTGAATAACACCCGTGAGCGGCAGACCCAACGGCATTCTGCCAAGTAGGAAAGACGTGTTCCTCACGTTATGAGGATAAGAGTGACAACGCTCGGATACTTTTTTTAAGCTTTTGAGCGCTTGTAAATTCAGGTGGTACCGCGAAGTCTATGGCTTTCGTCCTGTTATCGGGACGGGAGCCTTTTTTAATTCATAATTCATAACACTAAAAGCGAAG

INFERNAL output sequence >Infernal-CP002403.1:2974253-2974553
UGAAACGCUAUGACCGGGAGAAGUAACUCUGGU-AUUCACUCACAGAGAGCGCGGGAGAGGUGUGAgCCGCGCAGCAGAGCCUUUGUGAAUAACACCCGUGAGCGGCAGACCCAACGgcauucUGCCAAGUAGGAA-AGACGUGUUCcUCACGUUAUgaggauaagagugacaacgcucggaUACUUUUUUUAAGCUUUUGAGC--------GCUUGUAAAUUCAGGUGGUACCGCGAAGUCUAuggcUUUCGUCCUGUUA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP002403.1:2974253-2974553
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<____......_________>>>>>>>,<<<____.__>>>,,,,.........................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_____...._>>>>>>>>>:::