T-box Riboswitch Annotation Database - TBDB - ADLOSPNK from

T-box riboswitch ADLOSPNK

Putative VAL (GAC) T-box riboswitch from Dethiobacter alkaliphilus AHT 1

Source information

TBDB ID	ADLOSPNK
Host organism	Dethiobacter alkaliphilus AHT 1
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	ACJM01000011.1:18125-17850
Downstream protein description	branched-chain amino acid aminotransferase
Downstream protein ID	GenBank: EEG76911.1
T-box riboswitch length
Specifier loop sequence	AGUCA
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	GUC
Predicted tRNA family	VAL (GAC)
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 ADLOSPNK ACAAAAGCAATGATGGGGAGAGTATTCCAGGCTTATTTTGCAGAGAGCCGGTGGTTGCTGTGAACCGGTAAATAACCTTGATGAAAGTCACCCCGAAGCTGCCGTCTGAAAACTGCCACAGTTATTAGGCACGGCCGGTTCCTGCCCGTTACATGCAGGTTGAACCTAAGTCCGGTTATACCGGAGAATAAGGGTGGTACCGCGGAGGAATACTCTCGCCCCTTTCAGGGTGGGAGTTTTTTTTT

Predicted secondary structures

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

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

Specifier and tRNA predictions

Top specifier

Top predicted specifier: GUC
Top predicted tRNA family: VAL (GAC)

Best tRNA match for top specifier >VAL (GAC) tRNA from Dethiobacter alkaliphilus AHT 1
GGGTCGTTAGCTCAGGGGGAGAGCACTACCTTGACACGGTAGGGGCCACTGGTTCAAATCCAGTACGACCCACCA

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	-15.3
	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	128.4
Bias	0.0
CM Accuracy	0.92

*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		[7,99]
Stem II region
Stem III
Specifier region	-	[86,88]
T-box UGGN locus	-	[195,198]
Antiterminator		[191,223]
Terminator		[213,245]
All stems	-	[[7, 99], [102, 134], [136, 148], [171, 185], [191, 223]]

Input source sequence >ACJM01000011.1:18125-17850
ACAAAAGCAATGATGGGGAGAGTATTCCAGGCTTATTTTGCAGAGAGCCGGTGGTTGCTGTGAACCGGTAAATAACCTTGATGAAAGTCACCCCGAAGCTGCCGTCTGAAAACTGCCACAGTTATTAGGCACGGCCGGTTCCTGCCCGTTACATGCAGGTTGAACCTAAGTCCGGTTATACCGGAGAATAAGGGTGGTACCGCGGAGGAATACTCTCGCCCCTTTCAGGGTGGGAGTTTTTTTTTACTCATAATCATCTTTTAGTACTTTAGTGCT

INFERNAL output sequence >Infernal-ACJM01000011.1:18125-17850
ACAAAAGCAAUGAUGGGG-AGAGUAUUCCAGGC--UUAUUUUGCAGAGAGCCGGUGGUUGCUGUGAACCGGUAAAUAA-CCUUGAUGAAAGUCACCCCGAAGCUGCCGUCUGAAAAcugccaCAGUUAUUAGGCACGGCCGGUUCCuGCCCGUUACaugCAGGUUGAACCUAAGUCCGGUU-------AUACCGGAgAAUAAGGGUGGUACCGCGGAGgAAUAcUCUCGCCCCUUUC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-ACJM01000011.1:18125-17850
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<____......_________>>>>>>>,<<<____.__>>>,,,,...,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>.,,,,<<<<-------<<<<<_.____._>>>>>>>>>:::