T-box Riboswitch Annotation Database - TBDB - KBO1KSOC from

T-box riboswitch KBO1KSOC

Putative VAL (UAC) T-box riboswitch from Clostridium sp. CAG:356

Source information

TBDB ID	KBO1KSOC
Host organism	Clostridium sp. CAG:356
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	FR894104.1:8125-7847
Downstream protein description	putative aldose 1-epimerase
Downstream protein ID	ENA: CDD36523.1
T-box riboswitch length
Specifier loop sequence	GGUAG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	GUA
Predicted tRNA family	VAL (UAC)
Found cognate tRNA	False
Alternative specifiers	None
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence KBO1KSOC ATAAAAACGAAGAAAAAGAGGAGTACATTTATACTTATTTAGTAGAGAAAAGAAGTCGAAGGCTGGGAGCTTCTTAAACAAAGGTAAATGGAAGGTAGCTTTAGAGTTGATAATCTGACAATAAACTTAAGATTATCCGTATGCTGCGTTAAAGCAAAATAAGATGTTATCAAAAAACAAAATAGATAATAATTAAGGTGGTACCGTGAGATATAAACTCGCCCTTATGCAAATAAGCATATAGGCGAGTTATTTTTT

Predicted secondary structures

T-box riboswitch KBO1KSOC Antiterminator ......((......((((.......((((((.......(((.........((((((............))))))))).......))))))........))))...))..(((((((.............))))))).(((.....))).................((((((.............))))))....((((.......(((((.......)))))))))................................

T-box riboswitch KBO1KSOC Terminator ......((......((((.......((((((.......(((.........((((((............))))))))).......))))))........))))...))..(((((((.............))))))).(((.....))).................((((((.............)))))).........................((((((((..(((((......)))))..)))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: GUA
Top predicted tRNA family: VAL (UAC)

Best tRNA match for top specifier >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 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)	-5.4
Terminator	ΔG° (kcal/mol	-20.4
	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	107.5
Bias	17.4
CM Accuracy	0.87

*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		[7,107]
Stem II region
Stem III
Specifier region	-	[94,96]
T-box UGGN locus	-	[199,202]
Antiterminator		[195,226]
Terminator		[216,258]
All stems	-	[[7, 107], [110, 136], [138, 148], [166, 190], [195, 226]]

Input source sequence >FR894104.1:8125-7847
ATAAAAACGAAGAAAAAGAGGAGTACATTTATACTTATTTAGTAGAGAAAAGAAGTCGAAGGCTGGGAGCTTCTTAAACAAAGGTAAATGGAAGGTAGCTTTAGAGTTGATAATCTGACAATAAACTTAAGATTATCCGTATGCTGCGTTAAAGCAAAATAAGATGTTATCAAAAAACAAAATAGATAATAATTAAGGTGGTACCGTGAGATATAAACTCGCCCTTATGCAAATAAGCATATAGGCGAGTTATTTTTT

INFERNAL output sequence >Infernal-FR894104.1:8125-7847
AUAAAAACGAAGAAAAAGAGGAGUACAUUUAUACUUAUUUAgUAGAGAAAAGAAGUCGAAgGCUGGGAGCUUCUUAAACAaaGGUAAAUGGAAGGUAGCUUUAGAGUUGAUAAUCUGACAAUAAACUUAAGAUUAUCCGUAUG-CUGCGUUA--AAGCAAAAUAAGAUGUUAUCAAAAaacAAAAUAGAUAAUAAUUAAGGUGGUACCGUGAGAuAUAAACUCGCCCUUAUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-FR894104.1:8125-7847
::::::<<------<<<<-------<<<<<<-------<<<.--------<<<<<<____._______>>>>>>>>>---..-->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<___..._____>>>>>>>,,,,<<<<-------<<<<<_._____>>>>>>>>>:::