T-box Riboswitch Annotation Database - TBDB - FTY54GJS from

T-box riboswitch FTY54GJS

Putative ALA (GGC) T-box riboswitch from Acetobacterium woodii DSM 1030

Source information

TBDB ID	FTY54GJS
Host organism	Acetobacterium woodii DSM 1030
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP002987.1:1141402-1141847
Downstream protein description	alanyl-tRNA synthetase AlaS
Downstream protein ID	GenBank: AFA47770.1
T-box riboswitch length
Specifier loop sequence	UGCCG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	GCC
Predicted tRNA family	ALA (GGC)
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 FTY54GJS TAAAATGCATTGAGAACGAAGACTCTAAATAGTCAGTCCAGAGAAAGCGACATTGCTGAAAGTCGCTTATAATCATTTTGGAGTTGCCGCGTTTGAGCAGCTGGGAAAAGGTTTGAATAAATCGTTCGATTAGTATTTTCAGCCGGGAAATCGTTATTGATTAAGAGAGTTGCCGACGATATTGCAACTAATTTGGGTGGTACCGCGGTTTAAACTGTCCCTTGCATATTTGCATGGGATTTTTTTGTTT

Predicted secondary structures

T-box riboswitch FTY54GJS Antiterminator ......((......((((.......((((.....(.........((((((............)))))).)......)))).........))))...))..(((((((............................))))))).(((....)))..............((((((..........)))))).....(((.......(((((....)))))))).............................

T-box riboswitch FTY54GJS Terminator ......((......((((.......((((.....(.........((((((............)))))).)......)))).........))))...))..(((((((............................))))))).(((....)))..............((((((..........))))))............................((((.((((....)))).))))...........

Specifier and tRNA predictions

Top specifier

Top predicted specifier: GCC
Top predicted tRNA family: ALA (GGC)

Best tRNA match for top specifier >ALA (GGC) tRNA from Acetobacterium woodii DSM 1030
GGGGGTGTGGCGAAGTTGGGATCGCGTCTGACTGGCAGTCAGAAGGCCAGGGGTTCGAGTCCCCTCATCTCCACCA

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)	-5.5
Terminator	ΔG° (kcal/mol	-11.5
	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	85.3
Bias	0.0
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		[51,142]
Stem II region
Stem III
Specifier region	-	[129,131]
T-box UGGN locus	-	[242,245]
Antiterminator		[238,266]
Terminator		[262,294]
All stems	-	[[51, 142], [145, 186], [188, 197], [212, 233], [238, 266]]

Input source sequence >CP002987.1:1141402-1141847
CATTTAAATATAGAATTAATATAATCATCTTCATAGGTTAATATTAAAATGCATTGAGAACGAAGACTCTAAATAGTCAGTCCAGAGAAAGCGACATTGCTGAAAGTCGCTTATAATCATTTTGGAGTTGCCGCGTTTGAGCAGCTGGGAAAAGGTTTGAATAAATCGTTCGATTAGTATTTTCAGCCGGGAAATCGTTATTGATTAAGAGAGTTGCCGACGATATTGCAACTAATTTGGGTGGTACCGCGGTTTAAACTGTCCCTTGCATATTTGCATGGGATTTTTTTGTTTAACTAATTAAAAAAGTTGTTACAAATCGACAGTAAAGCCACGACTGTTTGACGTTTATGAGTTTCGCAATTGCTTAAAAAAGATAAATAATAAGGAGAAAAAATGAAACCATTAGGATTAAATGAAATCAGAGAAAAATACTTAGCATTTTT

INFERNAL output sequence >Infernal-CP002987.1:1141402-1141847
UAAAAUGCAUUGAGAACGAAGACUCUAAAU-----AGUCAGUCCAGAGAAAGCGACAUUGCUGAAAgUCGCUUAUAAUC--AUUUUGGAGUuGCCGCGUUUGAGCAGCUGGGAAAAGGuuugaauaaaucguuCGAUUAGUAUUUUCAGCCGGGAA--AUCGUUA-----UUGAUUAAGAGAGUUGCCGACGAUAUUGCAACUAAUUUGGGUGGUACCGCGGU-UUAA-ACUGUCCCUUGC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP002987.1:1141402-1141847
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>----->>>>>>----.---->>>>--->>,,<<<<<<<____..............._________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::