T-box Riboswitch Annotation Database - TBDB - KILNTHS6 from - Clostridium saccharoperbutylacetonicum N1-4(HMT)

T-box riboswitch KILNTHS6

Putative MET (CAU) T-box riboswitch from Clostridium saccharoperbutylacetonicum N1-4(HMT)

Source information

TBDB ID	KILNTHS6
Host organism	Clostridium saccharoperbutylacetonicum N1-4(HMT)
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP004121.1:2029186-2029498
Downstream protein description	methionine--tRNA ligase 1
Downstream protein ID	GenBank: AGF55613.1
T-box riboswitch length
Specifier loop sequence	AAUGG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AUG
Predicted tRNA family	MET (CAU)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Full

Genomic Context

Error loading NCBI Genome Browser - Cookies disabled To use the NCBI genome browser for visualizing genetic context of T-box riboswitch sequences, please enable cookies on your web browser.

Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence KILNTHS6 ACAAATGCAATGAAGAGGAAAGTAACTTTAAGAATACTTATACAGAGAGTTTCCATTGGTGAGAGGAAGCAAAGAATATTAAAGTGAAAATGGCCTTGGAGCGGTGTACCGAGATTTTTATTATAAAAATTAAGGCTGCAACGGATTCACCCGTTATAGTGATAGAGTATAATCATATGATATATGACGTACTTGATGAGGTGCATATTGTAAGGTATGCATGAAATAGGATGGTAACACGAAGTTTAGCTCTCGTTCCTAAGATTAATTTCTTAGGACGGGAGCTTTTTT

Predicted secondary structures

T-box riboswitch KILNTHS6 Antiterminator ......((......((((......((((((.......((.........((((((..........)))))).))......))))))........))))...))..((((.(........................).)))).(((......)))...............................................(((((((........))))))).....((((.......((((..........))))))))...............................

T-box riboswitch KILNTHS6 Terminator ......((......((((......((((((.......((.........((((((..........)))))).))......))))))........))))...))..((((.(........................).)))).(((......)))...............................................(((((((........)))))))..........................((((((((.(((((((......)))))))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AUG
Top predicted tRNA family: MET (CAU)

Best tRNA match for top specifier >MET (CAU) tRNA from Clostridium saccharoperbutylacetonicum N1-4(HMT)
CGCGGGGTGGAGCAGTTGGTAGCTCGTCGGGCTCATAACCCGAAGGTCGTAGGTTCAAGTCCTGCCCCCGCAACCA

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)	-4.8
Terminator	ΔG° (kcal/mol	-23.6
	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	118.9
Bias	8.6
CM Accuracy	0.95

*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		[7,102]
Stem II region
Stem III
Specifier region	-	[89,91]
T-box UGGN locus	-	[232,235]
Antiterminator		[228,260]
Terminator		[249,291]
All stems	-	[[7, 102], [105, 140], [142, 153], [201, 222], [228, 260]]

Input source sequence >CP004121.1:2029186-2029498
ACAAATGCAATGAAGAGGAAAGTAACTTTAAGAATACTTATACAGAGAGTTTCCATTGGTGAGAGGAAGCAAAGAATATTAAAGTGAAAATGGCCTTGGAGCGGTGTACCGAGATTTTTATTATAAAAATTAAGGCTGCAACGGATTCACCCGTTATAGTGATAGAGTATAATCATATGATATATGACGTACTTGATGAGGTGCATATTGTAAGGTATGCATGAAATAGGATGGTAACACGAAGTTTAGCTCTCGTTCCTAAGATTAATTTCTTAGGACGGGAGCTTTTTT

INFERNAL output sequence >Infernal-CP004121.1:2029186-2029498
ACAAAUGCAAUGAAGAGG-AAAGUAACUUUAAGAAUACUUAUACAGAGAGUUUCCAUU-GGUGAGAGGAAGCAAAGAAuAUUAAAGUGAAAAUGGCCUUGGAGCGGUGUACCGAGAUuuuuauuauAAAAAUUAAGGCUGCAACGGAUUCACCCGUUAUagugauagaguauaaucauaugauauauGACGUACUUGAUGAGGUGCAUAUUGUAAGGUAUGCAUgAAAUAGGAUGGUAACACGAAGUUUAgcUCUCGUUCCUAAG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP004121.1:2029186-2029498
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<____........._________>>>>>>>,<<<______>>>,,,,............................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>.,,,,<<<<-------<<<<<_____.._>>>>>>>>>:::