T-box Riboswitch Annotation Database - TBDB - NDRTII from

T-box riboswitch NDRTII

Putative VAL (UAC) T-box riboswitch from Clostridium isatidis

Source information

TBDB ID	NDRTII
Host organism	Clostridium isatidis
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP016786.1:770679-771071
Downstream protein description	valine--tRNA ligase
Downstream protein ID	GenBank: ASW42596.1
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	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 NDRTII AATTGAGCGATGATAAAGAGGAGTAGGGAATAGGAAGTATCAAAGAGAGGAAGGTTAGCAGCTGAGAGCCTTCTATACAGAATATCCTGAAGGTAGCTTTGGAGCATCTTTACTGAAATTTTAGTAAGTAAAGACGGTTATCTTAACCGTTAAAGATACAAGAGCCTATTAAATTTTTTAGTAGGAAAAAAGGTGGTACCGCGAGTCTTCGTCCTTTTGTGATGAAGACTCTTTTTTATTGT

Predicted secondary structures

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

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

Specifier and tRNA predictions

Top specifier

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

Best tRNA match for top specifier >VAL (UAC) tRNA from Clostridium isatidis
GGAAGCATAGCTCAGCTGGGAGAGCACCTGCCTTACAAGCAGGGGGTCACAGGTTCGATCCCTGTTGTTTCCACCA

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)	-3.0
Terminator	ΔG° (kcal/mol	-17.1
	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	135.8
Bias	1.5
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		[66,164]
Stem II region
Stem III
Specifier region	-	[151,153]
T-box UGGN locus	-	[253,256]
Antiterminator		[249,275]
Terminator		[262,301]
All stems	-	[[66, 164], [167, 192], [194, 208], [224, 244], [249, 275]]

Input source sequence >CP016786.1:770679-771071
TTTCTCGAACCAATGTTGACAAGAAAAATATAATATATTAATATTAGAAATAATTAAATAATTGAGCGATGATAAAGAGGAGTAGGGAATAGGAAGTATCAAAGAGAGGAAGGTTAGCAGCTGAGAGCCTTCTATACAGAATATCCTGAAGGTAGCTTTGGAGCATCTTTACTGAAATTTTAGTAAGTAAAGACGGTTATCTTAACCGTTAAAGATACAAGAGCCTATTAAATTTTTTAGTAGGAAAAAAGGTGGTACCGCGAGTCTTCGTCCTTTTGTGATGAAGACTCTTTTTTATTGTAAAATATAATAATTTTTAAATAGATTATAAGGAGGAAAAATAATGTCAGAGAAGAAAAATATTGCAACAACTTATGATCCTAAATCCTTTGA

INFERNAL output sequence >Infernal-CP016786.1:770679-771071
AAUUGAGCGAUGAUAAAGAGGAGUAGGGAAUAG-GAAGUAUCAAAGAGAGGAAGGUUAGcaGCUGAGAgCCUUCUAUACAGAAUAUCCUGAAGGUAGCUUUGGAGCAUCUUUACUGAA-AUUUUAGUAAGUAAAGACGGUUAUcuuAACCGUUA----AAGAUACAAGAGCCUAUUAA-AUUUUUUAGUAGGAAAAAAGGUGGUACCGCGAG---UC-UUCGUCCUUUUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP016786.1:770679-771071
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<____.._______.>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<____...__>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::