T-box Riboswitch Annotation Database - TBDB - LQEGTS1N from

T-box riboswitch LQEGTS1N

Putative LEU (CAG) T-box riboswitch from Clostridium bolteae CAG:59

Source information

TBDB ID	LQEGTS1N
Host organism	Clostridium bolteae CAG:59
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	HF988256.1:8560-8866
Downstream protein description	leucine--tRNA ligase
Downstream protein ID	ENA: CCX98667.1
T-box riboswitch length
Specifier loop sequence	ACUGG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	CUG
Predicted tRNA family	LEU (CAG)
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 LQEGTS1N GCAAATACGCAGATAGGGAAGAGTAGATAACCGGATGGATGCAGAGAGCCGGCGGCTGGTGAAAGCCGGTGACGGATGGTTGTTGAACTGGCCCTGGAGTAGCCTGCCCCAACGAGGAAGGACCGCCGGAAACGGGGGACCGGGAACCAGTAGGACGGGACGGAGACCTTACCGTTATAAGAGGATTAAGTGCATGCGTCAGACAGCATGAACCAGAGTGGTACCGCGCGGGGATTTTTAAGCCTTGCGTCTCTAGCAGTAGAGGCGCAGGGCTTTTTT

Predicted secondary structures

T-box riboswitch LQEGTS1N Antiterminator ......((......((((.......((((((.....(..........((((((...........))))))..).....)))))).......))))...))..((((.((...........................................)).)))).(((........)))..................(((((........)))))....((((.......((((((((.........)))))))))))).........................

T-box riboswitch LQEGTS1N Terminator ......((......((((.......((((((.....(..........((((((...........))))))..).....)))))).......))))...))..((((.((...........................................)).)))).(((........)))..................(((((........)))))...............................((((((((((((((....))))))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CUG
Top predicted tRNA family: LEU (CAG)

Best tRNA match for top specifier >LEU (CAG) tRNA from Clostridium bolteae CAG:59
GCAGAAGTGGCGGAATTGGCAGACGCGCACGGTTCAGGTCCGTGTGGTAGTAATACCTTGTGGGTTCGACTCCCATCTTCTGCACCA

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)	-12.2
Terminator	ΔG° (kcal/mol	-25.7
	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	108.4
Bias	0.4
CM Accuracy	0.94

*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		[7,100]
Stem II region
Stem III
Specifier region	-	[87,89]
T-box UGGN locus	-	[219,222]
Antiterminator		[215,254]
Terminator		[242,279]
All stems	-	[[7, 100], [103, 159], [161, 174], [193, 210], [215, 254]]

Input source sequence >HF988256.1:8560-8866
GCAAATACGCAGATAGGGAAGAGTAGATAACCGGATGGATGCAGAGAGCCGGCGGCTGGTGAAAGCCGGTGACGGATGGTTGTTGAACTGGCCCTGGAGTAGCCTGCCCCAACGAGGAAGGACCGCCGGAAACGGGGGACCGGGAACCAGTAGGACGGGACGGAGACCTTACCGTTATAAGAGGATTAAGTGCATGCGTCAGACAGCATGAACCAGAGTGGTACCGCGCGGGGATTTTTAAGCCTTGCGTCTCTAGCAGTAGAGGCGCAGGGCTTTTTT

INFERNAL output sequence >Infernal-HF988256.1:8560-8866
GCAAAUACGCAGAUAGGGAAGAGUAGAUAACCG--GAUGGAUGCAGAGAGCCGGCGGCUGGUGAAAGCCGGUGACGGAUGGUUGUUGAA-CUGGCCCUGGAGUAGCCUGCCCCAACgaggaaggaccgccggaaacgggggaccggGAACCAGUAGGACGGGACGGAGACcuUACCGUUA-UAAGAGGAUUAAGUGCAUGCGU----CAGACAGCAUGAACCAGAGUGGUACCGCGCGGggauu---UuuaagccUUGCGUCUCUAGC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-HF988256.1:8560-8866
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<____.............................._________>>>>>>>,<<<____..__>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_.....____......._>>>>>>>>>:::