T-box Riboswitch Annotation Database - TBDB - ESTVBGUS from

T-box riboswitch ESTVBGUS

Putative SER (GGA) T-box riboswitch from Dialister invisus DSM 15470

Source information

TBDB ID	ESTVBGUS
Host organism	Dialister invisus DSM 15470
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	ACIM02000001.1:663464-663704
Downstream protein description	putative phosphoserine transaminase
Downstream protein ID	GenBank: EEW96713.1
T-box riboswitch length
Specifier loop sequence	UUCCG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	UCC
Predicted tRNA family	SER (GGA)
Found cognate tRNA	True
Alternative specifiers	CCG
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 ESTVBGUS TTATGCACAAGGATGAAGAAGCGCTTTTGCAAGCTCTCCAGAGAGATGGTGGACGGTGGAAACCATCAGCAAACAATTGTCGTTCCGCTTCAGAGTGGTAGATGATGAATCTATCGGGTATGCCCGTTACAGCAGATTAAAGATGGCTGAAAAGCAATTTGGGTGGTATCGCGGGTGCTCTCGTCCCTTAGAGGATGAAGAGCGTTTTTT

Predicted secondary structures

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

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

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UCC
Top predicted tRNA family: SER (GGA)

Best tRNA match for top specifier >SER (GGA) tRNA from Dialister invisus DSM 15470
GGAGAGGTGTCCGAGCGGTTTAAGGTGCATGATTGGAAATCATGTTGCCGGCGAATACCGGCACGGGGGTTCGAATCCCCCTCTCTCCGCCA

Predicted tRNA structure (((((((...((...........))..(((((.......))))).((((((......)))))).(((((.......))))))))))))....

Alternative specifier 1

Alternative 1 for predicted specifier: CCG
Alternative 1 for predicted tRNA family: PRO (CGG)

Best tRNA match for alternative specifier 1 >PRO (CGG) tRNA from Dialister invisus DSM 15470
CGGGGCATAGCGCAGTTTGGTAGCGCACTTGGTTCGGGACCAAGGGGTCGCAGGTTCAAATCCTGCTGCTCCGACCA

Predicted tRNA structure (((((((..((((.........)))).(((((.......))))).....(((((.......))))))))))))....

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)	-7.2
Terminator	ΔG° (kcal/mol	-14.2
	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	80.0
Bias	0.0
CM Accuracy	0.92

*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		[7,96]
Stem II region
Stem III
Specifier region	-	[83,85]
T-box UGGN locus	-	[164,167]
Antiterminator		[160,188]
Terminator		[177,210]
All stems	-	[[7, 96], [99, 113], [115, 126], [146, 155], [160, 188]]

Input source sequence >ACIM02000001.1:663464-663704
TTATGCACAAGGATGAAGAAGCGCTTTTGCAAGCTCTCCAGAGAGATGGTGGACGGTGGAAACCATCAGCAAACAATTGTCGTTCCGCTTCAGAGTGGTAGATGATGAATCTATCGGGTATGCCCGTTACAGCAGATTAAAGATGGCTGAAAAGCAATTTGGGTGGTATCGCGGGTGCTCTCGTCCCTTAGAGGATGAAGAGCGTTTTTTATTACACAGGATATTTTGTCCCTTTTGGTTT

INFERNAL output sequence >Infernal-ACIM02000001.1:663464-663704
UUAUGCACAAGGAUGAAG------AAGCGCUUUUGCAAGCUCUcCAGAGAGAUGGUGGACGGUGGAAACCAUCAGCAAACAAUUGUCGU--UCCGCUUCAGAGUGGUAGAU--G--------AUGA--AUCUAUCGGGUAUGCCCGUUACAGCAGAUUAAAGAUGGCU*[ 4]*AGCAAUUUGGGUGGUAUCGCGGG--UGCUCUCGUCCCUUAG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-ACIM02000001.1:663464-663704
::::::<<------<<<<-------<<<<<<-------<<<--.------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<~~~~~~>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::