T-box Riboswitch Annotation Database - TBDB - LUGQQE6U from

T-box riboswitch LUGQQE6U

Putative TRP (CCA) T-box riboswitch from Butyrivibrio crossotus DSM 2876

Source information

TBDB ID	LUGQQE6U
Host organism	Butyrivibrio crossotus DSM 2876
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	ABWN01000043.1:25238-24951
Downstream protein description	trpE - anthranilate synthase component I
Downstream protein ID	GenBank: EFF67334.1
T-box riboswitch length
Specifier loop sequence	AUGGA
T-box 5'-UGGN-3' sequence	UGGC
Predicted specifier	UGG
Predicted tRNA family	TRP (CCA)
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 LUGQQE6U TTTAAACCGTTGAAGTGGAGATAACGTTAGTTGTTGCACACACAGAGAGCCTGGGATGGTGAGAGCTGGGTTGAACGCAGATTATCAAATGGACCACTGAGGGCATAGTGAACAGCTAAGGGCTTAGTATTCTATGACGTAGGGCATACGTTAGTTGCCTGGGATATGTTGGTATCTCGAAGAGAGCACATTTTATGTGAATCAAGGTGGCACCGCGGATTGAATATTCGCCCTTGACAATATTAATGATATTGTCAGGGGCTTTTTT

Predicted secondary structures

T-box riboswitch LUGQQE6U Antiterminator ......((......((((.......((.(.........((........((((((...........))))))))........).))........))))...)).(((((.(...................).))))).(((.......)))....................................(((((...)))))....((((.......((((((.....)))))))))).................................

T-box riboswitch LUGQQE6U Terminator ......((......((((.......((.(.........((........((((((...........))))))))........).))........))))...)).(((((.(...................).))))).(((.......)))....................................(((((...)))))..............................(((((((((((((((...)))))))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UGG
Top predicted tRNA family: TRP (CCA)

Best tRNA match for top specifier >TRP (CCA) tRNA from Butyrivibrio crossotus DSM 2876
AGGGGTATAGTTCAGCTGGTAGAATATCGGTCTCCAAAACCGCAGGTCGTGGGTTCGAATCCTACTGCCCCTGCCA

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)	-6.8
Terminator	ΔG° (kcal/mol	-22.7
	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	75.6
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		[7,102]
Stem II region
Stem III
Specifier region	-	[89,91]
T-box UGGN locus	-	[208,211]
Antiterminator		[204,235]
Terminator		[230,268]
All stems	-	[[7, 102], [104, 136], [138, 150], [187, 199], [204, 235]]

Input source sequence >ABWN01000043.1:25238-24951
TTTAAACCGTTGAAGTGGAGATAACGTTAGTTGTTGCACACACAGAGAGCCTGGGATGGTGAGAGCTGGGTTGAACGCAGATTATCAAATGGACCACTGAGGGCATAGTGAACAGCTAAGGGCTTAGTATTCTATGACGTAGGGCATACGTTAGTTGCCTGGGATATGTTGGTATCTCGAAGAGAGCACATTTTATGTGAATCAAGGTGGCACCGCGGATTGAATATTCGCCCTTGACAATATTAATGATATTGTCAGGGGCTTTTTTATTGCTTCCTGACAGGAAAG

INFERNAL output sequence >Infernal-ABWN01000043.1:25238-24951
UUUAAACCGUUGAAGUGG-AGAUAACGUUAGUUGUUGCACACACAGAGAGCCUGGGAU-GGUGAGAgCUGGGUUGAACGcAGAUUAUC-AAAUGGACCACUGAGG-GCAUAGUGAACAgcuaagGGCUUAGUAUUCUAUGACGUAGGGcAUACGUUAGuugccugggauauguugGUAUCUCGAAGAGAGCACAU-------UUU--AUGUGAAUCAAGGUGGCACCGCGGAUugAAU-AUUCGCCCUUGAC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-ABWN01000043.1:25238-24951
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<____......_________>>>>>>>,<<<____.__>>>,,,,.................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_.._____>>>>>>>>>:::