T-box Riboswitch Annotation Database - TBDB - MANB2Q6Y from

T-box riboswitch MANB2Q6Y

Putative GLN (UUG) T-box riboswitch from Bacillus thuringiensis str. Al Hakam

Source information

TBDB ID	MANB2Q6Y
Host organism	Bacillus thuringiensis str. Al Hakam
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP000485.1:2562123-2562431
Downstream protein description	permease, possible major facilitator superfamily
Downstream protein ID	GenBank: ABK85679.1
T-box riboswitch length
Specifier loop sequence	CCAAG
T-box 5'-UGGN-3' sequence	UGGC
Predicted specifier	CAA
Predicted tRNA family	GLN (UUG)
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 MANB2Q6Y TCAAATGCATTGAAGAGAAGAGTAAATAAAATGAATTTTTCACAGAGAGCTCCATTTAGCTGAAAAGGAGTAAAAATTCCTTATTGAACCAAGCCTCTGAGCAGCGCATCTGAATCTATTAATAGAGGGTGGTGTGACGGGAGCTCCCGTTATAGAGCTATGGTATAAGCATGAATGAAAATGCAGTACCAGATAAGGTTAATATGGTGACATATTAACAAACTAGGGTGGCACCGCGATGATAAATCTCGTCCCTAAGACTAAAAGTCTTGGGGGTGGGATTTTTTT

Predicted secondary structures

T-box riboswitch MANB2Q6Y Antiterminator ......((......(((.......(((((........(((........(((((.............))))))))......))))).........)))...))..((((((....................)))))).(((......)))................................................(((((((........))))))).....((((.......((((.........))))))))................................

T-box riboswitch MANB2Q6Y Terminator ......((......(((.......(((((........(((........(((((.............))))))))......))))).........)))...))..((((((....................)))))).(((......)))................................................(((((((........)))))))...........................((((((((((((((((...)))))))))))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CAA
Top predicted tRNA family: GLN (UUG)

Best tRNA match for top specifier >GLN (UUG) tRNA from Bacillus thuringiensis str. Al Hakam
TGGGCTATAGCCAAGCGGTAAGGCAACGGACTTTGACTCCGTCATGCGCTGGTTCGAATCCAGCTAGCCCAGCCA

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)	-6.0
Terminator	ΔG° (kcal/mol	-21.2
	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	135.0
Bias	0.4
CM Accuracy	0.97

*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	-	[229,232]
Antiterminator		[225,256]
Terminator		[247,288]
All stems	-	[[7, 102], [105, 136], [138, 149], [198, 219], [225, 256]]

Input source sequence >CP000485.1:2562123-2562431
TCAAATGCATTGAAGAGAAGAGTAAATAAAATGAATTTTTCACAGAGAGCTCCATTTAGCTGAAAAGGAGTAAAAATTCCTTATTGAACCAAGCCTCTGAGCAGCGCATCTGAATCTATTAATAGAGGGTGGTGTGACGGGAGCTCCCGTTATAGAGCTATGGTATAAGCATGAATGAAAATGCAGTACCAGATAAGGTTAATATGGTGACATATTAACAAACTAGGGTGGCACCGCGATGATAAATCTCGTCCCTAAGACTAAAAGTCTTGGGGGTGGGATTTTTTTATTGTTTTAAAACAATTTGGA

INFERNAL output sequence >Infernal-CP000485.1:2562123-2562431
UCAAAUGCAUUGAAGAGA-AGAGUAAAUAAAAUGAAUUUUUCACAGAGAGCUCCAUUUAGCUGAAAAGGAGUAAAAAUUCCUUAUUGAACCAAGCCUCUGAGCAGCGCAUCUGAAUcuauuAAUAGAGGGUGGUGUGACGGGAGCUCCCGUUAUagagcuaugguauaagcaugaaugaaaauGCAGUACCAGAUAAGGUUAAUAUGGUGACAUAUUAACAAAcUAGGGUGGCACCGCGAUGAUAAaUCUCGUCCCUAAG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP000485.1:2562123-2562431
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<____....._________>>>>>>>,<<<______>>>,,,,.............................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,.,<<<<-------<<<<<_____._>>>>>>>>>:::