T-box Riboswitch Annotation Database - TBDB - 7MHRFFR from

T-box riboswitch 7MHRFFR

Putative TRP (CCA) T-box riboswitch from Clostridium isatidis

Source information

TBDB ID	7MHRFFR
Host organism	Clostridium isatidis
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP016786.1:2740132-2739588
Downstream protein description	trpE - anthranilate synthase component I
Downstream protein ID	GenBank: ASW44303.1
T-box riboswitch length
Specifier loop sequence	AUGGG
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 7MHRFFR TTAAAATCTAGGAGCAGAAGGAGTAGATATAGGAGCTTAGTTTAAGCGAGTCTGGGATGGTGAGAGCCAGGTACTGTAGTCTATATTGAATGGGTCTGTGAGATGATATGTGAAATTATAGTAGCATTTTCCGGGAGTCAGCCGTTACAATGACAGGGTATCGATATTATTCCGTACCTGATAAAGATAAATTTGCATTTAGGTGGCATAGCGAGTATAACATCTCGTCCTATTGGACGAGGTGTTTTTTTGCTATATATGCTTGCTTAATAATGTGAATTTAATATGGGTGGCACCGCGAGTCACTTCGTCCCATTATAAGGATGAAGTGGCTTTTTTTT

Predicted secondary structures

T-box riboswitch 7MHRFFR Antiterminator ......((......((((.......((((((.......(((........((((((...........)))))))))......)))))).......))))...)).((.((((............)))).)).(((.......)))............................................(((((((................................................................................)))))))....((((.......(((((....)))))))))..........................

T-box riboswitch 7MHRFFR 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 Clostridium isatidis
AGGGGTATAGCTCAATTGGTAGAGTAGCGGTCTCCAAAACCGTTGGTTGTGGGTTCGATTCCTACTGCCCCTGCCA

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)	-6.3
Terminator	ΔG° (kcal/mol	-18.7
	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	110.1
Bias	2.2
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		[132,228]
Stem II region
Stem III
Specifier region	-	[215,217]
T-box UGGN locus	-	[416,419]
Antiterminator		[412,440]
Terminator		[427,466]
All stems	-	[[132, 228], [230, 255], [257, 269], [314, 407], [412, 440]]

Input source sequence >CP016786.1:2740132-2739588
AATAAAAACATCAAGCATTTGCTTGATGTTTTTTTGTTTTTATTAAAAATATTATTAAAAAGCTATTGACTAAATATTATGAGTGTAATAAAATGGATTAAAATATTATCAATGTAAAAAACAGGTTAAAATCTAGGAGCAGAAGGAGTAGATATAGGAGCTTAGTTTAAGCGAGTCTGGGATGGTGAGAGCCAGGTACTGTAGTCTATATTGAATGGGTCTGTGAGATGATATGTGAAATTATAGTAGCATTTTCCGGGAGTCAGCCGTTACAATGACAGGGTATCGATATTATTCCGTACCTGATAAAGATAAATTTGCATTTAGGTGGCATAGCGAGTATAACATCTCGTCCTATTGGACGAGGTGTTTTTTTGCTATATATGCTTGCTTAATAATGTGAATTTAATATGGGTGGCACCGCGAGTCACTTCGTCCCATTATAAGGATGAAGTGGCTTTTTTTTATTAAATTATAAGGATTGGAGGTTTTATTATGATCACTATGACCAAAGAGCAATTCAATGAATTAAAAAAGAGAAAGAA

INFERNAL output sequence >Infernal-CP016786.1:2740132-2739588
UUAAAAUCUAGGAGCAGAAGGAGUAGAUAUAGGAGCUUAGUUUAAGCGAGUCUGGGAU-GGUGAGAgCCAGGUACUGUAgUCUAUAUUGAA-UGGGUCUGUGAGA-UGAUAUGUGAA-AUUAUAGUAGCAUUUUCCGGGAGUcAGCCGUUACaaugacaggguaucgauauuauuccgua---CCUGAUAAAGAUAAAUUUGCAUuuagguggcauagcgaguauaacaucucguccuauuggacgagguguuuuuuugcuauauaugcuugcuuaaUAAUGUGAAUUUAAUAUGGGUGGCACCGCGAG--UCACUUCGUCCCAUUA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP016786.1:2740132-2739588
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<____.__>>>,,,,............................,,,,,,,,,,,,,,,<<<<<<<___........................................................................_____>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::