T-box Riboswitch Annotation Database - TBDB - 2RK3MWPN from

T-box riboswitch 2RK3MWPN

Putative LEU (CAG) T-box riboswitch from Clostridium saccharolyticum WM1

Source information

TBDB ID	2RK3MWPN
Host organism	Clostridium saccharolyticum WM1
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP002109.1:1791438-1791736
Downstream protein description	leucyl-tRNA synthetase
Downstream protein ID	GenBank: ADL04281.1
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

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence 2RK3MWPN AAAAATACTGTGATTAGGAGTAGTAAGCTGTCTGAAACATGCAGAGAGCCGGCGAGTGGTGAAAGCCGGTTGGGGATGTCAGCTGAACTGGCCTTTGAGTAGCGTGCTGAAGGAAGCTCTGTTTCTGAGTAGGCATTGCCGGTGTCCCGACCGTTACAGCGGGGGGATATGTTTTTCTATATCCAGTGAGAGCATACGAAACTTGTATGAAATAGAGTGGTACCACGCGGTAGATTCTGCGTCTCTATGGCCGTATAAACGGTTAGAGGCGCATTTTTTT

Predicted secondary structures

T-box riboswitch 2RK3MWPN Antiterminator ......((.......(((.......(((((.......((........((((((...........)))))))).......))))).......)))....))..((((((.......................)))).)).(((........))).......................................(((((((...)))))))....((((.......((((((......))))))))))..................................

T-box riboswitch 2RK3MWPN 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] saccharolyticum WM1
GCAGAAGTGGCGGAATTGGCAGACGCGCACGGTTCAGGTCCGTGTGGTAGCAATACCTTGAGGGTTCAAGTCCCTTCTTCTGCACCA

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)	-9.4
Terminator	ΔG° (kcal/mol	-21.6
	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	125.4
Bias	0.0
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		[7,100]
Stem II region
Stem III
Specifier region	-	[87,89]
T-box UGGN locus	-	[218,221]
Antiterminator		[214,246]
Terminator		[238,280]
All stems	-	[[7, 100], [103, 138], [140, 153], [193, 209], [214, 246]]

Input source sequence >CP002109.1:1791438-1791736
AAAAATACTGTGATTAGGAGTAGTAAGCTGTCTGAAACATGCAGAGAGCCGGCGAGTGGTGAAAGCCGGTTGGGGATGTCAGCTGAACTGGCCTTTGAGTAGCGTGCTGAAGGAAGCTCTGTTTCTGAGTAGGCATTGCCGGTGTCCCGACCGTTACAGCGGGGGGATATGTTTTTCTATATCCAGTGAGAGCATACGAAACTTGTATGAAATAGAGTGGTACCACGCGGTAGATTCTGCGTCTCTATGGCCGTATAAACGGTTAGAGGCGCATTTTTTTATGTTCTCTTACGGGTATC

INFERNAL output sequence >Infernal-CP002109.1:1791438-1791736
AAAAAUACUGUGAUUAGGAGUAGUAAGCUGUCU--GAAACAUGCAGAGAGCCGGCGAGUGGUGAAAGCCGGUUGGGGAUGUCAGCUGAA-CUGGCCUUUGAGUAGCG-UGCUGAAGgaagcucuguUUCUGAGUAGGCAUUGCCGGUGUCccGACCGUUACagcggggggauauguuuuucUAUAUCCAGUGAGAGCAUACGA-----AACUUGUAUGAAAUAGAGUGGUACCACGCGGuAGA-uuCUGCGUCUCUAUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP002109.1:1791438-1791736
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<____.........._________>>>>>>>,<<<____..__>>>,,,,....................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_.____.._>>>>>>>>>:::