T-box Riboswitch Annotation Database - TBDB - JUCM2GY7 from - Sporolactobacillus laevolacticus DSM 442

T-box riboswitch JUCM2GY7

Putative MET (CAU) T-box riboswitch from Sporolactobacillus laevolacticus DSM 442

Source information

TBDB ID	JUCM2GY7
Host organism	Sporolactobacillus laevolacticus DSM 442
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	AWTC01000009.1:45505-45851
Downstream protein description	methionyl-tRNA synthetase
Downstream protein ID	GenBank: EST11647.1
T-box riboswitch length
Specifier loop sequence	AAUGG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AUG
Predicted tRNA family	MET (CAU)
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 JUCM2GY7 TGACACGCGATGAAGAGAAAAAGTAGGTGGCGAATCTTTTCACAGAGAGCTTCGATACGGTGAAAGAAGCAAAGAAATGCTATCCGAAAAATGGCCTTGGAGCGGCATACTGAGTTTTCGCAGGGACTCTGCTAGTCCATTCCCAGCACCGAATCAGCTAGGCTATGACGAGTAATGGTTCTCGTTATAAAAACCACAGTATAAGAGCTATTGGAAGCTCCGTACTTGCAGAGACTAATGATGTGAATTATTAGTAAAATTAGGTGGTACCACGTGGATTATACCCTCGTCCTGATGCAATTGCATTAGGACGGGGGTTTTTT

Predicted secondary structures

T-box riboswitch JUCM2GY7 Antiterminator ......((......(((........((((((......(((........(((((............)))))))).....)))).))..........)))...))..((((((.................................................)).)))).(((..........))).................................................(((((((........))))))).....((((.......(((.((.......)).))))))).............................

T-box riboswitch JUCM2GY7 Terminator ......((......(((........((((((......(((........(((((............)))))))).....)))).))..........)))...))..((((((.................................................)).)))).(((..........))).................................................(((((((........)))))))............................(((((((((((((((....)))))))))))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AUG
Top predicted tRNA family: MET (CAU)

Best tRNA match for top specifier >MET (CAU) tRNA from Sporolactobacillus laevolacticus DSM 442
GGCGGTGTAGCTCAGCTGGCTAGAGCGTACGGTTCATACCCGTGAGGTCGAGGGTTCGATCCCCCCCGCCGCTACCA

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)	-7.9
Terminator	ΔG° (kcal/mol	-28.5
	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	97.2
Bias	0.0
CM Accuracy	0.88

*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		[7,103]
Stem II region
Stem III
Specifier region	-	[90,92]
T-box UGGN locus	-	[265,268]
Antiterminator		[261,294]
Terminator		[284,323]
All stems	-	[[7, 103], [106, 167], [169, 184], [234, 255], [261, 294]]

Input source sequence >AWTC01000009.1:45505-45851
TGACACGCGATGAAGAGAAAAAGTAGGTGGCGAATCTTTTCACAGAGAGCTTCGATACGGTGAAAGAAGCAAAGAAATGCTATCCGAAAAATGGCCTTGGAGCGGCATACTGAGTTTTCGCAGGGACTCTGCTAGTCCATTCCCAGCACCGAATCAGCTAGGCTATGACGAGTAATGGTTCTCGTTATAAAAACCACAGTATAAGAGCTATTGGAAGCTCCGTACTTGCAGAGACTAATGATGTGAATTATTAGTAAAATTAGGTGGTACCACGTGGATTATACCCTCGTCCTGATGCAATTGCATTAGGACGGGGGTTTTTT

INFERNAL output sequence >Infernal-AWTC01000009.1:45505-45851
UGACACGCGAUGAAGAGAAAAAGUAGGUGGCGA-AUCUUUUCACAGAGAGCUU-CGAUAcGGUGAAAG-AAGCAAAGAAAUGCUAuCCGAAAaAUGGCCUUGGAGCGGCAUA-CUGAG*[46]*GGCUAUGACGAGUAAugguUCUCGUUAUaaaaaccacaguauaagagcuauuggaagcUCCGUACUUGCAGAGACUAAUGAUGUGAAUUAUUAGUAAAaUUAGGUGGUACCACGUGGAUUAuacCCUCGUCCUGAUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AWTC01000009.1:45505-45851
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<____._______>>>>>>>>>----->>>>.>>----.---->>>>--->>,,<<<<<<<___~~~~~~>>>>>>>,<<<____....__>>>,,,,..............................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,.,<<<<-------<<<<<_____..._>>>>>>>>>:::