T-box Riboswitch Annotation Database - TBDB - GZMJXBD2 from

T-box riboswitch GZMJXBD2

Putative ASN (GUU) T-box riboswitch from Lactobacillus amylovorus

Source information

TBDB ID	GZMJXBD2
Host organism	Lactobacillus amylovorus
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP002559.1:1988584-1988878
Downstream protein description	asparagine synthetase AsnA
Downstream protein ID	GenBank: ADZ08150.1
T-box riboswitch length
Specifier loop sequence	AAACA
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AAC
Predicted tRNA family	ASN (GUU)
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 GZMJXBD2 TAAAAAGCTATGAAAAAGACGAGTAAATAATCTAATTCTTTCCAGTGAATTAGTGCTAGTGCGAAACTAATAGACCCTGGATTATTGAAAAACACTTTTAGCAGCTCACCGAACTAACAATTCTTATAGTAGGTTGAGACGTCTCCGGTACGTTACCACGCCGGTGGAGCATGATAGTGTTTCATGAGGAGGTCTATTTATAGACAACATGGGTGGTACCGCGGAAAAAGCCTTTCGTCCCTAACAATTAGGGAGCGAAGGGCTTTTT

Predicted secondary structures

T-box riboswitch GZMJXBD2 Antiterminator ......((......((((.......((((((.....(((.........((((((...........)))))))))......))))))........))))..))..((((((.....................)).)))).(((.......))).......................................(((((....))))).....(((.......((((((......)))))))))...........................

T-box riboswitch GZMJXBD2 Terminator ......((......((((.......((((((.....(((.........((((((...........)))))))))......))))))........))))..))..((((((.....................)).)))).(((.......))).......................................(((((....)))))........................(((((((((((((((...))))))).)))))))).....

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AAC
Top predicted tRNA family: ASN (GUU)

Best tRNA match for top specifier >ASN (GUU) tRNA from Lactobacillus amylovorus
TCCGGCTTAGCTCAGTTGGTAGAGCGCTTGACTGTTAATCAAGATGTCGTCAGTTCGAGTCTGACAGCCGGAGCCA

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	-21.9
	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	110.8
Bias	0.0
CM Accuracy	0.93

*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	-	[90,92]
T-box UGGN locus	-	[214,217]
Antiterminator		[210,242]
Terminator		[230,268]
All stems	-	[[7, 102], [105, 138], [140, 152], [192, 205], [210, 242]]

Input source sequence >CP002559.1:1988584-1988878
TAAAAAGCTATGAAAAAGACGAGTAAATAATCTAATTCTTTCCAGTGAATTAGTGCTAGTGCGAAACTAATAGACCCTGGATTATTGAAAAACACTTTTAGCAGCTCACCGAACTAACAATTCTTATAGTAGGTTGAGACGTCTCCGGTACGTTACCACGCCGGTGGAGCATGATAGTGTTTCATGAGGAGGTCTATTTATAGACAACATGGGTGGTACCGCGGAAAAAGCCTTTCGTCCCTAACAATTAGGGAGCGAAGGGCTTTTTCTTTACTCTCAACTAAAAACAAAAATA

INFERNAL output sequence >Infernal-CP002559.1:1988584-1988878
UAAAAAGCUAUGAAAAAGACGAGUAAAUAAUCU--AAUUCUUUcCAGUGAAUUAGUGCU-AGUGCGAaACUAAUAGACCCuGGAUUAUUGAAAAACACUUU-UAGCAGCUCA-CCGAACuaacaauuCUUAUAGUAGGUUGAGACGUCUCCgGUACGUUACcacgccgguggagcaugauaGUGUUUCAUGAGGAGGUCUAUU--------UAUAGACAACAUGGGUGGUACCGCGGAAAAAGccUUUCGUCCCUAAC

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP002559.1:1988584-1988878
::::::<<------<<<<-------<<<<<<-------<<<--.------<<<<<<___________.>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<____........_________>>>>>>>,<<<____.__>>>,,,,....................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_____.._>>>>>>>>>:::