T-box Riboswitch Annotation Database - TBDB - MOHAJCNC from

T-box riboswitch MOHAJCNC

Putative LEU (GAG) T-box riboswitch from Desulfosporosinus acidiphilus SJ4

Source information

TBDB ID	MOHAJCNC
Host organism	Desulfosporosinus acidiphilus SJ4
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	CP003639.1:4214928-4214679
Downstream protein description	leucyl-tRNA synthetase
Downstream protein ID	GenBank: AFM42914.1
T-box riboswitch length
Specifier loop sequence	ACUCG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	CUC
Predicted tRNA family	LEU (GAG)
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 MOHAJCNC TTAAAAGCTGGGAAAGGAAGCAGTACTCAAAAACCTTCTTTAGAGAAGCGGCGGTAGGTGCAAGTCGTTGAAGGGGATTGCAGGAACTCGTCCTGGAGCTGTGTTCAGGTAACAATGAACACCGGTGCGAACCGTTAAAGTCTTACGAGTGAATTTGGAAAATTGGGTGGTATCACGGGAGCAGGCCTCTCGTCCCTTGGGACGAGAGGATTTTT

Predicted secondary structures

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

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

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CUC
Top predicted tRNA family: LEU (GAG)

Best tRNA match for top specifier >LEU (GAG) tRNA from Desulfosporosinus acidiphilus SJ4
GCGGGAGTGGCGTAATTGGCAGACGCGCACGTTTGAGGGGCGTGTGGGTAACTCCGTACGGGTTCAAGTCCCGTCTTCCGCACCA

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)	-10.4
Terminator	ΔG° (kcal/mol	-19.3
	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	107.6
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		[7,99]
Stem II region
Stem III
Specifier region	-	[86,88]
T-box UGGN locus	-	[168,171]
Antiterminator		[164,197]
Terminator		[186,215]
All stems	-	[[7, 99], [102, 121], [123, 134], [150, 159], [164, 197]]

Input source sequence >CP003639.1:4214928-4214679
TTAAAAGCTGGGAAAGGAAGCAGTACTCAAAAACCTTCTTTAGAGAAGCGGCGGTAGGTGCAAGTCGTTGAAGGGGATTGCAGGAACTCGTCCTGGAGCTGTGTTCAGGTAACAATGAACACCGGTGCGAACCGTTAAAGTCTTACGAGTGAATTTGGAAAATTGGGTGGTATCACGGGAGCAGGCCTCTCGTCCCTTGGGACGAGAGGATTTTT

INFERNAL output sequence >Infernal-CP003639.1:4214928-4214679
UUAAAAGCUGGGAAAGGAAGCAGUACUCAAAA---ACCUUCUUUAGAGAAGCGGCGGUAGGUGCAAGUCGUUGAAGGGGAUUGCAGGAA-CUCGUCCUGGAGCUGUGUUCAGGUA-------ACAAUGAACACCGGUGCGAACCGUUA----AAGUCUUACGAGUGA-------A*[4]*-----GAAAAUUGGGUGGUAUCACGGGAGCAGgccUCUCGUCCCUUGG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-CP003639.1:4214928-4214679
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<____~~~~~>>>>>>>,,,,<<<<-------<<<<<_____..._>>>>>>>>>:::