T-box Riboswitch Annotation Database - TBDB - UU3AY4E from

T-box riboswitch UU3AY4E

Putative SER (GGA) T-box riboswitch from Phascolarctobacterium sp. CAG:207

Source information

TBDB ID	UU3AY4E
Host organism	Phascolarctobacterium sp. CAG:207
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	FR885210.1:65990-66244
Downstream protein description	d-3-phosphoglycerate dehydrogenase
Downstream protein ID	ENA: CDB45289.1
T-box riboswitch length
Specifier loop sequence	UUCCG
T-box 5'-UGGN-3' sequence	UGGC
Predicted specifier	UCC
Predicted tRNA family	SER (GGA)
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 UU3AY4E ATTTATCCGACGATGGAGAAAAGTAAGTTGGCAGGCGGCAAAGAGAAGCGGCGGTCAGTGTAAGCCGTAACGTCTAAAAACTGAATTCCGCTCCGGAGGAGACAGGGGTAGCAACCTGTCCGGGTCCGACCGATATATCGGCAATGAGGCCGCGCTGTGCGGCGAAAAAAGGTGGCACCACGTGAGTAGAACTCTCGTCCTTGATTGTAATTGATCAAGCCGGGAGTTTTTT

Predicted secondary structures

T-box riboswitch UU3AY4E Antiterminator ......((......((((.......((((......((..........(((((...........)))))..))......))))........))))...))..(((((........))))).(((......)))................((((((...)))))).....((((.......(((.((((...)))).)))))))..............................

T-box riboswitch UU3AY4E Terminator ......((......((((.......((((......((..........(((((...........)))))..))......))))........))))...))..(((((........))))).(((......)))................((((((...))))))............................((((((..((((((((....)))))))).))))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UCC
Top predicted tRNA family: SER (GGA)

Best tRNA match for top specifier >SER (GGA) tRNA from Phascolarctobacterium sp. CAG:207
GGAGAGATGACCGAGCGGTTGAAGGTGCACGCCTGGAAAGCGTGTGTACGGGAAACCGTACCGAGGGTTCGAATCCCTCTCTCTCCGCCA

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)	-9.7
Terminator	ΔG° (kcal/mol	-14.3
	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	100.0
Bias	0.0
CM Accuracy	0.92

*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	-	[173,176]
Antiterminator		[169,202]
Terminator		[192,232]
All stems	-	[[7, 99], [102, 119], [121, 132], [149, 163], [169, 202]]

Input source sequence >FR885210.1:65990-66244
ATTTATCCGACGATGGAGAAAAGTAAGTTGGCAGGCGGCAAAGAGAAGCGGCGGTCAGTGTAAGCCGTAACGTCTAAAAACTGAATTCCGCTCCGGAGGAGACAGGGGTAGCAACCTGTCCGGGTCCGACCGATATATCGGCAATGAGGCCGCGCTGTGCGGCGAAAAAAGGTGGCACCACGTGAGTAGAACTCTCGTCCTTGATTGTAATTGATCAAGCCGGGAGTTTTTT

INFERNAL output sequence >Infernal-FR885210.1:65990-66244
AUUUAUCCGACGAUGGAGAAAAGUAAGUUGGC---AGGCGGCAAAGAGAAGCGGCGGUCAGUGUAAGCCGUAACGUCUaAA--AACUGAAUUCCGCUCCGGAGGAGACAGGG-GU-------AGCAA-CCUGUCCGGGUCCGACCGAUA---UAUCGGCAAUGAGGCCGCGC-------UGUGCGGCgAAAAAAGGUGGCACCACGUGAguAGAAcUCUCGUCCUUGAU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-FR885210.1:65990-66244
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>.,,,,<<<<-------<<<<<_..____._>>>>>>>>>:::