T-box Riboswitch Annotation Database - TBDB - EYIENOJ from - Enterococcus casseliflavus ATCC 12755

T-box riboswitch EYIENOJ

Putative TRP (CCA) T-box riboswitch from Enterococcus casseliflavus ATCC 12755

Source information

TBDB ID	EYIENOJ
Host organism	Enterococcus casseliflavus ATCC 12755
Model used	Class I
Predicted regulation	Unknown
T-box riboswitch genomic accession	AEWT01000016.1:151802-152064
Downstream protein description	trpE - anthranilate synthase component I
Downstream protein ID	GenBank: EGC69405.1
T-box riboswitch length
Specifier loop sequence	AUGGA
T-box 5'-UGGN-3' sequence	UGGC
Predicted specifier	UGG
Predicted tRNA family	TRP (CCA)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Partial

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence EYIENOJ ATTAAGACTAAACAAAAGAGAAGTATGAGGACGTTCGTCTTGCAGAGAGCTGATGGTGGTGCAAATCAGCAGATTGACGCTTCAGAAATGGACTTTTGTGTCGAAAGGCTGAAATCAGTAGGCTTTTTCCGGGAACTCCCGTTACAGAGAACGATCGTTGATAGACGATCTAGAGAACCAATTGAGGTGGCACCGTGAGTAATCGCCCTCAGGCAGACAAGTTTGTTT

Predicted secondary structures

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

T-box riboswitch EYIENOJ Terminator Error: TBDB structure refinement failed to predict a terminator structure for this T-box

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UGG
Top predicted tRNA family: TRP (CCA)

Best tRNA match for top specifier >TRP (CCA) tRNA from Enterococcus casseliflavus ATCC 12755
AGGGGCATAGTTTAAAGGTAGAACAGCGGTCTCCAAAACCGTTAGTGTGGGTTCAATTCCTGCTGCCCCTGCCA

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	-30.0
	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	99.1
Bias	0.0
CM Accuracy	0.85

*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		[7,101]
Stem II region
Stem III
Specifier region	-	[88,90]
T-box UGGN locus	-	[188,191]
Antiterminator		[184,210]
Terminator		[205,228]
All stems	-	[[7, 101], [104, 128], [130, 141], [184, 210]]

Input source sequence >AEWT01000016.1:151802-152064
ATTAAGACTAAACAAAAGAGAAGTATGAGGACGTTCGTCTTGCAGAGAGCTGATGGTGGTGCAAATCAGCAGATTGACGCTTCAGAAATGGACTTTTGTGTCGAAAGGCTGAAATCAGTAGGCTTTTTCCGGGAACTCCCGTTACAGAGAACGATCGTTGATAGACGATCTAGAGAACCAATTGAGGTGGCACCGTGAGTAATCGCCCTCAGGCAGACAAGTTTGTTTGCCTGAGGGCTTTTTTGTTTTTCTTGCCCTTCAAC

INFERNAL output sequence >Infernal-AEWT01000016.1:151802-152064
AUUAAGACUAAACAAAAGAGAAGUAUGAGGACG-UUCGUCUUGCAGAGAGCUGAUGGU-GGUGCAAAUCAGCAGAUUGACGCUUCAGAAAUGGACUUUUGUGUCGAAAGGCUGAA---AUCAGUAGGCUUuUUCCGGGAACUCCCGUUAC---AGAGAACGAUCGUUGAUAG--A*[7]*-------gagaaccAAUUGAGGUGGCACCGUGA--GUAA--UCGCCCUCAGG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AEWT01000016.1:151802-152064
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>-------->>>>--->>,,<<<<<<<_____________>>>>>.>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<___~~~~~>>>>>>>.......,,,,<<<<-------<<<<<______>>>>>>>>>:::