T-box Riboswitch Annotation Database - TBDB - 5BAW16RI from - Erysipelatoclostridium ramosum DSM 1402

T-box riboswitch 5BAW16RI

Putative PHE (GAA) T-box riboswitch from Erysipelatoclostridium ramosum DSM 1402

Source information

TBDB ID	5BAW16RI
Host organism	Erysipelatoclostridium ramosum DSM 1402
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	ABFX02000008.1:156776-157078
Downstream protein description	3-deoxy-7-phosphoheptulonate synthase
Downstream protein ID	GenBank: EDS17411.1
T-box riboswitch length
Specifier loop sequence	AUUCA
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	UUC
Predicted tRNA family	PHE (GAA)
Found cognate tRNA	False
Alternative specifiers	AUU,UCA
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence 5BAW16RI ATAAATACTGTGAAAAGAAATAGTAGGTATTCAAAATAGTTTAGAGAGCTCTTGGCTGGTGTAAAAGAGTCTATTAGAGAATATTGAATTCATCTTGGAGTAGAGGACTGAATCGTTAGTAGTAGGTCTCTCCGGCAACACCCGTTAACGTGTAAGAGTATGAACTATTTGATTAGCGTACTCGATGAGGTTAGTGTAGCAATACATTAATAAATTAAGGTGGTATCACGAAGCATAAGCTCTCGTCCTTTTATAGGAAGAGAGTTTTTT

Predicted secondary structures

T-box riboswitch 5BAW16RI Antiterminator ......((......((((.......((((((.....(((........((((((...........)))))))))......)))))).......))))...))..((((((...............)))).)).(((......))).............................................(((((((........))))))).....((((.......((((.((....))..))))))))....................

T-box riboswitch 5BAW16RI Terminator ......((......((((.......((((((.....(((........((((((...........)))))))))......)))))).......))))...))..((((((...............)))).)).(((......))).............................................(((((((........)))))))............................(((((.((((.....)))).)))))......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: UUC
Top predicted tRNA family: PHE (GAA)

Best tRNA match for top specifier >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 1

Alternative 1 for predicted specifier: AUU
Alternative 1 for predicted tRNA family: ILE (AAU)

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: UCA
Alternative 2 for predicted tRNA family: ILE (UGA)

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)	-5.3
Terminator	ΔG° (kcal/mol	-11.9
	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	140.7
Bias	2.8
CM Accuracy	0.98

*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	-	[221,224]
Antiterminator		[217,250]
Terminator		[240,270]
All stems	-	[[7, 101], [104, 131], [133, 144], [190, 211], [217, 250]]

Input source sequence >ABFX02000008.1:156776-157078
ATAAATACTGTGAAAAGAAATAGTAGGTATTCAAAATAGTTTAGAGAGCTCTTGGCTGGTGTAAAAGAGTCTATTAGAGAATATTGAATTCATCTTGGAGTAGAGGACTGAATCGTTAGTAGTAGGTCTCTCCGGCAACACCCGTTAACGTGTAAGAGTATGAACTATTTGATTAGCGTACTCGATGAGGTTAGTGTAGCAATACATTAATAAATTAAGGTGGTATCACGAAGCATAAGCTCTCGTCCTTTTATAGGAAGAGAGTTTTTTATTTATATACAGAGTTGAAATAAAACAAAAGGG

INFERNAL output sequence >Infernal-ABFX02000008.1:156776-157078
AUAAAUACUGUGAAAAGAAAUAGUAGGUAUUCA--AAAUAGUUUAGAGAGCUCUUGGCUGGUGUAAAAGAGUCUAUUAgAGAAUAUUGAA-UUCAUCUUGGAGUAGAG-GACUGAAUcgUUAGUAGUAGGUCUCUCCGGCAACACCCGUUAAcguguaagaguaugaacuauuugauuAGCGUACUCGAUGAGGUUAGUGUAGCAAUACAUUAAUAAAuUAAGGUGGUAUCACGAAGcAUAAgcUCUCGUCCUUUUA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-ABFX02000008.1:156776-157078
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<____.._________>>>>>>>,<<<______>>>,,,,..........................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,.,<<<<-------<<<<<_.____.._>>>>>>>>>:::