T-box Riboswitch Annotation Database - TBDB - TWXREGPD from

T-box riboswitch TWXREGPD

Putative TRP (CCA) T-box riboswitch from Streptococcus salivarius SK126

Source information

TBDB ID	TWXREGPD
Host organism	Streptococcus salivarius SK126
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	ACLO01000062.1:194072-193776
Downstream protein description	hypothetical protein
Downstream protein ID	GenBank: EEK10316.1
T-box riboswitch length
Specifier loop sequence	UUGGG
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	UGG
Predicted tRNA family	TRP (CCA)
Found cognate tRNA	True
Alternative specifiers	UUG
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence TWXREGPD CAATAGTTAGTAAATCAGAAAGTAACTGGTCTTAGATTTTCAGGGAGCCTGCGGTGATTGTGAGTAGGTAATCGAGATGAGTGAACATTGGGCTGATTGGATGATAATGAGAAGGTAATACATATTCTTCTCGGTTGGCACCCCTTACCGTGCAACTCCTTGTTAGAGGAGATAGAGATGATGGTCGTTTTTTTGGAGACCATTAACTGAGGTGGTACCGTGTTAAACTAGATTTAATGCCCTCACAGAGTTTTTCTCTGTGAGGTTTTTT

Predicted secondary structures

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

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

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 Streptococcus salivarius SK126
ACGGGCATAGTTTAAAGGTAGAACTAAGGTCTCCAAAACCTTCAGTGTGGGTTCAATTCCTACTGCCCGTGCCA

Predicted tRNA structure (((((((..((((.......)))).(((((.......)))))....(((((.......))))))))))))....

Alternative specifier 1

Alternative 1 for predicted specifier: UUG
Alternative 1 for predicted tRNA family: LEU (CAA)

Best tRNA match for alternative specifier 1 >LEU (CAA) tRNA from Streptococcus salivarius SK126
GCCGGCGTGGCGGAATTGGCAGACGCGCTGGACTCAAAATCCAGTGTCCGCAAGGACGTGCCGGTTCGACCCCGGCCGCCGGTACCA

Predicted tRNA structure (((((((..(((...........))).(((((.......))))).((((....))))..(((((.......))))))))))))....

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)	-6.9
Terminator	ΔG° (kcal/mol	-17.7
	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	70.4
Bias	0.0
CM Accuracy	0.9

*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	-	[213,216]
Antiterminator		[209,244]
Terminator		[241,271]
All stems	-	[[7, 101], [104, 131], [133, 144], [180, 204], [209, 244]]

Input source sequence >ACLO01000062.1:194072-193776
CAATAGTTAGTAAATCAGAAAGTAACTGGTCTTAGATTTTCAGGGAGCCTGCGGTGATTGTGAGTAGGTAATCGAGATGAGTGAACATTGGGCTGATTGGATGATAATGAGAAGGTAATACATATTCTTCTCGGTTGGCACCCCTTACCGTGCAACTCCTTGTTAGAGGAGATAGAGATGATGGTCGTTTTTTTGGAGACCATTAACTGAGGTGGTACCGTGTTAAACTAGATTTAATGCCCTCACAGAGTTTTTCTCTGTGAGGTTTTTTGTTTACTTTTATCTTTAAAGAAGTGT

INFERNAL output sequence >Infernal-ACLO01000062.1:194072-193776
CAAUAGUUAGUAAAUCAG-AAAGUAACUGGUCU--UAGAUUUUCAGGGAGCCUGCGGUGAUUGUGAGUAGGUAAUCGA-GAUGAGUGAACauUGGGCUGAUUGGAUGAUAAUGAGAAgGUAAUACAUAUUCUUCUCGGUUGGCACCCCUUACcgugcaacuccuuguuAGAGGAGAUAGAGAUGAUGGUCGUUuuuUUGGAGACCAUUAACUGAGGUGGUACCGUGUUAaACUAgauuUAAUGCCCUCACA

INFERNAL output structure - (Antiterminator) >Infernal-Structure-ACLO01000062.1:194072-193776
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>----..---->>>>--->>,,<<<<<<<___.__________>>>>>>>,<<<______>>>,,,,................,,,,,,,,,,,,,,,<<<<<<<___..._____>>>>>>>,,,,<<<<-------<<<<<_.____...._>>>>>>>>>:::