T-box Riboswitch Annotation Database - TBDB - YYROUSSA from

T-box riboswitch YYROUSSA

Putative TRP (CCA) T-box riboswitch from Chloroflexi bacterium OLB15

Source information

TBDB ID	YYROUSSA
Host organism	Chloroflexi bacterium OLB15
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	LMZS01000133.1:17915-18228
Downstream protein description	trpE - anthranilate synthase component I
Downstream protein ID	GenBank: KXK16886.1
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	Full

Genomic Context

Error loading NCBI Genome Browser - Cookies disabled To use the NCBI genome browser for visualizing genetic context of T-box riboswitch sequences, please enable cookies on your web browser.

Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence YYROUSSA TCAATGATGTTGATCTGAACGAGTATGTGGCATACACCGTGTTCAGAGAGCCGCTAGCTGCTGCGAAGGCGGTACACAGGAAGCCACAGAATGGATCAGGGAGTCGCGCAGGCGAACCGCAAGCAGTAGCCCGCGCCGGGAAAGCGCACCCGTTATCAATGCGCGGGGTATCGGCTCTTAAACGCCCGTACCTTATGAATGAGCGGTCATCGTATTGATGATCATCAAGGTGGCACCACGGGAAAGCCTCTTCTCGTCCTTGTTACGGGAGAGGCTTTTT

Predicted secondary structures

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

T-box riboswitch YYROUSSA 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 Chloroflexi bacterium OLB15
AGGGGCGTGGTGAAACGGCATCATTACTCTCTCCAAAAGAGTCGTTCTTGGTTCGAATCCAGGCGCCCCTGCCA

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)	-8.0
Terminator	ΔG° (kcal/mol	-15.2
	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	110.1
Bias	0.0
CM Accuracy	0.96

*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		[7,104]
Stem II region
Stem III
Specifier region	-	[91,93]
T-box UGGN locus	-	[231,234]
Antiterminator		[227,261]
Terminator		[246,280]
All stems	-	[[7, 104], [107, 135], [137, 152], [206, 222], [227, 261]]

Input source sequence >LMZS01000133.1:17915-18228
TCAATGATGTTGATCTGAACGAGTATGTGGCATACACCGTGTTCAGAGAGCCGCTAGCTGCTGCGAAGGCGGTACACAGGAAGCCACAGAATGGATCAGGGAGTCGCGCAGGCGAACCGCAAGCAGTAGCCCGCGCCGGGAAAGCGCACCCGTTATCAATGCGCGGGGTATCGGCTCTTAAACGCCCGTACCTTATGAATGAGCGGTCATCGTATTGATGATCATCAAGGTGGCACCACGGGAAAGCCTCTTCTCGTCCTTGTTACGGGAGAGGCTTTTT

INFERNAL output sequence >Infernal-LMZS01000133.1:17915-18228
UCAAUGAUGUUGAUCUGAACGAGUAUGUGGCAUACACCGUGUUCAGAGAGCCGCUAGCUGCUGCGAaGGCGGUaCACAGGAAGCCACAGAA-UGGAUCAGGGAGUCGCGCAGGCGAAc-cgCAAGCAGUAGCCCGCGCCGGGAAAgcgcACCCGUUAUcaaugcgcgggguaucggcucuuaaacgcccguaCCUUAUGAAUGAGCGGUCAUCG-----UAUUGAUGAUCAUCAAGGUGGCACCACGGGAAAGCcucuUCUCGUCCUUGUU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-LMZS01000133.1:17915-18228
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>.>>>----->>>>>>-------->>>>--->>,,<<<<<<<___._.._________>>>>>>>,<<<____....__>>>,,,,..................................,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_____...._>>>>>>>>>:::