T-box Riboswitch Annotation Database - TBDB - KP5LPBFY from

T-box riboswitch KP5LPBFY

Putative ASN (GUU) T-box riboswitch from Bacillus subtilis gtP20b

Source information

TBDB ID	KP5LPBFY
Host organism	Bacillus subtilis gtP20b
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	AEHM01000050.1:55878-55598
Downstream protein description	-
Downstream protein ID	-
T-box riboswitch length
Specifier loop sequence	CAACA
T-box 5'-UGGN-3' sequence	UGGC
Predicted specifier	AAC
Predicted tRNA family	ASN (GUU)
Found cognate tRNA	True
Alternative specifiers	CAA
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence KP5LPBFY TTTGAACCAATAATGGAGAAGAGTAGGTCAGATTGCATGGCTAGAGAGGAACCGCCCCGGCTGAAAGCGGATCCCATTGCGTCTTTCTCGAAACAACACTCCGGAGGTTTCCTGCTGAACGCGTTAATCCCGTCATTAGGCAGTGAACGTGAACCTGCGTTAAAGGATCGAGCGGGAATATGAACATATTCCAACTAGGGTGGCACCACGGGTATAACTCTCGTCCCTACTATACATGTATAGTAGGGACGAGGGTTTTTTT

Predicted secondary structures

T-box riboswitch KP5LPBFY Antiterminator ......((......((((.......((..((.....(((........(((.((...............)).))))))......))..)).........))))...))..(((((((......................))))).)).(((......)))...............(((((((....)))))))....((((.......(((((.......)))))))))..................................

T-box riboswitch KP5LPBFY Terminator ......((......((((.......((..((.....(((........(((.((...............)).))))))......))..)).........))))...))..(((((((......................))))).)).(((......)))...............(((((((....))))))).........................(((((((((((((((((....))))))))))))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AAC
Top predicted tRNA family: ASN (GUU)

Best tRNA match for top specifier >ASN (GUU) tRNA from Bacillus subtilis gtP20b
TCCGCAGTAGCTCAGTGGTAGAGCTATCGGCTGTTAACCGATCGGTCGTAGGTTCGAATCCTACCTGCGGAGCCA

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

Alternative specifier 1

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

Best tRNA match for alternative specifier 1 >GLN (UUG) tRNA from Bacillus subtilis gtP20b
TGGGCTATAGCCAAGCGGTAAGGCAATGGACTTTGACTCCGTGATCGTTGGTTCGAATCCAGCTAGCCCAGCCA

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)	-7.6
Terminator	ΔG° (kcal/mol	-28.7
	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	111.3
Bias	0.0
CM Accuracy	0.94

*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		[7,107]
Stem II region
Stem III
Specifier region	-	[94,96]
T-box UGGN locus	-	[201,204]
Antiterminator		[197,228]
Terminator		[218,262]
All stems	-	[[7, 107], [110, 146], [148, 159], [175, 192], [197, 228]]

Input source sequence >AEHM01000050.1:55878-55598
TTTGAACCAATAATGGAGAAGAGTAGGTCAGATTGCATGGCTAGAGAGGAACCGCCCCGGCTGAAAGCGGATCCCATTGCGTCTTTCTCGAAACAACACTCCGGAGGTTTCCTGCTGAACGCGTTAATCCCGTCATTAGGCAGTGAACGTGAACCTGCGTTAAAGGATCGAGCGGGAATATGAACATATTCCAACTAGGGTGGCACCACGGGTATAACTCTCGTCCCTACTATACATGTATAGTAGGGACGAGGGTTTTTTTCATTTTCATCATTAACGAT

INFERNAL output sequence >Infernal-AEHM01000050.1:55878-55598
UUUGAACCAAUAAUGGAGAAGAGUAGGUCAGAU--UGCAUGGCUAGAGAGGAACCGCCCcgGCUGAAAgcGGAUCCCAUUGCgUCUUUCUCGAAAcAACACUCCGGAGGUUUCCUGCUGAACgcguuaaucCCGUCAUUAGGCAGuGAACGUGAACCUGCGUUA----AAGGAUCGAGCGGGAAUAU----GAACAUAUUCCAACUAGGGUGGCACCACGGGUAUAAcUCUCGUCCCUACU

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AEHM01000050.1:55878-55598
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<____.._______..>>>>>>>>>---.-->>>>>>----.---->>>>--->>,,<<<<<<<____........._________>>>>>.>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<_____._>>>>>>>>>:::