T-box Riboswitch Annotation Database - TBDB - 01OCB6Q from - Listeria seeligeri serovar 1/2b str. SLCC3954

T-box riboswitch 01OCB6Q

Putative HIS (GUG) T-box riboswitch from Listeria seeligeri serovar 1/2b str. SLCC3954

Source information

TBDB ID	01OCB6Q
Host organism	Listeria seeligeri serovar 1/2b str. SLCC3954
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	FN557490.1:1758373-1757919
Downstream protein description	amino acid ABC transporter, permease protein
Downstream protein ID	ENA: CBH27862.1
T-box riboswitch length
Specifier loop sequence	ACACA
T-box 5'-UGGN-3' sequence	UGGA
Predicted specifier	CAC
Predicted tRNA family	HIS (GUG)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence 01OCB6Q GTGAAAGCGTTGAACAGAACAAGTAGAGCGTGATTCTTTTCAAAGAGAGTCCTTGGTTGGTGCGAAAGGATAAAGATAGCGTTATCGAACACATCTAGGAGCTGGTTTGCTGAACAATTGTAAGTAGGTAAACTCGGGAAAAGCCCGTTATCGCTTGTTAGTCTAGAACTAACGGAGGCTAGTACTGCGAAGTATTAGTAAATTGAGGTGGAACCACGTGAATAATATTCTCGTCCTCTTGGCAATTTTATGCCAAGACGACGAGATTTTTTT

Predicted secondary structures

T-box riboswitch 01OCB6Q Antiterminator ......((.......(((.......((..((......(((........((((((...........)))))))))......))..)).......)))....))..(((((((...............))))))).(((.......)))..............................(((((((........))))))).....((((.......(((.((((...)))).)))))))...................................

T-box riboswitch 01OCB6Q Terminator ......((.......(((.......((..((......(((........((((((...........)))))))))......))..)).......)))....))..(((((((...............))))))).(((.......)))..............................(((((((........))))))).............................(((((((.((((((((......)))))))).))))))).......

Specifier and tRNA predictions

Top specifier

Top predicted specifier: CAC
Top predicted tRNA family: HIS (GUG)

Best tRNA match for top specifier >HIS (GUG) tRNA from Listeria seeligeri serovar 1/2b str. SLCC3954
GCGGGTGTGGCGAAGTGGTTAACGCACCTGATTGTGGTTCAGGCATTCGTGGGTTCGATTCCCATCATCCGCCCCA

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)	-9.9
Terminator	ΔG° (kcal/mol	-24.2
	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	133.3
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		[115,210]
Stem II region
Stem III
Specifier region	-	[197,199]
T-box UGGN locus	-	[317,320]
Antiterminator		[313,346]
Terminator		[337,381]
All stems	-	[[115, 210], [213, 241], [243, 255], [286, 307], [313, 346]]

Input source sequence >FN557490.1:1758373-1757919
TAAAATGCGGTAAACAAACGAAATACGAGTTGTTTACTGCTTTTTTATTGTTCAAAAATAAATAGTTGACTCTACCGCTTTATCGTGGTAGAGTATTAACAAGAAGAAGTGAAAGCGTTGAACAGAACAAGTAGAGCGTGATTCTTTTCAAAGAGAGTCCTTGGTTGGTGCGAAAGGATAAAGATAGCGTTATCGAACACATCTAGGAGCTGGTTTGCTGAACAATTGTAAGTAGGTAAACTCGGGAAAAGCCCGTTATCGCTTGTTAGTCTAGAACTAACGGAGGCTAGTACTGCGAAGTATTAGTAAATTGAGGTGGAACCACGTGAATAATATTCTCGTCCTCTTGGCAATTTTATGCCAAGACGACGAGATTTTTTTATGCAAAAAAAGGAGCGAATCAAAATGGACTATATCATGGAAATTTTACCGGCATTACTGGATGGAGCAAAAAC

INFERNAL output sequence >Infernal-FN557490.1:1758373-1757919
GUGAAAGCGUUGAACAGAACAAGUAGAGCGUGA-UUCUUUUCAAAGAGAGUCCUUGGUUGGUGCGAAAGGAUAAAGAUaGCGUUAUCGAA-CACAUCUAGGAGCUGGUUUGCUGAAc-aaUUGUAAGUAGGUAAACUCGGGAAAaGCCCGUUAUcgcuuguuaguCUAGAACUAACGGAGGCUAGUACUGCGAAGUAUUAGUAAAuUGAGGUGGAACCACGUGAAUAAuauUCUCGUCCUCUUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-FN557490.1:1758373-1757919
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<___._.._________>>>>>>>,<<<____.__>>>,,,,...........,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,.,<<<<-------<<<<<_____..._>>>>>>>>>:::