T-box Riboswitch Annotation Database - TBDB - RSZVYWZD from - Lactobacillus farraginis DSM 18382 = JCM 14108

T-box riboswitch RSZVYWZD

Putative HIS (GUG) T-box riboswitch from Lactobacillus farraginis DSM 18382 = JCM 14108

Source information

TBDB ID	RSZVYWZD
Host organism	Lactobacillus farraginis DSM 18382 = JCM 14108
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	BAKI01000007.1:13726-13418
Downstream protein description	histidinol dehydrogenase
Downstream protein ID	DDBJ: GAF36062.1
T-box riboswitch length
Specifier loop sequence	ACACA
T-box 5'-UGGN-3' sequence	UGGG
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 RSZVYWZD TATGAAGTTACGATTAGAAAAGTAAGCGATGAACTAACATAAAGAGAGTCCCGGCGGTGAGAACGGATTGTTGGTATTGCTGAAAACACATCTATGAACTGGATAATTGAACCAAGTAGGTTGTCCCGCTAGTGAGCGTTACCACGGCTGCTGTAACTGTTCTTCATTACTAATGGACGACTAGTTGCAGACAGTGTAAGGTCGTTTCATCGTGAGGTGGCGGCAAAATGAGGTGGGACCGCGAGAAATCGTCCTCAGGTATTGGATAACAATATCTGAGGACGATTTTTT

Predicted secondary structures

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

T-box riboswitch RSZVYWZD 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 Lactobacillus farraginis DSM 18382 = JCM 14108
GCGGTAGTGGTGAAGTGGTTAACACATCGGTTTGTGGATCCGACACGCGTGGGTTCGATTCCCACCTACCGCCCCA

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)	-7.3
Terminator	ΔG° (kcal/mol	-26.6
	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	94.8
Bias	0.0
CM Accuracy	0.95

*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		[7,99]
Stem II region
Stem III
Specifier region	-	[86,88]
T-box UGGN locus	-	[234,237]
Antiterminator		[230,256]
Terminator		[249,291]
All stems	-	[[7, 99], [102, 125], [127, 138], [201, 224], [230, 256]]

Input source sequence >BAKI01000007.1:13726-13418
TATGAAGTTACGATTAGAAAAGTAAGCGATGAACTAACATAAAGAGAGTCCCGGCGGTGAGAACGGATTGTTGGTATTGCTGAAAACACATCTATGAACTGGATAATTGAACCAAGTAGGTTGTCCCGCTAGTGAGCGTTACCACGGCTGCTGTAACTGTTCTTCATTACTAATGGACGACTAGTTGCAGACAGTGTAAGGTCGTTTCATCGTGAGGTGGCGGCAAAATGAGGTGGGACCGCGAGAAATCGTCCTCAGGTATTGGATAACAATATCTGAGGACGATTTTTT

INFERNAL output sequence >Infernal-BAKI01000007.1:13726-13418
UAUGAAGUUACGAUUAGA-AAAGUAAGCGAUGA-ACUAACAUAAAGAGAGUCCC--GGCGGUGAGAACGGAUUGUUGG-UAUUGCUGAAAaCACAUCUAUGAACUGGAUAAUUGAA---CCAAGUAGGUUGUCCCGCUAGUGAGCGUUACcacggcugcuguaacuguucuucauuacuaauggacgacuaguUGCAGACAGUGUAAGGUCGUUUCAUcgUGAGGUGGCGGCAAAaUGAGGUGGGACCGCGA--GAAA--UCGUCCUCAGG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-BAKI01000007.1:13726-13418
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________>>>>>>>>>----->>>>>>----.---->>>>--->>,,<<<<<<<_____________>>>>>>>,<<<______>>>,,,,...........................................,,,,,,,,,,,,,,,<<<<<<<___.._____>>>>>>>,,,.,<<<<-------<<<<<______>>>>>>>>>:::