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S.No.
Riboswitch Location and Strand
Riboswitch class
Downstream gene location and Strand
Downstream gene name/gene product description
Locus_tag of downstream gene
Single gene/within operon (According to DOOR database)
Operon details (List of genes within operon and their Locus_tag)
Predicted Structure
1
210150-210223
(+)
SAH
210245-212993 (+)
Varpa_0200
Methionine synthase (3) (5-methyltetrahydrofolate--homocysteine methyltransferase)
Varpa_0200
Operon
DOOR ID:
794661
Varpa_0200,
Varpa_0201,
Varpa_0202,
Varpa_0203
View Structure
2
867633-867749
(-)
glycine
866240-867542 (-)
Varpa_0770
D-amino-acid dehydrogenase
Varpa_0770
Single gene
DOOR ID:
3032004
Varpa_0770
View Structure
3
867783-867873
(-)
glycine
866240-867542 (-)
Varpa_0770
D-amino-acid dehydrogenase
Varpa_0770
Single gene
DOOR ID:
3032004
Varpa_0770
View Structure
4
2535882-2535989
(-)
glycine
2534655-2535834 (-)
Varpa_2332
Glycine cleavage system T protein
Varpa_2332
Single gene
DOOR ID:
3032404
Varpa_2332
View Structure
5
2536010-2536084
(-)
glycine
2534655-2535834 (-)
Varpa_2332
Glycine cleavage system T protein
Varpa_2332
Single gene
DOOR ID:
3032404
Varpa_2332
View Structure
6
2820984-2821091
(-)
TPP
2819551-2820907 (-)
Varpa_2607
Permease for cytosine/purines uracil thiamine allantoin
Varpa_2607
Single gene
DOOR ID:
3032482
Varpa_2607
View Structure
7
3642103-3642370
(-)
cobalamin
3640037-3642002 (-)
Varpa_3379
TonB-dependent receptor plug
Varpa_3379
Operon
DOOR ID:
795338
Varpa_3372,
Varpa_3373,
Varpa_3374,
Varpa_3375,
Varpa_3376,
Varpa_3377,
Varpa_3378,
Varpa_3379
View Structure
8
3795068-3795193
(+)
ZMP-ZTP
3795234-3796479 (+)
Varpa_3514
Serine hydroxymethyltransferase (SHMT) (Serine methylase)
Varpa_3514
Operon
DOOR ID:
795369
Varpa_3514,
Varpa_3515
View Structure
9
4149698-4149977
(-)
cobalamin
4147337-4149569 (-)
Varpa_3851
TonB-dependent siderophore receptor
Varpa_3851
Single gene
DOOR ID:
3032827
Varpa_3851
View Structure
10
4277632-4277795
(+)
FMN
4277895-4278408 (+)
Varpa_3966
6;7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (8)
Varpa_3966
Operon
DOOR ID:
795450
Varpa_3966,
Varpa_3967,
Varpa_3968
View Structure
11
5770661-5770730
(-)
SAH
5769146-5770586 (-)
Varpa_5312
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)
Varpa_5312
Operon
DOOR ID:
795746
Varpa_5311,
Varpa_5312
View Structure
12
5828228-5828333
(-)
TPP
5826253-5828140 (-)
Varpa_5365
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
Varpa_5365
Single gene
DOOR ID:
3033298
Varpa_5365
View Structure
13
6537875-6538052
(-)
yybP-ykoY
6537292-6537856 (-)
Varpa_6010
Varpa_6010
Single gene
DOOR ID:
3033510
Varpa_6010
View Structure
Genome:
Variovorax paradoxus EPS
(
NC_014931.1
);
Phylum:
Betaproteobacteria
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tetrahydrofolate interconversion [GO:0035999]";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_014931.1";i:2;s:25:"Variovorax paradoxus EPS ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4149698-4149977";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"4147337-4149569";i:10;s:1:"-";i:11;s:10:"Varpa_3851";i:12;s:35:"TonB-dependent siderophore receptor";i:13;s:10:"Varpa_3851";i:14;s:11:"Single gene";i:15;s:7:"3032827";i:16;s:10:"Varpa_3851";i:17;s:34:"siderophore transport [GO:0015891]";i:18;s:15:"View Structure ";}i:10;a:19:{i:0;i:10;i:1;s:11:"NC_014931.1";i:2;s:25:"Variovorax paradoxus EPS ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4277632-4277795";i:6;s:1:"+";i:7;s:3:"FMN";i:8;s:0:"";i:9;s:15:"4277895-4278408";i:10;s:1:"+";i:11;s:10:"Varpa_3966";i:12;s:84:"6;7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (8)";i:13;s:10:"Varpa_3966";i:14;s:6:"Operon";i:15;s:6:"795450";i:16;s:32:"Varpa_3966;Varpa_3967;Varpa_3968";i:17;s:44:"riboflavin biosynthetic process [GO:0009231]";i:18;s:15:"View Structure ";}i:11;a:19:{i:0;i:11;i:1;s:11:"NC_014931.1";i:2;s:25:"Variovorax paradoxus EPS ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"5770661-5770730";i:6;s:1:"-";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:15:"5769146-5770586";i:10;s:1:"-";i:11;s:10:"Varpa_5312";i:12;s:73:"Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)";i:13;s:10:"Varpa_5312";i:14;s:6:"Operon";i:15;s:6:"795746";i:16;s:21:"Varpa_5311;Varpa_5312";i:17;s:96:"one-carbon metabolic process [GO:0006730]; S-adenosylhomocysteine catabolic process [GO:0019510]";i:18;s:15:"View Structure ";}i:12;a:19:{i:0;i:12;i:1;s:11:"NC_014931.1";i:2;s:25:"Variovorax paradoxus EPS ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"5828228-5828333";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"5826253-5828140";i:10;s:1:"-";i:11;s:10:"Varpa_5365";i:12;s:176:"Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)";i:13;s:10:"Varpa_5365";i:14;s:11:"Single gene";i:15;s:7:"3033298";i:16;s:10:"Varpa_5365";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:13;a:19:{i:0;i:13;i:1;s:11:"NC_014931.1";i:2;s:25:"Variovorax paradoxus EPS ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"6537875-6538052";i:6;s:1:"-";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:15:"6537292-6537856";i:10;s:1:"-";i:11;s:10:"Varpa_6010";i:12;s:0:"";i:13;s:10:"Varpa_6010";i:14;s:11:"Single gene";i:15;s:7:"3033510";i:16;s:10:"Varpa_6010";i:17;s:0:"";i:18;s:15:"View Structure ";}}
