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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
172885-172993
(+)
SAH
173019-175770 (+)
Vapar_0171
Methionine synthase (3) (5-methyltetrahydrofolate--homocysteine methyltransferase)
Vapar_0171
Operon
DOOR ID:
569689
Vapar_0171,
Vapar_0172,
Vapar_0173,
Vapar_0174
View Structure
2
822763-822869
(-)
glycine
821370-822672 (-)
Vapar_0751
D-amino-acid dehydrogenase
Vapar_0751
Single gene
DOOR ID:
2591407
Vapar_0751
View Structure
3
822873-822972
(-)
glycine
821370-822672 (-)
Vapar_0751
D-amino-acid dehydrogenase
Vapar_0751
Single gene
DOOR ID:
2591407
Vapar_0751
View Structure
4
1118892-1119156
(-)
cobalamin
1117887-1118733 (-)
Vapar_1024
Precorrin-4 C11-methyltransferase (33)
Vapar_1024
Operon
DOOR ID:
569876
Vapar_1013,
Vapar_1014,
Vapar_1015,
Vapar_1016,
Vapar_1017,
Vapar_1018,
Vapar_1019,
Vapar_1020,
Vapar_1021
(cbiD)
,
Vapar_1022,
Vapar_1023,
Vapar_1024
View Structure
5
1985586-1985755
(-)
FMN
1984974-1985490 (-)
Vapar_1854
6;7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (8)
Vapar_1854
Operon
DOOR ID:
570057
Vapar_1852,
Vapar_1853,
Vapar_1854
View Structure
6
2562382-2562489
(-)
TPP
2560964-2562305 (-)
Vapar_2400
Permease for cytosine/purines uracil thiamine allantoin
Vapar_2400
Single gene
DOOR ID:
2591873
Vapar_2400
View Structure
7
2688294-2688542
(+)
cobalamin
2688733-2690581 (+)
Vapar_2547
TonB-dependent receptor plug
Vapar_2547
Operon
DOOR ID:
570186
Vapar_2547,
Vapar_2548,
Vapar_2549,
Vapar_2550,
Vapar_2551,
Vapar_2552,
Vapar_2553,
Vapar_2554,
Vapar_2555,
Vapar_2556,
Vapar_2557,
Vapar_2558,
Vapar_2559
View Structure
8
3260057-3260183
(+)
ZMP-ZTP
3260224-3261469 (+)
glyA
Serine hydroxymethyltransferase (SHMT) (Serine methylase)
Vapar_3100
Operon
DOOR ID:
570304
Vapar_3100
(glyA)
,
Vapar_3101
View Structure
9
3476392-3476482
(+)
glycine
3476655-3477834 (+)
Vapar_3299
Glycine cleavage system T protein
Vapar_3299
Single gene
DOOR ID:
2592077
Vapar_3299
View Structure
10
3476495-3476610
(+)
glycine
3476655-3477834 (+)
Vapar_3299
Glycine cleavage system T protein
Vapar_3299
Single gene
DOOR ID:
2592077
Vapar_3299
View Structure
11
4972729-4972797
(-)
SAH
4971222-4972662 (-)
Vapar_4683
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)
Vapar_4683
Operon
DOOR ID:
570658
Vapar_4682,
Vapar_4683
View Structure
12
5025784-5025888
(-)
TPP
5023806-5025693 (-)
Vapar_4728
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
Vapar_4728
Operon
DOOR ID:
570667
Vapar_4727,
Vapar_4728
View Structure
13
5614236-5614410
(-)
yybP-ykoY
5613655-5614219 (-)
Vapar_5289
Vapar_5289
Single gene
DOOR ID:
2592651
Vapar_5289
View Structure
Genome:
Variovorax paradoxus S110
(
NC_012791.1
);
Phylum:
Betaproteobacteria
a:14:{i:0;a:18:{i:0;s:5:"S.No.";i:1;s:9:"Genome_ID";i:2;s:11:"Genome_Name";i:3;s:13:"Taxonomy_name";i:4;s:6:"Tax_ID";i:5;s:19:"Riboswitch_Location";i:6;s:17:"Riboswitch_strand";i:7;s:16:"Riboswitch_class";i:8;s:14:"Tandem_Aptamer";i:9;s:24:"Downstream_gene_location";i:10;s:11:"Gene_Strand";i:11;s:20:"Downstream_gene_name";i:12;s:24:"Gene_product_description";i:13;s:9:"Locus_tag";i:14;s:25:"Single_gene/within_operon";i:15;s:9:"Operon_ID";i:16;s:14:"Operon_details";i:17;s:22:"Biological_process[GO]";}i:1;a:19:{i:0;i:1;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"172885-172993";i:6;s:1:"+";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:13:"173019-175770";i:10;s:1:"+";i:11;s:10:"Vapar_0171";i:12;s:82:"Methionine synthase (3) (5-methyltetrahydrofolate--homocysteine methyltransferase)";i:13;s:10:"Vapar_0171";i:14;s:6:"Operon";i:15;s:6:"569689";i:16;s:43:"Vapar_0171;Vapar_0172;Vapar_0173;Vapar_0174";i:17;s:60:"pteridine-containing compound metabolic process [GO:0042558]";i:18;s:15:"View Structure ";}i:2;a:19:{i:0;i:2;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"822763-822869";i:6;s:1:"-";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:13:"821370-822672";i:10;s:1:"-";i:11;s:10:"Vapar_0751";i:12;s:27:"D-amino-acid dehydrogenase ";i:13;s:10:"Vapar_0751";i:14;s:11:"Single gene";i:15;s:7:"2591407";i:16;s:10:"Vapar_0751";i:17;s:0:"";i:18;s:15:"View Structure ";}i:3;a:19:{i:0;i:3;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"822873-822972";i:6;s:1:"-";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:13:"821370-822672";i:10;s:1:"-";i:11;s:10:"Vapar_0751";i:12;s:27:"D-amino-acid dehydrogenase ";i:13;s:10:"Vapar_0751";i:14;s:11:"Single gene";i:15;s:7:"2591407";i:16;s:10:"Vapar_0751";i:17;s:0:"";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1118892-1119156";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"1117887-1118733";i:10;s:1:"-";i:11;s:10:"Vapar_1024";i:12;s:38:"Precorrin-4 C11-methyltransferase (33)";i:13;s:10:"Vapar_1024";i:14;s:6:"Operon";i:15;s:6:"569876";i:16;s:137:"Vapar_1013;Vapar_1014;Vapar_1015;Vapar_1016;Vapar_1017;Vapar_1018;Vapar_1019;Vapar_1020;Vapar_1021(cbiD);Vapar_1022;Vapar_1023;Vapar_1024";i:17;s:85:"cobalamin biosynthetic process [GO:0009236]; oxidation-reduction process [GO:0055114]";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1985586-1985755";i:6;s:1:"-";i:7;s:3:"FMN";i:8;s:0:"";i:9;s:15:"1984974-1985490";i:10;s:1:"-";i:11;s:10:"Vapar_1854";i:12;s:84:"6;7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (8)";i:13;s:10:"Vapar_1854";i:14;s:6:"Operon";i:15;s:6:"570057";i:16;s:32:"Vapar_1852;Vapar_1853;Vapar_1854";i:17;s:44:"riboflavin biosynthetic process [GO:0009231]";i:18;s:15:"View Structure ";}i:6;a:19:{i:0;i:6;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2562382-2562489";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"2560964-2562305";i:10;s:1:"-";i:11;s:10:"Vapar_2400";i:12;s:55:"Permease for cytosine/purines uracil thiamine allantoin";i:13;s:10:"Vapar_2400";i:14;s:11:"Single gene";i:15;s:7:"2591873";i:16;s:10:"Vapar_2400";i:17;s:0:"";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2688294-2688542";i:6;s:1:"+";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"2688733-2690581";i:10;s:1:"+";i:11;s:10:"Vapar_2547";i:12;s:28:"TonB-dependent receptor plug";i:13;s:10:"Vapar_2547";i:14;s:6:"Operon";i:15;s:6:"570186";i:16;s:142:"Vapar_2547;Vapar_2548;Vapar_2549;Vapar_2550;Vapar_2551;Vapar_2552;Vapar_2553;Vapar_2554;Vapar_2555;Vapar_2556;Vapar_2557;Vapar_2558;Vapar_2559";i:17;s:0:"";i:18;s:15:"View Structure ";}i:8;a:19:{i:0;i:8;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3260057-3260183";i:6;s:1:"+";i:7;s:7:"ZMP-ZTP";i:8;s:0:"";i:9;s:15:"3260224-3261469";i:10;s:1:"+";i:11;s:4:"glyA";i:12;s:58:"Serine hydroxymethyltransferase (SHMT) (Serine methylase) ";i:13;s:10:"Vapar_3100";i:14;s:6:"Operon";i:15;s:6:"570304";i:16;s:27:"Vapar_3100(glyA);Vapar_3101";i:17;s:100:"glycine biosynthetic process from serine [GO:0019264]; tetrahydrofolate interconversion [GO:0035999]";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3476392-3476482";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"3476655-3477834";i:10;s:1:"+";i:11;s:10:"Vapar_3299";i:12;s:33:"Glycine cleavage system T protein";i:13;s:10:"Vapar_3299";i:14;s:11:"Single gene";i:15;s:7:"2592077";i:16;s:10:"Vapar_3299";i:17;s:38:"glycine catabolic process [GO:0006546]";i:18;s:15:"View Structure ";}i:10;a:19:{i:0;i:10;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3476495-3476610";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"3476655-3477834";i:10;s:1:"+";i:11;s:10:"Vapar_3299";i:12;s:33:"Glycine cleavage system T protein";i:13;s:10:"Vapar_3299";i:14;s:11:"Single gene";i:15;s:7:"2592077";i:16;s:10:"Vapar_3299";i:17;s:38:"glycine catabolic process [GO:0006546]";i:18;s:15:"View Structure ";}i:11;a:19:{i:0;i:11;i:1;s:11:"NC_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4972729-4972797";i:6;s:1:"-";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:15:"4971222-4972662";i:10;s:1:"-";i:11;s:10:"Vapar_4683";i:12;s:73:"Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)";i:13;s:10:"Vapar_4683";i:14;s:6:"Operon";i:15;s:6:"570658";i:16;s:21:"Vapar_4682;Vapar_4683";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_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"5025784-5025888";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"5023806-5025693";i:10;s:1:"-";i:11;s:10:"Vapar_4728";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:"Vapar_4728";i:14;s:6:"Operon";i:15;s:6:"570667";i:16;s:21:"Vapar_4727;Vapar_4728";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_012791.1";i:2;s:26:"Variovorax paradoxus S110 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"5614236-5614410";i:6;s:1:"-";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:15:"5613655-5614219";i:10;s:1:"-";i:11;s:10:"Vapar_5289";i:12;s:0:"";i:13;s:10:"Vapar_5289";i:14;s:11:"Single gene";i:15;s:7:"2592651";i:16;s:10:"Vapar_5289";i:17;s:0:"";i:18;s:15:"View Structure ";}}
