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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
225367-225447
(+)
SAH
225476-228212 (+)
Alide_0204
Methionine synthase (3) (5-methyltetrahydrofolate--homocysteine methyltransferase)
Alide_0204
Single gene
DOOR ID:
3022759
Alide_0204
View Structure
2
737992-738074
(+)
SAH
738147-739578 (+)
Alide_0702
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)
Alide_0702
Single gene
DOOR ID:
3022876
Alide_0702
View Structure
3
1849241-1849343
(-)
TPP
1848082-1849201 (-)
Alide_1785
Glycine oxidase ThiO
Alide_1785
Operon
DOOR ID:
789296
Alide_1782,
Alide_1783,
Alide_1784,
Alide_1785
View Structure
4
1990607-1990768
(-)
ZMP-ZTP
1989325-1990570 (-)
Alide_1929
Serine hydroxymethyltransferase (SHMT) (Serine methylase)
Alide_1929
Operon
DOOR ID:
789325
Alide_1928,
Alide_1929
View Structure
5
2409682-2409778
(+)
glycine
2409940-2411074 (+)
Alide_2347
Glycine cleavage system T protein
Alide_2347
Single gene
DOOR ID:
3023301
Alide_2347
View Structure
6
2409793-2409895
(+)
glycine
2409940-2411074 (+)
Alide_2347
Glycine cleavage system T protein
Alide_2347
Single gene
DOOR ID:
3023301
Alide_2347
View Structure
7
3460417-3460661
(-)
cobalamin
3458474-3460268 (-)
Alide_3314
TonB-dependent receptor plug
Alide_3314
Operon
DOOR ID:
789623
Alide_3308,
Alide_3309,
Alide_3310,
Alide_3311,
Alide_3312,
Alide_3313,
Alide_3314
View Structure
8
3842405-3842515
(-)
TPP
3840470-3842318 (-)
Alide_3691
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
Alide_3691
Single gene
DOOR ID:
3023671
Alide_3691
View Structure
9
4606990-4607106
(-)
yybP-ykoY
4606304-4606883 (-)
Alide_4392
Alide_4392
Single gene
DOOR ID:
3023868
Alide_4392
View Structure
Genome:
Alicycliphilus denitrificans BC
(
NC_014910.1
);
Phylum:
Betaproteobacteria
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S-adenosylhomocysteine catabolic process [GO:0019510]";i:18;s:15:"View Structure ";}i:3;a:19:{i:0;i:3;i:1;s:11:"NC_014910.1";i:2;s:32:"Alicycliphilus denitrificans BC ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1849241-1849343";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"1848082-1849201";i:10;s:1:"-";i:11;s:10:"Alide_1785";i:12;s:20:"Glycine oxidase ThiO";i:13;s:10:"Alide_1785";i:14;s:6:"Operon";i:15;s:6:"789296";i:16;s:43:"Alide_1782;Alide_1783;Alide_1784;Alide_1785";i:17;s:43:"D-amino acid metabolic process [GO:0046416]";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_014910.1";i:2;s:32:"Alicycliphilus denitrificans BC ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1990607-1990768";i:6;s:1:"-";i:7;s:7:"ZMP-ZTP";i:8;s:0:"";i:9;s:15:"1989325-1990570";i:10;s:1:"-";i:11;s:10:"Alide_1929";i:12;s:58:"Serine hydroxymethyltransferase (SHMT) (Serine methylase) ";i:13;s:10:"Alide_1929";i:14;s:6:"Operon";i:15;s:6:"789325";i:16;s:21:"Alide_1928;Alide_1929";i:17;s:100:"glycine biosynthetic process from serine [GO:0019264]; tetrahydrofolate interconversion [GO:0035999]";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_014910.1";i:2;s:32:"Alicycliphilus denitrificans BC ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2409682-2409778";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"2409940-2411074";i:10;s:1:"+";i:11;s:10:"Alide_2347";i:12;s:33:"Glycine cleavage system T protein";i:13;s:10:"Alide_2347";i:14;s:11:"Single gene";i:15;s:7:"3023301";i:16;s:10:"Alide_2347";i:17;s:38:"glycine catabolic process [GO:0006546]";i:18;s:15:"View Structure ";}i:6;a:19:{i:0;i:6;i:1;s:11:"NC_014910.1";i:2;s:32:"Alicycliphilus denitrificans BC ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2409793-2409895";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:6:"Tandem";i:9;s:15:"2409940-2411074";i:10;s:1:"+";i:11;s:10:"Alide_2347";i:12;s:33:"Glycine cleavage system T protein";i:13;s:10:"Alide_2347";i:14;s:11:"Single gene";i:15;s:7:"3023301";i:16;s:10:"Alide_2347";i:17;s:38:"glycine catabolic process [GO:0006546]";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_014910.1";i:2;s:32:"Alicycliphilus denitrificans BC ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3460417-3460661";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"3458474-3460268";i:10;s:1:"-";i:11;s:10:"Alide_3314";i:12;s:28:"TonB-dependent receptor plug";i:13;s:10:"Alide_3314";i:14;s:6:"Operon";i:15;s:6:"789623";i:16;s:76:"Alide_3308;Alide_3309;Alide_3310;Alide_3311;Alide_3312;Alide_3313;Alide_3314";i:17;s:0:"";i:18;s:15:"View Structure ";}i:8;a:19:{i:0;i:8;i:1;s:11:"NC_014910.1";i:2;s:32:"Alicycliphilus denitrificans BC ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3842405-3842515";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"3840470-3842318";i:10;s:1:"-";i:11;s:10:"Alide_3691";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:"Alide_3691";i:14;s:11:"Single gene";i:15;s:7:"3023671";i:16;s:10:"Alide_3691";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_014910.1";i:2;s:32:"Alicycliphilus denitrificans BC ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4606990-4607106";i:6;s:1:"-";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:15:"4606304-4606883";i:10;s:1:"-";i:11;s:10:"Alide_4392";i:12;s:0:"";i:13;s:10:"Alide_4392";i:14;s:11:"Single gene";i:15;s:7:"3023868";i:16;s:10:"Alide_4392";i:17;s:0:"";i:18;s:15:"View Structure ";}}
