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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
475493-475563
(+)
SAH
475586-478484 (+)
Rfer_0466
Methionine synthase (3) (5-methyltetrahydrofolate--homocysteine methyltransferase)
Rfer_0466
Single gene
DOOR ID:
1775587
Rfer_0466
View Structure
2
675987-676101
(+)
SAH
676174-677635 (+)
Rfer_0652
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)
Rfer_0652
Operon
DOOR ID:
178986
Rfer_0652,
Rfer_0653,
Rfer_0654
View Structure
3
1372550-1372618
(+)
SAH
1373107-1374208 (-)
prfA
Peptide chain release factor 1 (RF-1)
Rfer_1280
Operon
DOOR ID:
179104
Rfer_1280
(prfA)
,
Rfer_1281
(hemA)
View Structure
4
1837798-1837900
(+)
TPP
1837995-1839870 (+)
Rfer_1708
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
Rfer_1708
Single gene
DOOR ID:
1776010
Rfer_1708
View Structure
5
2710968-2711076
(+)
TPP
2711155-2712463 (+)
Rfer_2463
Permease for cytosine/purines; uracil; thiamine; allantoin
Rfer_2463
Operon
DOOR ID:
179344
Rfer_2463,
Rfer_2464,
Rfer_2465,
Rfer_2466
(thiG)
,
Rfer_2467
View Structure
6
2718676-2718770
(-)
TPP
2717800-2718634 (-)
thiE
Hydroxyethylthiazole kinase (0) (4-methyl-5-beta-hydroxyethylthiazole kinase) (TH kinase) (Thz kinase)
Rfer_2472
Operon
DOOR ID:
179345
Rfer_2470,
Rfer_2471
(thiE)
,
Rfer_2472
View Structure
7
2890041-2890300
(-)
cobalamin
2887992-2889966 (-)
Rfer_2625
TonB-dependent receptor
Rfer_2625
Single gene
DOOR ID:
1776327
Rfer_2625
View Structure
8
2925225-2925356
(+)
ZMP-ZTP
2925401-2926646 (+)
glyA
Serine hydroxymethyltransferase (SHMT) (Serine methylase)
Rfer_2658
Operon
DOOR ID:
179387
Rfer_2658
(glyA)
,
Rfer_2659
(nrdR)
View Structure
9
3329752-3329892
(+)
glycine
3329894-3331106 (+)
Rfer_3019
Glycine cleavage system T protein
Rfer_3019
Single gene
DOOR ID:
1776442
Rfer_3019
View Structure
10
3599151-3599248
(-)
TPP
3598086-3599109 (-)
Rfer_3246
ABC transporter periplasmic binding protein; thiB subfamily
Rfer_3246
Operon
DOOR ID:
179521
Rfer_3241,
Rfer_3242,
Rfer_3243,
Rfer_3244,
Rfer_3245,
Rfer_3246
View Structure
11
4400341-4400428
(+)
c-di-GMP-I
4400907-4402677 (+)
Rfer_3937
Methyl-accepting chemotaxis sensory transducer
Rfer_3937
single gene
DOOR ID:
1776745
Rfer_3937
View Structure
12
4675140-4675244
(-)
fluoride
4673314-4674475 (-)
Rfer_4203
Integrase
Rfer_4203
Single gene
DOOR ID:
1776838
Rfer_4203
View Structure
Genome:
Rhodoferax ferrireducens T118
(
NC_007908.1
);
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_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1372550-1372618";i:6;s:1:"+";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:15:"1373107-1374208";i:10;s:1:"-";i:11;s:4:"prfA";i:12;s:37:"Peptide chain release factor 1 (RF-1)";i:13;s:9:"Rfer_1280";i:14;s:6:"Operon";i:15;s:6:"179104";i:16;s:31:"Rfer_1280(prfA);Rfer_1281(hemA)";i:17;s:0:"";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1837798-1837900";i:6;s:1:"+";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"1837995-1839870";i:10;s:1:"+";i:11;s:9:"Rfer_1708";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:9:"Rfer_1708";i:14;s:11:"Single gene";i:15;s:7:"1776010";i:16;s:9:"Rfer_1708";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2710968-2711076";i:6;s:1:"+";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"2711155-2712463";i:10;s:1:"+";i:11;s:9:"Rfer_2463";i:12;s:58:"Permease for cytosine/purines; uracil; thiamine; allantoin";i:13;s:9:"Rfer_2463";i:14;s:6:"Operon";i:15;s:6:"179344";i:16;s:55:"Rfer_2463;Rfer_2464;Rfer_2465;Rfer_2466(thiG);Rfer_2467";i:17;s:0:"";i:18;s:15:"View Structure ";}i:6;a:19:{i:0;i:6;i:1;s:11:"NC_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2718676-2718770";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"2717800-2718634";i:10;s:1:"-";i:11;s:4:"thiE";i:12;s:102:"Hydroxyethylthiazole kinase (0) (4-methyl-5-beta-hydroxyethylthiazole kinase) (TH kinase) (Thz kinase)";i:13;s:9:"Rfer_2472";i:14;s:6:"Operon";i:15;s:6:"179345";i:16;s:35:"Rfer_2470;Rfer_2471(thiE);Rfer_2472";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2890041-2890300";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"2887992-2889966";i:10;s:1:"-";i:11;s:9:"Rfer_2625";i:12;s:23:"TonB-dependent receptor";i:13;s:9:"Rfer_2625";i:14;s:11:"Single gene";i:15;s:7:"1776327";i:16;s:9:"Rfer_2625";i:17;s:0:"";i:18;s:15:"View Structure ";}i:8;a:19:{i:0;i:8;i:1;s:11:"NC_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2925225-2925356";i:6;s:1:"+";i:7;s:7:"ZMP-ZTP";i:8;s:0:"";i:9;s:15:"2925401-2926646";i:10;s:1:"+";i:11;s:4:"glyA";i:12;s:58:"Serine hydroxymethyltransferase (SHMT) (Serine methylase) ";i:13;s:9:"Rfer_2658";i:14;s:6:"Operon";i:15;s:6:"179387";i:16;s:31:"Rfer_2658(glyA);Rfer_2659(nrdR)";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_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3329752-3329892";i:6;s:1:"+";i:7;s:7:"glycine";i:8;s:0:"";i:9;s:15:"3329894-3331106";i:10;s:1:"+";i:11;s:9:"Rfer_3019";i:12;s:33:"Glycine cleavage system T protein";i:13;s:9:"Rfer_3019";i:14;s:11:"Single gene";i:15;s:7:"1776442";i:16;s:9:"Rfer_3019";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_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3599151-3599248";i:6;s:1:"-";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:15:"3598086-3599109";i:10;s:1:"-";i:11;s:9:"Rfer_3246";i:12;s:59:"ABC transporter periplasmic binding protein; thiB subfamily";i:13;s:9:"Rfer_3246";i:14;s:6:"Operon";i:15;s:6:"179521";i:16;s:59:"Rfer_3241;Rfer_3242;Rfer_3243;Rfer_3244;Rfer_3245;Rfer_3246";i:17;s:31:"thiamine transport [GO:0015888]";i:18;s:15:"View Structure ";}i:11;a:19:{i:0;i:11;i:1;s:11:"NC_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4400341-4400428";i:6;s:1:"+";i:7;s:10:"c-di-GMP-I";i:8;s:0:"";i:9;s:15:"4400907-4402677";i:10;s:1:"+";i:11;s:9:"Rfer_3937";i:12;s:46:"Methyl-accepting chemotaxis sensory transducer";i:13;s:9:"Rfer_3937";i:14;s:11:"single gene";i:15;s:7:"1776745";i:16;s:9:"Rfer_3937";i:17;s:32:"signal transduction [GO:0007165]";i:18;s:15:"View Structure ";}i:12;a:19:{i:0;i:12;i:1;s:11:"NC_007908.1";i:2;s:30:"Rhodoferax ferrireducens T118 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4675140-4675244";i:6;s:1:"-";i:7;s:8:"fluoride";i:8;s:0:"";i:9;s:15:"4673314-4674475";i:10;s:1:"-";i:11;s:9:"Rfer_4203";i:12;s:9:"Integrase";i:13;s:9:"Rfer_4203";i:14;s:11:"Single gene";i:15;s:7:"1776838";i:16;s:9:"Rfer_4203";i:17;s:70:"DNA integration [GO:0015074]; transposition; DNA-mediated [GO:0006313]";i:18;s:15:"View Structure ";}}
