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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
462555-462665
(+)
TPP
462762-464676 (+)
thiC
Phosphomethylpyrimidine synthase (7) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Thiamine biosynthesis protein ThiC)
Hsero_0427
Single gene
DOOR ID:
2900458
Hsero_0427
(thiC)
View Structure
2
576481-576664
(+)
yybP-ykoY
576672-577254 (+)
Hsero_0528
Putative manganese efflux pump MntP
Hsero_0528
Single gene
DOOR ID:
2900504
Hsero_0528
View Structure
3
1381288-1381387
(+)
ZMP-ZTP
1381527-1382772 (+)
glyA
Serine hydroxymethyltransferase (SHMT) (Serine methylase)
Hsero_1223
Single gene
DOOR ID:
2900759
Hsero_1223
(glyA)
View Structure
4
1439614-1439733
(-)
SAH
1438448-1438994 (+)
Hsero_1267
Aromatic compounds catabolic protein
Hsero_1267
Single gene
DOOR ID:
2900779
Hsero_1267
View Structure
5
2225947-2226115
(+)
FMN
2226202-2226712 (+)
ribH
6;7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (8)
Hsero_1967
Operon
DOOR ID:
727088
Hsero_1967
(ribH)
,
Hsero_1968
View Structure
6
2800602-2800675
(+)
fluoride
2800755-2802084 (+)
eriC
Chloride channel protein
Hsero_2467
Single gene
DOOR ID:
2901213
Hsero_2467
(eriC)
View Structure
7
3038673-3038919
(-)
cobalamin
3037564-3038290 (-)
Hsero_2658
Integral membrane protein
Hsero_2658
Operon
DOOR ID:
727237
Hsero_2658,
Hsero_2659
View Structure
8
4908117-4908206
(-)
SAH
4906660-4908067 (-)
ahcY
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)
Hsero_4289
Single gene
DOOR ID:
2901889
Hsero_4289
(ahcY)
View Structure
9
5115194-5115241
(-)
mini-ykkC
5111552-5115176 (-)
Hsero_4471
Hsero_4471
Operon
DOOR ID:
727599
Hsero_4470
(gatA)
,
Hsero_4471
View Structure
10
5118406-5118506
(-)
ykkC-yxkD
5117442-5118258 (-)
Hsero_4475
ABC-type nitrate/sulfonate/bicarbonate transport system; permease protein
Hsero_4475
Operon
DOOR ID:
727600
Hsero_4472,
Hsero_4473,
Hsero_4474,
Hsero_4475
View Structure
11
5119175-5119274
(+)
ykkC-yxkD
5119341-5120418 (+)
Hsero_4476
ABC-type nitrate/sulfonate/bicarbonate transport system; periplasmic component protein
Hsero_4476
Single gene
DOOR ID:
2901964
Hsero_4476
View Structure
Genome:
Herbaspirillum seropedicae SmR1
(
NC_014323.1
);
Phylum:
Betaproteobacteria
a:12:{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_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"462555-462665";i:6;s:1:"+";i:7;s:3:"TPP";i:8;s:0:"";i:9;s:13:"462762-464676";i:10;s:1:"+";i:11;s:4:"thiC";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:"Hsero_0427";i:14;s:11:"Single gene";i:15;s:7:"2900458";i:16;s:16:"Hsero_0427(thiC)";i:17;s:98:"thiamine biosynthetic process [GO:0009228]; thiamine diphosphate biosynthetic process [GO:0009229]";i:18;s:15:"View Structure ";}i:2;a:19:{i:0;i:2;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:13:"576481-576664";i:6;s:1:"+";i:7;s:9:"yybP-ykoY";i:8;s:0:"";i:9;s:13:"576672-577254";i:10;s:1:"+";i:11;s:10:"Hsero_0528";i:12;s:35:"Putative manganese efflux pump MntP";i:13;s:10:"Hsero_0528";i:14;s:11:"Single gene";i:15;s:7:"2900504";i:16;s:10:"Hsero_0528";i:17;s:0:"";i:18;s:15:"View Structure ";}i:3;a:19:{i:0;i:3;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1381288-1381387";i:6;s:1:"+";i:7;s:7:"ZMP-ZTP";i:8;s:0:"";i:9;s:15:"1381527-1382772";i:10;s:1:"+";i:11;s:4:"glyA";i:12;s:58:"Serine hydroxymethyltransferase (SHMT) (Serine methylase) ";i:13;s:10:"Hsero_1223";i:14;s:11:"Single gene";i:15;s:7:"2900759";i:16;s:16:"Hsero_1223(glyA)";i:17;s:100:"glycine biosynthetic process from serine [GO:0019264]; tetrahydrofolate interconversion [GO:0035999]";i:18;s:15:"View Structure ";}i:4;a:19:{i:0;i:4;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"1439614-1439733";i:6;s:1:"-";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:15:"1438448-1438994";i:10;s:1:"+";i:11;s:10:"Hsero_1267";i:12;s:36:"Aromatic compounds catabolic protein";i:13;s:10:"Hsero_1267";i:14;s:11:"Single gene";i:15;s:7:"2900779";i:16;s:10:"Hsero_1267";i:17;s:0:"";i:18;s:15:"View Structure ";}i:5;a:19:{i:0;i:5;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2225947-2226115";i:6;s:1:"+";i:7;s:3:"FMN";i:8;s:0:"";i:9;s:15:"2226202-2226712";i:10;s:1:"+";i:11;s:4:"ribH";i:12;s:84:"6;7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (8)";i:13;s:10:"Hsero_1967";i:14;s:6:"Operon";i:15;s:6:"727088";i:16;s:27:"Hsero_1967(ribH);Hsero_1968";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_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"2800602-2800675";i:6;s:1:"+";i:7;s:8:"fluoride";i:8;s:0:"";i:9;s:15:"2800755-2802084";i:10;s:1:"+";i:11;s:4:"eriC";i:12;s:24:"Chloride channel protein";i:13;s:10:"Hsero_2467";i:14;s:11:"Single gene";i:15;s:7:"2901213";i:16;s:16:"Hsero_2467(eriC)";i:17;s:0:"";i:18;s:15:"View Structure ";}i:7;a:19:{i:0;i:7;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"3038673-3038919";i:6;s:1:"-";i:7;s:9:"cobalamin";i:8;s:0:"";i:9;s:15:"3037564-3038290";i:10;s:1:"-";i:11;s:10:"Hsero_2658";i:12;s:25:"Integral membrane protein";i:13;s:10:"Hsero_2658";i:14;s:6:"Operon";i:15;s:6:"727237";i:16;s:21:"Hsero_2658;Hsero_2659";i:17;s:0:"";i:18;s:15:"View Structure ";}i:8;a:19:{i:0;i:8;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"4908117-4908206";i:6;s:1:"-";i:7;s:3:"SAH";i:8;s:0:"";i:9;s:15:"4906660-4908067";i:10;s:1:"-";i:11;s:4:"ahcY";i:12;s:73:"Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase)";i:13;s:10:"Hsero_4289";i:14;s:11:"Single gene";i:15;s:7:"2901889";i:16;s:16:"Hsero_4289(ahcY)";i:17;s:96:"one-carbon metabolic process [GO:0006730]; S-adenosylhomocysteine catabolic process [GO:0019510]";i:18;s:15:"View Structure ";}i:9;a:19:{i:0;i:9;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"5115194-5115241";i:6;s:1:"-";i:7;s:9:"mini-ykkC";i:8;s:0:"";i:9;s:15:"5111552-5115176";i:10;s:1:"-";i:11;s:10:"Hsero_4471";i:12;s:0:"";i:13;s:10:"Hsero_4471";i:14;s:6:"Operon";i:15;s:6:"727599";i:16;s:27:"Hsero_4470(gatA);Hsero_4471";i:17;s:0:"";i:18;s:15:"View Structure ";}i:10;a:19:{i:0;i:10;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"5118406-5118506";i:6;s:1:"-";i:7;s:9:"ykkC-yxkD";i:8;s:0:"";i:9;s:15:"5117442-5118258";i:10;s:1:"-";i:11;s:10:"Hsero_4475";i:12;s:73:"ABC-type nitrate/sulfonate/bicarbonate transport system; permease protein";i:13;s:10:"Hsero_4475";i:14;s:6:"Operon";i:15;s:6:"727600";i:16;s:43:"Hsero_4472;Hsero_4473;Hsero_4474;Hsero_4475";i:17;s:36:"transmembrane transport [GO:0055085]";i:18;s:15:"View Structure ";}i:11;a:19:{i:0;i:11;i:1;s:11:"NC_014323.1";i:2;s:32:"Herbaspirillum seropedicae SmR1 ";i:3;s:18:"Betaproteobacteria";i:4;s:5:"28216";i:5;s:15:"5119175-5119274";i:6;s:1:"+";i:7;s:9:"ykkC-yxkD";i:8;s:0:"";i:9;s:15:"5119341-5120418";i:10;s:1:"+";i:11;s:10:"Hsero_4476";i:12;s:86:"ABC-type nitrate/sulfonate/bicarbonate transport system; periplasmic component protein";i:13;s:10:"Hsero_4476";i:14;s:11:"Single gene";i:15;s:7:"2901964";i:16;s:10:"Hsero_4476";i:17;s:0:"";i:18;s:15:"View Structure ";}}
